|
| Status |
Public on Aug 01, 2009 |
| Title |
72-21-BX3, non-BRCA1/2 mutation associated breast tissue |
| Sample type |
RNA |
| |
|
| Source name |
Mammary tissue
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Preneoplastic breast tissue
gender: female
mutation: non-BRCA1/2 mutation
hybridization date: 10-31-08
beadchip barcode: 4380071010
beadchip section: C
|
| Treatment protocol |
Not applicable
|
| Growth protocol |
Not applicable
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA from sorted cell populations were prepared with the RNeasy Micro kit (Qiagen). RNA quality was ascertained using the Agilent Bioanalyser 2100 with the NanoChip protocol.
|
| Label |
Cy3
|
| Label protocol |
We labeled up to 500 ng with the Total Prep RNA amplification kit (Ambion).
|
| |
|
| Hybridization protocol |
Labeled cRNA (1.5 μg) was prepared for hybridization to Illumina HumanWG-6 V3 (R1) BeadChips.
|
| Scan protocol |
After washing, we coupled the chips with Cy3 and scanned them in an Illumina BeadArray Reader.
|
| Description |
none
|
| Data processing |
Un-normalized summary probe profiles were output from BeadStudio and analysed used the lumi and limma packages of the Bioconductor open-source software project (http://www.bioconductor.org). The raw intensities were normexp background corrected with offset 16, quantile normalized, then log2-transformed.
|
| |
|
| Submission date |
Jul 13, 2009 |
| Last update date |
Jul 23, 2009 |
| Contact name |
Jane E Visvader |
| E-mail(s) |
visvader@wehi.edu.au
|
| Phone |
(+61 3) 93452494
|
| Fax |
(+61 3) 93470852
|
| Organization name |
The Walter and Eliza Hall Institute of Medical Research
|
| Department |
Victorian Breast Cancer Research Consortium
|
| Lab |
Lindeman/Visvader Lab
|
| Street address |
1G Royal Parade
|
| City |
Parkville |
| State/province |
Victoria |
| ZIP/Postal code |
3052 |
| Country |
Australia |
| |
|
| Platform ID |
GPL6884 |
| Series (1) |
| GSE17072 |
Normal human mammary tissues from BRCA1 mutation carriers, non-BRCA1/2 mutation carriers and normal women |
|
