|
| Status |
Public on Oct 31, 2017 |
| Title |
Purified splenic CD4 T cells number 2 activated with anti-CD3/CD28 + Salp15deltaP11 day 2 |
| Sample type |
SRA |
| |
|
| Source name |
Purified splenic CD4 T cells, activated with anti-CD3/CD28 + Salp15deltaP11 day 2
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6(h-2b)
age: 8 weeks
tissue: Blood
cell type: CD4 T cells
treatment: Salp15deltaP11
time: day 2
|
| Growth protocol |
Mice were breed and housed at the Animal Facility of CIC bioGUNE under controled conditions according to the animal care international gidelines.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from CD4 T cells using PureLink RNA Micro Scale Kit (Thermo Fisher Scientific)
TruSeq® RNA Sample Preparation v2 (Illumina Inc.)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiScanSQ |
| |
|
| Description |
2SC2
2SC_vs_2S15
|
| Data processing |
Basecalls performed using CASAVA version 1.8.2
Individual FASTQ files for each sample were merged prior to the quality control & filtering steps
Quality control of the reads was carried out using FASTQC software (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Reads were filtered from the adapter sequences and their quality score using trim_galore software. (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and only are retained those with at least 20 phred quality score.
Reads were mapped to mm10 (Mus musculus) reference genome using Tophat (https://ccb.jhu.edu/software/tophat/index.shtml) to account for spliced reads alignments, allowing two mismatches (n = 2).
Resulting BAM aligment files were used in as input for a Differential Expression Analysis pipeline based on DESeq2 BioconductoR package (https://bioconductor.org/packages/release/bioc/html/DESeq2.html).
Genome_build: mm10
Supplementary_files_format_and_content: Tables of raw counts, obtained from the SAM files of the samples in each comparative. These tables are in tab separated plain text format.
|
| |
|
| Submission date |
May 09, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Jose Luis Lavin |
| E-mail(s) |
joluito@gmail.com
|
| Organization name |
CIC bioGUNE
|
| Street address |
Parque Tecnológico de Bizkaia Building 502, Floor 0
|
| City |
Derio |
| State/province |
Bizkaia |
| ZIP/Postal code |
48160 |
| Country |
Spain |
| |
|
| Platform ID |
GPL16173 |
| Series (1) |
| GSE98700 |
The immunosuppressive effect of the tick salivary protein, Salp15, is persistent and has long-term effects in a murine model of hematopoietic transplant |
|
| Relations |
| BioSample |
SAMN06920969 |
| SRA |
SRX2792702 |
