|
| Status |
Public on Feb 09, 2018 |
| Title |
Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain |
| Organism |
Danio rerio |
| Experiment type |
Expression profiling by high throughput sequencing
Other
|
| Summary |
The lineage relationships among the hundreds of cell types generated during development are difficult to reconstruct. A recent method, GESTALT, used CRISPR–Cas9 barcode editing for large-scale lineage tracing, but was restricted to early development and did not identify cell types. Here we present scGESTALT, which combines the lineage recording capabilities of GESTALT with cell-type identification by single-cell RNA sequencing. The method relies on an inducible system that enables barcodes to be edited at multiple time points, capturing lineage information from later stages of development. Sequencing of ∼60,000 transcriptomes from the juvenile zebrafish brain identified >100 cell types and marker genes. Using these data, we generate lineage trees with hundreds of branches that help uncover restrictions at the level of cell types, brain regions, and gene expression cascades during differentiation. scGESTALT can be applied to other multicellular organisms to simultaneously characterize molecular identities and lineage histories of thousands of cells during development and disease.
|
| |
|
| Overall design |
inDrops libraries of single-cell transcriptomes and scGESTALT barcodes, and genomic DNA GESTALT libraries
|
| |
|
| Contributor(s) |
Raj B |
| Citation(s) |
29608178 |
| |
| Submission date |
Oct 16, 2017 |
| Last update date |
Jul 25, 2021 |
| Contact name |
Bushra Raj |
| E-mail(s) |
bushra.raj@pennmedicine.upenn.edu
|
| Organization name |
University of Pennsylvania
|
| Street address |
421 Curie Boulevard
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platforms (2) |
| GPL20828 |
Illumina NextSeq 500 (Danio rerio) |
| GPL21930 |
Illumina MiSeq (Danio rerio) |
|
| Samples (72)
|
|
| Relations |
| BioProject |
PRJNA414416 |
| SRA |
SRP120009 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE105010_Danio_rerio.GRCz10.86.modified.gtf.gz |
18.4 Mb |
(ftp)(http) |
GTF |
| GSE105010_GSTLT_f1.noQ.genes.csv.gz |
15.6 Mb |
(ftp)(http) |
CSV |
| GSE105010_GSTLT_f2.noQ.genes.csv.gz |
15.7 Mb |
(ftp)(http) |
CSV |
| GSE105010_GSTLT_f3.noQ.genes.csv.gz |
20.2 Mb |
(ftp)(http) |
CSV |
| GSE105010_GSTLT_f4.noQ.genes.csv.gz |
18.4 Mb |
(ftp)(http) |
CSV |
| GSE105010_GSTLT_f5.noQ.genes.csv.gz |
17.0 Mb |
(ftp)(http) |
CSV |
| GSE105010_GSTLT_f6.noQ.genes.csv.gz |
10.7 Mb |
(ftp)(http) |
CSV |
| GSE105010_GSTLT_fore.noQ.genes.csv.gz |
6.3 Mb |
(ftp)(http) |
CSV |
| GSE105010_GSTLT_hind.noQ.genes.csv.gz |
2.6 Mb |
(ftp)(http) |
CSV |
| GSE105010_GSTLT_mid.noQ.genes.csv.gz |
6.4 Mb |
(ftp)(http) |
CSV |
| GSE105010_RAW.tar |
5.5 Mb |
(http)(custom) |
TAR (of TXT) |
| GSE105010_README.txt |
2.9 Mb |
(ftp)(http) |
TXT |
| GSE105010_fall.inDrops.RData.gz |
1.6 Gb |
(ftp)(http) |
RDATA |
| GSE105010_inDropsExpMatrix_noQ.txt.gz |
132.7 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
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