Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
DNMT3B

Cell type

Cell type Class
Epidermis
Cell type
Epidermal stem cells
NA
NA

Attributes by original data submitter

Sample

source_name
Epidermal Stem Cells
passage
2
tissue
Foreskin
chip-antibody
Dnmt3b (Novus Biotechnology. Cat: NB100-266)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
EpiSC and differentiated keratinocytes were trypsinized and crosslinked in 1% formaldehyde (FA) for 10 min at room temperature (RT). For ChIPs from EBs, crosslinking was performed for 30 min at RT in 4% FA. Crosslinking was quenched with 0.125 M glycine. Pelleted cells were lysed in 1 ml ChIP buffer and sonicated for 15 min in a Bioruptor (Diagenode). Soluble material was quantified by Bradford assays. To immunoprecipitate transcription factors, 2000 mg of protein and 100 mg of immunoprecipitated histone/histone modifications were used. Antibodies (10ug for DnmtA/3B and 3ug for histone modifications) were incubated overnight with the chromatin. Immunocomplexes were recovered with 30 ul of protein A bead slurry (Healthcare. Cat # 17-5280-01). Immunoprecipitated material was washed three times with low salt buffer and one time with high salt buffer. DNA complexes were decrosslinked at 65_C overnight, and DNA was then eluted in 50 ul of water using the PCR purification kit (QIAGEN)

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
47428344
Reads aligned (%)
77.2
Duplicates removed (%)
17.0
Number of peaks
2399 (qval < 1E-05)

hg38

Number of total reads
47428344
Reads aligned (%)
79.0
Duplicates removed (%)
15.8
Number of peaks
3205 (qval < 1E-05)

Base call quality data from DBCLS SRA