Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SMARCA4

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
BRG1 (Abcam, #ab110641)

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
37282941
Reads aligned (%)
83.1
Duplicates removed (%)
10.0
Number of peaks
20097 (qval < 1E-05)

hg38

Number of total reads
37282941
Reads aligned (%)
83.8
Duplicates removed (%)
9.8
Number of peaks
20353 (qval < 1E-05)

Base call quality data from DBCLS SRA