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Series GSE122009 Query DataSets for GSE122009
Status Public on May 26, 2020
Title A Multiplexed Barcodelet Single-Cell RNA-Seq Approach Elucidates Combinatorial Signaling Pathways that Drive ESC Differentiation
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Empirical optimization of stem cell differentiation protocols is time consuming, is labor intensive, and typi- cally does not comprehensively interrogate all relevant signaling pathways. Here we describe barcodelet sin- gle-cell RNA sequencing (barRNA-seq), which enables systematic exploration of cellular perturbations by tagging individual cells with RNA ‘‘barcodelets’’ to identify them on the basis of the treatments they receive. We apply barRNA-seq to simultaneously manipulate up to seven developmental pathways and study effects on embryonic stem cell (ESC) germ layer specification and mesodermal specification, uncovering combina- torial effects of signaling pathway activation on gene expression. We further develop a data-driven frame- work for identifying combinatorial signaling perturbations that drive cells toward specific fates, including several annotated in an existing scRNA-seq gastrulation atlas, and use this approach to guide ESC differen- tiation into a notochord-like population. We expect that barRNA-seq will have broad utility for investigating
Q2 and understanding how cooperative signaling pathways drive cell fate acquisition.
Overall design Multiplexed transcriptome profiling of 32-384 distinct populations per experiment at single-cell resolution
Contributor(s) Yeo GH, Lin L, Qi CY, Cha M, Gifford DK, Sherwood RI
Citation(s) 32459995
Submission date Oct 31, 2018
Last update date Jun 08, 2020
Contact name Richard I Sherwood
Organization name Brighan and Women's Hospital and Harvard Medical School
Department Division of Genetics, Department of Medicine
Street address 77 Avenue Louis Pasteur
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (20)
GSM3452920 Germ layer, barRNA-seq transcriptome
GSM3452921 Germ layer, barRNA-seq barcodelets
GSM3452922 Mesendoderm, barRNA-seq transcriptome
BioProject PRJNA503119
SRA SRP167310

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Supplementary file Size Download File type/resource
GSE122009_RAW.tar 288.2 Mb (http)(custom) TAR (of CSV, FA, MTX, TSV, TXT)
GSE122009_bulk.processed_data.csv.gz 539.1 Kb (ftp)(http) CSV
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Raw data are available in SRA
Processed data provided as supplementary file

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