|
| Status |
Public on Jan 14, 2008 |
| Title |
Bone OP-OA AMC 2631 23 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
OP34 - Total RNA from human OP trabecular bone labelled with Cyanine-5 (red)
|
| Organism |
Homo sapiens |
| Characteristics |
OP bone Age: 87 years Sex: female
|
| Extracted molecule |
total RNA |
| Extraction protocol |
As described in Kuliwaba et al Journal Bone & Mineral Research 2000 15:332-341
|
| Label |
Cy5
|
| Label protocol |
RNA was purified using RNeasy columns (Qiagen) according to the manufacturers instructions. RNA (5 micro grams) was amplified using a Message Amp II kit (Ambion) with indirect amino allyl-mediated incorporation of Cy5 (Amersham Biosciences) according to the manufacturers instructions. 5 micro grams of the labelled sample was used for hybridisation
|
| |
|
| Channel 2 |
| Source name |
OA13 - Total RNA from human OA trabecular bone, labelled with Cyanine-3 (green)
|
| Organism |
Homo sapiens |
| Characteristics |
OA bone Age: 82 years Sex: female
|
| Extracted molecule |
total RNA |
| Extraction protocol |
As described in Kuliwaba et al Journal Bone & Mineral Research 2000 15:332-341
|
| Label |
Cy3
|
| Label protocol |
RNA was purified using RNeasy columns (Qiagen) according to the manufacturers instructions. RNA (5 micro grams) was amplified using a Message Amp II kit (Ambion) with indirect amino allyl-mediated incorporation of Cy3 (Amersham Biosciences) according to the manufacturers instructions. 5 micro grams of the labelled sample was used for hybridisation
|
| |
|
| |
| Hybridization protocol |
see the Adelaide Microarray Facility website
|
| Scan protocol |
Slides were scanned with a GenePix 3000B Scanner (Axon Instruments) twice at slightly different PMT voltage
|
| Description |
This sample is part of a series (CTL-OA-OP human IT PF Bone study series) that spanned two array print runs (slides AMC_2609 - AMC_2638 and AMC_3104 - AMC_3119)
|
| Data processing |
Images were visually inspected for artefacts and boxplots and image plots of Red and Green channels examined. Arrays with poor hybridisation efficiency, or gross artefacts were excluded and repeated. Image analysis and spot identification and intensity extraction was performed using the Spot software package (see the CSIRO Australia SPOT web page. Spot uses a seeded region growing algorithm to identify spots and is able to identify non-uniform shaped spots. Each estimated grid was visually inspected to ensure accurate spot identification. Morphological opening background correction was applied to mean spot signal intensities. Arrays were normalised using intensity-dependent print-tip loess normalization followed by within slide scale normalisation (as implemented in the LIMMA package of BioConductor). As the design of this experiment did not include any technical replication, data obtained from duplicate scans were used for this purpose. Duplicate correlation was calculated in LIMMA and incorporated into the calculations similarly to the treatment commonly used for duplicate spots on the same array
|
| |
|
| Submission date |
Jul 06, 2007 |
| Last update date |
Jan 14, 2008 |
| Contact name |
Blair Hopwood |
| E-mail(s) |
blair.hopwood@imvs.sa.gov.au
|
| Organization name |
Institute of Medical and Veterinary Science
|
| Department |
Tissue Pathology
|
| Street address |
Frome Road
|
| City |
Adelaide |
| State/province |
South Australia |
| ZIP/Postal code |
5000 |
| Country |
Australia |
| |
|
| Platform ID |
GPL5391 |
| Series (1) |
| GSE8406 |
CTL-OA-OP human IT PF Bone - CompuGen H19K microarray study |
|
| Data table header descriptions |
| ID_REF |
|
| VALUE |
Normalised log2 fold change (Red/Green) ie M Value log2(R) - log2(G) - Scan1 |
| VALUE2 |
Normalised log2 fold change (Red/Green) ie M Value log2(R) - log2(G) – Scan2 |
| R1 |
Red (Cy5) spot mean intensity – Scan1 |
| R2 |
Red (Cy5) spot mean intensity - Scan2 |
| G1 |
Green (Cy3) spot mean intensity – Scan1 |
| G2 |
Green (Cy3) spot mean intensity – Scan2 |
| Rb1 |
Red (Cy5) background - morphological opening estimate from Spot (CSIRO) – Scan1 |
| Rb2 |
Red (Cy5) background - morphological opening estimate from Spot (CSIRO) – Scan2 |
| Gb1 |
Green (Cy3) background - morphological opening estimate from Spot (CSIRO) – Scan1 |
| Gb2 |
Green (Cy3) background - morphological opening estimate from Spot (CSIRO) – Scan2 |
