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Sample GSM1543792 Query DataSets for GSM1543792
Status Public on Jan 22, 2015
Title LNCaP_TOP1_ChIP-seq_30min_dht
Sample type SRA
 
Source name ChIP-seq with BLRP-tagged TOP1, 30min treatment with 100 nM DHT
Organism Homo sapiens
Characteristics cell line: LNCaP
chip antibody: BLRP-tagged TOP1
Growth protocol LNCaP cells were engineered to express BirA enzyme and the Tet-Repressor. This parental line was used to generate inducible cells that express biotin-tagged human topoisomerase I under the control of a Tet-on promoter that can be induced with doxycycline to obtain protein expression level similar to the endogenous one. Biotin ligase recognition peptide (BLRP)-tagged TOP1 cells were used for the ChIP experiment. Following doxycycline (2 μg/mL) induction for 24 h, the cells were stimulated with 100 nM DHT for 30 min and fixed with 1% formaldehyde for 10 min at room temperature.
Extracted molecule genomic DNA
Extraction protocol Isolated nuclei were sonicated and precipitation was carried out with Streptavidin Magnetic Microspheres (Solulink). Beads were washed with standard ChIP buffers. Additional extensive washes (4 times/20 min each with 1% SDS in TE buffer and two times with 1% Triton X-100 in TE buffer) were performed, before TEV (Life Technologies) cleavage. DNA was purified using QIAquick spin columns (Qiagen).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Description ChIP-seq with BLRP-tagged TOP1, 30min treatment with 100 nM DHT
Data processing ChIP-seq was sequenced with Illumina’s HiSeq 2000 system (San Diego, CA) according to the manufacturer’s instructions. The sequencing reads were aligned to the UCSC Homo sapiens reference genome (hg18) using SOAP3-dp (Luo et al., 2013: PLoS one 8, no. 5, e65632). The regions with DHT-increased/DHT-decreased TOP1-binding were calculated using SICER (with background control from 3 combined repeats from GEO database: GSM1543795). The TOP1 peaks were calculated with MACS. The 43653 peak summits in 64569 DHT-increased regions and 15073 peak summits in 26321 DHT-decreased regions were saved in "GSE63202_43653summitsIn64569increasedTOP1regions.bed.gz" and "GSE63202_15073summitsIn26321decreasedTOP1regions.bed.gz" files respectively in GEO database: GSE63202. Please note, not all regions have clearly defined peaks.
Genome build: hg18
Supplementary file format and content: BED (peaks)
 
Submission date Nov 12, 2014
Last update date May 15, 2019
Contact name Michael G Rosenfeld
E-mail(s) mrosenfeld@ucsd.edu
Organization name University of California, San Diego
Department School of Medicine
Lab Rosenfeld Lab
Street address 9500 Gilman Drive
City La Jolla
State/province CA
ZIP/Postal code 92093-0648
Country USA
 
Platform ID GPL11154
Series (1)
GSE63202 Ligand-Dependent Enhancer Activation Regulated by Topoisomerase-I Activity
Relations
BioSample SAMN03176976
SRA SRX758029

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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