 |
 |
GEO help: Mouse over screen elements for information. |
|
| 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)
|
| GSM3452923 |
Mesendoderm, barRNA-seq barcodelets |
| GSM4419011 |
Mixed, barRNA-seq transcriptome |
| GSM4419012 |
Mixed, barRNA-seq barcodelets |
| GSM4419013 |
Untransfected, Bulk RNA-seq, Replicate 1 |
| GSM4419014 |
Untransfected, Bulk RNA-seq, Replicate 2 |
| GSM4419015 |
Barcodelet72h, Bulk RNA-seq, Replicate 1 |
| GSM4419016 |
Barcodelet72h, Bulk RNA-seq, Replicate 2 |
| GSM4419017 |
Barcodelet24h, Bulk RNA-seq, Replicate 1 |
| GSM4419018 |
Barcodelet24h, Bulk RNA-seq, Replicate 2 |
| GSM4419019 |
Foxa2GFPplus, Bulk RNA-seq, Replicate 1 |
| GSM4419020 |
Foxa2GFPplus, Bulk RNA-seq, Replicate 2 |
| GSM4419021 |
Foxa2GFPplus, Bulk RNA-seq, Replicate 3 |
| GSM4419022 |
Foxa2GFPplus, Bulk RNA-seq, Replicate 4 |
| GSM4419023 |
Foxa2GFPminus, Bulk RNA-seq, Replicate 1 |
| GSM4419024 |
Foxa2GFPminus, Bulk RNA-seq, Replicate 2 |
| GSM4419025 |
Tdgf1GFPplus, Bulk RNA-seq, Replicate 1 |
| GSM4419026 |
Tdgf1GFPplus, Bulk RNA-seq, Replicate 2 |
|
| Relations |
| BioProject |
PRJNA503119 |
| SRA |
SRP167310 |
| 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 |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
Less...
More...