Antigen

Antigen Class

TFs and others

Antigen

DNMT3B

Cell type

Cell type Class

Pluripotent stem cell

Cell type

iPS cells

NA

NA

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

hg38

Number of total reads

40549229

Reads aligned (%)

98.3

Duplicates removed (%)

13.5

Number of peaks

5219 (qval < 1E-05)

hg19

Number of total reads

40549229

Reads aligned (%)

98.1

Duplicates removed (%)

13.7

Number of peaks

5172 (qval < 1E-05)