|
| Status |
Public on Feb 22, 2021 |
| Title |
45_185_11-12-15-16_d440_37 |
| Sample type |
SRA |
| |
|
| Source name |
PBMC
|
| Organism |
Macaca mulatta |
| Characteristics |
cell type: PBMC
animalid: 185_11
treatment: Untreated
days post art: D37
|
| Treatment protocol |
rhesus macaques (RM) were intravenously infected with SIVmac239 and at day (d) 35 post-infection (p.i.) initiated triple formulation ART17. 8 RM were administered rhesus rIL-21-IgFc (IL-21) at d42 and d189 p.i. in two cycles of four doses given once per week followed by weekly rhesus IFNaplha-IgFc (rIFNalpha) starting at d323 (3 doses) and d383 p.i. (2 doses; i.e. ART + IL-21 + rIFNalpha). Following ART analytical treatment interruption (ATI) treated animals transitioned to human PEGylated-IFNalpha (PEG-IFNalpha; 7 doses, once every 6-8 days, s.c., 7 ug/kg) starting at day 5 post-ATI. 5 RM served as cytokine treatment-naïve, ART-only controls. Blood was taken 24 hr following the first (d6 post-ATI) and the fifth PEG-IFNα dose (d37 post-ATI). Peripheral blood mononuclear cells (PBMCs) were isolated from whole blood by density gradient centrifugation
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was purified using RNAeasy Micro Kit (Qiagen). Standard quality control steps were included to determine total RNA quality using Agilent 2100 Bioanalyzer (RNA integrity number (RIN) >8.5; Eukaryote Total RNA Pico Kit, Agilent, USA)
Libraries were prepared on cDNA generated using Clontech SmartER kits. Illumina adapters were ligated using the NexteraXT DNA kit for Illumina sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| 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
Abundance estimation of raw read counts per transcript was done internally with STAR using the algorithm of htseq-count.
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 |
GPL23804 |
| Series (2) |
| GSE163441 |
IL-21 and IFNalpha therapy rescues terminally-differentiated NK cells and limit SIV reservoir in ART-treated macaques [cohort2] |
| GSE163443 |
IL-21 and IFNalpha therapy rescues terminally-differentiated NK cells and limit SIV reservoir in ART-treated macaques |
|
| Relations |
| BioSample |
SAMN17105989 |
| SRA |
SRX9698762 |
