|
| Status |
Public on Apr 07, 2021 |
| Title |
LNCaP_NMYC_shRB1_R2 |
| Sample type |
SRA |
| |
|
| Source name |
LNCaP cells
|
| Organism |
Homo sapiens |
| Characteristics |
genotype: MYCN+; shRB1
treatment: Androgen deprived
|
| Treatment protocol |
All LNCaP cells were maintained in androgen deprived media (phenol-red free RPMI medium (Gibco, 11835-030) supplemented with 5% charcoal stripped serum (Gibco, A33821-01) and 1% penicillin/streptomycin (Gibco, 15140-122)) for 96 hours.
|
| Growth protocol |
GEMM were created by crossing mice carrying an integrated CAG-LSL-MYCN gene at the Rosa26 locus with mice harboring homozygously-floxed Pten alleles and expressing Cre recombinase under the control of the probasin promoter. All LNCaP cells were grown in in RPMI 1640 (Gibco) supplemented with 10% FBS (Gemini), 100 U/ml penicillin, 100 ug/ml streptomycin (Gibco).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA extraction was performed using the NucleoSpin Tissue Extraction Kit (Macherey-Nagel) following the manufacturer’s recommendation.
Library preparation for reduced representation of bisulfite sequencing (RRBS) libraries, sequencing and post-processing of the raw data was performed at the Epigenomics Core at Weill Cornell Medicine
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Quality control of raw sequencing reads was performed using FastQC
Trimming and adapter removal using Trim Galore in non-directional mode with default parameters
Single-end bisulfite converted reads were aligned using Bismark with default parameters
MethylKit was used for identifying differentially methylated sites and annotating them to promoters (±1000bp from TSS), exons, introns, CpG islands and CpG shores (±2000bp from CpGi). Sites covered by at least 10X coverage were considered for methylation analysis
Sites with at least 25% difference in methylation between poorly differentiated and adenocarcinomas mice tumors with 5% False Discovery Rate (FDR) were considered as significantly differentially methylated
Genome_build: GEMM:GRCm38. LNCap: GRCh38
Supplementary_files_format_and_content: Differentially methylated sites with annotations
|
| |
|
| Submission date |
Jun 01, 2020 |
| Last update date |
Apr 07, 2021 |
| Contact name |
Nicholas Brady |
| E-mail(s) |
njb2003@med.cornell.edu
|
| Organization name |
Weill Cornell Medicine
|
| Department |
Pathology and Laboratory Medicine
|
| Street address |
1188 York Ave
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE151426 |
Temporal evolution of cellular heterogeneity during the progression to advanced, AR-negative prostate cancer |
| GSE151581 |
Temporal evolution of cellular heterogeneity during the progression to advanced, AR-negative prostate cancer [RRBS] |
|
| Relations |
| BioSample |
SAMN15077024 |
| SRA |
SRX8450089 |
