|
| Status |
Public on Sep 18, 2017 |
| Title |
1_270_c |
| Sample type |
SRA |
| |
|
| Source name |
fetal brain
|
| Organism |
Sus scrofa |
| Characteristics |
agent: none
Sex: female
mode: mock
|
| Treatment protocol |
infection with zika virus, strain PRVABC59 (GenBank: KU501215)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
brains were homogenized in trizol reagent and extracted as per TRIZOL protocol. Samples were then cleaned up using Norgen Biotek total RNA kit (cat#37500)
As per Illumina RIBO gold
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Sow 270
1_270_c
|
| Data processing |
reads were trimed of adaptor sequences and poor quality bases
reads were aligned to mRNA sequences obtained from ENSEMBL SusScrofa10.2 build
aligned bam files were quantified using DESeq2
differential expression was calculated using limma after transformation of the data using voom
aligments were uising bowtie 2.0
Genome_build: SusScrofa10.2
Supplementary_files_format_and_content: a table of voom transformed read counts
|
| |
|
| Submission date |
Sep 17, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Brian Joseph Cox |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Toronto
|
| Department |
Physiology
|
| Lab |
Cox System Biology
|
| Street address |
1 King's College Circle, Rm 3360
|
| City |
Toronto |
| State/province |
Ontario |
| ZIP/Postal code |
M5S1A8 |
| Country |
Canada |
| |
|
| Platform ID |
GPL20983 |
| Series (1) |
| GSE103932 |
Zika virus infections of porcine fetal brain |
|
| Relations |
| BioSample |
SAMN07661001 |
| SRA |
SRX3194388 |
