Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
ZSCAN5A

Cell type

Cell type Class
Placenta
Cell type
BeWo
Primary Tissue
Placenta
Tissue Diagnosis
Carcinoma

Attributes by original data submitter

Sample

source_name
Human BeWo cell line
cell line
Human BeWo
antibody
ZSCAN5A
treatment or control
treatment

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cross-linked chromatin was prepared and sonicated using Bioruptor UCD-200 in ice water bath to generate DNA fragments 200-300 bp in size. Twenty micrograms of each antibody preparation, or 20 µg IgG for mock pulldown controls, were incubated with chromatin prepared from nuclei of approximately 5 million cells. ChIP-seq libraries were generated using KAPA LTP Library Preparation Kits (Kapa Biosystems, KK8232) to yield two independent ChIP replicates for the antibody. We also generated libraries from sonicated genomic input DNA from the same chromatin preparations as controls. Libraries were bar-coded with Bioo Scientific index adapters and sequenced to generate 15-23 million reads per duplicate sample using the Illumina Hi-Seq 2000 instrument at the University of Illinois W.M. Keck Center for Comparative and Functional Genomics according to manufacturer’s instructions.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
11610075
Reads aligned (%)
90.8
Duplicates removed (%)
5.3
Number of peaks
310 (qval < 1E-05)

hg38

Number of total reads
11610075
Reads aligned (%)
91.2
Duplicates removed (%)
5.1
Number of peaks
278 (qval < 1E-05)

Base call quality data from DBCLS SRA