|
| Status |
Public on Oct 22, 2019 |
| Title |
M_2360_50D |
| Sample type |
SRA |
| |
|
| Source name |
Mastitic_milk somatic cells
|
| Organism |
Bos taurus |
| Characteristics |
breed: Holstein
group: Mastitic
lactation number: 2
dim: 44
cell type: Milk somatic cells
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Milk samples were collected using a 3 cm plastic cannula to ensure no bacteria contaminated the sample. Milk was kept on ice and immediately processed for RNA extraction using Trizol reagent to preserve the integrity of RNA.
Library construction was performed using the Illumina TruSeq RNA sample preparation kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
CLC genomics workbench (CLC Bio, Aarhus, Denmark) was used to map the genes to the annoated UMD3.1 bovine reference genome (release 90)
Transcript levels were quantified in reads per kilo base per million mapped reads (RPKM). By normalizing the data for transcript length and total reads in each gene for each sample, the RPKM measure facilitated comparisons of transcript levels between both groups.
Genome_build: UMD3.1
Supplementary_files_format_and_content: RPKM values normalized per gene and sample.
|
| |
|
| Submission date |
May 21, 2019 |
| Last update date |
Oct 22, 2019 |
| Contact name |
Angela Cánovas |
| E-mail(s) |
acanovas@uoguelph.ca
|
| Organization name |
University of Guelph
|
| Department |
Animal Biosciences
|
| Lab |
Cánovas Lab
|
| Street address |
50 Stone Road East
|
| City |
Guelph |
| State/province |
ON |
| ZIP/Postal code |
N1G 2W1 |
| Country |
Canada |
| |
|
| Platform ID |
GPL15749 |
| Series (1) |
| GSE131607 |
Genetic mechanisms regulating the host response during mastitis |
|
| Relations |
| BioSample |
SAMN11811717 |
| SRA |
SRX5880882 |
