|
Status |
Public on Jun 22, 2022 |
Title |
25T |
Sample type |
SRA |
|
|
Source name |
Rhesus macaque CD11b enriched brain microgla and macrophages
|
Organism |
Macaca mulatta |
Characteristics |
cell type: Enriched brain microglia and macrophages agent: SIVmac251, SIV protocol: Saline before and after SIVmac251 infection
|
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 monkey, SIVmac251-infected, 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 |
Jan 27, 2022 |
Last update date |
Jun 22, 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) |
GSE195574 |
Restoring a homeostatic microglia state by combination antiretroviral therapy in SIV-infected rhesus macaques |
|
Relations |
BioSample |
SAMN25337485 |
SRA |
SRX13952975 |