Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
HSF2

Cell type

Cell type Class
Digestive tract
Cell type
HCT 116
Primary Tissue
Colon
Tissue Diagnosis
Carcinoma

Attributes by original data submitter

Sample

source_name
HCT116
cell line
HCT116
cell type
colorectal carcinoma
antibody
HSF2_2C1

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
1x10^8 cells were fixed in 1% formaldehyde (Sigma, 252549) in PBS for 15- 20 min at room temperature and quenched with 1/10th volume of 1.25 M glycine for 5 minutes at room temperature. Cells were collected at 1,000xg for 5 minutes, washed in PBS, pelleted at 1,000xg for 5 min and pellets were flash frozen in liquid nitrogen and stored at -80°C until use. Pellets were thawed on ice and resuspended in 10 ml lysis buffer 1 (50 mM HEPES, pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% IGEPAL CA-630, 0.25% Triton X-100 with 5μl/ml Sigma 8340 protease inhibitor cocktail incubated on ice 10 minutes, pelleted 1,500xg and subsequently washed in lysis buffer 2 (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA and 5ul/ml protease inhibitor) as with lysis buffer 1 before resuspending in 1 ml lysis buffer 3 (10 mM tris-HCl pH 8.0, 1 mM EDTA, 0.1% SDS and 5 ul/ml protease inhibitors) for sonication. Chromatin was sheared in a 1 ml milliTUBE with AFA fiber on a Covaris E220 using 10% duty factor for 2 min. The sheared chromatin concentration was estimated with Nanodrop at OD 260 and diluted to 1 mg/ml in ChIP Dilution Buffer (10% Triton X-100, 1M NaCl and 1% Sodium deoxycholate). 1 mg chromatin was combined with 4 μg hybridoma tissue culture supernatant and rotated overnight at 4°C. 40 μl protein A/G Dynabeads was added and incubated for 2-4 hr rotating at 4°C. Samples were washed 5 times with 1 ml RIPA buffer, 2 times with TE with 50 mM NaCl. Chromatin was eluted with 800 μl elution buffer (50 mM Tris pH 8.0, 1 mM EDTA, 0.1% SDS) for 30 min at 65°C shaking at 1,500 rpm in a ThermoMixer (Eppendorf). Supernatants were collected, digested with 20 μl of 20 mg/ml Proteinase K and incubated overnight at 65°C. DNA was purified with phenol chloroform extraction. 500 μl of the aqueous phase was precipitated with 20 μl 5M NaCl, 1.5 μg glycogen and 1 ml EtOH on ice for 1 hr or at -20°C overnight. Sequencing libraries were prepared with the KAPA HTP library prep kit (Roche) using 1-10 ng DNA and libraries were size selected with AMPure XP beads (Beckman Coulter).

Sequencing Platform

instrument_model
NextSeq 500

hg38

Number of total reads
38528256
Reads aligned (%)
90.2
Duplicates removed (%)
12.7
Number of peaks
581 (qval < 1E-05)

hg19

Number of total reads
38528256
Reads aligned (%)
89.5
Duplicates removed (%)
13.4
Number of peaks
772 (qval < 1E-05)

Base call quality data from DBCLS SRA