Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
EZH2

Cell type

Cell type Class
Epidermis
Cell type
Dermal fibroblast
NA
NA

Attributes by original data submitter

Sample

source_name
Dermal Fibroblasts
chip antibody
EZH2 (Cell Signalling - 5246S, 1:40)
neoplastic stage
transformed

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were fixed with 1% formaldehyde in cell culture media for 10 minutes at room temperature. Cells were lysed in 1:1 SDS-containing buffer (100mM NaCl, 50mM Tris-HCl pH 8.0, 5mM EDTA pH 8.0, 0.2% NaN3, 0.5% SDS): triton-containing dilution buffer (100mM NaCl, 500mM Tris-HCl pH 8.6, 5mM EDTA pH 8.0, 0.2% NaN3, 5% Triton X-100) plus protease inhibitors (Cell Signalling). Chromatin was then sheared to 200-400bp using a Biouptor Pico Sonicator (Diagenode). Co-immunoprecipitation was performed by combining 1mg of clarified chromatin lysate and EZH2 (Cell Signalling - 5246S, 1:40) or H3K27me3 (Upstate - 07-449, 1:100) antibodies, which were then rotated at 4⁰C o/n. The following day, protein-G magnetic beads (ThermoFisher) were added to the immunoprecipitations and rotated at 4⁰C for 4 hours. The bead-antibody complexes were washed and chromatin was eluted by shaking at 65⁰C o/n 0.1M NaHCO3 1% SDS solution. Chromatin was isolated by PCR purification (Qiagen). Library preparation was undertaken with 5-10ng of DNA using the Illumina TruSeq ChIP protocol.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
54365708
Reads aligned (%)
84.6
Duplicates removed (%)
55.3
Number of peaks
625 (qval < 1E-05)

hg38

Number of total reads
54365708
Reads aligned (%)
86.4
Duplicates removed (%)
54.7
Number of peaks
953 (qval < 1E-05)

Base call quality data from DBCLS SRA