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Series GSE96769 Query DataSets for GSE96769
Status Public on Apr 26, 2018
Title Single-cell epigenomics maps the continuous regulatory landscape of human hematopoietic differentiation [scATAC-Seq]
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Normal human hematopoiesis involves cellular differentiation of multipotent cells into progressively more lineage-restricted states. While epigenomic landscapes of this process have been explored in immunophenotypically-defined populations, the single-cell regulatory variation that defines hematopoietic differentiation has been hidden by ensemble averaging. We generated single-cell chromatin accessibility landscapes across 8 populations of immunophenotypically-defined human hematopoietic cell types. Using bulk chromatin accessibility profiles to scaffold our single-cell data analysis, we constructed an epigenomic landscape of human hematopoiesis and characterized epigenomic heterogeneity within phenotypically sorted populations to find epigenomic lineage-bias toward different developmental branches in multipotent stem cell states. We identify and isolate sub-populations within classically-defined granulocyte-macrophage progenitors (GMPs) and use ATAC-seq and RNA-seq to confirm that GMPs are epigenomically and transcriptomically heterogeneous. Furthermore, we identified transcription factors and cis-regulatory elements linked to changes in chromatin accessibility within cellular populations and across a continuous myeloid developmental trajectory, and observe relatively simple TF motif dynamics give rise to a broad diversity of accessibility dynamics at cis-regulatory elements. Overall, this work provides a template for exploration of complex regulatory dynamics in primary human tissues at the ultimate level of granular specificity – the single cell.
 
Overall design Profiles of single cell epigenomes, assayed using scATAC-seq, across sorted cell types from CD34+ bone marrow.
 
Contributor(s) Buenrostro J
Citation(s) 29706549
Submission date Mar 17, 2017
Last update date Jul 03, 2019
Contact name Jason Daniel Buenrostro
E-mail(s) jdbuenrostro@gmail.com
Organization name Broad Institute
Street address 415 Main Street
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA
 
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (2784)
GSM2540299 BM1077-HSC-Frozen-160105-1
GSM2540300 BM1077-HSC-Frozen-160105-2
GSM2540301 BM1077-HSC-Frozen-160105-3
This SubSeries is part of SuperSeries:
GSE96772 Single-cell epigenomics maps the continuous regulatory landscape of human hematopoietic differentiation
Relations
BioProject PRJNA379613
SRA SRP102089

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE96769_PeakFile_20160207.bed.gz 8.4 Mb (ftp)(http) BED
GSE96769_scATACseq_counts.txt.gz 56.7 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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