Classifications

• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N35/00—Automatic analysis not limited to methods or materials provided for in any single one of groups G01N1/00 - G01N33/00; Handling materials therefor
  • G01N35/00584—Control arrangements for automatic analysers
  • G01N35/00594—Quality control, including calibration or testing of components of the analyser
  • G01N35/00693—Calibration
• • B—PERFORMING OPERATIONS; TRANSPORTING
  • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
  • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
  • B01L3/00—Containers or dishes for laboratory use, e.g. laboratory glassware; Droppers
• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N35/00—Automatic analysis not limited to methods or materials provided for in any single one of groups G01N1/00 - G01N33/00; Handling materials therefor
  • G01N35/00584—Control arrangements for automatic analysers
  • G01N35/00722—Communications; Identification
  • G01N35/00732—Identification of carriers, materials or components in automatic analysers
• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N35/00—Automatic analysis not limited to methods or materials provided for in any single one of groups G01N1/00 - G01N33/00; Handling materials therefor
  • G01N35/0098—Automatic analysis not limited to methods or materials provided for in any single one of groups G01N1/00 - G01N33/00; Handling materials therefor involving analyte bound to insoluble magnetic carrier, e.g. using magnetic separation
• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N35/00—Automatic analysis not limited to methods or materials provided for in any single one of groups G01N1/00 - G01N33/00; Handling materials therefor
  • G01N35/02—Automatic analysis not limited to methods or materials provided for in any single one of groups G01N1/00 - G01N33/00; Handling materials therefor using a plurality of sample containers moved by a conveyor system past one or more treatment or analysis stations
  • G01N35/026—Automatic analysis not limited to methods or materials provided for in any single one of groups G01N1/00 - G01N33/00; Handling materials therefor using a plurality of sample containers moved by a conveyor system past one or more treatment or analysis stations having blocks or racks of reaction cells or cuvettes
• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N35/00—Automatic analysis not limited to methods or materials provided for in any single one of groups G01N1/00 - G01N33/00; Handling materials therefor
  • G01N2035/00178—Special arrangements of analysers
  • G01N2035/00306—Housings, cabinets, control panels (details)
• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N35/00—Automatic analysis not limited to methods or materials provided for in any single one of groups G01N1/00 - G01N33/00; Handling materials therefor
  • G01N2035/00346—Heating or cooling arrangements
  • G01N2035/00445—Other cooling arrangements
• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N35/00—Automatic analysis not limited to methods or materials provided for in any single one of groups G01N1/00 - G01N33/00; Handling materials therefor
  • G01N35/00584—Control arrangements for automatic analysers
  • G01N35/00722—Communications; Identification
  • G01N35/00732—Identification of carriers, materials or components in automatic analysers
  • G01N2035/00742—Type of codes
  • G01N2035/00752—Type of codes bar codes
• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N35/00—Automatic analysis not limited to methods or materials provided for in any single one of groups G01N1/00 - G01N33/00; Handling materials therefor
  • G01N35/00584—Control arrangements for automatic analysers
  • G01N35/00722—Communications; Identification
  • G01N35/00732—Identification of carriers, materials or components in automatic analysers
  • G01N2035/00792—Type of components bearing the codes, other than sample carriers
  • G01N2035/00801—Holders for sample carriers, e.g. trays, caroussel, racks
• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N35/00—Automatic analysis not limited to methods or materials provided for in any single one of groups G01N1/00 - G01N33/00; Handling materials therefor
  • G01N35/02—Automatic analysis not limited to methods or materials provided for in any single one of groups G01N1/00 - G01N33/00; Handling materials therefor using a plurality of sample containers moved by a conveyor system past one or more treatment or analysis stations
  • G01N35/04—Details of the conveyor system
  • G01N2035/0401—Sample carriers, cuvettes or reaction vessels
  • G01N2035/0418—Plate elements with several rows of samples
• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N35/00—Automatic analysis not limited to methods or materials provided for in any single one of groups G01N1/00 - G01N33/00; Handling materials therefor
  • G01N35/10—Devices for transferring samples or any liquids to, in, or from, the analysis apparatus, e.g. suction devices, injection devices
  • G01N2035/1027—General features of the devices
  • G01N2035/103—General features of the devices using disposable tips
• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N35/00—Automatic analysis not limited to methods or materials provided for in any single one of groups G01N1/00 - G01N33/00; Handling materials therefor
  • G01N35/02—Automatic analysis not limited to methods or materials provided for in any single one of groups G01N1/00 - G01N33/00; Handling materials therefor using a plurality of sample containers moved by a conveyor system past one or more treatment or analysis stations
  • G01N35/028—Automatic analysis not limited to methods or materials provided for in any single one of groups G01N1/00 - G01N33/00; Handling materials therefor using a plurality of sample containers moved by a conveyor system past one or more treatment or analysis stations having reaction cells in the form of microtitration plates
• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N35/00—Automatic analysis not limited to methods or materials provided for in any single one of groups G01N1/00 - G01N33/00; Handling materials therefor
  • G01N35/10—Devices for transferring samples or any liquids to, in, or from, the analysis apparatus, e.g. suction devices, injection devices
  • G01N35/1009—Characterised by arrangements for controlling the aspiration or dispense of liquids
  • G01N35/1011—Control of the position or alignment of the transfer device
• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N35/00—Automatic analysis not limited to methods or materials provided for in any single one of groups G01N1/00 - G01N33/00; Handling materials therefor
  • G01N35/10—Devices for transferring samples or any liquids to, in, or from, the analysis apparatus, e.g. suction devices, injection devices
  • G01N35/1065—Multiple transfer devices
• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N35/00—Automatic analysis not limited to methods or materials provided for in any single one of groups G01N1/00 - G01N33/00; Handling materials therefor
  • G01N35/10—Devices for transferring samples or any liquids to, in, or from, the analysis apparatus, e.g. suction devices, injection devices
  • G01N35/1065—Multiple transfer devices
  • G01N35/1074—Multiple transfer devices arranged in a two-dimensional array

Definitions

• RNA- sequencing uses next-generation sequencing (NGS) to reveal the presence and quantity of RNA in a biological sample at a given moment.
• NGS next-generation sequencing
• RNA-Seq analyzes the transcriptome of gene expression patterns encoded within the RNA.
• RNA-Seq techniques analyze the RNA of an entire population of cells, but only yield a bulk average of the measurement instead of representing each individual cell’s transcriptome.
• the heterogeneity of a sample is captured and resolved to the fundamental unit of living organisms - the cell.
• Single-cell transcriptomics examines the gene expression level of individual cells in a given population by simultaneously measuring the messenger RNA (mRNA) concentration of hundreds to thousands of genes.
• mRNA messenger RNA
• Automated library generators have been developed integrating various components to achieve RNA sequencing. There is a need to provide an efficient and reliable automated library generator.
• One important component is a movable pipetting device. There is a need to improve the calibration of the device such that the calibration is reliable and efficient.
• One important aspect is consumable tracking and error detection. There is a need to provide a consumable tracking and error detection device such that consumables are loaded into the system correctly.
• Another important component is a magnetic separator which interacts with a fluid in a vial. There is a need to improve the interaction in a way that allows fluid to be used efficiently and to provide consistent results.
• Figure 1 illustrates a front view of one embodiment of an automated library generator 100.
• Figure 2 illustrates another view of one embodiment of an automated library generator 200.
• Figure 3 illustrates yet another view of one embodiment of an automated library generator 300.
• Figure 4 illustrates an embodiment of a multi-channel pipetting head 402.
• Figure 5 illustrates an embodiment of a teaching pendant 501.
• Figure 6 illustrates an embodiment of an array of teaching pendants 601 coupled to a multi-channel pipetting head 602 of a liquid handling gantry 638.
• Figure 7A illustrates a top view of an embodiment of a magnetic separator plate 702.
• Figure 7B illustrates a cross sectional view of the magnetic separator plate
• Figure 7C illustrates another view of the magnetic separator plate 702.
• Figure 8 illustrates an exemplary consumable 802 that may be loaded onto the magnetic separator plate 214 or magnetic separator plate 702 where magnetic bead-based cleanup may be performed.
• Figure 9B illustrates a cross sectional view of the magnetic separator plate adapter 902.
• Figure 9E illustrates another view of the bottom surface of the magnetic separator plate adapter 902.
• Figure 10A illustrates a cross sectional view of a teaching object 908.
• Figure 1 IB illustrates a cross sectional view of the magnetic separator plate adapter 902 being loaded onto the magnetic separator plate 702.
• Figure 12A illustrates a view of the magnetic separator plate adapter 902 about to be loaded onto the magnetic separator plate 702 and the 96-tube PCR plate 802 about to be loaded onto the magnetic separator plate adapter 902.
• Figure 13 illustrates another embodiment of a magnetic separator plate adapter
• Figure 16 illustrates another embodiment of a module 1602.
• Figure 18 illustrates an embodiment of a module 1802 with features, surfaces, or components that may be utilized as teaching objects.
• Figure 19 illustrates another embodiment of a module 1902 with features, surfaces, or components that may be utilized as teaching objects.
• Figure 23 illustrates an embodiment of a well detection process 2300.
• Figure 29 illustrates that barcodes on the deck module and the barcodes on the consumables may be read by the barcode readers through a plurality of mirrors.
• Figure 31 illustrates another embodiment in which barcodes are placed on a deck module 3101 and the consumables 3104A and 3104B that are loaded onto the module.
• Figure 32A illustrates a view of one embodiment of a thermal cycler 3200.
• Figure 33 illustrates a front view of the automated library generator 3300.
• Figure 1 illustrates a front view of one embodiment of an automated library generator 100.
• the system includes an automated controller 102 on deck for single cell partitioning and barcoding. Reagents and consumables may be loaded onto the instrument deck area 104 at the beginning of each run. Operations may be guided through an easy-to-use touchscreen computer 106 with Internet connectivity.
• System 100 includes a liquid handling gantry 108 that may perform pipetting steps throughout the entire workflow.
• System 100 further includes one or more barcode scanners that enable lot and reagent tracking for reagents and consumables.
• Automated pipetting enhances the throughput and the reproducibility of laboratory experiments. Automated pipetting takes the manual labor out of repeated pipetting, thereby shortening manual hands-on time. Reducing manual hands-on time frees up time and effort for other tasks, thereby greatly improving throughput. Furthermore, automated pipetting significantly reduces errors from manual pipetting, thereby enhancing reproducibility.
• the pipetting head may be moved to the position of the reagent module 240 to dispense liquid into a row 242 of eight wells of the reagent module 240
• the position of the reagent module 240 and the position of the row of wells may each be specified by a set of offset distances in the x, y, and z axes from one or more reference points within deck area 201
• the position of a certain module or labware may be recorded by library generator 200 as a first set of offset values (in x, y, and z) from a reference point within deck area 201
• the position of a row of wells within the module or labware may further be recorded by the system as another set of offset values from the position of the module or labware.
• different positions within the working area are recorded by library generator 200 as different sets of offset values from a single reference point within deck area 201.
• An array of teaching pendants is translated to a region where an array of teaching objects is located.
• a plurality of translation positions at which at least one pendant in the array of teaching pendants engages a teaching object in the array of teaching objects is detected.
• An adjustment offset based on the detected translation positions is determined.
• Figure 7 A illustrates a top view of an embodiment of a magnetic separator plate 702.
• Figure 7B illustrates a cross sectional view of the magnetic separator plate 702.
• Figure 7C illustrates another view of the magnetic separator plate 702.
• a tube received by a ring magnet may be a finger-like length of glass or plastic tubing that is open at the top and closed at the bottom.
• the position of the magnetic separator plate 702 may be specified by a reference position 706 (also referred to as the reference A1 position of the module) corresponding to the magnetic separator plate 702.
• the reference position may be recorded as a set of offset distances in the x, y, and z axes measured from the reference position 706 to a master reference point within the deck area.
• Figure 9 A illustrates a top view of a magnetic separator plate adapter
• each of the collars 904 constrains the x location and the y location of the tube holder plate by having a tube inserted into the collar.
• the magnetic separator plate adapter 902 further includes four cylindrical feet 906 at the four comers of the adapter, such that the magnetic separator plate adapter 902 may be mounted on the magnetic separator plate 702.
• magnetic separator plate adapter 902 may be formed of plastic and includes skirts. Magnetic separator plate adapter 902 may include a plurality of teaching objects 908.
• Figure 10A illustrates a cross sectional view of a teaching object 908.
• Automated library generator 200 may include circuitries or logic for detecting the teaching objects or other surfaces surrounding the teaching objects and determining the heights (or z positions) where the detections occur.
• System 200 may further include circuitries or logic for controlling the actuators in response to the detections.
• measurements of a combination of capacitance and conductivity while the teaching pendant is moving toward the teaching object or other surfaces may be used to detect the teaching object or other surfaces surrounding the teaching object.
• measurements of a combination of pressure and capacitance while the teaching pendant is moving toward the teaching object or other surfaces may be used to detect the teaching object or other surfaces surrounding the teaching object.
• Figure 11 A illustrates a top view of the magnetic separator plate adapter 902 being loaded onto the magnetic separator plate 702.
• Figure 1 IB illustrates a cross sectional view of the magnetic separator plate adapter 902 being loaded onto the magnetic separator plate 702.
• Figure 11C illustrates another cross sectional view of the magnetic separator plate adapter 902 being loaded onto the magnetic separator plate 702.
• Figure 1 ID illustrates a portion of a magnified cross sectional view of the magnetic separator plate adapter 902 being loaded onto the magnetic separator plate 702.
• a cylindrical foot 906 of the magnetic separator plate adapter 902 fits into a cylindrical hole on the magnetic separator plate 702, thereby mounting the magnetic separator plate adapter 902 on the magnetic separator plate 702 and raising the magnetic separator plate adapter 902 above the magnetic separator plate 702.
• Figure 12A illustrates a view of the magnetic separator plate adapter 902 about to be loaded onto the magnetic separator plate 702 and the 96-tube PCR plate 802 about to be loaded onto the magnetic separator plate adapter 902.
• Figure 12B illustrates another view of the magnetic separator plate adapter 902 being loaded onto the magnetic separator plate 702 and the 96-tube PCR plate 802 being loaded onto the magnetic separator plate adapter 902.
• the reference position 706 corresponding to the magnetic separator plate 702 is below the array of teaching objects 908 in the z direction.
• Each of the teaching objects 908 has a different offset from the reference position 706 in the x direction, and each of the teaching objects 908 has substantially the same offset from the reference position 706 in the y direction.
• the reference position 706 may be adjusted based on the results from detecting the array of teaching objects 908 with the array of teaching pendants.
• Figure 14 illustrates another embodiment of a module 1402.
• the module 1402 includes an array of eight teaching objects 1408.
• FIG. 18 illustrates an embodiment of a module 1802 with features, surfaces, or components that may be utilized as teaching objects.
• Module 1802 is an incubation module that includes a rectangular array of wells 1810. Each well 1810 has a shape of a cylinder.
• the stored information for each piece of labware may include the type of labware or deck object, its reference position, or the reference positions of different portions or components of that piece of labware.
• the stored information may also include the reference positions (x, y, and z positions) and the height of the teaching objects for calibrating the piece of labware.
• the stored information for the reagent module 240 may include the reference position of the reagent module 240 (also referred to as the reference A1 position of the reagent module) and the reference positions of different portions of reagent module 240, such as the row 242 of eight wells of the reagent module 240.
• step 2004 information corresponding to the current piece of labware on the list is loaded into the system.
• step 2006 the type of labware is determined based on the information corresponding to the current piece of labware. For some types of labware, the process proceeds to step 2008, and for other types of labware, process 2000 proceeds to step 2010.
• a teaching datum detection process is performed.
• the teaching datum detection process uses an array of teaching pendants to detect an array of teaching datums, such as the teaching datums as shown in Figures 10A and 10B.
• a well detection process is performed.
• the well detection process uses the array of teaching pendants to detect an array of wells and the surfaces surrounding the wells in certain types of labware, such as the labware as shown in Figures 18 and 19.
• the well detection process will be described in greater detail below.
• step 2008 or step 2010 process 2000 proceeds to step 2012.
• step 2012 the results from the teaching datum detection process or the well detection process are stored in a report, such as in a file or in a database.
• step 2014 it is determined whether there are any additional pieces of labware on the list that have not been processed. If there is another piece of labware to be processed, then process 2000 proceeds back to step 2004; otherwise, process 2000 proceeds to step 2016 and the process is terminated.
• Figure 21 illustrates an embodiment of a teaching datum detection process 2100.
• Process 2100 may be executed by step 2008 of process 2000 as shown in Figure 20.
• Teaching datum detection process 2100 uses an array of teaching pendants to detect an array of teaching datums, such as the teaching datum as shown in Figures 10A and 10B.
• the heights (or z positions) of the array of teaching pendants when the teaching pendants are translated to the x and y positions of the teaching datums are determined.
• a linear array of teaching pendants 601 is coupled to an 8-channel pipetting head 602 of liquid handling gantry 638.
• One or more actuators 640 may be used to move the x, y, and z positions of each of the teaching pendants 601.
• a translation actuator may be configured to translate the array of teaching pendants 601 to different x and y positions in a plane 642 substantially parallel to a floor of an instrument deck.
• the stored information for the current piece of labware includes the positions of the teaching datums for calibrating the piece of labware. Therefore, the translation actuator may be configured to translate the array of teaching pendants 601 to the x and y positions corresponding to the array of teaching datums.
• a plurality of height actuators is then configured to move each of the teaching pendants 601 independently in a direction 644 substantially perpendicular to the plane to detect the array of teaching datums.
• Different surfaces of the datum and different surfaces that are adjacent to the datum may be contacted and detected by a teaching pendant.
• the surfaces detected may include the top surface of the datum, the inner surfaces of the opening 1002, and the floor 1004 that is adjacent to the datum.
• a large z value corresponding to the teaching pendant may be recorded even when no surfaces have been detected by the teaching pendant.
• the base 1709d of the right vertical surface of the teaching post 1708 is not adjacent to any portion of the module floor surface.
• the teaching pendant will miss the top surface of the teaching post and will continuously go further in the z direction without hitting the module floor.
• a large z value corresponding to the teaching pendant is recorded even when no surfaces have been detected by the teaching pendant.
• the z value may be greater than a threshold value, such as Zi + H, where Zi is the z value at the top surface of the teaching post 1708, andH is the height of the post 1708.
• the detected heights of the array of teaching pendants when the teaching pendants are translated to the x and y positions of the teaching datums are used to determine whether the teaching pendants detect their corresponding teaching datums.
• a detected z value of a teaching pendant that is greater than a predetermined threshold indicates that the teaching pendant failed to detect its corresponding teaching datum
• a detected z value of a teaching pendant that is smaller than or substantially equal to the predetermined threshold indicates that the teaching pendant has detected its corresponding teaching datum.
• the predetermined threshold may be selected based on different factors, such as the type of the labware, the height of the teaching datum, the physical features and shapes of the teaching datum, and the like.
• process 2100 proceeds to step 2108.
• step 2108 a search for the teaching datums is performed. If the search fails at step 2109, process 2100 proceeds to step 2110, such that an error is logged and reported. If the entire array of teaching datums is detected, then process 2100 proceeds to step 2112.
• the array of teaching pendants is translated by a predetermined distance to verify that the array of teaching pendants is still able to engage and touch the array of teaching datums when the array of teaching pendants is being lowered in the z direction. If the positioning of the liquid handling gantry with the pipetting head is reasonably accurate, then initially each teaching pendant should be in relatively close contact with the center of the top surface of its corresponding teaching datum. Since the cross sectional area of the top surface of a teaching datum is greater than that of the tip of a teaching pendant, translating the array of teaching pendants by a predetermined distance away from its current position should still allow the array of teaching pendants to engage and touch the array of teaching datums. Therefore, the verification at step 2112 indicates that the positioning of the liquid handling gantry with the pipetting head is reasonably accurate.
• the array of teaching pendants is translated by a predetermined distance in a plurality of directions, and after each translation in one direction, it is verified that the array of teaching pendants is still engaging and touching the array of teaching datums.
• the array of teaching pendants is translated by 1 mm in four different directions (+x, -x, +y, and -y) from its original stored reference position, and after each translation in one direction, it is verified that the array of teaching pendants is still able to engage and touch the array of teaching datums.
• process 2100 proceeds to step 2116 and the results are logged into a report. However, if at least one direction fails, then process 2100 proceeds to step 2118, wherein the process enters a teaching phase to estimate the center points or new reference positions of the teaching datums. [00127] At step 2118, the edges or boundaries of the teaching datums are determined. For example, the left, right, upper, and lower edges of the teaching datums as viewed from the top are determined.
• the array of teaching pendants is translated by a predetermined distance in one direction and, after each translation, it is determined whether each of the teaching pendants is still able to engage and touch its corresponding teaching datum when the teaching pendant is lowered in the z direction.
• the incremental movement of the array of teaching pendants by the predetermined distance in one direction is continued until all of the teaching pendants are no longer engaging and touching their corresponding teaching datums.
• the total distance that each teaching pendant is moved in that direction until it no longer engages and touches its corresponding teaching datum is then recorded for each channel. This is the distance of each teaching pendant from its original reference position to the edge of its corresponding teaching datum in one direction.
• the same procedure is repeated for all four directions (+x, -x, +y, and -y) from the array’s original stored reference position.
• the array of teaching pendants may be translated by predetermined distance (e.g., 0.5 mm) in the +x direction (i.e., to the right) each time until all of the teaching pendants are no longer engaging and touching their corresponding teaching datums.
• the total distance that each teaching pendant is moved in the +x direction until it no longer engages and touches its corresponding teaching datum is then recorded for each channel.
• the distance for the i th channel is distance right(i).
• Figure 22 illustrates an example of determining the left and right edges of a teaching datum 908 in channel #1.
• a teaching pendant is moved from its original reference position 2202 (x ref(l), y ref(l)) to the right by a fixed distance (d) to position 2204A.
• the teaching pendant touches the top surface of the teaching datum 908.
• the teaching pendant is then translated by another fixed distance (d) to position 2204B.
• the teaching pendant no longer touches the top surface of the teaching datum 908.
• the total distance that the teaching pendant is moved to the right (distance right/ 1)) is then recorded for this channel.
• x right/ 1) x ref(l) + distance right(1).
• the array of teaching pendants is translated back to its original reference position.
• the array is then translated by a predetermined distance (e.g., 0.5 mm) in the -x direction (i.e., to the left) each time until all of the teaching pendants are no longer engaging and touching their corresponding teaching datums.
• the total distance that each teaching pendant has moved in the -x direction until it no longer engages and touches its corresponding teaching datum is then recorded for each channel.
• the distance for the i th channel is distance left(i).
• a teaching pendant is moved from its original reference position 2202 (x ref(l), y ref(l)) to the left by a fixed distance (d) to position 2204C.
• the teaching pendant touches the top surface of the teaching datum 908.
• the teaching pendant is then translated by another fixed distance (d) to position 2204D.
• the teaching pendant no longer touches the top surface of the teaching datum 908.
• the total distance that the teaching pendant has moved to the left is then recorded for this channel.
• x _ left/ 1 ) x ref(l) - distance _ left/ 1 ) .
• the array of teaching pendants is translated back to its original reference position.
• the array is then translated by 0.5 mm in the +y direction (i.e., in the up direction) each time until all of the teaching pendants are no longer engaging and touching their corresponding teaching datums.
• the total distance that each teaching pendant has moved in the +y direction before it no longer engages and touches its corresponding teaching datum is then recorded for each channel.
• the distance for the i th channel is distance up/i).
• the array of teaching pendants is translated back to its original reference position.
• the array is then translated by 0.5 mm in the -y direction (i.e., in the down direction) each time until all of the teaching pendants are no longer engaging and touching their corresponding teaching datums.
• the total distance that each teaching pendant has moved in the -y direction before it no longer engages and touches its corresponding teaching datum is then recorded for each channel.
• the distance for the i th channel is distance down(i).
• process 2100 proceeds to step 2122. However, if there is an error finding the edge of at least one teaching datum, then process 2100 proceeds to step 2110, such that the error is logged and reported.
• step 2122 the maximum difference of the distance from a reference position of a teaching datum to the edge of the teaching pendant in the +x/-x directions for all channels, DeltaXMax, is determined.
• step 2124 if either DeltaXMax or DeltaYMax is greater than a predetermined threshold (e.g., 1.5 mm), it indicates that the reference position of at least one teaching datum is significantly far away from its actual position and, accordingly, process 2100 proceeds to step 2110, such that an error is logged and reported. Otherwise, process 2100 proceeds to step 2126.
• a predetermined threshold e.g. 1.5 mm
• step 2126 the offset or adjustment in the x direction (x offset) and the offset in the y direction (y offset) are determined.
• process 2100 is completed and is terminated at 2128.
• These offset values may be used to correct the reference position of the labware or the reference positions of different portions or components of the labware.
• the x and y positions of the center points of the teaching datums are estimated based on the edge detection results that are obtained at step 2118 above.
• the offset from the original reference position of the teaching datum to the actual detected position of the teaching datum for the i th channel is then determined based on the estimated center point of the i th teaching datum and the original reference position of the i 1 * 1 teaching datum.
• the offset values (x offset and y offset) that may be used to correct the reference position of the labware or the reference positions of different portions or components of the labware may be determined based on the x offset® values and the y offset® values above.
• the offset values (x offset and y offset) that may be used to correct the reference position of the labware or the reference positions of different portions or components of the labware may be determined as an average of the x offset® values and an average of the y offset® values above.
• Figure 23 illustrates an embodiment of a well detection process 2300.
• Process 2300 may be executed by step 2010 of process 2000 as shown in Figure 20.
• Well detection process 2300 uses an array of teaching pendants to detect an array of wells, such as the wells in the modules as shown in Figures 18 and 19.
• the heights (or z positions) of the array of teaching pendants when the teaching pendants are translated to the x and y positions of the wells are determined.
• a linear array of teaching pendants 601 is coupled to an 8-channel pipetting head 602 of liquid handling gantry 638.
• One or more actuators 640 may be used to move the x, y, and z positions of each of the teaching pendants 601.
• a translation actuator may be configured to translate the array of teaching pendants 601 to different x and y positions in a plane 642 substantially parallel to a floor of an instrument deck.
• the stored information for the current piece of labware includes the positions of the wells for calibrating the piece of labware. Therefore, the translation actuator may be configured to translate the array of teaching pendants 601 to the x and y positions corresponding to a row of wells.
• a plurality of height actuators is then configured to move each of the teaching pendants 601 independently in a direction 644 substantially perpendicular to the plane to detect the array of wells.
• Different surfaces of the well and different surfaces that are adjacent to the well may be contacted and detected by a teaching pendant.
• the inner surfaces of the wells 1810 may serve as target teaching objects.
• the surfaces 1808 surrounding each of the wells 1810 are detected, it indicates that the teaching pendant has missed the target teaching object, i.e., the inner surfaces of the well 1810.
• the teaching pendant detects a surface, the z position or the height of the teaching pendant may be determined and recorded.
• the z positions when the teaching pendant touches the surfaces 1808 surrounding each of the wells 1810 and the bottom inner surface of each of the wells 1810 are Zi and Z , respectively.
• the value Z is equal to Zi + H, where FI is the depth of the well 1810.
• the detected heights of the array of teaching pendants when the teaching pendants are translated to the x and y positions of a row of wells are used to determine whether the teaching pendants detect their corresponding wells.
• a detected z value of a teaching pendant that is smaller than a predetermined threshold indicates that the teaching pendant failed to detect its corresponding well.
• the predetermined threshold may be selected based on different factors, such as the type of the labware, the depth of the well, the physical features and shapes of the well, and the like. For example, a z value that is smaller than Z (the z position when the teaching pendant touches the bottom inner surface of a well 1810) indicates that the teaching pendant failed to detect its corresponding well.
• step 2306 it is determined whether the entire linear array of wells is detected. If only some of the wells are detected, then the positioning of the liquid handling gantry with the pipetting head based on the stored reference positions is significantly misaligned. Accordingly, process 2300 proceeds to step 2310, such that an error is logged and reported. If the entire array of wells is detected, then process 2300 proceeds to step 2312.
• the array of teaching pendants is translated by a predetermined distance to verify that the array of teaching pendants is still within the wells and is still engaging and touching the bottom inner surfaces of the wells. If the positioning of the liquid handling gantry with the pipetting head is reasonably accurate, then initially each teaching pendant should be in relatively close contact with the center of the bottom inner surface of its corresponding well. Since the cross sectional area of the bottom inner surface of a well is greater than that of the tip of a teaching pendant, translating the array of teaching pendants by a predetermined distance away from its current position should still allow the array of teaching pendants to stay within the wells and engage and touch the bottom inner surfaces of the wells. Therefore, the verification at step 2312 indicates that the positioning of the liquid handling gantry with the pipetting head is reasonably accurate.
• the array of teaching pendants is translated by a predetermined distance in a plurality of directions, and after each translation in one direction, it is verified that the array of teaching pendants may be lowered and still able to engage and touch the bottom inner surfaces of the wells.
• the array of teaching pendants is translated by 1 mm in four different directions (+x, -x, +y, and -y) from its original stored reference position, and after each translation in one direction, it is verified that the array of teaching pendants may be lowered and is still able to engage and touch the bottom inner surfaces of the wells.
• process 2300 proceeds to step 2316 and the results are logged into a report. However, if at least one direction fails, then process 2300 proceeds to step 2318, when the process enters a teaching phase to estimate the center points of the wells.
• the edges or boundaries of the wells are determined. For example, the left, right, upper, and lower edges of the wells as viewed from above are determined.
• the array of teaching pendants is translated by a predetermined distance in one direction, and after each translation, it is determined whether each of the teaching pendants is still within its corresponding well. The incremental movement of the array of teaching pendants by the predetermined distance in one direction is continued until all of the teaching pendants are no longer within their corresponding wells. The total distance that each teaching pendant is moved in that direction until it no longer stays within its corresponding well is then recorded for each channel. This is the distance of each teaching pendant from its original reference position to the edge of its corresponding well in one direction.
• the array of teaching pendants is translated by 0.5 mm in the +x direction (i.e., to the right) each time until all of the teaching pendants are no longer detecting their corresponding wells.
• the total distance that each teaching pendant is moved in the +x direction until it is no longer within its corresponding well is then recorded for each channel.
• the distance for the i th channel is distance right(i).
• the array of teaching pendants is translated back to its original reference position.
• the array is then translated by 0.5 mm in the -x direction (i.e., to the left) each time until all of the teaching pendants are no longer within their corresponding wells.
• the total distance that each teaching pendant is moved in the -x direction until it no longer detects its corresponding well is then recorded for each channel.
• the distance for the i th channel is distance left(i).
• the x position of the left edge of the well, x left(i) is determined based on the distance and the well’s original reference position (x ref(i), y ref(i)), wherein x left(i)
• the array of teaching pendants is translated back to its original reference position.
• the array is then translated by 0.5 mm in the +y direction (i.e., in the up direction) each time until all of the teaching pendants are no longer within their corresponding wells.
• the total distance that each teaching pendant is moved in the +y direction before it no longer detects its corresponding well is then recorded for each channel.
• the distance for the i th channel is distance up(i).
• the array of teaching pendants is translated back to its original reference position.
• the array is then translated by 0.5 mm in the -y direction (i.e., in the down direction) each time until all of the teaching pendants are no longer within their corresponding wells.
• the total distance that each teaching pendant is moved in the -y direction before it no longer detects its corresponding well is then recorded for each channel.
• the distance for the i th channel is distance down(i).
• process 2300 proceeds to step 2322. However, if there is an error finding the edge of at least one well, then process 2300 proceeds to step 2310, such that the error is logged and reported.
• step 2322 the maximum difference of the distance from a reference position of a well to the edge of the well in the +x/-x directions for all channels, DeltaXMax, is determined.
• step 2324 if either DeltaXMax or DeltaYMax is greater than a predetermined threshold (e.g., 1.5 mm), it indicates that the reference position of at least one well is significantly far away from its actual position, and accordingly, process 2300 proceeds to step 2310, such that an error is logged and reported. Otherwise, process 2300 proceeds to step 2326.
• a predetermined threshold e.g. 1.5 mm
• step 2326 the offset or adjustment in the x direction (x offset) and the offset in the y direction (y offset) are determined.
• process 2300 is completed and is terminated at step 2328.
• These offset values may be used to correct the reference position of the labware or the reference positions of different portions or components of the labware.
• the x and y positions of the center points of the wells are estimated based on the edge detection results that are obtained at step 2318 above.
• the offset from the original reference position of the well to the actual detected position of the well for the i th channel is then determined based on the estimated center point of the i th well and the original reference position of the i th well.
• the offset values (x offset and y offset) that may be used to correct the reference position of the labware or the reference positions of different portions or components of the labware may be determined based on the x offset(i) values and the y offset® values above.
• the offset values (x offset and y offset) that may be used to correct the reference position of the labware or the reference positions of different portions or components of the labware may be determined as an average of the x offset® values and an average of the y offset® values above.
• the improved techniques of automatically calibrating the positioning of the liquid handling gantry with the pipetting head presented herein have many advantages. These techniques enhance the throughput and the reproducibility of laboratory experiments. Furthermore, these techniques significantly reduce errors, thereby enhancing reproducibility. In addition, these techniques eliminate the need for users to manually teach the system. This also eliminates the need of using a single high precision position. For example, other techniques may keep one high precision position (golden position), and whenever a high precision measurement is needed, the tips are measured at the golden position only.
• Reagents and consumables may be loaded onto the deck area at the beginning of each run.
• Consumables may include reagent reservoirs, plates (e.g., polymerase chain reaction (PCR) plates and deep well plates), tubes, and the like.
• PCR polymerase chain reaction
• loading the consumables onto the deck is prone to different types of errors. For example, consumables containing the wrong reagent may be loaded. In another example, consumables may be loaded at the wrong locations within the deck. In another example, consumables loaded onto the deck may be expired.
• a consumable tracking and error detection system comprises one or more barcode readers above an instrument deck.
• the system further comprises one or more mirrors on the instrument deck.
• the one or more barcode readers are controlled by a processor to read a plurality of barcodes on a plurality of objects on the instrument deck through the one or more mirrors.
• automated library generator 200 includes a consumable tracking and error detection system.
• the consumable tracking and error detection system may include one or more barcode readers for scanning barcodes that are placed at different locations of the deck and barcodes that are placed on different consumables.
• a barcode reader is an optical scanner that can read printed barcodes, decode the data contained in the barcode, and send the data to a computer.
• One or more barcode readers may be placed above the five carriers (202, 204, 206, 208, and 210) on deck 201.
• the consumable tracking and error detection system enables experiment tracking and prevents reagent mix-ups.
• Figure 24 illustrates one embodiment of a consumable tracking and error detection system 2400 for automated library generator 200.
• two barcode readers 2402 may be placed above the leftmost carrier on the deck.
• the barcode readers 2402 may be used to read the barcodes on different types of labware, deck modules, or deck objects that are placed at different locations of the deck.
• the barcode readers 2402 may also be used to read the barcodes on consumables that are loaded onto different labware or deck modules, such as reagent reservoirs, plates (e.g., polymerase chain reaction (PCR) plates and deep well plates), tubes, and the like.
• PCR polymerase chain reaction
• Consumable tracking and error detection system 2400 may further include a plurality of mirrors 223 to allow the barcode readers 2402 to read barcodes sideways and at more locations.
• barcodes may be placed on the sides or vertical surfaces of the cold plate reagent module 220 or the consumables that are loaded onto the module, and the barcode readers 2402 may read the barcodes through the plurality of mirrors 223.
• the barcodes on the cold plate reagent module 220 may encode information that enables experiment backing, such as the type of module, or the slot, row, or column number within the module.
• the barcodes on the consumables may encode information that enables experiment backing, such as the color code, part number, lot number, expiration date of the reagent, and the like.
• Reading the barcodes by the barcode readers through a plurality of mirrors has a number of advantages.
• One of the advantages is that the barcode readers do not need to occupy any deck space.
• Another advantage is that this enables the barcode readers to read from more locations on the deck.
• a barcode reader does not need to be placed on or close to the floor of the instrument deck, such that there is an unobstructed line of sight between the barcode reader and the barcode that is placed on the side or vertical surface of a labware, deck module, or consumable.
• a barcode reader may be placed anywhere above the instrument deck, such that the barcode reader has a sight along a line at the barcode’s image, thereby enabling the barcode reader to view the image of the barcode in the mirror.
• Figure 25 illustrates a plurality of strip tubes 2502 that may be loaded onto the cold plate reagent module 220.
• Each of the strip tubes 2502 includes eight tubes 2504.
• a barcode sticker 2506 may be added to a strip tube 2502.
• Figure 26 illustrates that four strip tubes 2502 are loaded onto the cold plate reagent module 220.
• Figure 27 illustrates one embodiment of one plate of an automated cell library and gel bead kit for the automated library generator 200.
• the kit may be tracked by the consumable tracking and error detection system 2400.
• Figure 28 illustrates a plurality of plates of an automated cell library and gel bead kit for the automated library generator 200.
• the kit includes three plates; each plate is color-coded. For example, as shown in Figure 28, the top plate is black, the middle plate is grey, and the bottom plate is white.
• each plate includes a plurality of strip tubes 2702.
• Each strip of tubes 2702 includes a plurality of tubes 2706 that are used to deliver a reagent.
• each strip 2702 may include eight tubes 2706.
• Each strip 2702 is pre-aliquoted and color-coded. During each run, three strips 2702, one from each plate (black, grey, and white), may be used per sample. One to eight samples may be run at a time.
• strip 2702 is optimized for automated liquid handling within the automated library generator 200.
• the strips 2702 may be easily loaded on the carriers (shown in Figure 2) on the deck.
• each strip 2702 may be labelled with a 2D barcode 2704 to prevent errors in handling the reagents or using reagents that are expired.
• a barcode 2704 may encode different information for tracking the reagent lots and expiration dates. The encoded information may include the part number, lot number, expiration date of the reagent, and the like.
• Consumable tracking and error detection system 2400 may include software logic to make sure that the correct consumables (with reagents) are put at the right slots or locations. Consumable tracking and error detection system 2400 may also detect that the consumables are missing such that the system may inform the user about these errors. The system may check for color matching, lot numbers, part numbers, and expiration dates.
• Figure 29 illustrates that barcodes on the deck module and the barcodes on the consumables may be read by the barcode readers through a plurality of mirrors.
• barcodes on the slots are covered by the strip tubes if they are put there. If the barcode reader reads the barcodes on the slots, then the slots are determined as being empty. If the barcode reader reads the barcodes on the strip tubes, then the system may match the two barcodes.
• Figure 30 illustrates an embodiment of a process 3000 for tracking consumables and detecting errors in loading the consumables in an automated library generator 200.
• a plurality of barcodes is read by the barcode reader.
• one of the barcodes read by the barcode reader is decoded to determine whether the barcode corresponds to a slot in a deck module.
• the barcode is determined as corresponding to a slot in a deck module, then it is determined that the slot of the deck module does not have any consumables loaded and is empty. Accordingly, the slot is reported as empty at step 3010, and process 3000 proceeds to step 3018. If the barcode is determined as not corresponding to a slot in a deck module, then the barcode is a barcode that is placed on a piece of consumable, and process 3000 proceeds to step 3012. At 3012, a number of attributes are checked, including the color code, lot number, part number, expiration date, and the like. At step 3014, it is determined whether any of the attributes indicate an error.
• step 3016 If there is any error, then the error is reported at step 3016, and process 3000 proceeds to step 3018; otherwise, process 3000 proceeds to step 3018.
• step 3018 it is determined whether there is another barcode to decode. If there is another barcode to decode, then process 3000 proceeds to step 3008; otherwise, process 3000 is completed and terminated at 3020.
• FIG 31 illustrates another embodiment in which barcodes are placed on a deck module 3101 and the consumables 3104 A and 3104B that are loaded onto the module.
• Deck module 3101 is a module for holding a plurality of tubes (e.g., tubes 3104A and 3104B).
• Each of the slots for holding the tubes is labeled with a barcode (e.g., barcodes 3102A and 3102B), and each of the tubes inserted into the slots is labeled with its barcode (e.g., barcodes 3108 A and 3108B).
• Consumable tracking and error detection system 2400 may read the barcode corresponding to a slot and the barcode corresponding to the tube inserted into the slot, which are adjacent to each other, and determine whether the two barcodes are compatible with each other. For example, the information decoded from the barcodes may be used to check the part numbers, lot number, and expiration date.
• An automated library generator may include components that generate heat, thereby creating heat spots within the system.
• automated library generator 200 may include an on-deck thermal cycler 224 (ODTC), as shown in Figure 2.
• Figures 32A and 32B illustrate two additional views of one embodiment of a thermal cycler 3200.
• Thermal cyclers may be used to amplify segments of Deoxyribonucleic acid (DNA) via the polymerase chain reaction (PCR). Thermal cyclers may also be used to facilitate other temperature-sensitive reactions.
• thermal cycler 3200 has a thermal block 3202 with holes 3204 where tubes holding reaction mixtures may be inserted. Thermal cycler 3200 then raises and lowers the temperature of the block 3202 in discrete, pre-programmed steps.
• Thermal cycler 3200 includes one or more heat sinks 3206 and fans 3208 for removing the heat from the elements and improving the efficiency of the system. Flowever, heat may still accumulate around thermal cycler 3200 and the deck components that are close to the thermal cycler.
• an air flow system for an automated library generator is disclosed. Air flow is created by the air flow system to eliminate hot spots within the automated library generator.
• the system includes an instrument deck having an instrument deck floor, wherein the instrument deck is configured to receive a plurality of deck modules or consumables.
• the instrument deck is enclosed by a frame.
• a first fan is mounted on the frame enclosing the instrument deck.
• a first air vent within the frame provides an opening to an air duct below the instrument deck floor.
• a second air vent on an outer surface of the frame provides an opening to the air duct.
• Figures 33 and 34 illustrate two different views of an exemplary configuration of an automated library generator 3300 in which airflow is created to eliminate hot spots within the system.
• Figure 33 illustrates a front view of the automated library generator 3300.
• Figure 34 illustrates a top view of the automated library generator 3300.
• automated library generator 3300 includes a frame 3320 housing the system 3300.
• the frame 3320 includes a top horizontal frame 3320A, a left vertical side frame 3320B, a right vertical side frame 3320C, and a bottom base frame 3320D.
• a deck floor 3340 is located above the bottom base frame 3320D.
• Automated library generator 3300 includes five carriers (3302, 3304, 3306, 3308, and 3310) and a disposal bin 3336 above the deck floor 3340.
• Thermal cycler 3200 is located in carrier 3304.
• automated library generator 3300 includes two top fans 3402 mounted on the top horizontal frame 3320A.
• the top fans 3402 are placed above the deck floor 3340 and the carriers (3302, 3304, 3306, 3308, and 3310).
• Figure 35 illustrates a view showing a portion of the left vertical side frame 3320B, the bottom base frame 3320D, and an integrated communication and power base compartment of automated library generator 3300.
• a plurality of air vents (3502, 3504, and 3506) is located on the outside surface of the bottom base frame 3320D.
• Figure 35 illustrates that cold air is brought into the bottom base frame 3320D through air vents 3502 and 3504, as indicated by arrows 1, and hot air is brought out of the bottom base frame 3320D through air vent 3506 as indicated by arrow 4.
• FIG 36 illustrates yet another view of automated library generator 3300.
• air vents 3602 are located within the frame and at the base of carrier 3302.
• the air vents 3602 are openings to air ducts below the deck floor 3340, as will be described in greater detail below.
• air vents may also be placed at the base of carrier 3304 or at the bases of other carriers (e.g., carrier 3306) adjacent to carrier 3304.
• the air vents are also shown in Figure 2 and Figure 3 as air vents 244 and 338, respectively.
• the heat sink is also shown in Figure 2 and Figure 3 as heat sinks 246 and 342, respectively.
• the top fans 3402 blow air out of the frame 3320 in an upward overall direction 3350.
• the top fans 3402 create a negative pressure in the enclosure within the frame 3320, which brings air into the frame 3320 through air vents 3502 and 3504 on the bottom base frame 3320D as indicated by the arrows 1 in Figure 33 and Figure 35, respectively.
• the air vents (3502 and 3504) on the bottom base frame 3320D are connected to a plurality of air ducts that are placed in the bottom base frame 3320D and below deck floor 3340 and at least some of the carriers ((3302, 3304, 3306, 3308, and 3310).
• cold air first flows horizontally in a direction as indicated by arrow 1 through the horizontal portions of the air ducts, and then the cold air flows upwards through the vertical portions of the air ducts and through the vents 3602 (see Figure 36) located at the base of carrier 3302 as indicated by arrow 2.
• the cold air is then directed to cool the internal components of the system as indicated by arrow 3.
• one or more fans 3208 in the thermal cycler 3200 may be used to create a forced convection that draws the cold air to the thermal cycler 3200 and its heat sink 3206 (as indicated by arrow 3) to cool down the thermal cycler 3200 and its heat sink 3206.
• the hot air is then directed out of the frame 3300 through air vent 3506 on the bottom base frame 3320D as indicated by arrow 4 in Figure 33 and Figure 35, respectively.
• the hot air enters the vents 3602 and flows downwards through the vertical portions of the air ducts.
• the hot air then flows horizontally through the horizontal portions of the air ducts and then exits the frame via air vent 3506.
• FIG 37 illustrates another exemplary configuration of an automated library generator 3700 in which airflow is created to eliminate hot spots within the system.
• Automated library generator 3700 is similar to automated library generator 3300 described above.
• One difference between automated library generator 3700 and automated library generator 3300 is that automated library generator 3700 has one or more top fans plus a FIEPA (high-efficiency particulate air) filter 3702 placed above the top horizontal frame 3320A.
• Figure 38 illustrates another embodiment of an automated library generator 3800 with a FIEPA filter hood 3802. [00180] As shown in Figure 37, the top fans blow cold air into the frame 3320 in a downward overall direction 3750. The cold air is then directed to cool the internal components of the system as indicated by arrow 3.
• FIEPA high-efficiency particulate air
• one or more fans 3208 in the thermal cycler 3200 may be used to create a forced convection that draws the cold air to the thermal cycler 3200 and its heat sink 3206 (as indicated by arrow 3) to cool down the thermal cycler 3200 and its heat sink 3206.
• the hot air then flows downwards through the vents 3602 located at the base of carrier 3302 and through the vertical portions of the air ducts, as indicated by arrow 2.
• the air vents (3502, 3504, and 3506) on the bottom base frame 3320D are connected to the plurality of air ducts that are placed in the bottom base frame 3320D and below deck floor 3340 and at least some of the carriers ((3302, 3304, 3306, 3308, and 3310).
• the hot air then flows horizontally in a direction as indicated by arrow 1 and arrow 4 through the horizontal portions of the air ducts, and then the hot air flows out of the frame through the air vents (3502, 3504, and 3506) on the bottom base frame 3320D as indicated by arrows 1 and arrow 4.
• the thermal cycler may be used to heat the PCR reaction mixtures to very high temperatures. As a result, the PCR reaction mixtures may evaporate, thereby causing unreliable PCR results. In addition, the PCR reaction mixtures may be contaminated during the thermos-cycling process. Therefore, in some embodiments, sealing lids may be used to cover the wells of a PCR plate during thermo-cycling to reduce evaporation and contamination of the reaction mixtures.
• Figure 39 illustrates a disposable PCR lid 3900.
• a disposable PCR lid 3900 may be picked up by a core gripper controlled by a movable gantry.
• Figure 40 illustrates a core gripper 4002 lifting a piece of labware 4004 up and moving the piece of labware 4004 to another position within the deck.
• the core gripper 4002 may be programmed to lift a disposable PCR lid 3900 from rack 226 (see Figure 2) for storing lids and place the disposable PCR lid 3900 to seal a PCR plate that has been loaded onto the thermal cycler. After the thermos cycling process, the core gripper 4002 may further be programmed to unseal the PCR plate by lifting the disposable PCR lid 3900 up.
• the core gripper 4002 may then be programmed to move the disposable PCR lid 3900 over a waste disposal bin (236, 336, or 3336) and drop the lid into the waste disposal bin.
• the waste disposal bin is also used to store recycled tips.
• Figure 41 illustrates a plurality of disposable tips that may be attached to the pipetting head.
• the pipetting head e.g., the multi-channel pipetting head 402 shown in Figure 4
• the pipetting head may be programmed to move to the waste disposal bin and drop the disposable tips into the waste disposal bin.
• the disposal PCR lids tend to stack up and topple over, causing contamination and system malfunctioning. Therefore, improved techniques of storing recycled tips and lids would be desirable.
• the automated library generator may alleviate the above problems by disposing the recycled tips and lids into different sections of the waste disposal bin.
• a divider may be added to the waste disposal bin for separating the recycled tips and lids.
• Figure 42 illustrates that with the added divider 4202, one side of the waste disposal bin is used for storing the tips and the other side of the waste disposal bin is used for storing the lids.
• One advantage is that it prevents the lids from stacking up and toppling over, thereby reducing system malfunctioning.
• Another advantage is that it allows the recycling of the tips and the lids while preventing contamination.
• the gantry may be programmed to translate the pipetting head to a set of x and y positions, wherein the x and y positions are measured in a plane substantially parallel to a floor of an instrument deck.
• the x and y positions are determined as the x and y positions corresponding to the portion of the waste disposal bin for storing disposable tips.
• the x and y positions are determined as the x and y positions of the pipetting head such that when the pipetting head is controlled to drop the disposable tips, the disposable tips are deposited on the portion of the waste disposal bin for storing tips.
• the gantry may be programmed to translate the core gripper to a set of x and y positions, wherein the x and y positions are measured in a plane substantially parallel to a floor of an instrument deck.
• the x and y positions are determined as the x and y positions corresponding to the portion of the waste disposal bin for storing disposable lids.
• the x and y positions are determined as the x and y positions of the core gripper such that when the core gripper is controlled to release the disposable lids, the disposable lids are deposited on the portion of the waste disposal bin for storing the disposable lids.
• An automated library generator may include an integrated communication and power base compartment.
• Figure 43 A illustrates a view of an automated library generator 4300 that includes an integrated communication and power base compartment 4310.
• Figure 43B and Figure 43C each illustrates a view of the integrated communication and power base compartment 4310.
• the integrated communication and power base compartment 4310 integrates a plurality of power and communication components at the base of the system by enclosing the components in a compartment below the bottom base frame 3320D.
• the integrated communication and power base compartment 4310 provides a clean design and ensures electric safety by eliminating the use of external power strips and external boxes/modules to provide power and connectivity to the automatic library generator.
• compartment 4310 includes a separate power plug/socket 4320 for powering the thermal cycler and another power plug/socket 4330 for powering the entire system.
• Each of the power plug/socket has its own switch to turn the power on or off.
• the switch for the entire system may be used to turn on the entire system, such that all components are up and running.
• compartment 4310 further includes a plurality of USB (Universal Serial Bus) receptacles 4340 for providing connection, communication, and power between the automatic library generator and other computers or peripherals.
• Compartment 4310 further includes a LAN (Local Area Networks) port 4350, which allows the automatic library generator to be connected with other client machines, server machines and network devices via the LAN port.
• USB Universal Serial Bus
• LAN Local Area Networks
• FIG. 44 illustrates an exemplary schematic diagram 4400 showing the connections of the integrated communication and power base compartment with other components of the automatic library generator.
• the integrated communication and power base compartment encloses at least one USB hub 4402, Ethernet switch 4404, and other ports for data transfer.
• USB hub 4402 provides USB connections to computers or peripherals, such as a tablet/touch screen computer 4406, a HEPA filter hood 4408, a chip manifold module 4410 (CMM), and a cold plate controller (CP AC) 4412.
• Ethernet switch 4404 provides communication of devices through a local area network (LAN).
• the devices connected to the LAN may include an on-deck thermal cycler controller (ODTC) 4414 that controls the ODTC 4416.
• Another device connected to the LAN is the tablet/touch screen computer 4406.
• ODTC thermal cycler controller
• Another device connected to the LAN is a pair of barcode scanners 4418.
• Another device connected to the LAN is a module 4420 that includes multiple components, including a module 4440 with two DC-DC converters, a barcode reader kit 4460, and a power supply 4480.
• the integrated communication and power base compartment encloses an alternating current (AC) & direct current (DC) power distribution module 4482.
• AC and DC power distribution module 4482 may be connected to a primary power source 4483.
• Module 4482 includes an AC power distributor 4484 that distributes AC power to various components of the automatic library generator, including Ethernet switch 4404, tablet/touch screen computer 4406, USB hub 4402, on-deck thermal cycler controller (ODTC) 4414, cold plate controller 4412, and module 4420.
• Module 4482 includes an AC to DC converter 4486 that distributes DC power to various components of the automatic library generator, including the pair of barcode scanners 4418, and the chip manifold module 4410.
• Magnetic separator plate 214 in Ligure 2 performs magnetic bead based cleanup. Magnetic beads are used for DNA purification and fragment size selection.
• Automated single cell sequencing system 200 uses the single-cell RNA-seq technology to analyze transcriptomes on a cell-by-cell basis through the use of microfluidic partitioning to capture single cells and prepare barcoded, next-generation sequencing (NGS) cDNA libraries. Specifically, single cells, reverse transcription (RT) reagents, gel beads containing barcoded oligonucleotides, and oil are combined on a microfluidic chip to form reaction vesicles called Gel Beads in Emulsion, or OEMs. After incubation, OEMs are broken and pooled fractions are recovered.
• RT reverse transcription
• Silane magnetic beads are used to purify the first-strand cDNA from the post GEM-RT reaction mixture, which includes leftover biochemical reagents and primers.
• consumables e.g., test tubes or wells
• the magnetic beads may be loaded onto the magnetic separator plate 214 where the magnetic bead based cleanup is performed. Barcoded, full-length cDNA is then amplified via PCR to generate sufficient mass for library construction.
• Figure 7A illustrates a top view of an embodiment of a magnetic separator plate 702.
• Figure 7B illustrates a cross sectional view of the magnetic separator plate 702.
• Figure 7C illustrates another view of the magnetic separator plate 702.
• magnetic separator plate 702 is a magnet holder plate that holds an array of magnets 704.
• Magnetic separator plate 702 is a 96-ring magnet plate
• the array of magnets 704 is an 8x12 array of magnets with eight magnets in a row and twelve magnets in a column.
• each of the magnets 704 is a ring magnet.
• a ring magnet may be a magnet with a shape of a hollow cylinder that is empty from inside and with differing internal and external radii. The hollow space of the cylinder allows a bottom end of a tube to be inserted therein.
• a tube received by a ring magnet may be a finger-like length of glass or plastic tubing that is open at the top and closed at the bottom.
• FIG 25 illustrates a plurality of strip tubes 2502 that may be loaded onto the magnetic separator plate 214 or magnetic separator plate 702 where the magnetic bead based cleanup may be performed.
• each of the strip tubes 2502 includes eight tubes 2504 for storing the reaction mixture and the magnetic beads.
• Figure 8 illustrates an exemplary consumable 802 that may be loaded onto the magnetic separator plate 214 or magnetic separator plate 702 where the magnetic bead based cleanup may be performed.
• consumable 802 is a 96-tube polymerase chain reaction (PCR) tube holder plate with an array of tubes 804 arranged as an 8x12 array of tubes with eight tubes in a row and twelve tubes in a column.
• PCR polymerase chain reaction
• Figure 45A illustrates a top view of the 96-tube PCR plate 802 being loaded onto the magnetic separator plate 702.
• Figure 45B illustrates a cross sectional view of the 96-tube PCR plate 802 being loaded onto the magnetic separator plate 702.
• Figure 45C illustrates a portion of a magnified cross-sectional view of the 96-tube PCR plate 802 being loaded onto the magnetic separator plate 702.
• the hollow space of a ring magnet (e.g., 704A or 704B) allows the bottom end of a tube (e.g., 804A or 804B) to be inserted therein.
• both the PCR plate 802 and the magnetic separator plate 702 are manufactured parts that have their respective sets of associated tolerances. All dimensions of a manufactured part have their associated tolerance, the amount that the particular dimension is allowed to vary. The tolerance is the difference between the maximum and minimum limits.
• the length 806A (the length from the center of the ring magnet 704A to the center of the ring magnet 704B) and the length 806B (the length from the center of the ring magnet 704B to the center of the ring magnet 704C) may not be the same.
• the length 808A (the length from the center of the tube 804A to the center of the tube 804B) and the length 808B (the length from the center of the tube 808B to the center of the tube 804C) may not be the same.
• an improved magnetic separator comprises an array of magnets configured to interact with an array of tubes, wherein the array of tubes is attached to a plate.
• the magnetic separator further includes a magnetic separator plate adapter.
• the adapter comprises a raised frame extending around a periphery of the array of magnets such that the raised frame is configured to support the plate, such that the array of tubes are suspended above the array of magnets.
• Figure 9 A illustrates a top view of a magnetic separator plate adapter
• magnetic separator plate adapter 902 includes four collars 904 at the four comers of the adapter. The collars 904 may be used to fix the location (the x and y location on the deck) of a consumable, such as a 96-tube PCR plate.
• each of the collars 904 constrains the x location and the y location of the tube holder plate by having a tube inserted into the collar.
• the magnetic separator plate adapter 902 further includes four cylindrical feet 906 at the four comers of the adapter, such that the magnetic separator plate adapter 902 may be mounted on the magnetic separator plate 702.
• magnetic separator plate adapter 902 may be formed of plastic and includes skirts.
• Magnetic separator plate adapter 902 may include a plurality of calibration posts 908.
• Figure 11 A illustrates a top view of the magnetic separator plate adapter
• Figure 12A illustrates a view of the magnetic separator plate adapter 902 about to be loaded onto the magnetic separator plate 702 and the 96-tube PCR plate 802 about to be loaded onto the magnetic separator plate adapter 902.
• Figure 12B illustrates another view of the magnetic separator plate adapter 902 being loaded onto the magnetic separator plate 702 and the 96-tube PCR plate 802 being loaded onto the magnetic separator plate adapter 902.
• Figure 46 A illustrates a top view of the magnetic separator plate adapter 902 being loaded onto the magnetic separator plate 702, and the 96-tube PCR plate 802 being loaded onto the magnetic separator plate adapter 902.
• Figure 46B illustrates a cross-sectional view of the magnetic separator plate adapter 902 being loaded onto the magnetic separator plate 702, and the 96-tube PCR plate 802 being loaded onto the magnetic separator plate adapter 902.
• Figure 46C illustrates another cross-sectional view of the magnetic separator plate adapter 902 being loaded onto the magnetic separator plate 702, and the 96-tube PCR plate 802 being loaded onto the magnetic separator plate adapter 902.
• Figure 46D illustrates a portion of a magnified cross-sectional view of the magnetic separator plate adapter 902 being loaded onto the magnetic separator plate 702, and the 96-tube PCR plate 802 being loaded onto the magnetic separator plate adapter 902.

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• 2020
  • 2020-11-18 EP EP20824795.7A patent/EP4062180A1/de active Pending
  • 2020-11-18 WO PCT/US2020/061116 patent/WO2021102043A1/en unknown
  • 2020-11-18 CN CN202080085125.2A patent/CN114868021A/zh active Pending

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