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
mESCs
tissue
Mouse embryonic stem cells (mESCs)
condition
Dox treated
chip antibody
none (input)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP-seq: Dox-induced were fixed with formaldehyde (final 1%) for 10 minutes. Fixed cells were then subjected to standard ChIP lysis protocol to release chromatin. Released Chromatin was sonicated for 15 cycles (30 sec on, 30 sec off) on a Biorupter at high setting. Soluble chromatin was collected and between 1-2 mg was used for IP with 4-8 ug of respective Dyna-protein G conjugated antibody complex. Captured fragments were subjected to several rounds of stringent salt washes before eluting with SDS buffer. ChIP-seq: Eluted DNA was purified and subjected to NGS library preparation using the NEBNext DNA ultra II kit. Constructed ChIP libraries were sequenced on the Illumina NextSeq or HiSeq platform.

Sequencing Platform

instrument_model
NextSeq 500

mm10

Number of total reads
56937855
Reads aligned (%)
98.4
Duplicates removed (%)
35.7
Number of peaks
282 (qval < 1E-05)

mm9

Number of total reads
56937855
Reads aligned (%)
98.2
Duplicates removed (%)
35.9
Number of peaks
266 (qval < 1E-05)

Base call quality data from DBCLS SRA