Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Unclassified
Antigen
Unclassified

Cell type

Cell type Class
Pluripotent stem cell
Cell type
ZHBTc4
NA
NA

Attributes by original data submitter

Sample

source_name
WT ES cells
cell type
ZHBTc4 ES cells
time after treatment
n/a
treatment
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For mRNA-sequencing, we obtained total RNAs from each sample and then poly(A) mRNA isolation from total RNA (5 µg) and fragmentation were performed using the Illumina Truseq RNA Sample Prep Kit Ver. 2 with poly-T oligo-attached magnetic beads, according to the manufacturer’s instructions. Reverse transcription of RNA fragments was performed using Superscript II reverse transcriptase (Life Technologies). For ChIP-sequencing, extracts containing DNA fragments with an average size of 400bp were immmunoprecipitated by using antibodies against GFP (control) or Pontin

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
63516307
Reads aligned (%)
94.1
Duplicates removed (%)
81.7
Number of peaks
176 (qval < 1E-05)

mm9

Number of total reads
63516307
Reads aligned (%)
94.0
Duplicates removed (%)
81.7
Number of peaks
146 (qval < 1E-05)

Base call quality data from DBCLS SRA