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Series GSE85066 Query DataSets for GSE85066
Status Public on Aug 02, 2016
Title In vitro cultured H7 human embryonic stem cells (WiCell) and H7-derived downstream early mesoderm progenitors
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Stem-cell differentiation to desired lineages requires navigating alternating developmental paths that often lead to unwanted cell types. Hence, comprehensive developmental roadmaps are crucial to channel stem-cell differentiation toward desired fates. To this end, here, we map bifurcating lineage choices leading from pluripotency to 12 human mesodermal lineages, including bone, muscle, and heart. We defined the extrinsic signals controlling each binary lineage decision, enabling us to logically block differentiation toward unwanted fates and rapidly steer pluripotent stem cells toward 80%–99% pure human mesodermal lineages at most branchpoints. This strategy enabled the generation of human bone and heart progenitors that could engraft in respective in vivo models. Mapping stepwise chromatin and single-cell gene expression changes in mesoderm development uncovered somite segmentation, a previously unobservable human embryonic event transiently marked by HOPX expression. Collectively, this roadmap enables navigation of mesodermal development to produce transplantable human tissue progenitors and uncover developmental processes. doi:10.1016/j.cell.2016.06.011
Overall design BioProject: PRJNA319573, Study: SRP073808, Bulk and single-cell RNA-seq, and ATAC-seq of of H7 human embryonic stem cells (ESC) and in vitro derived 10 diffrerent mesoderm progenitors from H7-ESC
Contributor(s) Sinha R, Koh PW
Citation(s) 27419872, 27996962
BioProject PRJNA319573
Submission date Aug 01, 2016
Last update date Jul 28, 2020
Contact name Rahul Sinha
Organization name Stanford University School of Medicine
Department ISCBRM
Lab Weissman
Street address 265 Campus Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
Platforms (2)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
Samples (12)
GSM2257291 H7_hESC_ATAC-seq
GSM2257292 H7_derived_APS_ATAC-seq
GSM2257293 H7_derived_MPS_ATAC-seq
SRA SRP073808

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

Supplementary file Size Download File type/resource
GSE85066_RAW.tar 30.9 Mb (http)(custom) TAR (of NARROWPEAK, TXT)
GSE85066_mergedPeaks_idr.narrowPeak.gz 1.8 Mb (ftp)(http) NARROWPEAK
GSE85066_pvalOverlappingMergedPeaks_idr.txt.gz 3.7 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

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