|
| Status |
Public on Jun 28, 2021 |
| Title |
O_W0D1_O8_Protected |
| Sample type |
SRA |
| |
|
| Source name |
Whole blood
|
| Organism |
Macaca mulatta |
| Characteristics |
animal_id: 29212
animal_name: O8
group: O
vaccination_route: Oral
vaccine_type: RhCMV_68-1
phase: Prime
outcome: Protected
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Whole blood was collected from RM in PAXgene RNA tubes (PreAnalytiX) following the manufacturer's procedures. (PreAnalytiX). RNA was isolated using PAXgene Blood miRNA kits (Qiagen) following the protocol provided with the kit that included an on-column DNase treatment.
Illumina TruSeq® Stranded mRNA HT kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Quality of mRNA-seq reads were assessed using FastQC version 0.11.3 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Both rhesus globin and ribosomal sequences were filtered via alignments with Bowtie v2.1.0.
Adapters were digitally removed using cutadapt, version 1.8.3.
Mapping was performed using STAR v2.4.0h1 .
Cene counts were generated using HTSeq-count v0.6.1p1.
Genome_build: Macaque mulatta genome Mmul1 (https://support.illumina.com/sequencing/sequencingsoftware/igenome.html )
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Nov 12, 2020 |
| Last update date |
Jun 28, 2021 |
| Contact name |
Michael Gale, Jr |
| E-mail(s) |
uw_galelab_geo@uw.edu
|
| Organization name |
University of Washington
|
| Department |
Immunology
|
| Street address |
750 Republican St. E360, Box 358059
|
| City |
Seattle |
| State/province |
Washington |
| ZIP/Postal code |
98109 |
| Country |
USA |
| |
|
| Platform ID |
GPL21120 |
| Series (1) |
| GSE160562 |
Host response to RhCMV/SIV immunization through subcutaneous and oral route |
|
| Relations |
| BioSample |
SAMN16785128 |
| SRA |
SRX9498956 |
