Illumina HiSeq 2500 sequencing; Genome-wide profiling of H3K27ac (ChIP-seq) in IMR90 cells
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
No description
Antigen
NA
Cell type
Cell type Class
Lung
Cell type
IMR-90
Primary Tissue
Lung
Tissue Diagnosis
Normal
Attributes by original data submitter
Sample
ENA first public
2018-04-12
ENA last update
2016-12-20
ENA-CHECKLIST
ERC000011
External Id
SAMEA32974918
INSDC center alias
Abt Vingron Max Planck Institute for Molecular Genetics
INSDC center name
Abt Vingron Max Planck Institute for Molecular Genetics
INSDC first public
2018-04-12T17:02:49Z
INSDC last update
2016-12-20T11:51:50Z
INSDC status
public
Submitter Id
E-MTAB-5355:IMR90_EtOH_input
broker name
ArrayExpress
cell line
IMR-90
common name
human
genotype
wild type genotype
sample name
E-MTAB-5355:IMR90_EtOH_input
Sequenced DNA Library
library_name
IMR90_EtOH_input_s
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were cultured to confluency and treated for 90 min with 1μM dexamethasone or vehicle control (ethanol). Chromatin was fixed at room temperature for 3 min with 1% formaldehyde. Approximately three million fixed IMR90 cells were lysed in 300 μl chromatin lysis buffer (50 mM Tris-HCl pH 8.1, 100 mM NaCl, 1% SDS, 3% Triton X-100, 5 mM EDTA, 0.2% NaN3) supplemented with 3x protease inhibitors (Roche complete protease inhibitor cocktail) on ice for 10 minutes. Lysates were then diluted 3x with dilution buffer (50 mM Tris-HCl pH 8.6, 100 mM NaCl, 5 mM EDTA, 0.2% NaN3) and homogenized ten times with a syringe (271/2 gauge). The lysate was then aliquoted (200 μl) into 1.5 ml TPX polymethylpentene tubes (Diagenode) and sheared at 4 °C in a Bioruptor Pico for 2x10 cycles. Chromatin Immunoprecipitation: The ChIP was performed using the Diagenode Auto Histone ChIPseq kit on an IPstar SX-8G compact automated system (Diagenode) using their indirect method (Ag + Ab → Beads). 1 μg of Diagenode ChIPseq grade rabbit polyclonal antibody (H3K27Ac; pAb-196-050) were used per ChIP. After de-crosslinking, RNAseA and proteinase K digestion, the DNA was isolated using ChIP DNA concentrator columns (Zymo Research D5205) according to the manufacturer's instructions.