|
Status |
Public on Aug 10, 2018 |
Title |
BA50_Baseline |
Sample type |
SRA |
|
|
Source name |
PBMC
|
Organism |
Macaca mulatta |
Characteristics |
donor id: BA50 time point: Baseline art-treatment: NO_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.
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|
|
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).
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|
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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 |
SAMN08766387 |
SRA |
SRX3828191 |