|
| Status |
Public on Mar 08, 2013 |
| Title |
Post-combination treatment patient 4 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Melanoma metastasis- treated with temsirolimus and bevacizumab
|
| Organism |
Homo sapiens |
| Characteristics |
patient: 4
treatment: temsirolimus and bevacizumab
days after treatment: 23 d
tumor: melanoma
tissue: lymph node
gender: female
tumor stage: 3
|
| Treatment protocol |
Biopsies of melanoma metastases were obtained prior to treatment and one day following treatment with temsirolimus alone. The following week patients received both bevacizumab and temsirolimus. One week later, they received temsirolimus alone and then the following week (day 23) they received bevacizumab and temsirolimus, after which another biopsy was obtained.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
microRNA extracted from sections cut from FFPE tissue using the miRNeasy FFPE kit
|
| Label |
Hy3
|
| Label protocol |
500ng of total RNA from sample and reference were labeled with Hy3 and Hy5 fluorescent label, respectively, using the miRCURY LNA microRNA Hi-Power Labeling Kit, Hy3/Hy5 (Exiqon, Denmark), following the procedure described by the manufacturer
|
| |
|
| Channel 2 |
| Source name |
total pooled microRNA from all samples
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: reference (total pooled microRNA from all samples)
|
| Treatment protocol |
Biopsies of melanoma metastases were obtained prior to treatment and one day following treatment with temsirolimus alone. The following week patients received both bevacizumab and temsirolimus. One week later, they received temsirolimus alone and then the following week (day 23) they received bevacizumab and temsirolimus, after which another biopsy was obtained.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
microRNA extracted from sections cut from FFPE tissue using the miRNeasy FFPE kit
|
| Label |
Hy5
|
| Label protocol |
500ng of total RNA from sample and reference were labeled with Hy3 and Hy5 fluorescent label, respectively, using the miRCURY LNA microRNA Hi-Power Labeling Kit, Hy3/Hy5 (Exiqon, Denmark), following the procedure described by the manufacturer
|
| |
|
| |
| Hybridization protocol |
Hy3-labeled samples and Hy5-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY LNA microRNA Array (6th gen- has, mmu, and mo). Hybridization was performed according to the miRCURY LNA microRNA Array instruction manual using a Tecan HS 4800 hybridization station (Tecan, Austria).
|
| Scan protocol |
Agilent G2565BA Microarray Scanner
Images were quantified using ImaGene 9.0 data analysis software
|
| Description |
PC-Mel-pt4
Melanoma metastasis following 23d of combination treatment
|
| Data processing |
LOWESS normalized, background subtracted data obtained from log2 of processed Hy3/processed Hy5 signal
The 2681 rows in GPL11434 list all the probes for the human, mouse, rat and related viral miRNAs. This project involved analysis of a single species (human), so information from capture probes specific for the other species are not included in this dataset.
|
| |
|
| Submission date |
Apr 10, 2012 |
| Last update date |
Mar 08, 2013 |
| Contact name |
Aubrey Wagenseller |
| Organization name |
University of Virginia
|
| Department |
Surgery
|
| Lab |
Craig Slingluff
|
| Street address |
345 Crispell Drive
|
| City |
Charlottesville |
| State/province |
Virginia |
| ZIP/Postal code |
22908 |
| Country |
USA |
| |
|
| Platform ID |
GPL11434 |
| Series (1) |
| GSE37131 |
Melanoma tissue samples from a clinical trial: no treatment vs. post-temsirolimus alone vs. post-combination temsirolimus and bevacizumab |
|
