Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K9ac

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
treatment
largazole 75nM
disease
colorectal carcinoma
chip antibody
H3K9ac (Abcam, ab4441)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
HCT116 cells were treated with largazole or vehicle for 16 hours and cross-linked with 1% formaldehyde for 15 minutes at room temperature (25°C). Cells were washed two times with PBS and membranes ruptured in hypotonic buffer (50 mM NaCl, 1% NP-40 alternative, 2 mM EDTA, 10 mM Tris, 1 mM DTT, 2 mM EDTA, 1X protease inhibitor cocktail (Roche # 04693124001). The cell nuclei were recovered by centrifugation and resuspended in lysate buffer (150 mM NaCl, 0.5% Triton X-100, 2 mM EDTA, 0.1% SDS, 20 mM Tris, 1 mM DTT, 1X protease inhibitor cocktail). Resuspended samples were sonicated for 25 cycles (30s ‘on’ at high level and 30s ‘off’ per cycle) using a Bioruptor (Diagenode; Denville, NJ, USA) and spun for 10 minutes at 16,000x g in a microcentrifuge. Samples were incubated for 5 hours at 4°C with 5 to 20 μg of antibodies and 20 μl of 50% slurry with protein A beads (Millipore; Billerica, MA, USA). The immunoprecipitated chromatin was then recovered and DNA purified using phenol chloroform extraction. ChIP sequencing libraries were prepared using an Illumina ChIP-Seq DNA Sample Prep Kit (cat. # IP-102-1001), with a starting sample varying from 2 to 20 ng of DNA isolated from the immunoprecipitation step. Libraries were prepared according to Illumina's protocol. Barcodes were assigned as follows: Input.fastq.gz;TAGCTT, ChIPSeq_DMSO_H3K27ac.fastq.gz;GATCAG, ChIPSeq_largazole_4.68nM_H3K27ac.fastq.gz;ACTTGA, ChIPSeq_largazole_9.37nM_H3K27ac.fastq.gz;CAGATC, ChIPSeq_largazole_18.75nM_H3K27ac.fastq.gz;GCCAAT, ChIPSeq_largazole_30nM_H3K27ac.fastq.gz;ACAGTG, ChIPSeq_largazole_37.5nM_H3K27ac.fastq.gz;TGACCA, ChIPSeq_largazole_75nM_H3K27ac.fastq.gz;TTAGGC, ChIPSeq_largazole_150nM_H3K27ac.fastq.gz;CGATGT, ChIPSeq_largazole_300nM_H3K27ac.fastq.gz;ATCACG, ChIPSeq_DMSO_H3K9ac.fastq.gz;ATCACG, ChIPSeq_largazole_4.68nM_H3K9ac.fastq.gz;CGATGT, ChIPSeq_largazole_9.37nM_H3K9ac.fastq.gz;TTAGGC, ChIPSeq_largazole_18.75nM_H3K9ac.fastq.gz;TGACCA, ChIPSeq_largazole_30nM_H3K9ac.fastq.gz;ACAGTG, ChIPSeq_largazole_37.5nM_H3K9ac.fastq.gz;GCCAAT, ChIPSeq_largazole_75nM_H3K9ac.fastq.gz;CAGATC, ChIPSeq_largazole_150nM_H3K9ac.fastq.gz;ACTTGA, ChIPSeq_largazole_300nM_H3K9ac.fastq.gz;GATCAG, ChIPSeq_DMSO_H3K4me1.fastq.gz;GCACTA, ChIPSeq_largazole_75nM_H3K4me1.fastq.gz;ACCTCA, ChIPSeq_largazole_300nM_H3K4me1.fastq.gz;GTGCTT, ChIPSeq_DMSO_H3K4me2.fastq.gz;AAGCCT, ChIPSeq_largazole_75nM_H3K4me2.fastq.gz;GTCGTA, ChIPSeq_largazole_300nM_H3K4me2.fastq.gz;AAGAGG, ChIPSeq_DMSO_RNAPII.fastq.gz;GATCAG, ChIPSeq_largazole_75nM_RNAPII.fastq.gz;TAGCTT, ChIPSeq_largazole_300nM_RNAPII.fastq.gz;GGCTAC, RNASeq_DMSO.fastq.gz;GCCAAT, RNASeq_largazole_4.68nM.fastq.gz;CGATTT, RNASeq_largazole_9.37nM.fastq.gz;CAGATC, RNASeq_largazole_18.75nM.fastq.gz;CTTGTA, RNASeq_largazole_30nM.fastq.gz;AGTCAA, RNASeq_largazole_37.5nM.fastq.gz;AGTTCC, RNASeq_largazole_75nM.fastq.gz;GTCCGC, RNASeq_largazole_150nM.fastq.gz;GTGAAA, RNASeq_largazole_300nM.fastq.gz;ACAGTG.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
28285015
Reads aligned (%)
94.3
Duplicates removed (%)
8.9
Number of peaks
1832 (qval < 1E-05)

hg19

Number of total reads
28285015
Reads aligned (%)
93.9
Duplicates removed (%)
9.3
Number of peaks
1923 (qval < 1E-05)

Base call quality data from DBCLS SRA