|
| Status |
Public on Aug 04, 2016 |
| Title |
aTr_H3K4me1_rep1 (Sample 40) |
| Sample type |
SRA |
| |
|
| Source name |
aTr_H3K4me1
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Spleen and peripheral lymph nodes
cell type: Activated Treg cells
source: mixed bone marrow chimeras generated with 90% Foxp3-GFP-DTR /10% Foxp3-GFP-CRE-ERT2XR26Y bone marrow
activating stimulus: Transient Treg cell depletion
days post-stimulus: 11 days
chip antibody: anti-H3K4me1 (Abcam; Cat #: ab8895; Lot:GR61306-1)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
FACS-sorted cell populations (1x105 cells) were crosslinked in 1% paraformaldehyde for 5 minutes at RT. The reaction was quenched by addition of 125mM glycine. Crosslinked cells were lysed and partially digested with micrococcal nuclease (12,000 units/ml) for 1 minute at 37 degrees. Digestion was stopped by addition of EDTA and digested nuclei were resuspended in nuclear lysis buffer containing 1% SDS. Following sonication, chromatin was incubated overnight with antibodies against H3K27me3, H3K27Ac, or H3K4me1 and immunocomplexes were precipitated with protein A Dynabeads. After washing, precipitated chromatin was decrosslinked overnight at 65 degrees in the presence of proteinase K and DNA fragments were isolated using Qiagen PCR-purification kit. Purified DNA was processed for sequencing on Illumina Hiseq.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
YFP+ GFP+ Treg cells were isolated from animals treated with tamoxifen and diphtheria toxin
|
| Data processing |
Sequences mapped using bowtie2 2.2.0
Peak was called with macs2 with p-value cutoff of 0.01
Peaks below the IDR cutoff of 0.05 were selected
The union of ATAC-seq peaks were found, and reads overlapping this peak atlas were counted.
Genome_build: mm9
Supplementary_files_format_and_content: [htseq.txt and bam-genes.txt] DESeq2-normalized read counts for RNA-Seq samples
Supplementary_files_format_and_content: [countsatatacseqpeaks.txt] peaks for ATAC-Seq and ChIP-Seq samples
|
| |
|
| Submission date |
Jun 13, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Hyein Sophia Cho |
| E-mail(s) |
[email protected]
|
| Organization name |
Memorial Sloan Kettering Cancer Center
|
| Department |
Developmental Biology
|
| Street address |
430 E 67th St
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE83315 |
Memory of inflammation in regulatory T cells |
|
| Relations |
| BioSample |
SAMN05240637 |
| SRA |
SRX1842267 |
