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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 12, 2020 |
| Title |
iTreg_JunD_ChIP-seq |
| Sample type |
SRA |
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| Source name |
Treg cells
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: spleen
age: post natal 8–12 weeks
genotype: wild type
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total CD4+ T cells were MACS-enrichment and FACS-sorted.
Cells were then transferred to a 96-well plate coated with anti-CD3ε and antiCD28 antibodies and cultured in RPMI complete media supplemented with TGF-β for 4 days.
2 x 107 cells were chemically crosslinked and sonicated on a Branson 450-D sonicator to generate fragmented genomic DNA
Chromatin immunoprecipitation was performed using the following antibodies: anti-BACH2 (N-2; Tohoku University), anti-JunD (sc-74; Santa Cruz) and (sc-586; Santa Cruz)
For sequencing of immunoprecipitated DNA, DNA fragments were blunt-end ligated to Illumina adaptors, amplified, and sequenced by using the HiSeq 2000 platform (Illumina)
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
The sequenced reads were aligned to the mouse genome (NCBIM37/mm9) with Bowtie 0.12.9; only uniquely mapped reads were retained
Peaks were called based on enrichment of ChIP-Seq reads over input reads (binomial distribution FDR < 5%)
Genome_build: mm9
Supplementary_files_format_and_content: MACS bed file, narrowPeak
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| Submission date |
Mar 19, 2019 |
| Last update date |
May 12, 2020 |
| Contact name |
Mohammed-Firas Sadiyah |
| E-mail(s) |
mfs37@cam.ac.uk
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| Organization name |
University of Cambridge
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| Street address |
The Old Schools, Trinity Ln
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| City |
Cambridge |
| ZIP/Postal code |
CB2 1TN |
| Country |
United Kingdom |
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| Platform ID |
GPL13112 |
| Series (2) |
| GSE127695 |
Distribution of genome-wide BACH2 or JunD binding sites identified by ChIP-Seq in iTreg cells |
| GSE128176 |
BACH2 is repurposed following Treg lineage commitment to drive the functional quiescence and maintenance of resting Treg cells |
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| Relations |
| BioSample |
SAMN11172710 |
| SRA |
SRX5548089 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3679893_ChIP-seq_iTreg_JunD_peaks.bed.gz |
75.0 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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