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
embryonic stem cells
strain
129S4/SvJae
genotype
wild type
chip antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
1×107 cells were fixed for 10 minutes with 1% formaldehyde, followed by chromatin extraction and sonication to generate 200-500bp fragments. The sheared chromatin was incubated overnight at 4°C with anti-Tet1 and Dynabeads Grotein A (Thermo Fisher, 10001D), or anti-Flag M2 and Dynabeads Protein G (Thermo Fisher, 10003D). ChIP washes were performed in the following order: 1×low-salt buffer, 3×high-salt buffer, 2×LiCl buffer and 1×TE buffer. Cross-linking was reversed with the addition of elution buffer (20 mM Tris-HCl, pH7.5, 5 mM EDTA, 50 mM NaCl, 1% SDS, 50 μg/mL Proteinase K) to washed beads and incubation at 68°C with rotation for three hours. DNA was purified with MinElute PCR purification kit (Qiagen, 28004). For ChIP-Seq, sequencing libraries were prepared using ThruPLEX DNA-seq 48D kit (Rubicon Genomics, R400406) following standard protocols.

Sequencing Platform

instrument_model
NextSeq 500

mm10

Number of total reads
45506535
Reads aligned (%)
95.0
Duplicates removed (%)
10.5
Number of peaks
221 (qval < 1E-05)

mm9

Number of total reads
45506535
Reads aligned (%)
94.8
Duplicates removed (%)
10.8
Number of peaks
275 (qval < 1E-05)

Base call quality data from DBCLS SRA