Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K27ac

Cell type

Cell type Class
Pluripotent stem cell
Cell type
mESC derived cells
NA
NA

Attributes by original data submitter

Sample

source_name
TKO_13D_H3K27ac
strain
R1 129/Sv
genotype/variation
Tet1-/- Tet2-/- Tet3-/-
cell type
mESC-derived cell
chip-antibody
Active Motif, Cat # 39133

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were crosslinked with 1% formaldehyde for 10 min at 37◦C; then, crude nuclei were purified. Chromatin was fragmented by sonication to obtain fragments 200–2000 bp in length. For each ChIP assay, 2–5 ug of antibodies were added and incubated at 4◦C overnight. Chromatin was reverse-crosslinked, purified and quantified with a Qubit fluorometer using the Quant-iT dsDNA HS assay kit DNA was end-repaired, adenylated, and ligated to TruSeq sequencing adaptors. DNA was purified by AMPure beads or DNA purification kit according to the DNA amount. Library DNA was amplified by Phusion HF (NEB, Cat. M0530L). The amplified DNA was size selected using 2% agarose gel for 200-500bp DNA fragments.

Sequencing Platform

instrument_model
HiSeq X Ten

mm10

Number of total reads
22660419
Reads aligned (%)
86.6
Duplicates removed (%)
21.0
Number of peaks
12398 (qval < 1E-05)

mm9

Number of total reads
22660419
Reads aligned (%)
86.5
Duplicates removed (%)
20.9
Number of peaks
12340 (qval < 1E-05)

Base call quality data from DBCLS SRA