Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SMC1A

Cell type

Cell type Class
Neural
Cell type
KELLY
Primary Tissue
Brain
Tissue Diagnosis
Neuroblastoma

Attributes by original data submitter

Sample

source_name
TAE resistant Kelly cells
antibody
SMC1
tae response
resistant
treatment
shBORIS
cell line
Neuroblastoma Kelly cells

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were crosslinked with formaldehyde and lysed to obtain purified nuclei that were sonicated to shear chromatin. Protein-DNA complexes were then isolated using Dynabeads with corresponding antibodies, and DNA was isolated through reverse crosslinking and purified by phenol chloroform extraction in order to be used for library construction. Libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit from NEB (E7645), according to the manufacturer's protocol.

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
19597649
Reads aligned (%)
88.1
Duplicates removed (%)
8.3
Number of peaks
955 (qval < 1E-05)

hg38

Number of total reads
19597649
Reads aligned (%)
90.2
Duplicates removed (%)
6.9
Number of peaks
972 (qval < 1E-05)

Base call quality data from DBCLS SRA