GSM2610546: LNCaP DNase-seq; Homo sapiens; DNase-Hypersensitivity
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
DNase-seq
Antigen
DNase-Seq
Cell type
Cell type Class
Prostate
Cell type
LNCAP
Primary Tissue
Prostate
Tissue Diagnosis
Carcinoma
Attributes by original data submitter
Sample
source_name
LNCaP prostate cancer cell
tissue
Prostate
cell line
LNCaP
chip-antibody
DNase1 (Roche, #04716728001)
Sequenced DNA Library
library_strategy
DNase-Hypersensitivity
library_source
GENOMIC
library_selection
DNase
library_construction_protocol
Cells (7x10^6 per sample) were scraped, centrifuged and washed with PBS. Cell pellets were resuspended in nuclear extraction buffer (10mM Tris-HCl pH7.4, 12.5mM NaCl, 3mM MgCl, 0.1mM EDTA, 0.5% IGEPAL) and dounced until nuclei were visible under light microscope with 0.4% Trypan Blue staining. DNase1 (Roche, #04716728001) was added to nuclei pellets of LNCaP (24U) and PrEC (12U) and incubated at 37°C for 15 minutes. DNaseI reactions were terminated by the addition of 36mM EDTA and Proteinase K was added before incubating at 55°C overnight. DNA was purified by phenol-chloroform extraction and ethanol precipitation. Samples were separated using electrophoresis on a 1% agarose gel. 100-300bp sections were excised and purified using the QIAquick Gel Extraction kit. Library preparation and sequencing were performed by the USC Epigenome Center. Libraries were prepared using the Illumina TruSeq Chip Library Prep Kit. The resulting libraries were sequenced on the Illumina HiSeq 2000 or 2500 platform configured for 50bp single-end reads.