Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
TAZ

Cell type

Cell type Class
Digestive tract
Cell type
SW 480
Primary Tissue
unresolved
Tissue Diagnosis
unresolved

Attributes by original data submitter

Sample

source_name
SW480_wild type
cell line
SW480
source tissue
colon
genotype/variation
WT
chip antibody
TAZ antibody

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Micrococcal nuclease treated chromatin was pulled down with TAZ antibody. The MicroPlex Library Preparation Kit v2 (Diagenode) was used to prepare indexed libraries from 1ng of ChIP DNA. The resulting libraries were then size-selected (selecting a 200-800bp range) by adding 0.55X volume of AMPure XP beads (Beckman Coulter). To the supernatant, 0.3X the original sample volume of AMPure XP beads were added. The supernatant was discarded and the beads washed with 70% ethanol before drying and eluting the size-selected library. Library quality was checked using the Agilent Bioanalyzer. Libraries were quantified by qPCR using the KAPA Library Quantification Kit for Illumina (Kapa Biosystems Inc.). 1.7 pM pooled libraries were loaded onto the NextSeq 500 and 2x75bp sequencing was carried out using a NextSeq 500/550 High Output v2 kit (Illumina Inc.).

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
32129533
Reads aligned (%)
158.1
Duplicates removed (%)
13.8
Number of peaks
537 (qval < 1E-05)

hg38

Number of total reads
32129533
Reads aligned (%)
159.6
Duplicates removed (%)
13.6
Number of peaks
587 (qval < 1E-05)

Base call quality data from DBCLS SRA