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Sample GSM241090 Query DataSets for GSM241090
Status Public on Aug 30, 2010
Title Biopsy_metastatic_M01_dye-swap_rep 2
Sample type RNA
 
Channel 1
Source name Total RNA from osteosarcoma biopsy of metastatic patient labelled with AlexaFluor555
Organism Homo sapiens
Characteristics Female, 76 years, left tibia
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.
 
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 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.
 
 
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

Data table header descriptions
ID_REF
VALUE log2 of PRE_VALUE (i.e., log2 of LOWESS normalized ratio of test/reference)
RANGE
PRE_VALUE LOWESS normalized ratio of test/reference

Data table
ID_REF VALUE RANGE PRE_VALUE
1 null null
2 null null
3 null null
4 null null
5 null null
6 null null
7 -1.4112 0.376
8 null null
9 null null
10 null null
11 null null
12 null null
13 0.6799 1.602
14 null null
15 null null
16 0.3696 1.292
17 null null
18 null null
19 null null
20 null null

Total number of rows: 41059

Table truncated, full table size 694 Kbytes.




Supplementary file Size Download File type/resource
GSM241090_M01-B-rep2-Green.txt.gz 4.5 Mb (ftp)(http) TXT
GSM241090_M01-B-rep2-Red.txt.gz 4.5 Mb (ftp)(http) TXT
Processed data included within Sample table

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