|
| Status |
Public on Nov 17, 2021 |
| Title |
CWR22_shNCOR2_RT_X1 |
| Sample type |
genomic |
| |
|
| Source name |
genomic DNA from xenograft tissue
|
| Organism |
Homo sapiens |
| Characteristics |
gender: Male
sample type: PCa xenograft
disease stage: RT
shRNA: shNCOR2_V2LHS-251658
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted from all samples using the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen), following manufacturer’s protocol.
|
| Label |
Cy5 and Cy3
|
| Label protocol |
Standard Illumina Protocol
|
| |
|
| Hybridization protocol |
DNA methylation profiles were obtained using the Infinium MethylationEPIC BeadChip (EPIC array) platform, performed in the RP Genomics Shared Resource.
|
| Scan protocol |
DNA methylation profiles were obtained using the Infinium MethylationEPIC BeadChip (EPIC array) platform, performed in the RP Genomics Shared Resource.
|
| Data processing |
Data Importing and subsequent processing was accomplished using ChAMP. Detectible beta values for all probed CpG sites were initially compiled and filtered to remove those associated with multiple alignments and known SNPs. To adjust for probe design bias (Infinium Type-I, Type-II), a beta-mixture quantile normalization method (BMIQ) was employed. Additionally, cross-array batch effect was corrected using ComBat.
|
| |
|
| Submission date |
Jun 24, 2021 |
| Last update date |
Nov 17, 2021 |
| Contact name |
Mark D Long |
| E-mail(s) |
mark.long@roswellpark.org
|
| Organization name |
Roswell Park Comprehensive Cancer Center
|
| Department |
Bioinformatics & Biostatistics
|
| Street address |
Elm & Carlton Streets
|
| City |
Buffalo |
| State/province |
NY |
| ZIP/Postal code |
14263 |
| Country |
USA |
| |
|
| Platform ID |
GPL23976 |
| Series (2) |
| GSE178819 |
NCOR2 controls androgen deprivation therapy failure in advanced prostate cancer through re-wiring of the onco-epigenome [CWR22_EPIC] |
| GSE178820 |
NCOR2 controls androgen deprivation therapy failure in advanced prostate cancer through re-wiring of the onco-epigenome |
|
