|
Status |
Public on May 16, 2019 |
Title |
2398_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 |
SAMN10714790 |
SRA |
SRX5227511 |