|
| Status |
Public on Jun 28, 2021 |
| Title |
X_W18D7_X11_Unprotected |
| Sample type |
SRA |
| |
|
| Source name |
Whole blood
|
| Organism |
Macaca mulatta |
| Characteristics |
animal_id: 29548
animal_name: X11
group: X
vaccination_route: Subcuraneous
vaccine_type: RhCMV_68-1/68-1.2
phase: Boost
outcome: Unprotected
|
| 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) |
mgale@umn.edu
|
| Organization name |
University of Minnesota
|
| Department |
Microbiology and Immunology
|
| Street address |
689 23rd Ave SE
|
| City |
Minneapolis |
| State/province |
Minnesota |
| ZIP/Postal code |
55455 |
| Country |
USA |
| |
|
| Platform ID |
GPL21120 |
| Series (1) |
| GSE160562 |
Host response to RhCMV/SIV immunization through subcutaneous and oral route |
|
| Relations |
| BioSample |
SAMN16785277 |
| SRA |
SRX9498878 |
