Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
TP53

Cell type

Cell type Class
Lung
Cell type
IMR-90
Primary Tissue
Lung
Tissue Diagnosis
Normal

Attributes by original data submitter

Sample

source_name
IMR90 fetal lung fibroblasts
cell line
IMR90
treatment
DMSO (6hrs)
passages
30-35
antibody
p53 (EMD Millipore (DO1))

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP-seq, cells were crosslinked with formaldehyde (1% final) for 10min at room temperature, and harvested for sonication. Nuclei were extracted and chromatin was sheared to an average size of 200bp using a Diagenode Bioruptor. For RNA-seq, cells were harvested and PolyA+ RNA was isolated using the NEBNext Ultra RNA-seq Isolation Module. For ATAC-seq, cells were harvested, nuclei were prepped,and transposase was added for 30 minutes at 30C. Sequencing libraries for ChIP-seq were constructd using the NEBNext Ultra kit as per manufacturer's recommended instructions Sequencing libraries for ATAC-seq were constructed using custom Nextera-compatible primers, from Nextera-adapted DNA fragments

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
121883390
Reads aligned (%)
63.6
Duplicates removed (%)
23.7
Number of peaks
1663 (qval < 1E-05)

hg38

Number of total reads
121883390
Reads aligned (%)
65.5
Duplicates removed (%)
22.1
Number of peaks
1845 (qval < 1E-05)

Base call quality data from DBCLS SRA