|
| Status |
Public on Mar 20, 2016 |
| Title |
108_ns_rt |
| Sample type |
SRA |
| |
|
| Source name |
rectal tissue
|
| Organism |
Bos taurus |
| Characteristics |
tissue: rectum
phenotypes: negative for E. coli O157
|
| Treatment protocol |
Cattle with two phenotypes, one is negative for E. coli O157, one is shedding > 10^4 CFU E. coli O157/g of feces
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Two 2 cm2 biopsies 3-5 cm proximal to the rectal-anal junction were collected from each animal and immediately flash frozen in liquid nitrogen within 10 min after death of the animal. Samples were stored at -80 °C until RNA was extracted. 100 mg of powdered rectal tissue was used for RNA extraction using a mirVana total RNA Isolation Kit
Illumina truseq_stranded_total_rna_sample_preparation kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Alignment to Genome with Tophat2
Alignment output piped to Ht-seq-count
Reads mapped were normlized into counts per million
Differential analysis was performed using edgeR
Functional anlaysis with Ingenuity Pathway Anlaysis
Genome_build: umd3.1
Supplementary_files_format_and_content: csv files, content is normalized expressional abundance of each gene each animal
|
| |
|
| Submission date |
Mar 20, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Guanxiang Liang |
| E-mail(s) |
liangguanxiang@gmail.com
|
| Organization name |
University of Alberta
|
| Street address |
410 Agriculture/Forestry Centre
|
| City |
Edmonton |
| State/province |
Alberta |
| ZIP/Postal code |
T6G 2P5 |
| Country |
Canada |
| |
|
| Platform ID |
GPL15749 |
| Series (1) |
| GSE67099 |
Transcriptome analysis of rectal tissues of E. coli O157 super-shedding and E. coli O157 negative cattle |
|
| Relations |
| BioSample |
SAMN03435375 |
| SRA |
SRX960500 |
