|
| Status |
Public on Apr 04, 2022 |
| Title |
metastasis, sample 8 |
| Sample type |
RNA |
| |
|
| Source name |
metastasis, left adrenal gland
|
| Organism |
Homo sapiens |
| Characteristics |
type: tumor tissue
site: tumor tissue
organ: adrenal gland
side: left
|
| Treatment protocol |
no treatment was induced
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from biological samples using AllPrep DNA/RNA Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions with a maximum of 30 mg frozen tissue.
|
| Label |
biotin
|
| Label protocol |
Tissues were homogenized in RLT buffer using TissueLyser (Qiagen) followed by passing the lysate through a blunt 23-gauge. Genomic DNA purification and RNA isolation were performed according to the manufacturer's instructions. DNase digestion done also for RNA and integrity was checked using RNA 6000 NanoChips with the Agilent 2100 Bioanalyzer (Agilent, Diegem, Belgium). Only RNA preparations with a RNA integrity number (RIN) >6.9 were considered for further microarray analysis.
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| |
|
| Hybridization protocol |
Total RNA samples were hybridized to Human Transcriptome Array 2.0 GeneChips as recommended by the manufacturer (Affymetrix, Santa Clara, USA). Sample processing, labeling and hybridization were performed using the GeneChip WT PLUS Reagent Kit and the GeneChip Hybridization/Wash/Stain Kit, according to the manufacturer's guidelines (ThermoFischer Scientific). Scanning and data extraction of the microarray were followed by the transformation of fluorescence data into CEL files employing the Affymetrix GeneChip Command Console (AGCC) software.
|
| Scan protocol |
The resulting CEL files were processed using the oligo package available performed in R/Bioconductor (3). The SCAN.UPC package were then employed for data normalization and background correction using the BRAINARRAY custom CDF file for directly mapping Affymetrix probe to Entrez gene identifiers (hta20_Hs_ENTREZG version 21.0.0) (4). The signal distribution was further quality controlled by box plots as implemented in R (Fig. S1, panel B ).
|
| Description |
Gene expression data from a metastasis of the left adrenal gland
|
| Data processing |
the statistical filtration of the genes differentially expressed (DE) among the three sample classes (C1-C3) was performed using AMEN (7) (Table S2, Fig. S2, panel B). Briefly, we first filtered genes with at least one signal above the background expression cutoff (BEC = 0.189, corresponding to the overall median intensity) and with a minimal fold change of 1.5 across sample classes. Finally, a statistical test implemented in the LIMMA package (F-value adjusted with the false discovery rate method: P ≤ 0.05) was used to identify significantly DE genes across sample classes (8). The resulting genes were then partitioned into three gene expression clusters (named G1 to G3) using the k-means method (k = 3) implemented in R.
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| |
|
| Submission date |
Apr 16, 2018 |
| Last update date |
Apr 05, 2022 |
| Contact name |
Frédéric Chalmel |
| E-mail(s) |
frederic.chalmel@inserm.fr
|
| Organization name |
Inserm U1085-Irset
|
| Department |
Physiology and physiopathology of the urogenital tract
|
| Street address |
9 avenue du Pr. Léon Bernard
|
| City |
Rennes |
| State/province |
France |
| ZIP/Postal code |
35000 |
| Country |
France |
| |
|
| Platform ID |
GPL24299 |
| Series (2) |
| GSE113204 |
A complex seeding of multiple metastases in clear cell renal cell carcinoma (expression) |
| GSE113206 |
A complex seeding of multiple metastases in clear cell renal cell carcinoma |
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