|
| Status |
Public on Nov 25, 2013 |
| Title |
L_D_25U_100-200bp |
| Sample type |
SRA |
| |
|
| Source name |
Prostate cancer cell line LNCaP
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LNCaP
passage: 14-17
digestion level: 25U
fragment size: 100-200bp
|
| Treatment protocol |
LNCaP and MCF-7 cells were starved in phenol-red-free medium supplemented with 10% charcoal stripped FBS for 3 days before hormone stimulation.
|
| Growth protocol |
The prostate cancer cell line LNCaP and breast cancer cell line MCF7 were obtained from the American Type Culture Collection. LNCaP cells were maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS), 2mM glutamine, 100 U/mL penicillin and 100 mg/mL streptomycin. MCF-7 cells were maintained in DMEM medium supplemented with 10% fetal bovine serum (FBS), 2 mM glutamine, 100 U/mL penicillin, 100 mg/mL streptomycin.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
LNCaP and MCF-7 cells were harvested by trypsinization followed by nuclei extraction. Entact nuclei were treated with Dnase I for desired time.
Libraries were prepared according to Rubicon's instructions accompanying the ThruPLEX-FD kit.
|
| |
|
| Library strategy |
DNase-Hypersensitivity |
| Library source |
genomic |
| Library selection |
DNAse |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
DNase-seq
|
| Data processing |
Illumina Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie v2.0.0
MACS2 was used to call peaks and generate bigwiggle file
Genome_build: hg19
Supplementary_files_format_and_content: mapped bed file
|
| |
|
| Submission date |
Oct 30, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Housheng Hansen He |
| E-mail(s) |
hansen.he@uhn.ca
|
| Phone |
4165679687
|
| Organization name |
UNIVERSITY HEALTH NETWORK
|
| Department |
Medical Biophysics
|
| Lab |
Housheng Hansen He
|
| Street address |
101 College Street, PMCRT 11-305
|
| City |
Toronto |
| State/province |
Ontario |
| ZIP/Postal code |
M5G1L7 |
| Country |
Canada |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE51915 |
Systematic evaluation of DNase-seq experimental parameters |
|
| Relations |
| BioSample |
SAMN02389281 |
| SRA |
SRX371581 |
