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Series GSE117075 Query DataSets for GSE117075
Status Public on Dec 01, 2019
Title Decoding neuronal diversity by single cell Convert-seq
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary The conversion of cell fates is controlled by hierarchical gene regulatory networks (GRNs) that induce remarkable alterations of cellular and transcriptome states. The identification of key regulators within these networks from myriad of candidate genes, however, poses a major research challenge. Here we present Convert-seq, combining single-cell RNA sequencing (scRNA-seq) and pooled (mutiplexed) ectopic gene expression with a new strategy to discriminate sequencing reads derived from exogenous and endogenous transcripts. We demonstrate Convert-seq by associating hundreds of single cells at multiple time-points during direct conversion of human fibroblasts to induced neurons (iN) with exogenous and endogenous transcriptional signatures. Convert-seq simultaneously identified GRNs that modulate the emergence of parallel developmental trajectories during iN conversion and predicted combinatorial interactions of exogenous transcription factors controlling iN subtype specification. Validation of iN subtypes generated by novel combinations of exogenous transcription factors establish Convert-seq as a broadly applicable workflow to rapidly identify key transcription factors and GRNs orchestrating the direct conversion of virtually any cell type.
 
Overall design Single-cell transcriptomes of human fibroblasts reprogrammed into induced neurons via chemicals or ectopic expression of transcription factors at multiple time-points
 
Contributor(s) Luginbühl J, Shin JW
Citation(s) 33711266
Submission date Jul 13, 2018
Last update date May 06, 2021
Contact name Joachim Felix Luginbühl
E-mail(s) joachim.luginbuhl@riken.jp
Organization name RIKEN
Street address 1-7-22 Suehiro-cho
City Yokoham
State/province Kanagawa
ZIP/Postal code 230-0045
Country Japan
 
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (674)
GSM3270141 FIB.A01
GSM3270142 FIB.A02
GSM3270143 FIB.A03
Relations
BioProject PRJNA481008
SRA SRP153373

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
GSE117075_10x.mat.count.csv.gz 9.8 Mb (ftp)(http) CSV
GSE117075_10x.mat.cpm.qc.csv.gz 84.4 Mb (ftp)(http) CSV
GSE117075_tc.mat.count.qc.csv.gz 15.4 Mb (ftp)(http) CSV
GSE117075_tc.mat.tpm.qc.csv.gz 20.7 Mb (ftp)(http) CSV
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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