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Sample GSM4825336 Query DataSets for GSM4825336
Status Public on Dec 07, 2020
Title 3727_I0
Sample type SRA
 
Source name Blood
Organism Bos taurus
Characteristics breed: Holstein
tissue: Blood
age: 15 month
immunization protocol: Intramuscular immunization with heat-killed E.coli P4 and boost with same vaccine
time: 0 days after first immunization
immunization routes: Intramuscular (x2)
Extracted molecule total RNA
Extraction protocol Whole blood samples were lysed using the buffer provided in the kit and stored at -80°C. Total RNA was extracted on silica columns with Nucleospin RNA blood kit (Macherey-Nagel).
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Data processing Read quality was assessed with FastQC software. Reads were aligned in comparison to the bovine reference genome (UMD3.1.87) with STAR software
Count table was generated with Cufflinks/RSEM
Identification of differentially expressed genes (DEGs) was performed with DESeq2 package within the R environment
Genome_build: Bos_taurus.UMD3.1.87
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
 
Submission date Oct 09, 2020
Last update date Dec 07, 2020
Contact name gilles FOUCRAS
E-mail(s) gilles.foucras@envt.fr
Organization name ENVT INRA
Street address 23 Chemin des Capelles
City TOULOUSE
State/province State/Province/Region
ZIP/Postal code 31300
Country France
 
Platform ID GPL21659
Series (1)
GSE159286 Whole blood transcriptome analysis during immunization and mammary challenge with E. coli
Relations
BioSample SAMN16402826
SRA SRX9269539

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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