Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
NEUROD2

Cell type

Cell type Class
Digestive tract
Cell type
LoVo
Primary Tissue
Colon
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
LoVo
cell line
LoVo
cell type
colon adenocarcinoma
hgn
NEUROD2
antibody
Santa Cruz Biotechnology, Inc. : sc-98674 X
control sample
batch3_chrom2_LoVo_IgG_Rabbit
qc successful
FailedQC
fraction of peaks close to tss
0.029508
lowest e-value for a high complexity de novo motif
8.5e+03

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were cross-linked by 1% formaldehyde, and DNA was sonicated to 200- 400 bp fragments. Antibodies (5 µg) were added and collected using protein G Sepharose (GE). Cross-links were reversed and proteins digested by incubation with proteinase K at 65 °C overnight. DNA was then purified using Qiagen PCR purification kit. Libraries were constructed according to Illuminas standard protocol. The concentration of the library was determined by Nanodrop spectrophotometer (Thermo Fisher Scientific Inc.) and 10 pmol of the DNA was applied for one flow-cell lane. Sequencing was performed using one lane of Illumina GAIIx, or alternatively, samples were indexed with DNA barcodes and four to six different samples were multiplexed in one library and sequenced using Illumina HiSeq 2000 (single 36 bp reads).

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
18475440
Reads aligned (%)
51.7
Duplicates removed (%)
8.3
Number of peaks
863 (qval < 1E-05)

hg38

Number of total reads
18475440
Reads aligned (%)
53.1
Duplicates removed (%)
6.8
Number of peaks
734 (qval < 1E-05)

Base call quality data from DBCLS SRA