|
| Status |
Public on Aug 29, 2012 |
| Title |
Prostate_tumor_pretreated_needle_biopsy_vs._posttreated_prostatectomy_KP-03 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
KP-03_LCM_pretreated_tumor
|
| Organism |
Homo sapiens |
| Characteristics |
gender: male
age: 56
clinical stage: T2b
surgical margin status: Negative
nodal status at surgery: Negative
gleason sum score (biopsy): 7
gleason sum score (surgical): 7
psa pre-chemotherapy: 1.43
psa post-chemotherapy: 0.77
tissue: prostate needle biopsy tissue frozen in OCT blocks
cell type: neoplastic epithelium
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from captured neoplastic epithelium using a Picopure RNA isolation kit according to the manufacturer's instructions (Arcturus). Extracted RNA underwent two rounds of amplification by a linear T7-RNA polymerase method developed by Eberwine et al. using a messageAMP aRNA kit (Ambion).
|
| Label |
Cy5
|
| Label protocol |
cDNA was separately synthesized from 3 μg aRNA amplified from pretreated and posttreated specimens as described previously. To eliminate potential dye bias, we randomly alternated Cy3 and Cy5 labeling to pretreated and posttreated specimens across 31 samples.
|
| |
|
| Channel 2 |
| Source name |
KP-03_LCM_posttreated_tumor
|
| Organism |
Homo sapiens |
| Characteristics |
gender: male
age: 56
clinical stage: T2b
surgical margin status: Negative
nodal status at surgery: Negative
gleason sum score (biopsy): 7
gleason sum score (surgical): 7
psa pre-chemotherapy: 1.43
psa post-chemotherapy: 0.77
tissue: prostatectomy tissue frozen in OCT blocks
cell type: neoplastic epithelium
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from captured neoplastic epithelium using a Picopure RNA isolation kit according to the manufacturer's instructions (Arcturus). Extracted RNA underwent two rounds of amplification by a linear T7-RNA polymerase method developed by Eberwine et al. using a messageAMP aRNA kit (Ambion).
|
| Label |
Cy3
|
| Label protocol |
cDNA was separately synthesized from 3 μg aRNA amplified from pretreated and posttreated specimens as described previously. To eliminate potential dye bias, we randomly alternated Cy3 and Cy5 labeling to pretreated and posttreated specimens across 31 samples.
|
| |
|
| |
| Hybridization protocol |
Labeled cDNA probes were hybridized in a head-to-head fashion, pretreated versus posttreated from the same individual, simultaneously to custom-made microarrays composed of ∼6,800 clones derived from the Prostate Expression DataBase, a public sequence repository of expressed sequence tag data derived from human prostate cDNA libraries.
|
| Scan protocol |
Fluorescent array images were collected for both Cy3 and Cy5 emissions using a GenePix 4000B fluorescent scanner (Axon Instruments)
|
| Description |
Prostate_tumor_pretreated_needle_biopsy_vs._posttreated_prostatectomy_KP-03
|
| Data processing |
GenePix Pro 4.1 software was used to grid and extract image intensity data. Spots of poor quality as determined by visual inspection were removed from further analysis. Print tip-specific Loess normalization was performed in R using the Limma Bioconductor package, using these settings: span=0.2, bc.method=subtract, offset=10.
|
| |
|
| Submission date |
Aug 28, 2012 |
| Last update date |
Aug 29, 2012 |
| Contact name |
Ilsa Coleman |
| E-mail(s) |
icoleman@fredhutch.org
|
| Phone |
206-667-1703
|
| Organization name |
Fred Hutchinson Cancer Center
|
| Department |
Human Biology
|
| Lab |
Peter Nelson
|
| Street address |
1100 Fairview Ave N, E2-112
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109 |
| Country |
USA |
| |
|
| Platform ID |
GPL4767 |
| Series (1) |
| GSE40434 |
Molecular alterations in prostate carcinomas that associate with in vivo exposure to chemotherapy |
|
