Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
DNMT3B

Cell type

Cell type Class
Pluripotent stem cell
Cell type
hESC H1
NA
NA

Attributes by original data submitter

Sample

source_name
H1 human embryonic stem cell
tissue
human embryonic stem cell
mutation
Wild type
passage
44-60
antibody
anti-human DNMT3B rabbit monoclonal antibody (Clone D3C8T, Cell Signaling Technologies, custom-made antibody)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
1) ChIP-seq:Cell were fixed with 1% formaldehyde and insoluble chromatin fraction were isolated. Chromatin were sonicated to 100 to 500 base pair and protein-DNA complexes were pulled down by antbodies. 2) RNA-seq: RNA was harvested by trizol followed by DNAseI treatment and Qiagen RNA mini column for further purification. 3) WGBS: gDNA was harvested by lysing the cells in 50mM Tris-HCl pH8, 100mM NaCl, 25mM EDTA and 1%SDS buffer with 1mg/mL of proteinase K and incubate at 65C overnight. 1) ChIP-seq: Libraries were prepared using ThruPLEX DNA-seq kit (R400428) according to manufacturer's instruction. Constructed libraries were PAGE purified and only libraries with 250 to 500bp were used for sequencing 2) RNA-seq: Librarries were prepared using Scriptseq V2 RNA-seq Library preparation kit (SSV21124) according to manufacturer's instruction. Constructed libraries were PAGE purified and only libraries with 250 to 500bp were used for sequencing. 3) WGBS library were prepared by BGI using standard Illumina WGBS protocol.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
38346584
Reads aligned (%)
182.8
Duplicates removed (%)
6.0
Number of peaks
345 (qval < 1E-05)

hg38

Number of total reads
38346584
Reads aligned (%)
183.8
Duplicates removed (%)
5.9
Number of peaks
648 (qval < 1E-05)

Base call quality data from DBCLS SRA