|
| Status |
Public on Apr 08, 2016 |
| Title |
Dex rep#1 DNase-seq GH1564 |
| Sample type |
SRA |
| |
|
| Source name |
MCF-7 breast cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: ZR-75-1
cell type: Ascites from a ductal carcinoma of the breast
treatment: Dexamethasone
concentration: 100nM
time: 30 minutes
replicate: replicate 1
growth proptocol: For maintenance cells were cultured in RPMI containing 2mM L-glutamine supplemented 10% calf serum, 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_ZR-75-1_Dex_RC_GH1564xGH1568_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(http://sorceforge.net/proujects/dnase2hotspots/) 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
|
| Lab |
LRBGE
|
| 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 |
|
| Relations |
| BioSample |
SAMN04004005 |
| SRA |
SRX1161160 |
