Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me2

Cell type

Cell type Class
Blood
Cell type
CD4+ T cells
NA
NA

Attributes by original data submitter

Sample

source_name
Blast-cultured splenic CD4+ T-cells
cell type
Blast-cultured splenic CD4+ T-cells
pma treatment
120 min
antibody
H3K4me2

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin was prepared and immunoprecipitation was carried out as previously described (Lichtinger et al) for the antibodies, H3K27ac (ab4729) and H3K4me2 (Millipore 07-030). For all other antibodies, JunB (sc-46), Runx1 (ab23980), Ets1 (sc-111), and BRD4 (Bethyl laboratories), chromatin was prepared as follows. Cells were resuspended in PBS at 3.3x106 cells/ml and cross-linked with 0.83mg/ml disuccinimidyl glutarate (DSG) for 45 minutes at room temperature with rotation. Cells were washed four times with PBS and further crosslinked in PBS at 2x106 cells/ml with 1% formaldehyde for 10 minutes at room temperature. Crosslinking was quenched with 0.125M glycine, cells were washed twice in PBS and incubated with Buffer A at 4oC for 10 minutes followed by buffer B at 4oC for 10 minutes. Double cross-linked chromatin was then used for immunoprecipitation as previously described (Lichtinger et al). Libraries were prepared from approximately 10ng DNA from ChIP samples. Libraries for sequencing on the Solid platform were prepared according to the manufacturer’s instructions. Samples were sequenced using 50bp reads. All other libraries were prepared using the Tru-Seq library preparation kit according to the manufacturer’s instructions (Illumina). These samples were sequenced on the Illumina HiSeq platforms using 50bp single end reads

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
67439153
Reads aligned (%)
98.3
Duplicates removed (%)
17.9
Number of peaks
28450 (qval < 1E-05)

mm9

Number of total reads
67439153
Reads aligned (%)
98.2
Duplicates removed (%)
18.0
Number of peaks
28490 (qval < 1E-05)

Base call quality data from DBCLS SRA