Sample information curated by ChIP-Atlas

Antigen

Antigen Class
RNA polymerase
Antigen
RNA polymerase II

Cell type

Cell type Class
Breast
Cell type
IMEC
NA
NA

Attributes by original data submitter

Sample

source_name
IMEC cell line
generation of cells
primary breast epithelial cells
antibody
Ser5p_RNAPII
dox treatment
DOX
construct
pInducer21-MYC-K52o-HA

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Where indicated, MYC K52o-HA was induced with doxycycline (pInducer samples) or treated with EtOH as solvent control. Where indicated MG-132 (10 µM) or EtOH as a control was added to the cells 4 hr prior to fixation. Cells were crosslinked with 1% formaldehyde 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 was precipitated by incubation with specific antibodies pre-adsorbed to 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
NextSeq 500

hg38

Number of total reads
17331613
Reads aligned (%)
96.3
Duplicates removed (%)
33.2
Number of peaks
22951 (qval < 1E-05)

hg19

Number of total reads
17331613
Reads aligned (%)
96.0
Duplicates removed (%)
33.2
Number of peaks
23326 (qval < 1E-05)

Base call quality data from DBCLS SRA