|
| Status |
Public on Aug 27, 2008 |
| Title |
Ref_SSA_female_83 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
pooled normal colonic tissue
|
| Organism |
Homo sapiens |
| Characteristics |
pooled normal colonic tissue
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total cellular RNA was harvested with Trizol (Invitrogen, Carlsbad, CA) and further purified with the RNeasy RNA purification kit (Qiagen, Valencia, CA) according to the manufacturers instructions. cDNA was generated using 25-40 ug total RNA as a template and primed with PolyT(V)N (4.0 ug) and random hexamers (1.0 ug, Amersham, UK).
|
| Label |
Cy3
|
| Label protocol |
cDNA was labeled with Cy5 or Cy3 dyes using the Cy-Scribe post-labeling kit (Amersham) as per the instructions.
|
| |
|
| Channel 2 |
| Source name |
Sessile serrated adenoma
|
| Organism |
Homo sapiens |
| Characteristics |
Polyp type: SSA Gender: Female Age:83
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total cellular RNA was harvested with Trizol (Invitrogen, Carlsbad, CA) and further purified with the RNeasy RNA purification kit (Qiagen, Valencia, CA) according to the manufacturers instructions. cDNA was generated using 25-40 ug total RNA as a template and primed with PolyT(V)N (4.0 ug) and random hexamers (1.0 ug, Amersham, UK).
|
| Label |
Cy5
|
| Label protocol |
cDNA was labeled with Cy5 or Cy3 dyes using the Cy-Scribe post-labeling kit (Amersham) as per the instructions.
|
| |
|
| |
| Hybridization protocol |
Labeled cDNA was hybridized to microarray slides printed with the CompuGen Human OligoLibrary (Compugen Human Oligo Library (v1) containing 18861 60-mer oligonucleotides, representing approximately 16,000 unique genes) by the Adelaide Microarray Centre (Australia).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 |
np.385.38
|
| Data processing |
Data analysis was performed in R (www.r-project.org) using the Limma package of Bioconductor (Gentleman, Carey et al. 2004; Smyth 2004). Loess print tip method was used to correct for dye-bias and intensity within each group of adjacent spots printed by one pin (Yang, Dudoit et al. 2002). Linear modelling was performed with the Limma package of Bioconductor (Smyth 2004).
|
| |
|
| Submission date |
Aug 21, 2008 |
| Last update date |
Aug 26, 2008 |
| Contact name |
maria caruso |
| E-mail(s) |
maria.caruso@imvs.sa.gov.au
|
| Organization name |
SA Pathology
|
| Street address |
Frome Road
|
| City |
Adelaide |
| State/province |
SA |
| ZIP/Postal code |
5000 |
| Country |
Australia |
| |
|
| Platform ID |
GPL5391 |
| Series (1) |
| GSE12514 |
Sessile serrated adenomas and conventional adenomas of the colon |
|
