|
| Status |
Public on May 28, 2024 |
| Title |
1484803_Foxp3_Traditional |
| Sample type |
SRA |
| |
|
| Source name |
Male mice
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
Sex: Male
cell type: In vitro induced wild-type regulatory T cells
chip antibody: Rabbit anti-Foxp3 (Abcam, ab150743)
|
| Treatment protocol |
iTr cells were treated with 0.25 mM ascorbic acid 2-phosphate for 4 days during Treg induction to induce Tet-mediated DNA demethylation naturally occurring during Tr differentiation in vivo.
|
| Growth protocol |
CD4 naïve T cells from male Foxp3-gfp reporter mice were sorted to induce regulatory T cells in vitro (iTr) by plate-bound anti-CD3 and anti-CD28 antibodies, recombinant Interleukin-2 (IL-2), and TGF-beta, and ascorbic acid-2-phosphate. Four days later, iTr cells were used for Foxp3 PSI or traditional ChIP sequencing.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For Foxp3-PSI ChIP, cell fixation and intracellular staining was performed with Foxp3 staining kit (eBioscience). After Foxp3 PSI reaction, cells were fixed with 1% methanol-free formaldehyde at room temperature for 5 min and then sonicated for enrichment of biotinylated chromatins with streptavidin beads. Precipitated DNA was released by proteinase K digestion, phenol: chloroform extraction, and 2-propanol precipitation. Traditional Foxp3 ChIP was conducted according to standard protocols (PMID: 23021222).
Libraries were constructed according to standard protocols for ChIP
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Traditional ChIP
|
| Data processing |
ChIP-seq data analysis: Single reads of 50 bp were mapped mouse genome mm9 (MGSCv37 from Sanger) by BWA (version 0.7.12-r1039, default parameter), duplicated reads were then marked with biobambam2 (version v2.0.87), and non-duplicated reads were chosen by samtools (parameter “-q 1 -F 1024” version 1.2).
We followed ENCODE guideline for quality control of our data. All our samples passed QC criterion and have more than 30M non-duplicated reads.
After assessing the data quality, we extended reads to fragment size (detected by SPP v1.1) and generated bigwig tracks (normalized to 15 million uniquely mapped reads) for visualization. We then called peaks using MACS2(version 2.1.1.20160309, parameters “--nomodel --extsize fragment size”). We confirmed the PSI samples were highly reproducible that > 90% of peaks in one replicate could be called in another.
Genome_build: mm9(MGSCv37 )
Supplementary_files_format_and_content: bigwig
|
| |
|
| Submission date |
Apr 30, 2020 |
| Last update date |
May 28, 2024 |
| Contact name |
Beisi Xu |
| E-mail(s) |
beisi.xu@stjude.org
|
| Organization name |
St Jude Children's Research Hosipital
|
| Department |
Center for Applied Bioinformatics
|
| Street address |
262 Danny Thomas Pl
|
| City |
Memphis |
| State/province |
Tennessee |
| ZIP/Postal code |
38105 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE149672 |
Dynamic Foxp3-chromatin interaction controls tunable Treg cell function [PSI-ChIP] |
| GSE149674 |
Dynamic Foxp3-chromatin interaction controls tunable Treg cell function |
|
| Relations |
| BioSample |
SAMN14783602 |
| SRA |
SRX8218319 |
