|
| Status |
Public on Apr 14, 2012 |
| Title |
Post-op quadriceps muscle sample Sample63 |
| Sample type |
RNA |
| |
|
| Source name |
quadriceps muscle biopsy post operative
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: skeletal muscle
condition: cancer-free
age: 63
Sex: F
bmi: 22.5
weightlossfromusual: -16.25
crp: 5
height(cm): 175
currentwgt: 68.8
quadsstr(n/kg): 3.23
stepsperday: 3295
tumour: Oesophagus
|
| Treatment protocol |
Biopsies were harvested from human quadriceps muscle using a Bergstrom needle under suction
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tissue was homogenised in Qiazol (Qiagen, UK) reagent using a Polytron PT1200E (Kinematica AG, Switzerland). Total RNA was extracted using miRNEasy columns (Qiagen, UK) as directed by the manufacturer with an on column DNAse digestion step.
|
| Label |
biotin
|
| Label protocol |
Reverse transcription of RNA was carried out using the Ovation RNA Amplification system v2 (Nugen Technologies Inc, USA). 100ng of total RNA was reverse transcribed as per the manufacturer’s protocol. cDNA was purified using qiaQuick PCR purification kit (Qiagen, UK) and quantified using the Nanodrop instrument. For the microarray study, 3.75ug of cDNA was fragmented and labeled with the FL-Ovation cDNA Biotin Module V2 (Nugen Technologies, USA) and hybridised to each Affymetrix U133+2 array (Affymetrix, USA) using protocols provided by Nugen Technologies Inc.
|
| |
|
| Hybridization protocol |
For the microarray study, 3.75ug of cDNA was fragmented and labeled with the FL-Ovation cDNA Biotin Module V2 (Nugen Technologies, USA) and hybridised to hgu133aplus2 arrays.
|
| Scan protocol |
As per Affymetrix recommendations using Affymetrix equipment
|
| Description |
Post-op quadriceps muscle sample
gene expression in human skeletal muscle post tumour removal
|
| Data processing |
Raw chip data were analysed using MAS 5.0 with global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. Further analysis used the bioconductor suite (bioC 2.8 / R 2.13) and further data processing were performed by RMA.
|
| |
|
| Submission date |
Dec 02, 2011 |
| Last update date |
Apr 14, 2012 |
| Contact name |
Iain Gallagher |
| E-mail(s) |
iaingallagher@gmail.com
|
| Phone |
00 44 1786 46 6024
|
| Organization name |
University of Stirling
|
| Department |
Faculty of Health Sciences and Sport
|
| Street address |
Room 4B133 Cottrell Building, University of Stirling, Airthrey Road
|
| City |
Stirling |
| ZIP/Postal code |
FK9 4LA |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE34111 |
Gene expression in skeletal muscle of cancer patients before and after potentially curative surgery |
|
