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| Status |
Public on Feb 21, 2018 |
| Title |
Single cell profiling of the developing mouse brain and spinal cord with split-pool barcoding |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
To facilitate scalable profiling of single cells, we developed Split Pool Ligation-based Transcriptome sequencing (SPLiT-seq), a single-cell RNA-seq (scRNA-seq) method that labels the cellular origin of RNA through combinatorial barcoding. SPLiT-seq is compatible with fixed cells or nuclei, allows efficient sample multiplexing and requires no customized equipment. We used SPLiT-seq to analyze 156,049 single-nucleus transcriptomes from postnatal day 2 and 11 mouse brains and spinal cords. Over 100 cell types were identified, with gene expression patterns corresponding to cellular function, regional specificity, and stage of differentiation. Pseudotime analysis revealed transcriptional programs driving four developmental lineages, providing a snapshot of early postnatal development in the murine central nervous system. SPLiT-seq provides a path towards comprehensive single-cell transcriptomic analysis of other similarly complex multicellular systems.
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| Overall design |
Single-cell/nucleus RNA-seq was performed using SPLiT-seq
This code explains how to read the data from the paper into python:
https://gist.github.com/Alex-Rosenberg/5ee8b14ea580144facad9c2b87cebf10
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| |
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| Contributor(s) |
Rosenberg A, Roco C |
| Citation(s) |
29545511 |
| |
| Submission date |
Feb 20, 2018 |
| Last update date |
Jan 15, 2019 |
| Contact name |
Alexander B Rosenberg |
| E-mail(s) |
abros@uw.edu
|
| Organization name |
University of Washington
|
| Department |
Electrical Engineering
|
| Lab |
Seelig Lab
|
| Street address |
4000 15th Ave NE
|
| City |
Seattle, WA 98195 |
| State/province |
WA |
| ZIP/Postal code |
98195 |
| Country |
USA |
| |
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| Platforms (2) |
| GPL21626 |
NextSeq 550 (Mus musculus) |
| GPL24625 |
NextSeq 550 (Homo sapiens; Mus musculus) |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA434658 |
| SRA |
SRP133097 |
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