Sample information curated by ChIP-Atlas

Antigen

Antigen Class
No description
Antigen
NA

Cell type

Cell type Class
Pancreas
Cell type
PANC-1
Tissue
Pancreas/Duct
Disease
Epithelioid Carcinoma

Attributes by original data submitter

Sample

ENA first public
2018-12-18
ENA last update
2018-07-20
ENA-CHECKLIST
ERC000011
External Id
SAMEA4799820
INSDC center alias
Section of Tumor Epigenetics, Department of General, Visceral and Pediatric Surgery, University Medical Center Gottingen, 37075 Gottingen, Germany
INSDC center name
Section of Tumor Epigenetics, Department of General, Visceral and Pediatric Surgery, University Medical Center Gottingen, 37075 Gottingen, Germany
INSDC first public
2018-12-18T17:02:52Z
INSDC last update
2018-07-20T14:51:18Z
INSDC status
public
Submitter Id
E-MTAB-7034:Panc_BRD4_rep_1
broker name
ArrayExpress
cell line
Panc1
cell type
epithelial cell
common name
human
disease
pancreatic ductal adenocarcinoma
organism part
pancreas
sample name
E-MTAB-7034:Panc_BRD4_rep_1

Sequenced DNA Library

library_name
Panc_BRD4_rep_1_s
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Briefly, cells were crosslinked with 1% formaldehyde for 20 minutes and quenched by Glycine (125mM final concentration). Upon cell scraping, nuclear pellets were prepared in and washed with the nuclear preparation buffer (150mM NaCl, 20 mM EDTA, 50 mM Tris-HCl (pH 7.5), 0.5% v/v NP-40, 1% v/v Triton-X-100, 20 mM NaF). Then samples were sonicated in sonication buffer (150mM NaCl, 20 mM EDTA, 50 mM Tris-HCl (pH 8), 1% v/v NP-40, 0.5% v/v Sodium deoxycholate, 20 mM NaF, 0.1% SDS) for 30 cycles (in L3.6pl) and 25 cycles (in BxPC-3 and Panc-1) using a Bioruptor Pico (Diagenode) and a cycle setting of 30s on and 30s off. Consequently, samples were precleared by incubation with 50% slurry of Sepharose 4B (GE Healthcare) and incubated with antibody overnight. Antibodies included 1µg of p63 (4A4) (sc-8431, Santa-Cruz), 1µg of H3K27ac (196-050, Diagenode), 2µg of BRD4 (C15410337, Diagenode), and 1µg of Rabbit IgG (C15410206, Diagenode). Sepharose beads with Protein A (for rabbit antibodies) or Protein G (for mouse antibodies, 4A4 p63) were added to samples and incubated for 2 hours followed by washes, de-crosslinking, and DNA extraction. Extraction of DNA was performed using Roti(R)-phenol/chloroform/Isoamylalcohol (Roth) extraction followed by precipitation in 100% Ethanol and washes with 70% Ethanol. Libraries for DNA from ChIP were made using the Microplex Library Preparation kit v2 (Diagenode) according to the manufacturer's instructions.

Sequencing Platform

instrument_model
Illumina HiSeq 4000

hg19

Number of total reads
18999593
Reads aligned (%)
68.8
Duplicates removed (%)
28.2
Number of peaks
8062 (qval < 1E-05)

hg38

Number of total reads
18999593
Reads aligned (%)
71.0
Duplicates removed (%)
26.4
Number of peaks
8122 (qval < 1E-05)

Base call quality data from DBCLS SRA