|
| Status |
Public on Feb 22, 2021 |
| Title |
13_M1_GSK138_Pax_7-28 |
| Sample type |
SRA |
| |
|
| Source name |
PBMC
|
| Organism |
Macaca mulatta |
| Characteristics |
cell type: PBMC
animalid: T020
week post infection: Wk8
|
| Treatment protocol |
rhesus macaques were infected with SIVmac251, then treated with ART, and followed while on ART treatment. Blood samples were collected in paxgene tubes 1 week prior to infection, 8 weeks later immediately prior to ART initiation, and at 9 weeks and 18 weeks post ART treatment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared using QIAGEN Paxgene RNA kits. Globin transcripts were depleted using Ambion GlobinClear solution.
500-1000 ng of Globin depleted RNA was used for library preparation. Libraries were prepared using the Illumina (Illumina Inc. San Diego, CA, USA) TruSeq™ mRNA stranded kit as per manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1000 |
| |
|
| Data processing |
Illumina bcl2fastq v2.17.1.14 was used for demultiplexing.
Reads were aligned using STAR v2.4.0g1.(Dobin et al.)
Transcripts were annotated using the UNMC rhesus annotation v 7.6.8
Transcript abundance was estimated using htseq-count v0.6.1p1
Genome_build: MacaM v7 (MacaM_Rhesus_Genome_v7.fasta,MacaM_Rhesus_Genome_Annotation_v7.8.2.gtf available at https://www.unmc.edu/rhesusgenechip/index.htm)
Supplementary_files_format_and_content: tab delimited text file containing raw read counts for each sample (in columns) and each annotated transcript (in rows).
|
| |
|
| Submission date |
Dec 17, 2020 |
| Last update date |
Feb 22, 2021 |
| Contact name |
Gregory K Tharp |
| E-mail(s) |
gktharp@emory.edu
|
| Phone |
404-727-7797
|
| Organization name |
Yerkes National Primate Research Center
|
| Department |
Developmental and Cognitive Neuroscience
|
| Lab |
Genomics Core
|
| Street address |
954 Gatewood Dr
|
| City |
Atlanta |
| State/province |
GA |
| ZIP/Postal code |
30329-4208 |
| Country |
USA |
| |
|
| Platform ID |
GPL20313 |
| Series (2) |
| GSE163442 |
IL-21 and IFNalpha therapy rescues terminally-differentiated NK cells and limit SIV reservoir in ART-treated macaques [cohort3] |
| GSE163443 |
IL-21 and IFNalpha therapy rescues terminally-differentiated NK cells and limit SIV reservoir in ART-treated macaques |
|
| Relations |
| BioSample |
SAMN17106011 |
| SRA |
SRX9698778 |
