|
| Status |
Public on Oct 19, 2023 |
| Title |
P4_(miRNA-4_0) |
| Sample type |
RNA |
| |
|
| Source name |
Borderline mucinous tumors
|
| Organism |
Homo sapiens |
| Characteristics |
gender: female
|
| Treatment protocol |
none
|
| Growth protocol |
none
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA from FFPE sample was extracted using Nucleospin® total RNA FFPE Kit (Ma-cherey-Nagel, Hoert, France). We estimated the amount of tissue of FFPE nodes according to their surface (R*r*π) and the equivalence provided by the fabricant: 1 slice of 10µm thick and 1cm² equates 1mg of material. We calculated the numbers of 20µm thick slice necessary to obtain 17-19mg of material from each node. Slices were cut by microtome and the excess of paraffin was removed with a scalpel. According to the manufacturer’s protocol, the slices were incubated 5 minutes at 56°C in paraffin dissolver provided in the kit. The deparaffined samples were next incubated with proteinase K for 3 hours at 56°C to digest the fixed tissue, release acid nucleic acids and remove the crosslinks. Optimal binding conditions for small RNA were adjusted and the lysate was applied to Nucleo-spin® RNA column. Finally, the RNA was purified by washing steps and eluted. The quantification of total RNA was assessed using Nanodrop 2000 (Thermo Scientific, Les Ulis, France). One of malignant tumor was excluded due to its low amount of RNA, which was insufficient for further analyses
|
| Label |
biotin
|
| Label protocol |
Microarrays were processed according to manufacturer’s recommendations. For each sample, 200 ng of RNAs were labeled with FlashTag Biotin HSR RNA Labeling Kit (Genisphere Affymetrix UK Ltd, High Wycombe, United Kingdom).
|
| |
|
| Hybridization protocol |
Samples were hybridized for 16 h at 48°C on GeneChip microRNA 4.0 Array (Affymetrix)
|
| Scan protocol |
arrays were scanned with a GC30007G scanner (Affymetrix)
|
| Description |
Gene expression data from Borderline mucinous tumors
|
| Data processing |
Raw data were normalized using the Expression Console (Affymetrix) with the RMA method, algorithmically based on microarrays spike-in.
|
| |
|
| Submission date |
Oct 18, 2023 |
| Last update date |
Oct 19, 2023 |
| Contact name |
frédéric leprêtre |
| E-mail(s) |
frederic.lepretre@univ-lille.fr
|
| Organization name |
Lille University
|
| Department |
CHU of Lille, CBP
|
| Lab |
plateforme de génomique fonctionnelle et structurale
|
| Street address |
Boulevard du Pr Leclercq
|
| City |
lille |
| ZIP/Postal code |
59037 |
| Country |
France |
| |
|
| Platform ID |
GPL19117 |
| Series (1) |
| GSE245725 |
Double ratio of microRNA signatures as promising diagnosis biomarkers for mucinous borderline and malignant ovarian tumors |
|
