Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Pluripotent stem cell
Cell type
hESC H1
NA
NA

Attributes by original data submitter

Sample

source_name
H1 hESCs
cell line
H1
cell type
Embryonic stem cells (ESCs)
genotype/variation
overexpressing HA-tagged ZFP57
chip antibody
None

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were harvested, washed 2x (in KO medium), fixed in 10mL per 1x10^7 cells (10 min in 1% formaldehyde), quenched with TrisHCl in 50mL (at 250 mM final), washed with PBS, and pelleted. Each pellet containing 1x10^7 cells was lysed, resuspended in 1 mL of sonication buffer on ice (10 mM Tris at pH 8, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% NaDOC, 0.25% NLS, and protease inhibitors), transferred to TC 12x12 tubes (Covaris), and sonicated (Covaris settings: 20 min, 5% duty cycle, 140W, 200 cycles). Sonication was assessed by reverse cross-linking (65°C, RNase A at 1μg/μL, overnight), followed by DNA extraction. Fragment size (between 200-400bp) was checked on a Bioanalyzer (Agilent 2100). Immunoprecipitations were performed with chromatin from 1x10^7 cells with Dynabeads (ThermoFisher) in IP buffer (16.25 mM Tris at pH 8.1, 137.5 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1.25% Triton X-100, and protease inhibitors) overnight. Chromatin was reversed cross-linked (65°C, Proteinase K at 400ng/μL, overnight) and DNA was further extracted for analysis. Single-end libraries were prepared and sequenced in 100bp reads runs according to Illumina instructions.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
65254569
Reads aligned (%)
94.9
Duplicates removed (%)
5.0
Number of peaks
2315 (qval < 1E-05)

hg19

Number of total reads
65254569
Reads aligned (%)
94.0
Duplicates removed (%)
6.7
Number of peaks
1341 (qval < 1E-05)

Base call quality data from DBCLS SRA