Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SATB1

Cell type

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

Attributes by original data submitter

Sample

source_name
SH-SY5Y cells
cell line
SH-SY5Y
cell type
neural cells
passages
8-10
treated with
100 nM amyloid-beta1-42 oligomers for 4 h
chip antibody
anti-SATB1 (sc-5990)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were cross-linked with paraformaldehyde, lysed and sonicated prior to extraction of DNA-protein complexes with antibody ChIP-seq samples were individually barcoded with Illumina TruSeq® adapter sequences for library construction at the Donnelly Sequencing Centre (Toronto, ON) according to the manufacturer's instructions

Sequencing Platform

instrument_model
Illumina Genome Analyzer

hg19

Number of total reads
13720699
Reads aligned (%)
35.7
Duplicates removed (%)
50.6
Number of peaks
4214 (qval < 1E-05)

hg38

Number of total reads
13720699
Reads aligned (%)
38.3
Duplicates removed (%)
47.9
Number of peaks
4187 (qval < 1E-05)

Base call quality data from DBCLS SRA