|
Status |
Public on Feb 24, 2021 |
Title |
51_RJh14_A5 |
Sample type |
SRA |
|
|
Source name |
blood
|
Organism |
Macaca mulatta |
Characteristics |
tissue: blood subject: RJh14 timepoint: Phase II D7 group: Double
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was prepared using QIAGEN Paxgene RNA kits. Globin transcripts were depleted using Ambion GlobinClear solution. 500-1000 ng of Globin depleted RNA was used for library preparation. Libraries were prepared using the Illumina (Illumina Inc. San Diego, CA, USA) TruSeq™ mRNA stranded kit as per manufacturer’s instructions.
|
|
|
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. RNA-seq data were aligned to the MacaM v7.8 assembly of the Indian rhesus macaque genome ( available at https://www.unmc.edu/rhesusgenechip/index.htm ) Alignment was performed using STAR v2.4.0g1 using the annotation as a splice junction reference. Transcripts were annotated using the MacaM v7.8.2 annotation. Transcript abundance was estimated using htseq-count v0.6.1p1 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) 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 05, 2018 |
Last update date |
Feb 24, 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 (1) |
GSE111435 |
Combination Anti-PD-1 and Anti-retroviral Therapy Provides Therapeutic Benefit Against SIV |
|
Relations |
BioSample |
SAMN08636730 |
SRA |
SRX3765904 |