Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SVIL

Cell type

Cell type Class
Neural
Cell type
SH-SY5Y
Primary Tissue
Brain
Tissue Diagnosis
Neuroblastoma

Attributes by original data submitter

Sample

source_name
Cultured SH-SY5Y cells
cell line
SH-SY5Y
antibody
SVIL (S8695; Sigma)
infection
control shRNA
neuronal maturation
B3

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were fixed with 1% formaldehyde for 10 minutes at room temperature before termination with 0.125 M glycine. Cells were then lysed in ChIP buffer (0.6% SDS, 10 mM EDTA, and 50 mM Tris-HCl, pH 8.1) and cross-linked chromatin was sonicated to obtain DNA fragments of 300–800 bp. Immunoprecipitations were performed following the Upstate protocol (http://www.upstate.com). DNA was recovered by phenol-chloroform extraction and ethanol precipitation. ChIP-seq libraries were prepared using NEBNext DNA library preparation reagents (E6000) and the protocol and reagents concentrations described in the Illumina Multiplex ChIP-seq DNA sample Prep Kit. Libraries were indexed using a single indexed PCR primer. After PCR amplification, 300-600 bp DNA fragments were selected on an agarose gel. Libraries were quantified by Qubit (Invitrogen), and library size was assessed by Bioanalyzer (Agilent). Libraries were sequenced using a HiSeq 2000 (Illumina) to generate 50 bp single end reads.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
31524009
Reads aligned (%)
69.7
Duplicates removed (%)
24.6
Number of peaks
1342 (qval < 1E-05)

hg38

Number of total reads
31524009
Reads aligned (%)
71.5
Duplicates removed (%)
23.4
Number of peaks
1296 (qval < 1E-05)

Base call quality data from DBCLS SRA