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
E14, mouse embryonic stem cell line
genotype
wild type
cell line
E14
antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP-seq: Cells were lysed in RIPA buffer (10 mM Tris-HCl pH 8.0, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate) supplemented with protease inhibitor (details see Yan et al). Hi-C and 4C-seq: Briefly, 2 million cells were cross-linked with 1% formaldehyde for 10min at RT and reaction was quenched using 125 mM of Glycine for 5 min at RT. Nuclei were isolated and directly applied for digestion using 4 cutter restriction enzyme MboI (NEB) at 37 °C o/n. All libraries were constructed using standard illumina TruSeq LT library prep.

Sequencing Platform

instrument_model
Illumina HiSeq 4000

mm10

Number of total reads
37409101
Reads aligned (%)
95.2
Duplicates removed (%)
8.5
Number of peaks
473 (qval < 1E-05)

mm9

Number of total reads
37409101
Reads aligned (%)
95.1
Duplicates removed (%)
8.6
Number of peaks
487 (qval < 1E-05)

Base call quality data from DBCLS SRA