|
| Status |
Public on Aug 19, 2021 |
| Title |
liver_C_ULST_2 [1_Exiqon_19713595] |
| Sample type |
RNA |
| |
|
| Source name |
liver, late stage, group C
|
| Organism |
Mus musculus |
| Characteristics |
strain background: FVBn
genotype/variation: double transgenic LAP-Tta/TRE-c-MYC (LT2/MYC: conditional doxycycline-regulatable transgenic c-Myc driven mouse model of liver cancer)
Sex: Male
tumor stage: late stage_developing
tissue: Liver
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extraccted from liver or liver tumor tissues, as per the group. Quality was subsequently assessed on an Agilent 2100 Bioanalyzer.
|
| Label |
miRCURY LNATM microRNA Hi-Power Labeling Kit, Hy3TM/Hy5TM
|
| Label protocol |
700 ng total RNA from sample and reference was labeled with Hy3TM and Hy5TM fluorescent label, respectively, using the miRCURY LNATM microRNA Hi-Power Labeling Kit, Hy3TM/Hy5TM (Exiqon, Denmark) following the procedure described by the manufacturer.
|
| |
|
| Hybridization protocol |
The Hy3TM-labeled samples and a Hy5TM-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY LNATM microRNA Array 7'th (Exiqon, Denmark), which contains capture probes targeting all microRNAs for human, mouse or rat registered in the miRBASE 18.0. The hybridization was performed according to the miRCURY LNATM microRNA Array Instruction manual using a Tecan HS4800TM hybridization station (Tecan, Austria).
|
| Scan protocol |
Slides were scanned and stored in an ozone free environment (ozone level below 2.0 ppb) in order to prevent potential bleaching of the fluorescent dyes. The miRCURY LNATM microRNA Array slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and the image analysis was carried out using the ImaGene 9.0 software (BioDiscovery, Inc., USA).
|
| Data processing |
The quantified signals were background corrected (Normexp with offset value 10, see Ritchie et al. 2007) and normalized using quantile normalization method, which we have found produces the best between-slide normalization to minimize the intensity-dependent differences between the samples.
|
| |
|
| Submission date |
Jun 21, 2020 |
| Last update date |
Aug 19, 2021 |
| Contact name |
Asha Balakrishnan |
| E-mail(s) |
balakrishnan.asha@mh-hannover.de
|
| Organization name |
Hannover Medical School (MHH)
|
| Department |
Gastroenterology, Hepatology, and Endocrinology
|
| Street address |
carl neuberg str. 1
|
| City |
Hannover |
| State/province |
Lower saxony |
| ZIP/Postal code |
30625 |
| Country |
Germany |
| |
|
| Platform ID |
GPL19715 |
| Series (1) |
| GSE152920 |
MicroRNA expression profiling of livers from the conditional doxycyline-regulatable c-Myc-driven liver tumor mouse model during tumor development and regression. |
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