Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

Cell type

Cell type Class
Pluripotent stem cell
Cell type
ES cells
NA
NA

Attributes by original data submitter

Sample

source_name
Dnmt TKO ESCs
cell type
ESC
construct
WWD H3K4me3
passages
7 to 10
chip antibody
H3K4me3 (Abcam, 8580)
cell line
J1 ES

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin from formaldehyde fixed cell (2x107 cells per ChIP) was fragmented to a size range of 160-480 bp using a combination of micrococcal nuclease digestion and sonication with Bioruptor (Diagenode). Solubilized chromatin was immunoprecipitated with antibody. To generate libraries for Illumina high-throughput sequencing of ChIP and input DNA, end repair, adenylation, ligation with indexed adaptors, and 18 cycles of PCR with Illumina primers were performed following the TruSeq ChIP Sample Preparation guide (Illumina).

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
36492449
Reads aligned (%)
86.7
Duplicates removed (%)
81.6
Number of peaks
24994 (qval < 1E-05)

mm9

Number of total reads
36492449
Reads aligned (%)
86.6
Duplicates removed (%)
81.7
Number of peaks
25048 (qval < 1E-05)

Base call quality data from DBCLS SRA