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Sample GSM3874708 Query DataSets for GSM3874708
Status Public on Feb 21, 2020
Title Brg1 deleted tregs from rko1 mice
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(no 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(without reversal)
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 SAMN11964669
SRA SRX5979904

Supplementary file Size Download File type/resource
GSM3874708_rko1without_reversal.txt.gz 297.1 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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