Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Unclassified
Cell type
Unclassified
NA
NA

Attributes by original data submitter

Sample

source_name
wig
generation of cells
primary breast epithelial cells
antibody
none
construct
pRRL-MYC-HA

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were crosslinked with 1% formaldehyde at 37°C for 10min. Cells were lysed and after centrifugation nuclei were re-suspended in RIPA buffer. DNA was sonicated with a Branson sonifier to obtain DNA fragments at nucleosomal size. Chromatin bound to target proteins (HA-tag) was precipitated by incubation with Protein A dynabeads beads overnight. After several washings chromatin was eluted with 1 % SDS and crosslinking was reverted overnight. DNA was purified by Phenol/Chloroform extraction and enrichments were checked by qPCR. Libraries for ChIP-seq samples were contructed following manufactor's intructions using the NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina (E6240). Briefly, ChIP DNA was end repaired, A-tailed and Illumina adaptors were ligated. DNA fragments of about 200 bps were cut out of a agarose gel and extracted with a Qiagen PCR purification column. Size-selected DNA was amplified with 18 PCR cycles.

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

hg38

Number of total reads
24220464
Reads aligned (%)
98.8
Duplicates removed (%)
1.6
Number of peaks
636 (qval < 1E-05)

hg19

Number of total reads
24220464
Reads aligned (%)
98.3
Duplicates removed (%)
2.3
Number of peaks
891 (qval < 1E-05)

Base call quality data from DBCLS SRA