Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CTCF

Cell type

Cell type Class
Neural
Cell type
SK-N-AS
Primary Tissue
Brain
Tissue Diagnosis
Neuroblastoma

Attributes by original data submitter

Sample

source_name
Neuroblastoma
cell type
SK-N-AS
chip antibody
CTCF
antibody vendor
Abcam
antibody catalog
ab70303
antibody lot
gr20146-2
young_id
20171106_6512

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
37825419
Reads aligned (%)
68.2
Duplicates removed (%)
25.8
Number of peaks
52147 (qval < 1E-05)

hg38

Number of total reads
37825419
Reads aligned (%)
69.5
Duplicates removed (%)
24.8
Number of peaks
52559 (qval < 1E-05)

Base call quality data from DBCLS SRA