|
| Status |
Public on Oct 13, 2022 |
| Title |
75T |
| Sample type |
SRA |
| |
|
| Source name |
Rhesus macaque CD11b enriched brain microglia and macrophages
|
| Organism |
Macaca mulatta |
| Characteristics |
tissue: Enriched brain microglia and macrophages
treatment: morphine, SIV-latent virus
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Brains were removed at necropsy, microglia/macrophage enriched cells were isolated from the brain and cryopreserved. Isolates were immunomagnetically enriched for CD11b+ cells, and then flow cytometry sorted for CD11b positive, live events, and processed for scRNA.
scRNA10x Genomics Chromium GEM Chip and placed into Chromium Controller for library preparation. The prepared libraries were sequenced using Illumina Nextseq550 sequencer for Sample 1 to sample 7 and Novaseq6000 fro sample 8 to sample 23.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Cellranger pipeline was used here. Cellranger mkfastq was used for demultiplexing and generate fastq files and cellranger count was used to align the reads to Mmul10 and M33262.1 reference genomes.
M33262.1 was split and annotated into 5 regions as described in the manuscript.
Assembly: Mmul10
Assembly: M33262.1
Supplementary files format and content: H5 files were created from cellranger count to store the matrix of UMI per gene per cell for each sample
|
| |
|
| Submission date |
Jul 23, 2022 |
| Last update date |
Oct 13, 2022 |
| Contact name |
Meng Niu |
| E-mail(s) |
vincentnue@gmail.com
|
| Phone |
4025595925
|
| Organization name |
University of Nebraska Medical Center
|
| Department |
Department of Neurological sciences
|
| Street address |
42nd and Emile
|
| City |
OMAHA |
| State/province |
NE |
| ZIP/Postal code |
68198 |
| Country |
USA |
| |
|
| Platform ID |
GPL29319 |
| Series (1) |
| GSE209606 |
Morphine Alters Systemic Responses to SIV Infection of Rhesus Monkeys and Changes Brain Macrophage and Microglia Gene Expression Favoring Neuropathogenesis |
|
| Relations |
| BioSample |
SAMN29921434 |
| SRA |
SRX16541810 |
