Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
TBP

Cell type

Cell type Class
Lung
Cell type
Bronchial tracheal epithelial cells
NA
NA

Attributes by original data submitter

Sample

source_name
HBTEC_wt_MOI5_dl312_Pol2_12hpi
Sex
male
cell type
Primary Human Bronchial/Tracheal Epithelial Cells (HBTEC)
infected with
a mixture of the wt E1A-expressing vector at an MOI of 5 with an Ad5 mutant containing an E1A deletion (dl312) at an MOI of 95
passage
<28
chip antibody
Mouse monoclonal anti-TBP Diagenode Cat#C15200002
molecule subtype
genomic DNA and viral DNA

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
1x10^7 low-passage HBTEC were infected with indicated Ad vector 3 days after reaching confluence. 24h p.i. cells were cross-linked for 1% formaldehyde for 10 minutes at room temperature on rotator. Formaldehyde crosslinking was quenched with 0.14M glycine for 30 minutes at room temperature on rotator. Cells were washed with PBS and scraped from plates in PBS with Roche protease inhibitor cocktail. Cells were pelleted and lysed in 400uL lysis buffer (1% SDS, 50mM Tris-HCl pH8, 20mM EDTA, Roche complete protease inhibitors) and sonicated at 4°C using the Qsonica Q800R2 at 20% amplitude 10s on 30s off until DNA fragments from sheared chromatin were mostly between the sizes of 200-600 base pairs. 100uL of sonicated chromatin was diluted in 10X lysis dilution buffer (16.7 mM Tris-HCl, 1.1% Triton X-100, 1.2mM EDTA, 167mM NaCl) and precleared for 1h 4°C with 30uL of protein A dynabeads washed 10X lysis dilution buffer on nutator. IPs were performed O/N at 4°C on nutator with precleared chromatin and 2ug of anti-Pol2, -H3K27ac or 5uL of H3K18ac anti-rabbit sera. 50uL of protein A dynabeads were added for 4h on nutator at 4°C. Bead-immunocomplexes were washed for 5min 2X with each of the following buffers in order: wash buffer A (50mM Hepes pH 7.9, 0.1% SDS, 1% Triton X-100, 0.1% Deoxycholate, 1mM EDTA, 140mM NaCl), wash buffer B (50mM Hepes pH 7.9, 0.1% SDS, 1% Triton X-100, 0.1% Deoxycholate, 1mM EDTA, 500mM NaCl), LiCl buffer (20mM Tris-HCl pH8, 0.5% NP-40, 0.5% Deoxycholate, 1mM EDTA, 250mM LiCl), TE (50mM Tris-HCl pH8, 1mM EDTA). Elution was performed in 150uL of elution buffer (50mM Tris HCl pH8, 1mM EDTA, 1% SDS) then ChIP samples and inputs (10uL of precleared chromatin lysis plus 140uL elution buffer) were reverse crosslinked O/N at 65°C. Samples were RNase A treated for 1h at 37°C and DNA was purified and extracted with phenol/chloroform and ethanol precipitated. DNA pellets were resuspended in 12uL of TE and measured using Qubit fluorometer. ChIP sequencing libraries were constructed from 1 ng of immunoprecipitated and input DNA using the KAPA Hyper Prep Kit from KAPA Biosystems and NEXTflex ChIP-Seq barcodes purchased from Bioo Scientific.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
40218561
Reads aligned (%)
18.5
Duplicates removed (%)
15.5
Number of peaks
13874 (qval < 1E-05)

hg38

Number of total reads
40218561
Reads aligned (%)
18.8
Duplicates removed (%)
15.0
Number of peaks
13834 (qval < 1E-05)

Base call quality data from DBCLS SRA