|
| Status |
Public on Dec 24, 2022 |
| Title |
2015-B-12381 |
| Sample type |
RNA |
| |
|
| Source name |
TNBC sample
|
| Organism |
Homo sapiens |
| Characteristics |
gender: female
|
| Extracted molecule |
total RNA |
| Extraction protocol |
After tumour area selection, total RNA was isolated from macrodissected sections using the Agilent Absolutely RNA FFPE Kit; reverse-transcribed to corresponding cDNA and in vitro transcribed with the Sigma TransPlex Whole Transcriptome Amplification Kit.
|
| Label |
Cy3
|
| Label protocol |
cDNA was amplified and labelled with the Agilent SureTag DNA Labeling Kit.
|
| |
|
| Hybridization protocol |
Hybridisation was performed by means of the Agilent Gene Expression Hybridization Kit on whole genome SurePrint G3 Human GE 8x60K V3 microarrays containing probes for 26,803 coding RNAs and 30,606 lncRNAs; slides were washed using the Gene Expression Wash Buffer Kit.
|
| Scan protocol |
Slides were then scanned with the Agilent scanner version C. All protocols and kits were purchased from Agilent Technologies.
|
| Data processing |
After scanning, array image analysis was carried out using the Agilent Feature Extraction Software v12.1, and then raw expression data was processed by background subtraction (normexp offset = 50) followed by within and between array normalisation, using the LIMMA (LInear Models for Microarray Analysis) package in R software. This dataset contains log normalised intensities.
|
| |
|
| Submission date |
Jun 24, 2022 |
| Last update date |
Dec 24, 2022 |
| Contact name |
Paola Ostano |
| Organization name |
Fondazione Edo ed Elvo Tempia
|
| Street address |
via Malta 3
|
| City |
Biella |
| ZIP/Postal code |
13900 |
| Country |
Italy |
| |
|
| Platform ID |
GPL21185 |
| Series (1) |
| GSE206912 |
Identification of a minimum number of genes to predict triple negative breast cancer subgroups from gene expression profiles |
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