|
Status |
Public on Aug 30, 2018 |
Title |
SAMPLE 72: Patient25.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: -4.35596746188494 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: Chip8 Batch number: 3 OriginalSampleNumbers: 22
|
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 |
|