|
| Status |
Public on May 16, 2019 |
| Title |
2176_P2 |
| Sample type |
SRA |
| |
|
| Source name |
parotid salivary gland - ventral section
|
| Organism |
Bos taurus |
| Characteristics |
tissue: parotid salivary gland
sample collection time during experimental trial: 33 months' post-experimental challenge
|
| Treatment protocol |
Tissue collected from two groups of cattle - A) Challenged group - group challenged with bacteria MAP; B) Control no MAP-Challenged group
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Trizol and using RNeasy Mini Kit (Qiagen) as per manufacturer’s instructions
TruSeq (Illumina TruSeq RNA Library v2 construction)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
FASTQC was used to assess the quality of sequence reads. Low quality reads and adapters were trimmed using Trimmomatic software
Trimmed reads were mapped to Bovine Reference Genome Assembly BTA_UMD3.1 (ftp://ftp.ensembl.org/pub/release-91/fasta/bos_taurus/dna/) using STAR RNA-seq aligner and to generate read counts
Differential expression analysis carried out using DESEq2 software
Genome_build: Bovine Reference Genome Assembly BTA_UMD3.1
Supplementary_files_format_and_content: excel files with read counts of each sample
|
| |
|
| Submission date |
Jan 08, 2019 |
| Last update date |
May 16, 2019 |
| Contact name |
Sanjay Mallikarjunappa |
| E-mail(s) |
smallika@uoguelph.ca
|
| Organization name |
University of Guelph
|
| Department |
Animal Biosciences
|
| Street address |
50 Stone Road East
|
| City |
Guelph |
| State/province |
ON |
| ZIP/Postal code |
N1G 2W1 |
| Country |
Canada |
| |
|
| Platform ID |
GPL26012 |
| Series (1) |
| GSE124789 |
Characterization of the Bovine Salivary Gland Transcriptome Associated with Mycobacterium avium subsp. paratuberculosis Experimental Challenge |
|
| Relations |
| BioSample |
SAMN10714721 |
| SRA |
SRX5227491 |
