Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
DNMT3B

Cell type

Cell type Class
Pluripotent stem cell
Cell type
iPS cells
NA
NA

Attributes by original data submitter

Sample

source_name
253G1_SALL3 shRNA_DNMT3B_ChIPSeq
cell type
Human induced pluripotent stem cell (iPSC)
genotype
SALL3 KD
chip antibody
anti-DNMT3B

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Active Motif Epigenetic Services performed ChIP assays. Cells fixed with 1% formaldehyde for 15 min were quenched with 0.125 M lysine, and then swollen in lysis buffer for 30 min on ice. Chromatin was isolated after sonication to shear the DNA to an average length of 300-500 bp. ChIP and input DNAs were prepared for amplification by converting overhangs into phosphorylated blunt ends and adding an adenine to the 3' ends. Illumina adaptors were added and the library was size-selected (175-225 bp) on an agarose gel. The adaptor- ligated libraries were amplified for 18 cycles. The resulting DNA libraries were purified, quantified, and tested by qPCR at the same specific genomic regions as the original ChIP DNA to assess quality of the amplification reactions.

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
40549229
Reads aligned (%)
84.7
Duplicates removed (%)
13.7
Number of peaks
5172 (qval < 1E-05)

hg38

Number of total reads
40549229
Reads aligned (%)
85.1
Duplicates removed (%)
13.5
Number of peaks
5219 (qval < 1E-05)

Base call quality data from DBCLS SRA