Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SALL4

Cell type

Cell type Class
Liver
Cell type
SNU-398
Primary Tissue
Liver
Tissue Diagnosis
Carcinoma Hepatocellular

Attributes by original data submitter

Sample

source_name
Hepatocarcinoma cell
cell line
SNU398
cell type
Hepatocarcinoma
chip antibody
SALL4 (Cell Signaling Technolog, cat# 8459BF, Lot 2)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cell were fixed with 1% formaldehyde and insoluble chromatin fraction were isolated. Chromatin were sonicated to 100 to 500 base pair and protein-DNA complexes were pulled down by antbodies Libraries were prepared using ThruPLEX DNA-seq kit (R400428) according to manufacturer's instruction. Constructed libraries were PAGE purified and only libraries with 250 to 500bp were used for sequencing

Sequencing Platform

instrument_model
Illumina MiniSeq

hg19

Number of total reads
37534587
Reads aligned (%)
184.6
Duplicates removed (%)
5.6
Number of peaks
2722 (qval < 1E-05)

hg38

Number of total reads
37534587
Reads aligned (%)
186.7
Duplicates removed (%)
5.3
Number of peaks
3442 (qval < 1E-05)

Base call quality data from DBCLS SRA