Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
GATA6

Cell type

Cell type Class
Digestive tract
Cell type
LS-174T
Primary Tissue
Colon
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
LS174T, GATA6 ChIP
cell line
LS174T
cell type
colorectal carcinoma
antibody
anti-hGATA6 (R&D AF1700)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were lysed in 0.5% SDS, lysates were sonicated and clarified. Chromatin was diluted 5 fold and incubated with beads for pre-clearing. After pre-clearing, chromatin was incubated o/n with anti-GATA6 antibody. 20ng of DNA, as quantitated by fluorometry, was resolved by electrophoresis and fractions of 50-250bp were extracted. Fractions were processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq DNA Sample Preparation Guide" (part # 15005180 Rev. C). Adapter-ligated libraries were completed by limited-cycle PCR with Illumina PE primers (12 cycles). The resulting purified DNA library was applied to an Illumina flow cell for cluster generation (TruSeq cluster generation kit v5) and sequenced on the Genome Analyzer IIx with SBS TruSeq v5 reagents by following manufacturer's protocols.

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

hg19

Number of total reads
12270621
Reads aligned (%)
89.4
Duplicates removed (%)
7.4
Number of peaks
3556 (qval < 1E-05)

hg38

Number of total reads
12270621
Reads aligned (%)
91.3
Duplicates removed (%)
6.3
Number of peaks
3430 (qval < 1E-05)

Base call quality data from DBCLS SRA