Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me1

Cell type

Cell type Class
Blood
Cell type
Treg
NA
NA

Attributes by original data submitter

Sample

source_name
rTr_H3K4me1
tissue
Spleen and peripheral lymph nodes
cell type
Resting Treg cells
source
mixed bone marrow chimeras generated with 90% Foxp3-GFP-DTR /10% Foxp3-GFP-CRE-ERT2XR26Y bone marrow
activating stimulus
none
days post-stimulus
NA
chip antibody
anti-H3K4me1 (Abcam; Cat #: ab8895; Lot:GR61306-1)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_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.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
16686003
Reads aligned (%)
88.6
Duplicates removed (%)
12.8
Number of peaks
216 (qval < 1E-05)

mm9

Number of total reads
16686003
Reads aligned (%)
88.3
Duplicates removed (%)
12.9
Number of peaks
340 (qval < 1E-05)

Base call quality data from DBCLS SRA