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Series GSE117089 Query DataSets for GSE117089
Status Public on Aug 29, 2018
Title Joint profiling of chromatin accessibility and gene expression in thousands of single cells
Organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Here we describe sci-CAR, a combinatorial indexing strategy to jointly profile chromatin accessibility and mRNA in each of thousands of single cells. As a proof-of-concept, we apply sci-CAR to 4,825 cells comprising a time-series of dexamethasone treatment, as well as to 11,233 cells from the mouse kidney.
Overall design single cell RNA-seq and ATAC-seq co-profiling for HEK293T cells, NIH/3T3 cells, A549 cells across three treatment conditions (DEX 0 hour, 1 hour and 3 hour treatment), and wild type mouse kidney.
Contributor(s) Cao J, Cusanovich DA, Ramani V, Pliner H, Hill A, Aghamirzaie D, Daza RM, McFaline J, Packer JS, Christiansen L, Steemers FJ, Adey A, Trapnell C, Shendure J
Citation(s) 30166440
Submission date Jul 13, 2018
Last update date Mar 25, 2019
Contact name Junyue Cao
Organization name University of Washington
Department Department of Genome Sciences
Lab Shendure lab
Street address Foege Building S-210, 3720 15th Ave NE
City Seattle
State/province WA
ZIP/Postal code 98195-5065
Country USA
Platforms (2)
GPL19057 Illumina NextSeq 500 (Mus musculus)
GPL19415 Illumina NextSeq 500 (Homo sapiens; Mus musculus)
Samples (6)
GSM3271040 HEK293T, NIH/3T3, A549 cells, sci-CAR RNA-seq
GSM3271041 HEK293T, NIH/3T3, A549 cells, sci-CAR ATAC-seq
GSM3271042 HEK293T, NIH/3T3, A549 cells, sci-RNA-seq
BioProject PRJNA481032
SRA SRP153396

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE117089_RAW.tar 232.2 Mb (http)(custom) TAR (of CSV, TXT)
GSE117089_README.txt 5.5 Kb (ftp)(http) TXT
GSE117089_README_filenames_to_SRR.txt 113.1 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data provided as supplementary file

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