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
etoposide (100uM, 6hrs)
passages
Passage # 30-35
antibody
p53

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 constructed 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
69283594
Reads aligned (%)
62.4
Duplicates removed (%)
30.6
Number of peaks
3416 (qval < 1E-05)

hg38

Number of total reads
69283594
Reads aligned (%)
64.4
Duplicates removed (%)
29.0
Number of peaks
3822 (qval < 1E-05)

Base call quality data from DBCLS SRA