Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
EP300

Cell type

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

Attributes by original data submitter

Sample

source_name
Lung Fibroblasts
cell line
IMR90 human primary lung embryo fibroblasts
cell type
contact-inhibited IMR90
infection
dl1500-infected
chip antibody
anti-p300 (N-15) (Santa Cruz, catalog# sc-584)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
24 h post infection (p.i.), formaldehyde was added for 10 min at 37°C. After PBS washing, cross-linked cells were scraped from the plates and washed with 1 ml of PBS containing protease inhibitors (Roche). 2x10^7 Cells were resuspended in 450 ul of lysis buffer and incubated for 10 min on ice and immediately sonicated using Misonix cup-horn sonicator. 100 ul of the lysate (corresponding to 5x10^6 cells) were used for each immunoprecipitation with a given antibody (listed below); 10 ul of the lysate was used as input. After overnight reversal of crosslinking at 65°C, samples were treated with RNase A for 30 min at 37°C, proteinase K for 2 h at 56°C. DNA was subsequently purified using phenol/chloroform extraction and precipitation. DNA concentration was measured using Qubit (Invitrogen). At least 10 ng of dsDNA for both input and IP was used for library preparation according to the manufacturer's instructions (NuGen). Sequencing libraries were constructed from 1 ng of immunoprecipitated and input DNA using the NuGen Ovation Ultralow DR Multiplex System 1-8 kit according to protocol.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
22972089
Reads aligned (%)
46.4
Duplicates removed (%)
27.4
Number of peaks
0 (qval < 1E-05)

hg19

Number of total reads
22972089
Reads aligned (%)
46.4
Duplicates removed (%)
27.5
Number of peaks
0 (qval < 1E-05)

Base call quality data from DBCLS SRA