|
| Status |
Public on Feb 21, 2020 |
| Title |
Brg1 deleted tregs subset from rko1 mice, isolated on day 7 after tam |
| Sample type |
SRA |
| |
|
| Source name |
Treg cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Spleen and LN
cell type: Treg cells
age: 3-4 weeks
genotype: R26CAG-FlpoERBrgF/deltaRFoxp3YFP-Cre/YFP-Cre(treatment)
|
| Treatment protocol |
Tregs were harvested from lymph nodes and spleens of various mice, including reversible KO mice treated with tamoxifen.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from 0.1 million Tregs using RNAprep Pure Micro Kit (TIANGEN), and cDNA synthesized from mRNA using SMART-Seq® v4 Ultra™ Low Input RNA Kit (Clontech). Library was then constructed and sequenced on Illumina HiSeq platform with the PE150 strategy, which yielded 25~ 60 million reads per sample.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
rko1(-)
|
| Data processing |
Reads were aligned to the reference genome using Hisat2 (v2.0. 5)
The mapped reads of each sample were assembled by StringTie (v1.3.3b)
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped each gene.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
Jun 11, 2019 |
| Last update date |
Feb 21, 2020 |
| Contact name |
Zhengyu Jing |
| E-mail(s) |
jingzhy@shanghaitech.edu.cn
|
| Organization name |
ShanghaiTech University
|
| Department |
School of Life Science and Technology
|
| Lab |
Chi Lab
|
| Street address |
393 Middle Huaxia Road, Pudong
|
| City |
Shanghai |
| ZIP/Postal code |
201210 |
| Country |
China |
| |
|
| Platform ID |
GPL21273 |
| Series (1) |
| GSE132562 |
A reversible KO model reveals therapeutic potentials of defective Tregs |
|
| Relations |
| BioSample |
SAMN11964671 |
| SRA |
SRX5979902 |
