|
| Status |
Public on Dec 01, 2020 |
| Title |
34T |
| Sample type |
SRA |
| |
|
| Source name |
Saline before and after SIVmac251 infection
|
| Organism |
Macaca mulatta |
| Characteristics |
tissue: CD11b enriched brain microgla and macrophages
treatment: SIVmac251, SIVE, saline
|
| Treatment protocol |
Animals were infected with SIV and treated with either saline or methamphetamine injections.
|
| 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.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
Saline-treated SIV-infected rhesus monkey with encephalitis, enriched microglia/brain macrophages
|
| Data processing |
Cellranger pipeline (version 3.1.0) 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.
Genome_build: Mmul10
Genome_build: 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 |
Oct 29, 2020 |
| Last update date |
Dec 01, 2020 |
| 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) |
| GSE160384 |
Methamphetamine increases the proportion of SIV-infected microglia/macrophages, alters metabolic pathways, and elevates cell death pathways: a single-cell analysis |
|
| Relations |
| BioSample |
SAMN16591530 |
| SRA |
SRX9397265 |
