Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
TEAD1

Cell type

Cell type Class
Digestive tract
Cell type
Pharynx cancer cells
NA
NA

Attributes by original data submitter

Sample

source_name
human pharynx cancer cells
age
Adult
chip antibody
anti TEF1/TEAD-1 (Abcam, ab133533)
treatment
DMSO

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were plated and dosed with either DMSO or small molecular (Compound 2) at 10 mM for 24 hrs. For dual cross-linking, cells were first incubated with 2 mM disuccinimidyl glutarate (ThermoFisher, 20593) for 20 min and then with formaldehyde at 1% (v/v) for an additional 10 min. Nuclei were extracted and sheared to an average length of 300-600 bp using truChIP Chromatin Shearing Kit (Covaris, 520154) following the manufacturer's guidelines. All chromatin immunoprecipitation samples were supplemented with 20 ng of Drosophila chromatin (Active Motif, 53083) and 2 µg of a Drosophila-specific antibody (Active Motif, 61686) for normalization of ChIP-seq samples. For immunoprecipitations, 20 µg of sheared chromatin was incubated with 3-5 µg of antibody at 4 °C overnight. Complexes were captured by incubating with 40 mL Protein A Dynabeads (ThermoFisher, 10002D) for 2 hr at 4 °C. ChIP'd DNA was purified using ChIP DNA Clean & Concentrator (Zymo Research, D5205) following elution from magnetic beads, digestion with RNase and proteinase K, and reversal of crosslink by heating at 65 °C. 10 ng of purified DNA was used to generate libraries with the Ovation Ultra Low Library Prep Kit (NuGEN, 0344NB-32). Sequencing was performed on an Illumina HiSeq 2500 platform. Libraries were prepared using standard protocols for the Ovation Ultralow System. Briefly, samples were PCR-amplified and sized using the Agilent 2100Bioanalyzer. Barcoded libraries were sequenced 50 bp single end on HiSeq 2500 (Illumina).

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
21804718
Reads aligned (%)
94.3
Duplicates removed (%)
3.5
Number of peaks
1039 (qval < 1E-05)

hg38

Number of total reads
21804718
Reads aligned (%)
96.3
Duplicates removed (%)
2.4
Number of peaks
866 (qval < 1E-05)

Base call quality data from DBCLS SRA