Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Hdac5

Cell type

Cell type Class
Pancreas
Cell type
Pancreatic ductal adenocarcinoma
NA
NA

Attributes by original data submitter

Sample

source_name
PDAC escaper cells
strain
C57BL/6
cell type
HDAC5-driven PDAC escaper cells
chip-antibody
HDAC5 (CST, 20458s)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
HDAC5 escaper cells were crosslinked by 1% paraformaldehyde for 10 minutes at room temperature and then quenched by 0.125M glycine for 5 minutes. Cells were lysed on ice for 30 minutes with lysis buffer containing 10 mM Tris-HCl (pH 8.0), 1 mM EDTA (pH 8.0), 140 mM NaCl, 1% Triton X-100, 0.2% SDS, 0.1% deoxycholic acid. Chromatin DNA was fragmented to around 200-500bp by Diagenode BioruptorPico sonicator for 45 cycles of 30 seconds on and 30 second off, and then incubated overnight with anti-HDAC5 antibody and Dynabead (Life Technologies) at 4C. Next day, immune complexes were washed once with RIPA buffer with 500mM NaCl and once with LiCl wash buffer (10 mM Tris-HCl (pH 8.0), 1 mM EDTA (pH 8.0), 250 mM LiCl, 0.5% NP-40, 0.5% deoxycholic acid). DNA was then reverse crosslinked and eluted overnight in elution buffer (10 mM Tris-Cl (pH 8.0), 5 mM EDTA, 300 mM NaCl, 0.5% SDS, 20 mg/ml proteinase K) at 65C. The third day, eluted DNA was purified by AMPure beads (Beckman-Coulter). NEB Next Ultra DNA Library kit was used to prepare library

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
10851197
Reads aligned (%)
47.2
Duplicates removed (%)
8.6
Number of peaks
885 (qval < 1E-05)

mm9

Number of total reads
10851197
Reads aligned (%)
47.1
Duplicates removed (%)
8.9
Number of peaks
876 (qval < 1E-05)

Base call quality data from DBCLS SRA