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Sample GSM3790870 Query DataSets for GSM3790870
Status Public on Oct 22, 2019
Title M_2457_70G
Sample type SRA
 
Source name Mastitic_milk somatic cells
Organism Bos taurus
Characteristics breed: Holstein
group: Mastitic
lactation number: 1
dim: 236
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 SAMN11811709
SRA SRX5880890

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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