|
| Status |
Public on Aug 10, 2018 |
| Title |
29512_Wk19 |
| Sample type |
SRA |
| |
|
| Source name |
PBMC
|
| Organism |
Macaca mulatta |
| Characteristics |
donor id: 29512
time point: Wk19
art-treatment: ART
ifn-1ant treatment: IF13x
|
| Treatment protocol |
Samples for RNA extraction were resuspended in 10% DMSO-FBS and store in liquid nitrogen until use
|
| Growth protocol |
PBMC were isolated using ficoll
|
| Extracted molecule |
total RNA |
| Extraction protocol |
After thaw and wash, PBMC pellets were resuspended in RNAzolRT prior to RNA extraction. Purified RNA was used for transcriptome analysis. Polyadenylated transcripts were purified on oligo-dT magnetic beads, fragmented, reverse transcribed using random hexamers and incorporated into barcoded cDNA libraries based on the Illumina TruSeq platform.
Modified Illumina TruSeq. Illumina-ready libraries were sequenced by 2x75 paired-end reads on a HiSeq 4000.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Reads were aligned to an assembly of Indian Rhesus macaque (Macaca mulatta) (MacaM_Rhesus_Genome_v7.fasta) using STAR software (v2.5.2b)
Insert size was estimated with Picard Tools v1.74
Transcripts were annotated using the UNMC rhesus annotation v 7.6.8
unsorted bam files were sorted and indexed using samtools and converted to HTSeq-count format.
Estimates of gene-wise and isoform-wise expression levels for individual genes were performed using the R package DESeq2 with R version 3.3.3.
Genome_build: MacaM v7 (MacaM_Rhesus_Genome_v7.fasta,MacaM_Rhesus_Genome_Annotation_v7.8.2.gtf)
Supplementary_files_format_and_content: tab delimited text file containing normalized read counts for each sample (in columns) and each annotated transcript (in rows).
|
| |
|
| Submission date |
Mar 21, 2018 |
| Last update date |
Aug 10, 2018 |
| 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 |
GPL23949 |
| Series (1) |
| GSE112148 |
Type I IFN signaling blockade during ART-treated and untreated chronic SIV infection suppresses inflammation but does not increase virus replication |
|
| Relations |
| BioSample |
SAMN08766254 |
| SRA |
SRX3828112 |
