Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Blood
Cell type
EML
NA
NA

Attributes by original data submitter

Sample

source_name
EML_C1
strain
C57BL/6
passage
4-5
antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
H3K27Me3 ChIP samples were fixed using a 1% formaldehyde (FA) fixation protocol for 10 min, while a 60 min, 2 mM DSG and a 60 min 1% FA double fixation protocol was used for Ezh2 and Runx1 antibodies. Fixed chromatin samples were fragmented using a S220 Focused-ultrasonicators (Covaris) for 10 min with 10% duty cycle, 5 intensity, 200 cycle per burst with frequent sweeping mode and constant degassing at 4°C to an average size of 200-500bps. Antibody:chromatin complexes were collected with a mixture of protein A and Protein G Dynabeads (Life Technologies) collected with a magnet, and washed 3X with a solution of 50 mM HEPES-KOH, pH 7.6, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Na-Deoxycholate. After a TE wash, samples were eluted, de-crosslinked, RNase and Proteinase K treated, and purified using a QIAGEN PCR purification kit. ChIP samples were quantified relative to inputs. A 50 μl aliquot taken from each of 1 ml of sonicated, diluted chromatin before antibody incubation serves as the input, thus the signal from the input samples represents 5% of the total chromatin used in each ChIP. The library prep was performed on the Apollo system (Wafergen) with the kit PrepX Complete ILMN 32i DNA Library Kit (cat # 400076) and custom adapters.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
49602639
Reads aligned (%)
98.5
Duplicates removed (%)
8.8
Number of peaks
702 (qval < 1E-05)

mm9

Number of total reads
49602639
Reads aligned (%)
98.3
Duplicates removed (%)
9.5
Number of peaks
736 (qval < 1E-05)

Base call quality data from DBCLS SRA