|
| Status |
Public on Mar 09, 2020 |
| Title |
55A_2447_27W_PBMC |
| Sample type |
SRA |
| |
|
| Source name |
Peripheral blood mononuclear cells
|
| Organism |
Macaca mulatta |
| Characteristics |
set: A
subject id: 2447
siv genotype: ctl
tissue: PBMC
timepoint (weeks): 27W
infection status: uninfected
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Qiagen RNeasy Mini kits with DNase digest and QIAcube automation stations. RNA was quantified on NanoDrop 2000 spectrophotometer and the quality was assessed by Bioanalyzer analysis.
Set A samples: Libraries were prepared using the Illumina TruSeq mRNA stranded kit, as per manufacturer’s instructions, with 400 ng of total RNA as input. The amplified libraries were validated by capillary electrophoresis on the Agilent 4200 TapeStation. The libraries were normalized, pooled and sequenced on the Illumina HiSeq 3000 system employing a single-end 101 cycles run at average read depths of 16 million reads/sample.
Set B samples: 10 ng of total RNA was used as input for cDNA amplification using 5’ template-switch PCR with the Clontech SMART-Seq v4 Ultra Low Input RNA kit. Amplified cDNA was fragmented and appended with dual indexed bar codes using Illumina NexteraXT DNA Library Prep kits. The amplified libraries were validated by capillary electrophoresis on the Agilent 4200 TapeStation. The libraries were normalized, pooled and sequenced on the Illumina HiSeq 3000 system employing a single-end 101 cycles run at average read depths of 25 million reads/sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
The sequencing data was demultiplexed using Illumina bcl2fastq v2.20.0.422.
The quality of raw reads was assessed with FastQC v0.11.8.
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 htseq-count algorithm.
Normalized expression (normalized read counts) was obtained with DESeq2 v1.22.1.
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 |
Dec 08, 2019 |
| Last update date |
Apr 10, 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 |
GPL23804 |
| Series (1) |
| GSE141626 |
Nef-mediated downmodulation of CD3 dampens immune activation and is critical for maintenance of high virus loads in SIV-infected macaques |
|
| Relations |
| Reanalyzed by |
GSM7158656 |
| BioSample |
SAMN13508255 |
| SRA |
SRX7285913 |
