|
| Status |
Public on May 11, 2021 |
| Title |
treg_Bach2-cKO rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Regulatory T cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: lymphocytes
cell subtype: Regulatory T cells
strain: C57BL/6
genotype: Bach2-cKO
treatment: CD3 and CD28 stimulation in vitro for 24h
|
| Treatment protocol |
Treated sorted cells with plate-bound CD3 and CD28 for 24h
|
| Growth protocol |
Sorted fresh B220-CD4+YFP+cells from WT and Bach2 KO mice spleen
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cells were havest and RNA was extract by Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#RS-122-2001) was used with 0.1-1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.
|
| |
|
| Submission date |
Jan 15, 2021 |
| Last update date |
May 13, 2021 |
| Contact name |
Heng Zhang |
| E-mail(s) |
zh123@sjtu.edu.cn
|
| Organization name |
Shanghai Jiao Tong University School of Medicine
|
| Street address |
No.227 Sounth Chongqing Road
|
| City |
Shanghai |
| ZIP/Postal code |
200025 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE164937 |
Bach2 attenuates IL-2R signalling to control Treg homeostasis and Tfr development |
|
| Relations |
| BioSample |
SAMN17348067 |
| SRA |
SRX9859551 |
