Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K27ac

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
Human colorectal cancer cell-line HCT116
antibody
H3K27Ac, Active Motif #39133, lot# 21311004
cell line
HCT116
clone
Control Clone 1

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For RNA-seq, RNA was prepared using Trizol (Life Technologies, Carlsbad, CA) For ChIP-seq, cells were crosslinked using 1% formaldehyde andl lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. For 4C-seq, cells were cross linked using 1% formalehyde for 10 minutes and nuclei were isolated, followed by chromatin is digested with a first restriction enzyme (DpnII) and ligated. After reverse cross-linking, DNA is treated with secondary restriction enzyme (Csp6I) followed by second ligation. RNA-seq:Single-end libraries were prepared using the Illumina TruSeqV2 Sample Prep Kit (Catalog #15596-026), starting with 1 ug total RNA. Libraries were barcoded (NEXTflex™ DNA Barcodes), pooled, and sequenced using an NextSeq500. ChIP-seq: Libraries were barcoded (NEXTflex™ DNA Barcodes), pooled, and sequenced using an Illumina HiSeq2000 or NextSeq500 4C-seq: Libraries were made through inverse PCR using primers that anneal to the bait fragment-end, customized barcode and adaptor seqeunces. Libraries were sequenced using an Illumina HiSeq2500

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
30760304
Reads aligned (%)
99.1
Duplicates removed (%)
2.9
Number of peaks
15330 (qval < 1E-05)

hg19

Number of total reads
30760304
Reads aligned (%)
98.2
Duplicates removed (%)
3.8
Number of peaks
15261 (qval < 1E-05)

Base call quality data from DBCLS SRA