|
| Status |
Public on Jun 06, 2019 |
| Title |
RNA-Seq_CD8_TIM_S2 |
| Sample type |
SRA |
| |
|
| Source name |
Thymus
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Thymocytes
Stage: CD8SP Innate Memory
strain: BALB/c
genotype: wild type
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA from 106 sorted CD8SP populations was extracted using RNeasy Plus Mini kit according to manufacturer’s instructions
RNA library was prepared using Truseq Ribo zero gold kit for TIM and Naive, and Truseq kit for CD8SP WT and CD8SP EomesTg following manufacturer's instruction.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Truseq Ribo zero gold kit
RNA-Seq_CD8_TIMvsNaive.xlsx
|
| Data processing |
reads were filtered using FastX 0.0.13 and ShortRead 1.16.3, polyA-reads (more than 90% of the bases equal A), ambiguous reads (containing N), low quality reads (more than 50% of the bases < Q25) and artifact reads (all but 3 bases in the read equal one base type) were removed
reads were aligned to the reference genome mm10 using Tophat v2.0.13 with the following parameters: --library-type fr-firststrand --min-intron-length 50 --max-intron-length 500000 --no-coverage-search --no-mixed --read-realign-edit-dist 3
reads from the alignment that are non-primary mappings or have a mapping quality ≤20 were removed
read counts were estimated using featureCounts v1.4.6 with the following parameters: -Q 0 -s 2 -t exon -g gene_id and genes that have less than 1 counts-per-million were removed
raw read counts were normalised with the EDASeq package and FPKM values were obtained
differential expression analysis was performed with edgeR 3.4.0 package by applying a corrected p value FDR<0.05 and absolute log2-ratio larger than 1.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file containing raw read counts and FPKM normalized counts (TIM vs Naive) and tab-delimited text files containing normalized read counts (such as total read count=20M) for each sample and gene and differential analysis results (EomesTG vs WT)
|
| |
|
| Submission date |
Jan 10, 2019 |
| Last update date |
Jun 06, 2019 |
| Contact name |
Stanislas Goriely |
| E-mail(s) |
stgoriel@ulb.ac.be
|
| Phone |
+3226509586
|
| Organization name |
Université Libre de Bruxelles
|
| Lab |
IMI
|
| Street address |
Rue Adrienne Bolland 8
|
| City |
Gosselies |
| ZIP/Postal code |
B-6041 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE124913 |
EOMES-dependent epigenetic reprogramming during CD8 T cell development leads to acquisition of memory traits (RNA-Seq) |
| GSE124914 |
EOMES-dependent epigenetic reprogramming during CD8 T cell development leads to acquisition of memory traits |
|
| Relations |
| BioSample |
SAMN10721935 |
| SRA |
SRX5236604 |
