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
A300-351A (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
32624235
Reads aligned (%)
68.3
Duplicates removed (%)
26.4
Number of peaks
1008 (qval < 1E-05)

hg38

Number of total reads
32624235
Reads aligned (%)
70.3
Duplicates removed (%)
24.8
Number of peaks
973 (qval < 1E-05)

Base call quality data from DBCLS SRA