Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CTCF

Cell type

Cell type Class
Neural
Cell type
NB69
Primary Tissue
Brain
Tissue Diagnosis
Neuroblastoma

Attributes by original data submitter

Sample

source_name
Neuroblastoma
cell type
NB69
chip antibody
CTCF
antibody vendor
Abcam
antibody catalog
ab70303
antibody lot
gr20146-2
young_id
20171106_6510

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified. Lysates were clarified from sonicated nuclei and target bound fragments were isolated with antibody.

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
71124235
Reads aligned (%)
64.0
Duplicates removed (%)
30.8
Number of peaks
64284 (qval < 1E-05)

hg38

Number of total reads
71124235
Reads aligned (%)
65.1
Duplicates removed (%)
29.9
Number of peaks
65032 (qval < 1E-05)

Base call quality data from DBCLS SRA