Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Pluripotent stem cell
Cell type
ES cells
NA
NA

Attributes by original data submitter

Sample

source_name
ES cell culture
strain
V6.5
cell type
embryonic stem cell
shRNA
RNAi of Zic2
chip antibody
no antibody

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP-Seq, 5×107 ES cells (V6.5) were used per immunoprecipitation according to previously described protocols (Lee et al., 2006). ChIP-Seq libraries were prepared with Illumina's kit.For RNA-seq, ES cells (V6.5) were infected with lentivirus carrying either Non-targeting shRNA, Zic2, Mbd3 or Mta2 shRNA in the presence of 8 ug/ml of polybrene. 24 hours later, ES cells were selected with 2 ug/ml of puromycin for additional 48 hours and then were grown one passage off feeders for 30 min before harvesting. Total RNA was isolated with the RNeasy (74106 Qiagen) kit, treated with DNase I (M0303L NEB), and re-purified with RNeasy. For total RNA-seq analyses, total RNA was depleted of ribosomal RNA using Ribozero (Illumina) before library preparation performing Tru-seq sample prep (Illumina). ChIP-seq and RNA-seq libraries were prepared for sequencing using standard Illumina protocols

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
40558544
Reads aligned (%)
98.2
Duplicates removed (%)
14.6
Number of peaks
506 (qval < 1E-05)

mm9

Number of total reads
40558544
Reads aligned (%)
97.9
Duplicates removed (%)
14.6
Number of peaks
546 (qval < 1E-05)

Base call quality data from DBCLS SRA