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Series GSE75748 Query DataSets for GSE75748
Status Public on Jul 21, 2016
Title Snapshot and temporal scRNA-seq of progenitor cells to dissect human embryonic stem cells entry into endoderm progenitors
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Human pluripotent stem cells (hPSCs) offer a unique cellular model to study lineage specifications of the primary germ layers during human development. We profiled single-cell RNA-seq (scRNA-seq) on four lineage-specific progenitor cells derived from hESCs. Our scRNA-seq analyses revealed each type of progenitors display various extend of heterogeneity. Specifically, definitive endoderm cells (DECs) not only show a greater degree of heterogeneity, but are also enriched in metabolic signatures. Followed by detailed temporal scRNA-seq profiling along DEC differentiation, we reconstructed a differentiation trajectory using a novel statistical pipeline named Wave-Crest. Wave-Crest further identifies candidate regulators during the transitioning phase from Brachyury (T)+ mesendoderm towards CXCR4+ DEC state. To functionally test identified novel regulators; we generated a live cell monitoring system, a T-2A-EGFP knock-in reporter cell line via CRISPR/CAS9. We demonstrated that, among the top candidate genes, KLF8 plays a pivotal role modulating mesendoderm to DEC differentiation. In this submission, 1810 raw fastq files are provided; 212 are re-analysis from GSE64016. Four expected count matrices are provided - 1) 1018 single cells from snapshot progenitors; 2) 758 single cells from time couse profiling; 3) 19 bulk RNA-seq sample from snapshot progenitors; 4) 15 bulk RNA-seq sample from time course profiling.
 
Overall design Total 1018 single cells from snapshot progenitors and 758 single cells from time couse profiling. Matchd population bulk RNA-seq samples for both the progenitors snapshot (19 samples) and time course profiling (15 samples) also included in this submission. These data set are used to detect the transitioning phase from mesendoderm to definitive endoderm.
 
Contributor(s) Chu L, Leng N
Citation(s) 27534536
Submission date Dec 07, 2015
Last update date May 15, 2019
Contact name Ning Leng
E-mail(s) lengning1@gmail.com
Organization name Morgridge Institute for Research
Street address 330 N Orchard St
City Madison
State/province WI
ZIP/Postal code 53715
Country USA
 
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (1810)
GSM1964932 bulk H1 hESC cell [H1_rep1]
GSM1964933 bulk H1 hESC cell [H1_rep2]
GSM1964934 bulk H1 hESC cell [H1_rep3]
Relations
BioProject PRJNA305280
SRA SRP067036

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
GSE75748_bulk_cell_type_ec.csv.gz 894.7 Kb (ftp)(http) CSV
GSE75748_bulk_time_course_ec.csv.gz 421.2 Kb (ftp)(http) CSV
GSE75748_sc_cell_type_ec.csv.gz 22.8 Mb (ftp)(http) CSV
GSE75748_sc_time_course_ec.csv.gz 13.1 Mb (ftp)(http) CSV
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Processed data are available on Series record
Raw data are available in SRA
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