|
Status |
Public on May 12, 2020 |
Title |
Foxp3-GFP+Treg_BACH2-RFP_HI_Male2_RNA-seq |
Sample type |
SRA |
|
|
Source name |
Treg cells
|
Organism |
Mus musculus |
Characteristics |
strain: C57BL/6 tissue: spleen age: post natal 12–13 weeks genotype: Foxp3EGFP-DTR Bach2tdRFP/+
|
Extracted molecule |
total RNA |
Extraction protocol |
Single-cell suspensions were purified by total CD4+ T cell enrichment followed by FACS-sorting stored in 40 µl RNAlater™ Stabilization Solution at -80 °C Samples were processed using the QIAshredder Kit (Qiagen) according to the manufacturer’s protocol RNA was extracted from samples using the RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s protocol RNA Libraries were prepared using the SmartSeq2 protocol on an automated Hamilton NGS-STAR library preparation system and sequenced using a HiSeq 2500 System (Illumina)
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|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
|
|
Description |
RNA-seq_Foxp3-GFP_BACH2-RFP_HI_M2
|
Data processing |
FastQ files underwent quality control with FastQC, adaptor trimming with Cutadapt and alignment to the NCBIM37 Mus musculus genome annotation with hisat2 using ClusterFlow pipelines Differential gene expression analysis was performed using Cufflinks44 and differentially expressed genes were futher analysed using R Genome_build: mm9 Supplementary_files_format_and_content: tab-delimited text files include FPKM values
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|
|
Submission date |
Mar 01, 2019 |
Last update date |
May 12, 2020 |
Contact name |
Mohammed-Firas Sadiyah |
E-mail(s) |
mfs37@cam.ac.uk
|
Organization name |
University of Cambridge
|
Street address |
The Old Schools, Trinity Ln
|
City |
Cambridge |
ZIP/Postal code |
CB2 1TN |
Country |
United Kingdom |
|
|
Platform ID |
GPL17021 |
Series (2) |
GSE127698 |
Heterogeneous Bach2 expression distinguishes rTreg cells and aTreg cells |
GSE128176 |
BACH2 is repurposed following Treg lineage commitment to drive the functional quiescence and maintenance of resting Treg cells |
|
Relations |
BioSample |
SAMN11106055 |
SRA |
SRX5508327 |