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Sample GSM1858663 Query DataSets for GSM1858663
Status Public on Apr 08, 2016
Title Dex rep#1 DNase-seq GH1502
Sample type SRA
Source name MCF-7 breast cancer cell line
Organism Homo sapiens
Characteristics cell line: MCF-7
cell type: Pleural effusion from an adenocarcinoma of the breast
treatment: Dexamethasone
concentration: 100nM
time: 30 minutes
replicate: replicate 1
growth proptocol: For maintenance cells were cultured in DMEM supplemented 10% calf serum, 2mM L-glutamine, 1mM sodium pyruvate, 1X non-essential amino acids, and 1% penicillin-streptomycin
Treatment protocol Cells were plated for experiments in phenol red free growth medium supplemented with 10% charcoal-dextran serum twenty-four hours before hormone treatment. Cells were left untreated or induced with 100nM dexamethasone or 100nM estradiol for 30 minutes.
Growth protocol see additional columns of the SAMPLES section
Extracted molecule genomic DNA
Extraction protocol Lysates were digested with DNase-I and DNA fragments of 100-500bp were purified using a sucrose gradient.
Library strategy DNase-Hypersensitivity
Library source genomic
Library selection DNAse
Instrument model Illumina NextSeq 500
Description hs_RC_MCF7_DHS_Dex_RC_GH1502_3xGH1572_3_FDR0.csv
Data processing RTA 1.12.42 was used for Basecalling and Casava 1.8.2 ws used for demultiplexing.
Alignment was performed by Bowtie2 software with the hg19 reference genome.
Areas of enrichment were identified using DNase2Hotspots software( software with FDR 0%.
Raw signal density graphs were generated by counting tags at each genomic coordinate after extending the length of sequences to 150bp by strands.
Values for tag densities were normalized to 10 million reads to adjust for differences in the sequencing depth between samples.
Genome_build: hg19
Supplementary_files_format_and_content: comma-delimited (CSV) text files include genomic locations (Chromosome, start, end ), z-score, p-value and the maximum density of hotspots. Bedgraph files contain genomic locations and normalized tag density profiles.
Submission date Aug 20, 2015
Last update date May 15, 2019
Contact name Songjoon Baek
Organization name NCI / NIH
Department CCR
Street address 41 Library Drive
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
Platform ID GPL18573
Series (2)
GSE72250 Characterization of chromatin accessibility through the DNaseI hypersensitivity assay in breast cancer cells treated with either Dex or E2
GSE72252 DNaseI hypersensitivity assay and ER, GR, and FoxA1 binding patterns in breast cancer cells
BioSample SAMN04003999
SRA SRX1161154

Supplementary file Size Download File type/resource
GSM1858663_GH1502_MCF-7_DHS_hg19.bedgraph.gz 121.2 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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