|
| Status |
Public on Aug 30, 2018 |
| Title |
SAMPLE 84: Patient3.Pre_Replicate2 |
| Sample type |
RNA |
| |
|
| Source name |
Breast tumour
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Breast tumour
gender: Female
her2_status: HER2+
er_status: ER+
pr_status: PR-
pakt_response: Non-Responder_pAKT
changeki67: 1.40283096059537
ki67_response: Non-Responder_Ki67
|
| Treatment protocol |
Women recruited were to receive 5 mg of everolimus pre-operative treatment daily for 14 days prior to primary surgery
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Paired biopsies were taken at diagnosis and at surgery; half of the tissue was immediately frozen in liquid nitrogen and stored at −196°C. Frozen sections were removed, sectioned and stained with haematoxylin and eosin to assess tumour content. Approximately 100-mg tissue from pre- and post-treatment biopsies from 27 patients who completed everolimus treatment were placed in RNAlater® ICE (Ambion, Warrington, United Kingdom) overnight at −20°C prior to RNA extraction using the RNeasy Mini Kit, including RNase-Free DNase treatment (Qiagen, Crawley, United Kingdom). Aliquots of RNA were analysed by electrophoresis and quantified on a Bioanalyser 2100 (G2938c, Agilent Technologies, Stockport, United Kingdom).
|
| Label |
biotin
|
| Label protocol |
100-ng RNA per patient was amplified and biotinylated using Illumina® TotalPrep RNA Amplification Kit (Ambion) and quantified on a Bioanalyser 2100.
|
| |
|
| Hybridization protocol |
Standard Illumina hybridization protocol
|
| Scan protocol |
Standard Illumina scanning protocol
|
| Description |
ChipNumber: Chip11
Batch number: 4
OriginalSampleNumbers: 34
|
| Data processing |
The data were normalised using quantile normalisation using the Beadarray package
|
| |
|
| Submission date |
Aug 30, 2018 |
| Last update date |
Aug 30, 2018 |
| Contact name |
Andrew H Sims |
| E-mail(s) |
andrew.sims@ed.ac.uk
|
| Organization name |
University of Edinburgh
|
| Department |
Institute of Genetics and Molecular Medicine
|
| Lab |
Applied Bioinformatics of Cancer
|
| Street address |
Systems Medicine Building
|
| City |
Carrington Crescent |
| State/province |
Edinburgh |
| ZIP/Postal code |
EH4 2XR |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL6104 |
| Series (1) |
| GSE119262 |
Gene expression profiling of pre-operative mTOR inhibitor everolimus treatment in breast cancer |
|
