Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Neural
Cell type
SJNB3
NA
NA

Attributes by original data submitter

Sample

source_name
Neuroblastoma
cell type
SJNB3
chip antibody
None
young_id
20171106_6507

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

hg38

Number of total reads
49213032
Reads aligned (%)
93.5
Duplicates removed (%)
10.0
Number of peaks
1846 (qval < 1E-05)

hg19

Number of total reads
49213032
Reads aligned (%)
92.5
Duplicates removed (%)
11.7
Number of peaks
1262 (qval < 1E-05)

Base call quality data from DBCLS SRA