|
| Status |
Public on Jan 22, 2021 |
| Title |
86T_ Cryo |
| Sample type |
SRA |
| |
|
| Source name |
Rhesus macaque CD11b enriched brain microgla and macrophages
|
| Organism |
Macaca mulatta |
| Characteristics |
tissue: Enriched brain microglia and macrophages, capture from cryopreserved isolates
tissue preparation: cryo
condition: SIVmac251 infection, cART d35 post SIV infection, 6 months latent virus (<50 copies SIV/ml plasma). Treated with four drug cART, 4 mg/ml DTG, 1mg/ml tenofovir alafenamide fumerate (TAF), 40 mg/ml FTC, and 12 mg/ml maraviroc (MVC).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Brain isolates were either cryopreserved or used that day for GEM chip capture. Fresh isolates were immunomagnetically enriched for CD11b microglia and macrophages, and then sorted using flow cytometry for CD11b+, live events. Fresh sorted cells were captured on 10X Genomics Chromium GEM Chip and subsequently processed for scRNA. Cryopreserved were thawed, adapted to room temperature in media containing DNase1 and then immunomagnetically enriched, sorted using flow cytometry, and captured on 10X Genomics Chromium GEM Chip and subsequently processed for scRNA.
Next Generation Sequencing performed on the Illumina NextSeq550
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 |
SIVmac251, latent, cART cryo
|
| 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 D01065.1 reference genomes.
Genome_build: Mmul10
Genome_build: D01065.1
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 |
Dec 04, 2020 |
| Last update date |
Jan 22, 2021 |
| 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) |
| GSE162663 |
Cryopreservation of microglia enables single-cell RNA sequencing with minimal effects on disease-related gene expression patterns |
|
| Relations |
| BioSample |
SAMN17002091 |
| SRA |
SRX9632463 |
