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
SA-tTA-Ascl2 Embryonic Stem Cells
strain
MC1 mouse ES cells derived from 129S6/SvEvTac
antibody
input control

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP-seq was performed on samples of 10M formaldehyde-fixed murine ES cells. Frozen samples were thawed and lysed to purify nuclei. Nuclei were then incubated in nuclear lysis/ChIP buffer and sonicated using a Diagenode standard sonicator for a total of 35 minutes. Samples were centrifuged to remove cellular debris, and antibodies added. Antibody-binding incubation was performed, rotating overnight at 4C. Sequential washes to remove nonspecific genomic template were performed using Life Technologies Protein G Dynabeads, and immunopurified samples were further purified. Samples were eluted from Dynabeads using a 70C benchtop shaker, and crosslink reversal performed overnight at 65C using heated shaker, prior to proteinase K and RNAse treatment. Detailed description, including buffer components and formulae, is described in the text. Library preparation was performed according to manufacturer-supplied literature (NEB E6240L). Libraries were prepared using NEB ChIP purification reagents (E6240L) and Illumina indexing primers were used to facilitate demultiplexing.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
19523416
Reads aligned (%)
95.2
Duplicates removed (%)
10.9
Number of peaks
510 (qval < 1E-05)

mm9

Number of total reads
19523416
Reads aligned (%)
95.0
Duplicates removed (%)
11.0
Number of peaks
523 (qval < 1E-05)

Base call quality data from DBCLS SRA