Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
JUND

Cell type

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

Attributes by original data submitter

Sample

source_name
JunD ChIP-seq
cell line
Calu-3 cells
cell type
Lung adenocarcinoma cells
chip antibody
JunD (sc-74)
input used for homer peak calling
Calu-3 Input

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 performed on an Illumina Hi-Seq.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
15566239
Reads aligned (%)
85.0
Duplicates removed (%)
4.6
Number of peaks
2961 (qval < 1E-05)

hg38

Number of total reads
15566239
Reads aligned (%)
85.9
Duplicates removed (%)
4.0
Number of peaks
2858 (qval < 1E-05)

Base call quality data from DBCLS SRA