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 cells
strain
R1/E
construct
TOBF1 tagged in BAC
cell type
embryonic stem (ES) cells
chip antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were extracted from sonicated chromatin and processed with indicated Antibodies Immunoprecipitated fragments were end-repaired with NEBnext End Repair Module (NEB) and purified by using Agencourt Ampure XP - beads (Beckman Coulter) and A-tailed using the NEBnext dA-Tailing Module according to manufacturers’ instructions. After purification, adaptors were ligated (Adaptor-Oligo 1: 5'ACACTCTTTCCCTACACGACGCTCTTCCGATCT-3', Adaptor-Oligo 2: 5'-P-GATCGGAAGAGCACACGTCTGAACTCCAGTCAC-3') by using 1x NEBnext Quick Ligation Buffer (NEB), 10x excess of DNA Adaptors, 5 µl Quick T4 DNA Ligase (NEB) at 50 µl total volume. Large-scale amplification of library constructs was performed by using the PCR Enrich Adaptor Ligated cDNA Library module (NEB).

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
70034926
Reads aligned (%)
94.2
Duplicates removed (%)
29.4
Number of peaks
2598 (qval < 1E-05)

mm9

Number of total reads
70034926
Reads aligned (%)
94.1
Duplicates removed (%)
29.4
Number of peaks
2670 (qval < 1E-05)

Base call quality data from DBCLS SRA