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Series GSE158013 Query DataSets for GSE158013
Status Public on Apr 02, 2021
Title Simultaneous trimodal single cell measurement of transcripts, epitopes, and chromatin accessibility using TEA-seq
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary Single-cell measurements of cellular characteristics have been instrumental in understanding the heterogeneous pathways that drive differentiation, cellular responses to signals, and human disease. Recent advances have allowed paired capture of protein abundance and transcriptomic state, but a lack of epigenetic information in these assays has left a missing link to gene regulation. Using the heterogeneous mixture of cells in human peripheral blood as a test case, we developed a novel scATAC-seq workflow that increases signal-to-noise and allows paired measurement of cell surface markers and chromatin accessibility: Integrated Cellular Indexing of Chromatin Landscape and Epitopes (ICICLE-seq). We extended this approach using a droplet-based multiomics platform to develop a trimodal assay that simultaneously measures Transcriptomics (scRNA-seq), Epitopes, and chromatin Accessibility (scATAC-seq) from thousands of single cells, which we term TEA-seq. Together, these multimodal single-cell assays provide a novel toolkit to identify type-specific gene regulation and expression grounded in phenotypically defined cell types.
 
Overall design PBMCs were profiled using a variety of multi-modal sequencing assays. We processed PBMCs through a number of single-cell and single-nuclei ATAC-seq protocols during development and identification of an optimized scATAC-seq assay. We processed PBMCs through our ICICLE-seq assay: a novel method for simultaneous profiling of chromatin accessibility and surface epitopes. We processed PBMCs through TEA-seq: a novel method for simulaneous single-cell profling of transcripts, epitopes, and chromatin accessiblity. As part of TEA-seq testing we prepared CITE-seq, scATAC-seq, single-cell and single-nuclei 10x Multiome ATAC + Gene Expression, and TEA-seq libraries from the same PBMC sample in parallel.

**The submitter declares that the raw data are being deposited in dbGaP due to patient privacy concerns. dbGap: phs002316**
 
Contributor(s) Swanson E, Lord C, Green R, Bumol TF, Graybuck LT, Skene PJ
Citation(s) 33835024
Submission date Sep 15, 2020
Last update date Apr 29, 2021
Contact name Allen Institute For Immunology
E-mail(s) xiaojun.li@alleninstitute.org
Phone 2065487135
Organization name Allen Institute
Street address 615 Westlake Ave N, Seattle, WA
City Seattle
State/province Washington
ZIP/Postal code 98109
Country USA
 
Platforms (2)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (34)
GSM4784064 scATAC-seq of leukapheresis-purified, 0.01% digitonin permeabilized, unsorted PBMCs
GSM4784065 scATAC-seq of leukapheresis-purified, 0.01% digitonin permeabilized, FACS neutrophil-depleted PBMCs
GSM4784066 scATAC-seq of ficoll-purified, 1x 10xNIB isolated nuclei, unsorted PBMCs
Relations
BioProject PRJNA663623

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Supplementary file Size Download File type/resource
GSE158013_RAW.tar 13.9 Gb (http)(custom) TAR (of CSV, H5, TSV)
Raw data not provided for this record
Processed data provided as supplementary file

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