|
| Status |
Public on Jan 17, 2022 |
| Title |
WT3 |
| Sample type |
SRA |
| |
|
| Source name |
Spleen_CD8 T cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Spleen
genotype: WT
|
| Treatment protocol |
WT and KO CD8+ T cells were sorted from the spleens of recipient mice 7 days after LM-OVA infection in the co-transfer model.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol. RNA concentration was detected by the Qubit RNA broad range assay in the Qubit Fluorometer (Invitrogen). After quality control by RNase free agarose gel and Agilent 2100 (Agilent Technologies, Palo Alto, CA, USA), RNA-Seq libraries were prepared using 200ng total RNA with the TruSeq RNA sample prep kit according to manufacturer’s instructions (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Hiseq 6000 sequencer software used for basecalling.
The double-stranded cDNA library was finished through PCR enrichment and size selection. The prepared cDNA library was sequenced with the Illumina Hiseq 2000 sequencer (Illumina HiSeq 6000 v4 Single-Read 50 bp) after pooling according to its expected data volume and effective concentration.
Firstly, the raw reads were trimmed by using Trim Galore (version 0.5.0_dev, Cutadapt version 1.15) with default parameters. After removing low-quality bases RNAs, the clean data were mapped to mouse genome (mm10), and quantified by using Salmon5. The transcript-level quantification results were converted to the gene-level quantities with tximport R package.
DESeq2 R package was used to normalize the gene-level quantities and followed by differential expression analysis between selected samples with the same package.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Jan 13, 2022 |
| Last update date |
Jan 17, 2022 |
| Contact name |
Cangang Zhang |
| E-mail(s) |
cg.zhang20195028@stu.xjtu.edu.cn
|
| Phone |
13636810556
|
| Organization name |
xian jiaotong university
|
| Street address |
Yanta district, xi 'an city, shaanxi province
|
| City |
xian |
| State/province |
State... |
| ZIP/Postal code |
710000 |
| Country |
China |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE193624 |
Med1 controls effector CD8+ T cell differentiation and survival through mediating the transcriptional regulation of C/EBPβ on T-bet |
|
| Relations |
| BioSample |
SAMN24957182 |
| SRA |
SRX13775745 |
