Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
UBE3A

Cell type

Cell type Class
Pluripotent stem cell
Cell type
hESC H9
NA
NA

Attributes by original data submitter

Sample

source_name
hESCs
cell type
H9 hESCs with homozygous UBE3A deletion
weeks of differentiation
no differentiation
genotype
UBE3A KO
antibody
anti-UBE3A
antibody catalog number and manufacturer
A300-352A (Bethyl)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
hESCs, NPCs, and neurons were processed for ChIP-seq as previously described (Cotney & Noonan (2015), Cold Spring Harb Protoc 2015(4): 419 Libraries were prepared from ChIPed DNA using the Takara ThruPLEX DNA-seq library preparation kit according to manufacturer's instructions. Libraries were quantified with the NEBNext Library Quant Kit for Illumina

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
32471576
Reads aligned (%)
64.8
Duplicates removed (%)
30.7
Number of peaks
990 (qval < 1E-05)

hg38

Number of total reads
32471576
Reads aligned (%)
66.7
Duplicates removed (%)
29.1
Number of peaks
983 (qval < 1E-05)

Base call quality data from DBCLS SRA