|
| Status |
Public on Dec 07, 2020 |
| Title |
IMM-inoculated |
| Sample type |
SRA |
| |
|
| Source name |
CD45+ CD4+ T cells
|
| Organism |
Bos taurus |
| Characteristics |
breed: Holstein
cell type: CD45+ CD4+ T cells
age: 15 month
treatment: immunized intramuscularly using heat-killed E. coli P4 emulsified in adjuvant plus a mammary boost with 50 µg of protein concentrate prepared from a E. coli P4 supernate
inoculation: challenged with E. coli P4
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mononuclear cells were isolated from 2 g of mammary tissue after collagenase type IV and DNAse digestion. Cells were recovered through Percoll gradient centrifugation and stained with PE-labeled CD45 (CC1, BIO-RAD) and FITC-labeled CD4 (CC8, BIO-RAD) mAbs, before cell sorting using a MoFlo Astrios EQ (Beckman Coulter). Total RNA was extracted from samples with Nucleospin XS RNA 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) |
| GSE159283 |
Transcriptome analysis of mammary CD45+ CD4+ lymphocytes after immunization against E. coli P4 strain and homologous challenge |
|
| Relations |
| BioSample |
SAMN16402568 |
| SRA |
SRX9269381 |
