Abstract: A method includes receiving an image of a plurality of fiducial markers, where the plurality of fiducial markers has at least one predetermined height relative to a substrate. The method also includes determining at least one optical metric associated with the plurality of fiducial markers within the image, and determining a calibration model based on the at least one predetermined height and the at least one optical metric.

Abstract: The present disclosure relates to methods to deconvolute a mixture sample of genetic material from different origins or sources. The disclosed methods can be used in various applications, including, the non-invasive determination of a fetal genome, a fetal -ome (e.g. exome). or other targeted fetal locus from cell-free nucleic acids in maternal plasma or other body fluids; the determination of cancer-associated mutations from cell-free nucleic acids in a body fluid sample that contains a mixture of nucleic acids from normal cells and tumor cells; and quantification of donor cell contamination using a body fluid from a transplantation recipient to monitor and/or predict the outcome of a transplantation procedure.

Abstract: The present disclosure relates to materials and methods for spatially analyzing nucleic acids that have been fragmented with a transposase enzyme, alone or in combination with other types of analytes.

Abstract: Described herein are methods, compositions, and systems useful for detecting transplant rejection and associated abnormal conditions in solid organ transplant recipients, such as kidney transplant recipients. Methods described herein may involve combined assessment of blood gene expression profiles from an assessment of particular, related mRNA transcript levels and donor-derived cell-free nucleic acids (dd-cfDNA).

Abstract: Many regions of genomic DNA are highly similar to other regions of the genome and thus are very difficult to capture without also capturing the similar, undesired regions. This leads to over-sequencing of regions for which there is no interest and lowers coverage of the desired regions. To minimize the capture of non-desired regions, blocking baits have been designed to prevent similar but non-desired fragments from being captured. This allows more directed sequencing of the regions of interest. Blocking baits differ from capture baits in that they have modestly different sequence that preferentially bind the non-desired DNA and do not contain a biotin or other modification so remain behind when the capture baits are selected.

Abstract: The disclosure provides devices, systems and methods for the generation of encapsulated reagents and the partitioning of encapsulated reagents for use in subsequent analyses and/or processing, such as in the field of biological analyses and characterization.

Abstract: Disclosed herein, inter alia, are compositions and methods of use thereof for interrogating a sample comprising a cell.

Abstract: A computer-implemented method is provided for identifying V(D)J cells from at least one data set including a plurality of sequence barcode records from a plurality of single cells. Embodiments of the method include analyzing nucleic acid sequences from nucleic acid sequencing data set(s), comprising comparing a plurality of barcode records in a V(D)J sequencing data set(s) to a plurality of barcode records in a gene expression (GEX) data set(s), to identify a plurality of single V(D)J cells from V(D)J sequencing data set(s), wherein each single V(D)J cell has one or more full length V(D)J contigs.

Abstract: Provided is primers, where the primers specifically bind to a polynucleotide and are used to amplify the polynucleotide; and the polynucleotide comprises or consists of the following sequence: 1) the nucleotide sequence represented by SEQ ID NO: 5; or 2) the complete complementary sequence of the sequence represented by SEQ ID NO: 5; or 3) a nucleotide sequence being identical to 300 bp or more contiguous nucleotides in the sequence of the above 1) or 2), where the nucleotide sequence being identical to 300 bp or more contiguous nucleotides is unique to a male Ginkgo biloba plant; and the sequences of the primers are respectively represented by SEQ ID NO: 1 and SEQ ID NO: 2.

Abstract: The application provides compositions including engineered reverse transcriptases with at least one altered reverse-transcriptase related activity. The engineered reverse transcriptases or reverse transcription enzymes unexpectedly exhibit one or more altered reverse transcriptase related activities such as but not limited to altered template switching efficiency, altered transcription efficiency or both.

Abstract: A machine vision system for calibrating and/or positioning of various motion control modules of an opto-fluidic instrument/tool/instrument having integrated optics and fluidics modules configured for imaging of biological specimens is disclosed. The machine vision system includes determining 3D positions of an object within a reference coordinate system based on a plurality of stereo-images comprising the object; generating a transformation matrix based on the determined 3D positions of the object with respect to a reference position; and calibrating one or more motion control systems based on the determined transformation matrix. The methods also include determining a 3D position of an object within a reference coordinate system based on a stereo-image of the object; generating a 3D offset value between the determined 3D position and a reference location of the object; updating the 3D position using the 3D offset value; and positioning the object based on the corrected 3D position.

Abstract: The application provides compositions including engineered fusion reverse transcriptases with at least one altered reverse-transcriptase related activity. The engineered fusion reverse transcriptases or reverse transcription enzymes unexpectedly exhibit one or more altered reverse transcriptase related activities such as but not limited to altered template switching efficiency, altered transcription efficiency or both.

Abstract: Embodiments of the invention include methods of identifying microorganisms and/or diagnosing infections in subjects cause by microorganisms. Embodiments of the invention may also include further characterizing (e.g., determining the presence of one or more antibiotic resistance markers) the microorganisms and determining a strain identity of the microorganisms.

Abstract: Various embodiments of the present disclosure disclose methods and systems for heat exchange in an opto-fluidic instrument. The opto-fluidic instrument includes a sample interface module (SIM), an illumination module, a camera module, and a reagent deck. A coolant from a coolant reservoir is directed into one or more of the modules so that heat exchange occurs at each module with the coolant. The heated coolant from the one or more modules flows to a radiator for cooling, for example, with fans flowing ambient air over the radiator, before the cooled coolant is returned to the coolant reservoir for subsequent use in cooling the modules.

Abstract: Various embodiments of the present disclosure disclose methods and systems for dispensing a reagent into a sample well and efficiently extracting the dispensed reagent from the sample well after the reagent is used for detecting molecules in a sample. The amount of probe reagents dispensed may be no more than what is needed to immerse the sample and allow effective probing of the sample by the probes in the reagent.

Abstract: An optical assembly of a machine vision system for calibrating and/or positioning of various motion control modules of an analytical system/tool/instrument having integrated optics and fluidics modules configured for imaging of biological specimens is disclosed. The optical assembly includes one or more light sources configured to generate a first light beam and a second light beam that intersects the first light beam at an intersection region to illuminate an object within the intersection region; a sensor array configured to receive the first light beam and the second light beam to thereby form a stereo-image based on received light from the first light beam and the second light beam; a first imaging mirror configured to reflect the first beam after the intersection region and towards the sensor array; and a second imaging mirror configured to reflect the second beam after the intersection region and towards the sensor array.

Abstract: Provided in some aspects are methods for light-controlled in situ surface patterning of a substrate. Compositions such as nucleic acid arrays produced by the methods are also disclosed. In some embodiments, a method disclosed herein comprises using photocontrollable ligation of nucleic acid molecules with splints, wherein at least one of the splints comprises a photo-crosslinkable moiety. Photo-induced crosslinking of the splint to oligonucleotide molecules immobilized on a substrate allows the splint to remain attached to the oligonucleotide molecules during subsequent rounds of photoresist application and removal. A large diversity of barcodes can be created in molecules on the substrate via sequential rounds of light exposure, hybridization, and ligation.

Abstract: Various embodiments of the present disclosure disclose methods and systems for actively monitoring an opto-fluidic instrument for vibrational disturbances and correcting images obtained during the detected disturbances. In various embodiments, an optical imaging system may acquire Z-stack images of samples supported by an XY-stage. Vibrations can cause individual stacks to be sheared, i.e., to not be co-located with respect to neighboring Z-stacks. In various embodiments, an offset between the measured positions and the expected positions of the sheared stacks may be computed, and a determination as to whether to correct or reacquire the Z-stack images may be made based at least in part on the computed offset.

Abstract: A bottle connection assembly is configured to seal a bottle and provide a fluidic path between the interior of the bottle and its exterior for drawing fluids therefrom. The fluids can be reagents used for preparing a sample for the identification of target molecules. A bottle cap for capping the bottle is positioned below the bottle interface assembly and includes a female fitting configured to engage with a male fitting of the bottle interface assembly to form a sealed fluidic connection.

Abstract: An imaging system includes an optical mounting plate having an aperture disposed between a first portion and a second portion, an imaging sensor disposed on the first portion, an objective lens disposed on the second portion, and an illumination assembly arranged within the aperture and disposed between the imaging sensor and the objective lens. The imaging system includes a heat sink coupled to the illumination assembly and configured to transfer heat away from light sources of the illumination assembly via a working fluid that flows through the heat sink.