Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
HAND2

Cell type

Cell type Class
Neural
Cell type
BE(2)-C
Primary Tissue
Brain
Site of Extraction
Bone Marrow
Tissue Diagnosis
Neuroblastoma

Attributes by original data submitter

Sample

source_name
Neuroblastoma
cell type
BE2C
chip antibody
HAND2
antibody catalog
sc9409X
antibody lot
c230
young_id
20161217_5285

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
50141075
Reads aligned (%)
81.2
Duplicates removed (%)
16.1
Number of peaks
61300 (qval < 1E-05)

hg38

Number of total reads
50141075
Reads aligned (%)
82.1
Duplicates removed (%)
15.6
Number of peaks
61332 (qval < 1E-05)

Base call quality data from DBCLS SRA