Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
PROX1

Cell type

Cell type Class
Digestive tract
Cell type
SW 480
Primary Tissue
unresolved
Tissue Diagnosis
unresolved

Attributes by original data submitter

Sample

source_name
SW480R
cell type
Epithelial tumor cells isolated from human colorectal adenocarcinoma
cell line
SW480
chip antibody
goat anti–human PROX1 antibody (R&D Systems)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
0.5x107 SW480R cells were cross-linked with formaldehyde, chromatin was fragmented using Simple ChIP Enzymatic Chromatin IP Kits (Cell Signaling) and immunoprecipitated using 5µg goat anti–human PROX1 antibody (R&D Systems) complexed with protein G Sepharose (GE Healthcare). 10 ng of ChIP sample was quantified using the Qubit fluorometer (Invitrogen) and DNA were prepared using the ChIP-Seq Sample Preparation Kit (Illumina) according to the manufacturer’s protocol.

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

hg19

Number of total reads
47046783
Reads aligned (%)
86.7
Duplicates removed (%)
11.1
Number of peaks
27061 (qval < 1E-05)

hg38

Number of total reads
47046783
Reads aligned (%)
88.0
Duplicates removed (%)
10.3
Number of peaks
26999 (qval < 1E-05)

Base call quality data from DBCLS SRA