|
| Status |
Public on Aug 30, 2010 |
| Title |
Biopsy_metastatic_M03_rep 1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Total RNA from osteosarcoma biopsy of metastatic patient labelled with AlexaFluor647
|
| Organism |
Homo sapiens |
| Characteristics |
Female, 19 years, right femur
|
| Treatment protocol |
Biopsies were removed from patients and immediately frozen in dry ice, before long-term storage at -80oC.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted from 100 mg of tumour biopsy with 900 uL Trizol and 100 uL 2M acetic acid.
|
| Label |
AlexaFluor647
|
| Label protocol |
20 ug of total RNA incubated with 5 ug anchored oligo(dT)12-18 primer 70oC/10 min. Reverse transcription performed at 42oC/2 h with 0.65 uL aminoallyl dNTP - 25 mM dATP, dGTP, dCTP, 7.5 mM dTTP, 15 mM aminoallyl d-UTP, and 400 U Superscript II. The RNA was labelled at room temperature/1 hour with AlexaFluor555 or AlexaFluor647 in the presence of 0.3M NaHCO3 and DMSO.
|
| |
|
| Channel 2 |
| Source name |
Total RNA pooled from 8 cancer cell lines
|
| Organism |
Homo sapiens |
| Characteristics |
HDF, COLO-16, LNCap, DU145, SK-BR3, U2OS, HT29, DG75
|
| Treatment protocol |
Biopsies were removed from patients and immediately frozen in dry ice, before long-term storage at -80oC.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted from 100 mg of tumour biopsy with 900 uL Trizol and 100 uL 2M acetic acid.
|
| Label |
AlexaFluor555
|
| Label protocol |
20 ug of total RNA incubated with 5 ug anchored oligo(dT)12-18 primer 70oC/10 min. Reverse transcription performed at 42oC/2 h with 0.65 uL aminoallyl dNTP - 25 mM dATP, dGTP, dCTP, 7.5 mM dTTP, 15 mM aminoallyl d-UTP, and 400 U Superscript II. The RNA was labelled at room temperature/1 hour with AlexaFluor555 or AlexaFluor647 in the presence of 0.3M NaHCO3 and DMSO.
|
| |
|
| |
| Hybridization protocol |
Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers, as described by the manufacturer. Washing was performed following solutions and protocols recommended by Agilent.
|
| Scan protocol |
Scanned on an Agilent G2565AA scanner.
|
| Description |
none
|
| Data processing |
LOWESS normalized, background subtracted data obtained from log of ratio of processed test signal/processed reference signal using GeneSpring version 7.2.
|
| |
|
| Submission date |
Nov 02, 2007 |
| Last update date |
Feb 08, 2012 |
| Contact name |
Liliana Beatriz Endo-Munoz |
| E-mail(s) |
l.munoz@uq.edu.au
|
| Phone |
+61734436929
|
| Organization name |
University of Queensland
|
| Department |
Diamantina Institute
|
| Lab |
Saunders
|
| Street address |
TRI, 37 Kent St
|
| City |
Woolloongabba |
| State/province |
Queensland |
| ZIP/Postal code |
4102 |
| Country |
Australia |
| |
|
| Platform ID |
GPL6076 |
| Series (1) |
| GSE9508 |
Gene expression profiling of metastatic and non-metastatic osteosarcoma biopsies |
|
