|
| Status |
Public on Jul 07, 2011 |
| Title |
838T rep1 |
| Sample type |
RNA |
| |
|
| Source name |
xenograft tumor
|
| Organism |
Homo sapiens |
| Characteristics |
tumor id: 838T
tumor type: human breast tumor xenograft
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Invotrogen Trizol Reagent in accordance with the prescribed protocol provided with the kit. DNase treatment was performed using the QIAGEN RNase free DNase Set prior to RNA purification using the QIAGEN RNAeasy kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
|
| Label |
biotin
|
| Label protocol |
Human total RNA was quality ascertained using the Agilent Bioanalyser 2100 using the NanoChip protocol. A total of 500ng was labelled using the Ambion Total Prep RNA amplification kit (Cat. No. IL1791). The quantity of labelled product was ascertained using the Agilent Bioanalyser 2100 using the NanoChip protocol. A total of 750ng of labelled cRNA was then prepared for hybridisation to the Sentrix Human- HT12v4 Beadchip by preparing a probe cocktail (cRNA @ 0.05ug/ul) that includes GEX-HYB Hybridisation Buffer (supplied with the beadchip).
|
| |
|
| Hybridization protocol |
A total hybridisation volume of 15ul is prepared for each sample and 15ul loaded into a single array on the Sentrix Human-HT12v4 Beadchip. A total of 12 different labelled samples can be loaded into 12 individual arrays per beadchip. The chip is hybridised at 58C for 16 hours in an oven with a rocking platform. After hybridisation, the chip is washed using the appropriate protocols as outlined in the illumina manual. Upon completion of the washing, the chips are then coupled with Cy3 and scanned in the illumina BeadArray Reader.
|
| Scan protocol |
Arrays were scanned in the Illumina BeadArray Reader.
|
| Description |
838T replicate 1
|
| Data processing |
The scanner operating software, GenomeStudio, converts the signal on the array into a TXT file for analysis. The data were then calibrated and quantile normalized using the neqc method of Shi et al. (2010) [PMID:20929874]. This analysis was was carried out in R using the limma package.
|
| |
|
| Submission date |
Apr 12, 2011 |
| Last update date |
May 24, 2013 |
| Contact name |
Matthew Ritchie |
| E-mail(s) |
[email protected]
|
| Organization name |
The Walter and Eliza Hall Institute of Medical Research
|
| Department |
Epigenetics and Development Division
|
| Street address |
1G Royal Parade
|
| City |
Parkville |
| State/province |
Victoria |
| ZIP/Postal code |
3052 |
| Country |
Australia |
| |
|
| Platform ID |
GPL10558 |
| Series (1) |
| GSE28570 |
Characterization of human breast cancer xenografts |
|
| Relations |
| Reanalyzed by |
GSM1148256 |
