|
| Status |
Public on Dec 31, 2016 |
| Title |
165_NS |
| Sample type |
SRA |
| |
|
| Source name |
rectal tissue_negative for E. coli O157
|
| Organism |
Bos taurus |
| Characteristics |
tissue: rectum
phenotype: negative for E. coli O157
|
| Treatment protocol |
Cattle with two phenotypes, control group was cattle negative for E. coli O157, experimental group was cattle shedding > 10^4 CFU E. coli O157/g of feces
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Two 2 cm^2 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 Small RNA Sample Preparation kit
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
165
|
| Data processing |
sRNAbench: expression profiling of microRNAs based on genome mappings generated by Bowtie aligner
sRNAde: differntially expressed microRNA identification, differentially expressed microRNA were defined from edgeR output table
miRNAconsTargets: consensus microRNA target prediction, using miRNAda and PITA
Functional anlaysis for target genes with Ingenuity Pathway Anlaysis
Genome_build: BosTau7
Supplementary_files_format_and_content: excel file, content is normalized expressional abundance (counts per million) of each microRNA from each animal
|
| |
|
| Submission date |
Nov 03, 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) |
| GSE74627 |
microRNA study of rectal tissue collected from super-shedders vs cattle negative for E. coli O157:H7 |
|
| Relations |
| BioSample |
SAMN04231518 |
| SRA |
SRX1410883 |
