|
| Status |
Public on Aug 15, 2007 |
| Title |
YBp2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
YB mammary tumor. Strain YB, Gender: female, Age:..., Tissue: breast tumor
|
| Organism |
Mus musculus |
| Characteristics |
YBp2
|
| Treatment protocol |
Tumours were flash frozen in liquid nitrogen and stored in liqiud nitrogen until further use.
|
| Growth protocol |
Mammary tumours and lung tissue were harvested from mice that were tumour-bearing for 6 weeks.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from 10 individual flash frozen mammary tumour samples derived from our MMTV/neundl-NYPD, -YB, -YC, -YD, -YE and the parental MMTV/neu NDL2-5 strains using the RNeasy Midi Kit (QIAGEN, Valencia, CA). RNA quantity and quality was determined using a spectrophotometer (Nanodrop), the BioAnalyzer 2100 and the RNA 6000 Pico Assay Kit (Agilent Technologies, Palo Alto, CA). Two RNA pools, containing equal amount of total RNA from five individual tumours, were generated from each strain and functioned as a biological repeat. Five hundred nanograms of total RNA from each pool was subjected to one round of T7 linear amplification using the Amino Allyl MessageAmpTM aRNA Kit (Ambion, Austin, Texas)
|
| Label |
Cy3 or Cy5
|
| Label protocol |
Ten micrograms of the resulting aRNA was labelled with Cy3 and Cy5 dyes (CyTMPost-labelling Reactive Dye Pack; Amersham Biosciences, UK)
|
| |
|
| Channel 2 |
| Source name |
Universal Mouse Reference RNA (Stratagene).
|
| Organism |
Mus musculus |
| Characteristics |
Reference
|
| Treatment protocol |
Tumours were flash frozen in liquid nitrogen and stored in liqiud nitrogen until further use.
|
| Growth protocol |
Mammary tumours and lung tissue were harvested from mice that were tumour-bearing for 6 weeks.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from 10 individual flash frozen mammary tumour samples derived from our MMTV/neundl-NYPD, -YB, -YC, -YD, -YE and the parental MMTV/neu NDL2-5 strains using the RNeasy Midi Kit (QIAGEN, Valencia, CA). RNA quantity and quality was determined using a spectrophotometer (Nanodrop), the BioAnalyzer 2100 and the RNA 6000 Pico Assay Kit (Agilent Technologies, Palo Alto, CA). Two RNA pools, containing equal amount of total RNA from five individual tumours, were generated from each strain and functioned as a biological repeat. Five hundred nanograms of total RNA from each pool was subjected to one round of T7 linear amplification using the Amino Allyl MessageAmpTM aRNA Kit (Ambion, Austin, Texas)
|
| Label |
Cy3 or Cy5
|
| Label protocol |
Ten micrograms of the resulting aRNA was labelled with Cy3 and Cy5 dyes (CyTMPost-labelling Reactive Dye Pack; Amersham Biosciences, UK)
|
| |
|
| |
| Hybridization protocol |
Seven hundred fifty nanograms of labelled aRNA was hybridized onto Agilent Whole Mouse Genome Oligo Microarray Kit (G4122A; 44K) using the Agilent In situ Hybridization Plus Kit Large for 17 hrs at 65°C (Agilent Technologies). Microarrays were washed according to the manufacturer’s protocol (Agilent microarray processing protocol)
|
| Scan protocol |
Microarray slides were scanned using a Microarray Scanner (Model G2565BA, Agilent Technologies) at 10 µm resolution according to the manufacturer’s protocol (manual ID #G4140- 90030).
|
| Description |
YBp2
|
| Data processing |
Data from dyeswap hybridizations were condensed as part of the data processing strategy. Raw feature intensities were background corrected using the RMA background correction algorithm. The resulting expression estimates were converted to log2-ratios. Within array normalization was performed using 2D loess correction and intensity dependent loess correction of log-ratios. The resulting data set was scale-normalized using Linear Models for Microarray Analysis (LIMMA) package from BioConductor (version 1.8) and R (version 2.3.0).
|
| |
|
| Submission date |
Apr 24, 2007 |
| Last update date |
Jul 05, 2007 |
| Contact name |
Daniela Cernea |
| E-mail(s) |
danacery@gmail.com
|
| Organization name |
McGill
|
| Department |
Computer Science
|
| Lab |
McGill Centre for Bioinformatics
|
| Street address |
3775 University Street, Room 332
|
| City |
Montreal |
| State/province |
Quebec |
| ZIP/Postal code |
H3A 2B4 |
| Country |
Canada |
| |
|
| Platform ID |
GPL2872 |
| Series (1) |
| GSE7595 |
Distinct ErbB-2-coupled signalling pathways promote mammary tumors with unique pathological and transcriptional profiles |
|
