|
| Status |
Public on Feb 16, 2018 |
| Title |
OUH_miR_091 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Primary breast tumour of patient with relapse
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: primary breast tumour
gender: female
pair no.: 46
metastasis (1= yes; 0=no): 1
tumour type: IDC
esr1 expression (1=yes; 0=no): 1
lymph node status (1=positive; 0=negative): 0
status at last follow up (1=dead, 0=alive): 1
|
| Treatment protocol |
After surgical removal, tumor samples were snap-frozen and stored at -80°C.
|
| Growth protocol |
not applicable
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from tumor samples with Trizol (Invitrogen) and further purified with the RNeasy micro kit (Qiagen), including DNase treatment. NanoDrop Spectrophotometer (NanoDrop Technologies) was used for RNA quantification. The quality of extracted RNA was assessed with Bioanalyzer 2100 (Agilent Technologies) using the RNA 6000 Nano Kit (Agilent Technologies).
|
| Label |
Hy3
|
| Label protocol |
The miRCURY Power labeling kit (Exiqon), miRCURY LNA Array hybridization buffer (Exiqon) and miRCURY LNA Array Washing buffer kit (Exiqon) were used for sample labelling, hybridization and washing, respectively.
|
| |
|
| Channel 2 |
| Source name |
common reference pool of all samples
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: primary breast tumour
gender: female
|
| Treatment protocol |
After surgical removal, tumor samples were snap-frozen and stored at -80°C.
|
| Growth protocol |
not applicable
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from tumor samples with Trizol (Invitrogen) and further purified with the RNeasy micro kit (Qiagen), including DNase treatment. NanoDrop Spectrophotometer (NanoDrop Technologies) was used for RNA quantification. The quality of extracted RNA was assessed with Bioanalyzer 2100 (Agilent Technologies) using the RNA 6000 Nano Kit (Agilent Technologies).
|
| Label |
Hy5
|
| Label protocol |
The miRCURY Power labeling kit (Exiqon), miRCURY LNA Array hybridization buffer (Exiqon) and miRCURY LNA Array Washing buffer kit (Exiqon) were used for sample labelling, hybridization and washing, respectively.
|
| |
|
| |
| Hybridization protocol |
Hybridization, washing, and scanning (Agilent G2565CA Microarray scanner) were performed according to the recommendations provided by Exiqon.
|
| Scan protocol |
Scanned images were imported into GenePixPro6.0 software (Molecular Devices) for quality control and raw data extraction.
|
| Description |
Total RNA extracted from fresh frozen primary breast tumour of a female patient with relapse
|
| Data processing |
Signals from 3 spots were compiled, only human microRNAs were selected, the R-package limma was used for LOESS normalization and quantile normalization of raw signal intensities, and the ComBat function embedded in the sva R-package was used for adjustment of the normalized intensities and to eliminate potential batch effects
|
| |
|
| Submission date |
Aug 28, 2017 |
| Last update date |
Jan 29, 2019 |
| Contact name |
Ines Block |
| Organization name |
Odense University Hospital
|
| Department |
Department of Clinical Genetics
|
| Street address |
J.B. Winsløws Vej 4
|
| City |
Odense |
| ZIP/Postal code |
5000 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL23960 |
| Series (1) |
| GSE103161 |
MicroRNA profiles of 110 primary breast cancer tumors of systemically untreated, lymph node negative and estrogen receptor positive patients |
|
