Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
EHF

Cell type

Cell type Class
Lung
Cell type
Calu-3
Primary Tissue
Lung
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
Lung adenocarcinoma cells
cell line
Calu-3
cell type
Lung adenocarcinoma
chip antibody
EHF (Clone 5A.5), Pierce
-style parameter used for homer peak calling
factor
input used for homer peak calling
Input 1

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were lysed in lysis buffer (5mM PIPEs pH 8.0, 85mM KCL, 0.5% NP-40, 1x Protese Inhibitor Cocktail (Roche)). Nuclear preparation was isolated by centrifugation, lysed in RIPA buffer (1x PBS, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, Protease Inhibitor Cocktail), and sonicated. Protein-DNA complexes were isolated with antibody. DNA ends were blunted using T4 DNA polymerase, Klenow DNA polymerase, and T4 polynucleotide kinase. DNA was then incubated with Klenow exo- to add 5’ adenine overhangs. Multiplex adaptors were ligated to the ends and converted to dsDNA using 5 cycles of PCR. DNA was size-selected to contain fragments between 200 and 300bp and PCR amplified for 5 cycles. DNA was purified with 1.2x AMPusreXP beads. Sequencing was preformed on an Illumina Hi-Seq.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
14000252
Reads aligned (%)
88.4
Duplicates removed (%)
3.2
Number of peaks
539 (qval < 1E-05)

hg38

Number of total reads
14000252
Reads aligned (%)
90.3
Duplicates removed (%)
1.9
Number of peaks
427 (qval < 1E-05)

Base call quality data from DBCLS SRA