|
| Status |
Public on Apr 01, 2021 |
| Title |
breast tumour 133C |
| Sample type |
RNA |
| |
|
| Source name |
breast tumour
|
| Organism |
Homo sapiens |
| Characteristics |
Sex: female
timepoint: 16 weeks
tissue: breast tumor
patient: IRSS133
age: 92
size: 3.3
grade: 2
nodal status: N0
her2 status: 0
pgr status pre_treatment: 1
response: Partial/Complete Response
|
| Extracted molecule |
total RNA |
| Extraction protocol |
mRNA from tumour biopsies taken 16 weeks after commencement of anastrazole treatement were extracted with an RNeasy Mini Kit (Qiagen), as per the manufacturer's instructions, and quantification performed using the Agilent 2100 Bioanalyzer (Santa Clara, CA, USA).
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays
|
| |
|
| Hybridization protocol |
Standard Illumina hybridization protocol
|
| Scan protocol |
Standard Illumina scanning protocol of iScan
|
| Description |
133C
|
| Data processing |
The data was filtered to remove any non-expressed probes using the detection p-value from Illumina. Across all samples probes for which the intensity values were not significantly different (p>0.01) from the negative controls were removed from the analysis. Following filtering the data was transformed and normalized using variance-stabilizing transformation and robust spline normalization (RSN) method in the lumi package in R. The RSN combines the features of quantile and loess normalization.
|
| |
|
| Submission date |
Nov 19, 2020 |
| Last update date |
Apr 01, 2021 |
| Contact name |
Anita Dunbier |
| E-mail(s) |
anita.dunbier@otago.ac.nz
|
| Organization name |
University of Otago
|
| Department |
Biochemistry
|
| Lab |
Anita Dunbier
|
| Street address |
710 Cumberland Street
|
| City |
Dunedin |
| State/province |
... |
| ZIP/Postal code |
9076 |
| Country |
New Zealand |
| |
|
| Platform ID |
GPL13376 |
| Series (1) |
| GSE161830 |
Molecular profiling of 16 week aromatase inhibitor-treated post-menopausal breast tumors |
|
