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| Status |
Public on Dec 31, 2018 |
| Title |
Deep single-cell RNAseq of postnatal day 7 microglia from wild type and Trem2 knockout brains |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
We generated single-cell RNAseq profiles of 369 microglia (183 from wild type and 186 from Trem2 knock-out), sorted in the gate CD45lowCD11+ or CD45lowCD11+Gpnmb+Clec7a+ (PAM enrichment), to compare gene expression of wild type vs. Trem2 knock-out microglia on the postnatal day 7. Single cells were FACS index sorted from the whole brain followed by Smart-seq2 library preparation and Illumina Nextseq (sequence depth > 1 million per cell). A total of 334 cells passed quality control for data analysis. Microglia in the Trem2 knock-out contained a similar PAM population with characteristic gene expression, suggesting that the presence of early postnatal PAM do not depend on TREM2.
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| Overall design |
Single microglia were FACS sorted from male animals (C57BL/6J background) into 96-well plates. Libraries were prepared with a semi-automated Smart-seq2 protocol. Three QC criteria were used (Y=passed, N=not passed), and only cells that passed all three criteria were used for downstream analysis.
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| Contributor(s) |
Li Q, Barres B |
| Citation(s) |
30606613 |
| |
| Submission date |
Nov 27, 2018 |
| Last update date |
Apr 01, 2019 |
| Contact name |
Qingyun Li |
| E-mail(s) |
tristan.qingyun.li@gmail.com
|
| Phone |
702-686-6685
|
| Organization name |
Stanford University
|
| Department |
Neurobiology
|
| Street address |
299 Campus Drive
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (369)
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| This SubSeries is part of SuperSeries: |
| GSE123030 |
Developmental heterogeneity of microglia and brain myeloid cells revealed by deep single-cell RNA sequencing |
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| Relations |
| BioProject |
PRJNA507267 |
| SRA |
SRP170963 |
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