Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SS18

Cell type

Cell type Class
Neural
Cell type
NGP
NA
NA

Attributes by original data submitter

Sample

source_name
Neuroblastoma
cell line
NGP
cell type
ARID1A-/- #1
chip antiboy
SS18 (CST, #21792)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and target bound fragments were isolated with antibody. 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.

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
40002616
Reads aligned (%)
33.9
Duplicates removed (%)
64.6
Number of peaks
1189 (qval < 1E-05)

hg38

Number of total reads
40002616
Reads aligned (%)
34.9
Duplicates removed (%)
63.8
Number of peaks
1280 (qval < 1E-05)

Base call quality data from DBCLS SRA