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
embryonic stem cells
strain
129S4/SvJae
genotype
wild type
chip antibody
anti-H3K4me3 (Millipore, 07-473)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
2×106 cells were fixed for 10 minutes with 1% formaldehyde, followed by chromatin extraction and sonication to generate 200-500bp fragments. The sheared chromatin was incubated overnight at 4°C with H3K4me3 or H3K27me3 antibody. After incubation, 10 µl of Dynabeads Protein A magnetic beads previously washed in RIPA buffer was added, and samples were incubated for an additional 2 hours at 4°C. Bead-protein complexes were washed three times with RIPA buffer and twice with TE buffer. Genomic DNA was eluted for 2 hours at 68°C in 100 µl of Complete Elution Buffer (20 mM Tris, pH7.5, 5 mM EDTA, 50 mM NaCl, 1% SDS, 50 µg/ml proteinase K) and purified with MinElute PCR purification kit (Qiagen, 28004). For ChIP-Seq, sequencing libraries were prepared using ThruPLEX DNA-seq 48D kit (Rubicon Genomics, R400406) following standard protocols.

Sequencing Platform

instrument_model
NextSeq 500

mm10

Number of total reads
11533044
Reads aligned (%)
96.5
Duplicates removed (%)
7.7
Number of peaks
31387 (qval < 1E-05)

mm9

Number of total reads
11533044
Reads aligned (%)
96.3
Duplicates removed (%)
7.9
Number of peaks
31288 (qval < 1E-05)

Base call quality data from DBCLS SRA