Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Epitope tags

Cell type

Cell type Class
Neural
Cell type
LN-229
Primary Tissue
Brain
Tissue Diagnosis
Glioma

Attributes by original data submitter

Sample

source_name
LN229 human glioblastoma cell line with SOX4 overexpression
cell line
LN229 glioblastoma cell line
genotype/variation
Flag-SOX4-HA
chip antibody
anti-Flag (Sigma, Catalog# F3165)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and SOX4-DNA complexes were isolated with anti-Flag antibody. The negative control experiment used LN229-GFP cell and anti-Flag antibody. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# IP-102-1001). 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 ~300 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

Sequencing Platform

instrument_model
Illumina Genome Analyzer II

hg38

Number of total reads
24276847
Reads aligned (%)
83.2
Duplicates removed (%)
0.5
Number of peaks
495 (qval < 1E-05)

hg19

Number of total reads
24276847
Reads aligned (%)
81.9
Duplicates removed (%)
0.6
Number of peaks
276 (qval < 1E-05)

Base call quality data from DBCLS SRA