|
Status |
Public on Feb 22, 2021 |
Title |
37_O1_GSK162_Pax_12_1-4 |
Sample type |
SRA |
|
|
Source name |
PBMC
|
Organism |
Macaca mulatta |
Characteristics |
cell type: PBMC animalid: T020 week post infection: Wk26
|
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 |
SAMN17106023 |
SRA |
SRX9698790 |