Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CTCF

Cell type

Cell type Class
Neural
Cell type
SH-SY5Y
Primary Tissue
Brain
Tissue Diagnosis
Neuroblastoma

Attributes by original data submitter

Sample

source_name
Neuroblastoma
cell type
SH-SY5Y
chip antibody
CTCF
antibody vendor
Abcam
antibody catalog
ab70303
antibody lot
gr20146-2
young_id
20171106_6514

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
36436682
Reads aligned (%)
62.3
Duplicates removed (%)
32.9
Number of peaks
45675 (qval < 1E-05)

hg38

Number of total reads
36436682
Reads aligned (%)
63.0
Duplicates removed (%)
32.5
Number of peaks
45888 (qval < 1E-05)

Base call quality data from DBCLS SRA