|
Status |
Public on Feb 22, 2021 |
Title |
51_269_10-12-15-16_d415_37 |
Sample type |
SRA |
|
|
Source name |
PBMC
|
Organism |
Macaca mulatta |
Characteristics |
cell type: PBMC animalid: 269_10 treatment: Treated 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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 3000 |
|
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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).
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|
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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 |
SAMN17105985 |
SRA |
SRX9698766 |