|
|
GEO help: Mouse over screen elements for information. |
|
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 |
Oct 04, 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 |
GSM4784067 |
scATAC-seq of ficoll-purified, 0.25x 10xNIB isolated nuclei, unsorted PBMCs |
GSM4784068 |
scATAC-seq of ficoll-purified, 0.1x 10xNIB isolated nuclei, unsorted PBMCs |
GSM4784069 |
scATAC-seq of ficoll-purified, 1x ANIB isolated nuclei, unsorted PBMCs |
GSM4784070 |
scATAC-seq of ficoll-purified, 0.01% digitonin permeabilized, unsorted PBMCs 7811BW |
GSM4784071 |
scATAC-seq of ficoll-purified, 0.05% digitonin permeabilized, unsorted PBMCs |
GSM4784072 |
scATAC-seq of ficoll-purified, 0.1% digitonin permeabilized, unsorted PBMCs |
GSM4784073 |
scATAC-seq of ficoll-purified, 0.2% digitonin permeabilized, unsorted PBMCs |
GSM4784074 |
scATAC-seq of ficoll-purified, 0.01% digitonin permeabilized, unsorted PBMCs BRH1291132 |
GSM4784075 |
scATAC-seq of ficoll-purified, 0.01% digitonin permeabilized, FACS neutrophil-depleted PBMCs |
GSM4784076 |
scATAC-seq of ficoll-purified, 0.01% digitonin permeabilized, undepleted PBMCs |
GSM4784077 |
scATAC-seq of ficoll-purified, 0.01% digitonin permeabilized, magnetic bead anti-CD15-depleted PBMCs |
GSM4784078 |
scATAC-seq of leukapheresis-purified, 0.01% digitonin permeabilized, undepleted PBMCs |
GSM4784079 |
scATAC-seq of leukapheresis-purified, 0.01% digitonin permeabilized, magnetic bead anti-CD15-depleted PBMCs |
GSM4784080 |
scATAC-seq of ficoll-purified, 1x 10xNIB isolated nuclei, unsorted PBMCs from donor RG1131 |
GSM4784081 |
scATAC-seq of ficoll-purified, 1x 10xNIB isolated nuclei, FACS dead cell/debris-depleted PBMCs from donor RG1131 |
GSM4784082 |
scATAC-seq of ficoll-purified, 1x 10xNIB isolated nuclei, FACS neutrophil-depleted PBMCs from donor RG1131 |
GSM4784083 |
scATAC-seq of ficoll-purified, 0.01% digitonin permeabilized, unsorted PBMCs from donor RG1131 |
GSM4784084 |
scATAC-seq of ficoll-purified, 0.01% digitonin permeabilized, FACS dead cell/debris-depleted PBMCs from donor RG1131 |
GSM4784085 |
scATAC-seq of ficoll-purified, 0.01% digitonin permeabilized, FACS neutrophil-depleted PBMCs from donor RG1131 |
GSM4784086 |
ICICLE-seq of leukapheresis-purified, 0.01% digitonin permeabilized PBMCs, well 1 |
GSM4784087 |
ICICLE-seq of leukapheresis-purified, 0.01% digitonin permeabilized PBMCs, well 2 |
GSM4784088 |
ICICLE-seq of leukapheresis-purified, 0.01% digitonin permeabilized PBMCs, well 3 |
GSM4949911 |
TEA-seq of leukapheresis-purified, 0.01% digitonin permeabilized, FACS neutrophil-depleted PBMCs, well 1 |
GSM5123948 |
scATAC-seq of leukapheresis-purified, 0.01% digitonin permeabilized, FACS neutrophil-depleted PBMCs, method comparison |
GSM5123949 |
Multiome RNA/ATAC of leukapheresis-purified, isolated nuclei, FACS neutrophil-depleted PBMCs, method comparison |
GSM5123950 |
Multiome RNA/ATAC of leukapheresis-purified, 0.01% digitonin perm, FACS neutrophil-depleted PBMCs, method comparison |
GSM5123951 |
TEA-seq of leukapheresis-purified, 0.01% digitonin perm, FACS neutrophil-depleted PBMCs, method comparison, well 1 |
GSM5123952 |
TEA-seq of leukapheresis-purified, 0.01% digitonin perm, FACS neutrophil-depleted PBMCs, method comparison, well 2 |
GSM5123953 |
TEA-seq of leukapheresis-purified, 0.01% digitonin perm, FACS neutrophil-depleted PBMCs, method comparison, well 3 |
GSM5123954 |
TEA-seq of leukapheresis-purified, 0.01% digitonin perm, FACS neutrophil-depleted PBMCs, method comparison, well 4 |
GSM5123955 |
CITE-seq of leukapheresis-purified, 0.01% digitonin permeabilized, FACS neutrophil-depleted PBMCs, method comparison |
|
Relations |
BioProject |
PRJNA663623 |
Supplementary file |
Size |
Download |
File type/resource |
GSE158013_RAW.tar |
14.3 Gb |
(http)(custom) |
TAR (of CSV, H5, TSV) |
Raw data not provided for this record |
Processed data provided as supplementary file |
|
|
|
|
|