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TXG 10x Genomics

APP
Utility
Systems and Methods for Correcting Sample Preparation Artifacts In Droplet-based Sequencing
21 Oct 21
A method for filtering open chromatin regions on a cell barcode genomic sequence dataset is provided, comprising receiving, by one or more processors, a cell barcode genomic sequence dataset, the method comprising a plurality of fragment sequence reads and barcodes associated with the plurality of fragment sequence reads.
Preyas Shah, Li Wang, Brett Olsen
Filed: 15 Apr 21
APP
Utility
Methods for Generating Spatially Barcoded Arrays
21 Oct 21
This disclosure relates to methods for generating spatially barcoded arrays using concentration gradients.
Eswar Prasad Ramachandran Iyer, Michael Schnall-Levin, Augusto Manuel Tentori, Tarjei Sigurd Mikkelsen, Benjamin Hindson, Michael Ybarra Lucero, Rajiv Bharadwaj, Yifeng Yin, Zachary Bent, Jennifer Chew, Meghan L. F. Frey, Linda Kvastad, Joakim Lundeberg, Eva Gracia Villacampa
Filed: 27 Aug 19
APP
Utility
Systems and Methods for Analyzing and Aggregating Open Chromatin Signatures at Single Cell Resolution
21 Oct 21
A method for conducting a customized analysis of open chromatin regions on a cell, comprising receiving an output file for a cell barcode genomic sequence dataset, the output file comprising a peak-barcode matrix, wherein each peak is defined by a plurality of fragment sequences aligned within a peak region, a unique barcode is associated with each fragment sequence in the dataset, and the peak-barcode matrix pairs each peak with the barcodes of the aligned fragments; and cell clusters with cells aggregated based on similarity in accessibility of specific transcription factor binding motifs associated with each cell, wherein the accessibility is determined via a differential accessibility analysis.
Preyas SHAH, Li WANG, Brett OLSEN
Filed: 15 Apr 21
APP
Utility
Systems and Methods for Visualizing Adaptive Immune Cell Clonotyping Data
21 Oct 21
An interactive visualization system is disclosed herein.
David Jaffe, Sreenath Krishnan, Wyatt McDonnell, Michael Stubbington
Filed: 16 Apr 21
APP
Utility
Resolving Spatial Arrays
14 Oct 21
Methods for determining a location of a feature in a spatial array of features include: providing a spatial array including a plurality of features on a substrate, where a feature of the plurality of features has a capture probe, and where the capture probe has a spatial barcode and a constant sequence; hybridizing a first sequencing probe to the spatial barcode, where the first sequencing probe has a first label and a first nucleotide sequence; obtaining a first image of the first label with the first sequencing probe hybridized to the spatial barcode; determining, based on the first image, a first portion of a sequence of the spatial barcode; and associating the feature with a location in the spatial array based on a location of the first label in the first image.
Michael Ybarra Lucero, Michael Schnall-Levin, Tarjei Sigurd Mikkelsen, Eswar Prasad Ramachandran Iyer, Paul Giresi, Benjamin Hindson
Filed: 27 Aug 19
GRANT
Utility
Instrument systems for integrated sample processing
5 Oct 21
An integrated system for processing and preparing samples for analysis may include a microfluidic device including a plurality of parallel channel networks for partitioning the samples including various fluids, and connected to a plurality of inlet and outlet reservoirs, at least a portion of the fluids comprising reagents, a holder including a closeable lid hingedly coupled thereto, in which in a closed configuration, the lid secures the microfluidic device in the holder, and in an open configuration, the lid is a stand orienting the microfluidic device at a desired angle to facilitate recovery of partitions or droplets from the partitioned samples generated within the microfluidic device, and an instrument configured to receive the holder and apply a pressure differential between the plurality of inlet and outlet reservoirs to drive fluid movement within the channel networks.
Donald A. Masquelier, Benjamin Hindson, Kevin Ness, Rajiv Bharadwaj
Filed: 12 Feb 19
APP
Utility
Methods for Analyzing Nucleic Acids
30 Sep 21
Aspects of the present invention include analyzing nucleic acids from single cells using methods that include using tagged polynucleotides containing multiplex identifier sequences.
Sydney Brenner, Gi Mikawa, Robert Osborne, Andrew Slatter
Filed: 3 Feb 21
GRANT
Utility
Methods and systems for macromolecule labeling
28 Sep 21
The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing and analyte characterization from one or more cells.
Katherine Pfeiffer, Sarah Taylor, Michael Stubbington
Filed: 4 Apr 19
GRANT
Utility
Systems and methods for nucleic acid sequence assembly
28 Sep 21
Determination of a nucleic acid sequence using sequence reads of the nucleic acid.
Michael Schnall-Levin, Iain MacCallum
Filed: 2 Nov 17
APP
Utility
Methods and Devices for Detecting and Sorting Droplets or Particles
23 Sep 21
Devices, systems, and their methods of use, for detecting and/or sorting droplets or particles are provided.
Rajiv BHARADWAJ, Jianying CAO, Mohammad Rahimi LENJI, Anthony MAKAREWICZ, Alireza SALMANZADEH
Filed: 9 Jun 21
APP
Utility
Systems and Methods for Determining Structural Variation and Phasing Using Variant Call Data
23 Sep 21
Systems and methods for determining structural variation and phasing using variant call data obtained from nucleic acid of a biological sample are provided.
Sofia Kyriazopoulou-Panagiotopoulou, Patrick Marks, Michael Schnall-Levin, Xinying Zheng, Mirna Jarosz, Serge Saxonov, Kristina Giorda, Patrice Mudivarti, Heather Ordonez, Jessica Terry, William Haynes Heaton
Filed: 13 Nov 20
APP
Utility
Generating Capture Probes for Spatial Analysis
16 Sep 21
The present disclosure relates to compositions and methods for generating capture probes on a substrate for identifying the location of analytes in a biological sample.
Yifeng Yin, Eswar Prasad Ramachandran Iyer, Zachary Bent, Stefania Giacomello, Meghan L. F. Frey, Alexander Gagnon, Erik Leonard Henrik Borgstrom
Filed: 25 Mar 21
APP
Utility
Systems and Methods for Nucleic Acid Processing Using Degenerate Nucleotides
16 Sep 21
Provided herein are compositions, systems and methods for tagging molecular events, reactions, species, etc., but without the need for complex, highly diverse libraries of tagging molecules.
Paul Ryvkin, Jason Underwood, Michael Schnall-Levin, Tarjei Mikkelsen, Benjamin Hindson
Filed: 13 Mar 20
APP
Utility
Methods for Spatial Analysis Using Rna-templated Ligation
16 Sep 21
Provided herein are methods of detecting an analyte of interest to interrogate spatial gene expression in a sample using RNA-templated ligation.
James Michael Chell, Marlon Stoeckius, Jonathan Alles, Caroline Julie Gallant, Christina Galonska, Felice Alessio Bava, Layla Katiraee
Filed: 1 Apr 21
APP
Utility
Functionalized Gel Beads
9 Sep 21
The present disclosure provides methods of generating supports (e.g., beads) comprising barcode molecules coupled thereto.
Zachary Bent, Elliott Meer, Daniel Riordan, Paul Ryvkin, Niranjan Srinivas, Jessica Terry, Alex Gagnon
Filed: 11 Nov 20
APP
Utility
Three-dimensional Spatial Transcriptomics with Sequencing Readout
9 Sep 21
In some embodiments described herein are methods for three-dimensional analysis of a biological sample, comprising migrating a population of spatial probes into the biological sample in each of three dimensions, wherein each spatial probe comprises a targeting domain and a migration domain.
Felice Alessio BAVA
Filed: 4 Mar 21
APP
Utility
Methods and Systems for Processing Polynucleotides
9 Sep 21
The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing.
Benjamin Hindson, Christopher Hindson, Michael Schnall-Levin, Kevin Ness, Mirna Jarosz, Serge Saxonov, Paul Hardenbol
Filed: 7 May 21
APP
Utility
Cell Population Analysis Using Single Nucleotide Polymorphisms from Single Cell Transcriptomes
9 Sep 21
The disclosure provides methods and systems for producing single cell RNA sequencing data.
Xinying Zheng, Jason H. Bielas, Mark T. Gregory, Benjamin Hindson, Tarjei Sigurd Mikkelsen, Ryan Wilson, Paul Ryvkin
Filed: 23 Sep 20
APP
Utility
Method for Isolating Nuclei and Cells from Tissues
2 Sep 21
A method of extracting and isolating fixed biological particles, such as fixed cells and/or fixed nuclei from snap-frozen biological tissue yields dramatically improved amounts of ligation products and an increase in targeted single cell RNA sequence data quality and sensitivity in subsequent RNA-templated ligation.
Jawad N. Abousoud
Filed: 26 Feb 21
APP
Utility
Methods and Systems for Detection of Protein-dna Interactions Using Proximity Ligation
2 Sep 21
The present disclosure provides systems and methods that facilitate, at the single cell level, the linking of information from multiple different antibodies (e.g., antibodies specific for different proteins) to the genomic locations of the protein binding sites, while being able to distinguish these distinct events between antibodies.
Paul GIRESI
Filed: 19 Feb 21
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