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
mouse embryonic stem cells (E14)
strain
C57BL/6
chip antibody
mouse IgG (Santa Cruz, sc-2025)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were cross-linked with 1% (v/v) formaldehyde for 5 minutes at 37℃ and lysed. Then, nuclear pellets were sheared with Focused-ultrasonicator (Covaris) and immunoprecipitated. The immune complexes were eluted by adding 250ul of elution buffer containing 1% (w/v) SDS and 0.1M NaHCO3 two times. Cross-linking was reversed by adding of 20ul of 5M NaCl and incubated overnight at 65C. DNA was precipitated with ethanol and kept in -20℃ for the further use. The immunoprecipitated (20ng/μL) samples were used for library preparation for Illumina sequencing using the TruSeq ChIP kit (Illumina, San Diego, CA) following the manufacturer's protocol. Briefly, 20 ng of immunoprecipitated DNA samples was end repaired-ligated to Illumina adaptors and selected for a fragment size of approximately 300 bp by gel extraction. Multiplex Illumina primers were used to amplify gel-extracted products.

Sequencing Platform

instrument_model
NextSeq 500

mm10

Number of total reads
80587868
Reads aligned (%)
92.4
Duplicates removed (%)
61.1
Number of peaks
402 (qval < 1E-05)

mm9

Number of total reads
80587868
Reads aligned (%)
91.9
Duplicates removed (%)
61.1
Number of peaks
486 (qval < 1E-05)

Base call quality data from DBCLS SRA