|
| Status |
Public on Dec 12, 2014 |
| Title |
VCaP_D_LSD1 |
| Sample type |
SRA |
| |
|
| Source name |
Prostate cancer cell line VCaP
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: VCaP
transfection: no treatment
passage: 14-17
antibody: LSD1 antibody (Abcam, ab17721, lot # GR79477-2)
|
| Treatment protocol |
LNCaP and VCaP 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 VCaP 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. VCaP 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 VCaP cells were harvested by scraping from the plates.
Libraries were prepared according to Rubicon's instructions accompanying the ThruPLEX-FD kit (for ChIP-seq) or Illumina TruSeq RNA Sample Prep Kit v2 (for RNA-seq)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 1000 |
| |
|
| 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 or tophat v2.0.4
MACS2 was used to call peaks and generate bigwiggle file, cuffdiff v2.0.1 was used to identify differentially expressed genes
Genome_build: hg19
Supplementary_files_format_and_content: Peaks files for ChIP-seq samples.
Supplementary_files_format_and_content: Abundance counts for RNA-seq samples.
|
| |
|
| Submission date |
Dec 04, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Housheng Hansen He |
| E-mail(s) |
housheng@jimmy.harvard.edu
|
| Phone |
617-632-4738
|
| Organization name |
Dana-Farber Cancer Institute
|
| Department |
Medical Oncology
|
| Lab |
Myles Brown
|
| Street address |
450 Brookline Ave
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL15433 |
| Series (1) |
| GSE52201 |
Lysine-Specific Demethylase 1 Has Dual Functions as a Major Regulator of Androgen Receptor Transcriptional Activity |
|
| Relations |
| BioSample |
SAMN02436031 |
| SRA |
SRX387195 |
| Named Annotation |
GSM1279770_VCaP_D_LSD1_peaks.bed.gz |
