|
| Status |
Public on Feb 24, 2021 |
| Title |
34_REc14_A5 |
| Sample type |
SRA |
| |
|
| Source name |
blood
|
| Organism |
Macaca mulatta |
| Characteristics |
tissue: blood
subject: REc14
timepoint: Phase II D0
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 |
SAMN08636747 |
| SRA |
SRX3765887 |
