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Series GSE68102 Query DataSets for GSE68102
Status Public on May 07, 2015
Title Multiplex Single Cell Profiling of Chromatin Accessibility by Combinatorial Cellular Indexing [RNA-seq]
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Technical advances have enabled the collection of genome and transcriptome data sets with single-cell resolution. However, single-cell characterization of the epigenome has remained challenging. Furthermore, because cells must be physically separated prior to biochemical processing, conventional single-cell preparatory methods scale linearly. We applied combinatorial cellular indexing to measure chromatin accessibility in thousands of single cells per assay, circumventing the need for compartmentalization of individual cells. We report chromatin accessibility profiles from over 15,000 single cells and use these data to cluster cells on the basis of chromatin accessibility landscapes. We identify modules of coordinately regulated chromatin accessibility at the level of single cells both between and within cell types, with a scalable method that may accelerate progress toward a human cell atlas.
Overall design 3 replicates from GM12878 and HL-60 cell lines collected for differential gene expression analysis.
Contributor(s) Cusanovich DA, Daza R, Adey A, Pliner H, Christiansen L, Gunderson KL, Steemers FJ, Trapnell C, Shendure J
Citation(s) 25953818
Submission date Apr 21, 2015
Last update date May 15, 2019
Contact name Darren A. Cusanovich
Organization name University of Arizona
Department Cellular and Molecular Medicine
Street address 1230 N Cherry Avenue, BSRL 421
City Tucson
State/province AZ
ZIP/Postal code 85721
Country USA
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (6)
GSM1663002 GM12878 RNA-seq Replicate 1
GSM1663003 GM12878 RNA-seq Replicate 2
GSM1663004 GM12878 RNA-seq Replicate 3
This SubSeries is part of SuperSeries:
GSE68103 Multiplex Single Cell Profiling of Chromatin Accessibility by Combinatorial Cellular Indexing
BioProject PRJNA281746
SRA SRP057508

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE68102_gencodev17idx.gff.gz 8.6 Mb (ftp)(http) GFF
GSE68102_gene_exp.diff.gz 1.5 Mb (ftp)(http) DIFF
GSE68102_genes.count_tracking.txt.gz 712.9 Kb (ftp)(http) TXT
GSE68102_genes.fpkm_tracking.gz 2.1 Mb (ftp)(http) FPKM_TRACKING
GSE68102_genes.read_group_tracking.txt.gz 2.3 Mb (ftp)(http) TXT
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Processed data are available on Series record

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