|
| Status |
Public on Jun 05, 2015 |
| Title |
E24 |
| Sample type |
SRA |
| |
|
| Source name |
mammary epithelial cell line
|
| Organism |
Bos taurus |
| Characteristics |
cell type: MAC-T cell
treatment: Challenged by Escherichia coli (E. coli) strain P4
time points: 24 hours
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Rumen, mid-jejunum and ileum were collected from cavles, flash frozen on dry ice, and RNA was harvested using mirVana™ miRNA Isolation Kit (Ambion, Carlsbad, CA). Illumina TruSeq Small RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiScanSQ |
| |
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to miRBase Version19 using miRDeep2.
The expression of miRNAs in each library was normalized to counts per million reads (CPM) by the following method: CPM = (miRNA reads number / total reads number per library) × 1000000
Genome_build: Bos_taurus_UMD_3.1
Supplementary_files_format_and_content: Tab-delimited text files include reads number for each Sample
|
| |
|
| Submission date |
Oct 31, 2013 |
| 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 |
GPL17875 |
| Series (1) |
| GSE51979 |
Transcriptome microRNA profiling of bovine mammary epithelial cells challenged with Escherichia coli or Staphylococcus aureus bacteria reveals pathogen directed microRNA expression profiles |
|
| Relations |
| BioSample |
SAMN02389842 |
| SRA |
SRX372041 |
