Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
ASCL1

Cell type

Cell type Class
Unclassified
Cell type
Unclassified
NA
NA

Attributes by original data submitter

Sample

source_name
G523NS-ASCL1 KO-pBAC-ASCL1
tumor
glioblastoma
derived cell line
G523NS
genotype
knockout ASCL1

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and ASCL1-DNA complexes were isolated with antibody. Libraries were prepared according to NEBNext ChIP-Seq library preparation protocol. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were selected with Ampure beads. Library was validated by Bioanalzyer and Kapa qPCR assay and sequenced on an Illumina HiSeq 2500 platform, using a Rapid Run mode flowcell to generate paired end reads of 100 bases.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
29060175
Reads aligned (%)
179.5
Duplicates removed (%)
1.3
Number of peaks
610 (qval < 1E-05)

hg38

Number of total reads
29060175
Reads aligned (%)
181.7
Duplicates removed (%)
1.2
Number of peaks
1084 (qval < 1E-05)

Base call quality data from DBCLS SRA