|
| Status |
Public on Feb 09, 2022 |
| Title |
RVt10_Pre-ART [reanalysis] |
| Sample type |
SRA |
| |
|
| Source name |
PBMC
|
| Organism |
Macaca mulatta |
| Characteristics |
subjectid: RVt10
treatment: IL-21
processinggroup: Gr3
processday: day59
timepoint: Pre-ART
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared using the QIAGEN RNEasy Micro Kit.
Libraries were generated using the CLONTECH SMARTer HV kit, barcoding and sequencing primers were added using NexteraXT DNA kit. Libraries were validated by microelectrophoresis, quantified, pooled and clustered on Illumina TruSeq v3 flowcell. Pre-Infection samples were sequenced on an Illumina HiSeq3000, the remaining samples were sequenced on an Illumina HiSeq 1000 in 100-base single-read reactions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1000 |
| |
|
| Description |
re-analysis of GSM1889031
X9_RVt10_Gr3_day59_ATGTCA_L002
|
| Data processing |
Illumina bcl2fastq v2.17.1.14 was used for demultiplexing.
Reads were mapped to the Rhesus macaque (MacaM v7) genomic reference with STAR (v2.5.2b) with default alignment parameters.
Abundance estimation of raw read counts per transcript was done internally with STAR using the algorithm of htseq-count.
Normalized expression (normalized read counts) was performed with DESeq2 (v1.10.1)
Genome_build: MacaM v7 (MacaM_Rhesus_Genome_v7.fasta,MacaM_Rhesus_Genome_Annotation_v7.8.2.gtf) https://www.unmc.edu/rhesusgenechip/index.htm#NewRhesusGenome
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 |
Feb 04, 2022 |
| Last update date |
Aug 07, 2023 |
| 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 (1) |
| GSE196182 |
Interleukin-10 contributes to reservoir establishment and persistence in antiretroviral therapy-treated, SIV-infected macaques |
|
| Relations |
| Reanalysis of |
GSM1889031 |
| BioSample |
SAMN25656327 |
| SRA |
SRX14047215 |
