|
| Status |
Public on Dec 31, 2013 |
| Title |
7420028_AOM d15 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Universal Reference (Miltenyi Biotec GmbH)
|
| Organism |
synthetic construct |
| Characteristics |
reference: syntethic miRNA pool of 954 synthetic miRNAs in equimolar concentrations from human, mouse, rat, and virus
|
| Treatment protocol |
AOM 12 mg/kg in PBS, one intraperitoneal injection at day 1. DSS 2% in drinkable water, 3 cycles administration of 5 days followed by 16 days recovery. Fisrt day of first DSS cycle at day 7.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA were extracted from the whole colon with 8 mL Tripur according to the manufacturer's instructions.
|
| Label |
Hy3
|
| Label protocol |
2 µg of respective total RNA as well as 2 fmol of the Universal Reference (Miltenyi Biotec GmbH) were each mixed with 2.5 fmol of each of 18 RNA oligonucleotides reverse complement to miRControl 3 probes and subsequently fluorescently labeled using a commercial kit (miRCury™ LNA microRNA Array Power labeling kit, Exiqon) following the instructions of the manufacturer. The total RNA and Universal Reference mix was hybridized in a dual colour approach to miRXplore™ microarrays (Miltenyi Biotec GmbH).
|
| |
|
| Channel 2 |
| Source name |
AOM d15
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57bl6
tissue: Whole colonic tissue
treatment: AOM treated-mice for 15 days
|
| Treatment protocol |
AOM 12 mg/kg in PBS, one intraperitoneal injection at day 1. DSS 2% in drinkable water, 3 cycles administration of 5 days followed by 16 days recovery. Fisrt day of first DSS cycle at day 7.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA were extracted from the whole colon with 8 mL Tripur according to the manufacturer's instructions.
|
| Label |
Hy5
|
| Label protocol |
2 µg of respective total RNA as well as 2 fmol of the Universal Reference (Miltenyi Biotec GmbH) were each mixed with 2.5 fmol of each of 18 RNA oligonucleotides reverse complement to miRControl 3 probes and subsequently fluorescently labeled using a commercial kit (miRCury™ LNA microRNA Array Power labeling kit, Exiqon) following the instructions of the manufacturer. The total RNA and Universal Reference mix was hybridized in a dual colour approach to miRXplore™ microarrays (Miltenyi Biotec GmbH).
|
| |
|
| |
| Hybridization protocol |
Hy3 and Hy5 labeled (sample_ch1 and sample_ch2) RNA were combined and hybridized overnight to miRXplore™ microarrays (Miltenyi Biotec GmbH) using the a-Hyb™ Hybridization Station (Miltenyi Biotec)
|
| Scan protocol |
Image capture and signal quantification of hybridized miRXplore™ microarrays microarrays were done with the Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA) and ImaGene software Version 8.0.1 (BioDiscovery, Los Angeles, CA, USA).
|
| Description |
0007420028_raw
biological replicate 4 of 5. First point of 2 time points
|
| Data processing |
Signal quantification was done using ImaGene software version 8.0.1 (BioDiscovery, Los Angeles, MA). Median normalization was performed using the calibration oligos
|
| |
|
| Submission date |
Jun 04, 2012 |
| Last update date |
Dec 31, 2013 |
| Contact name |
Claire Josse |
| E-mail(s) |
[email protected]
|
| Phone |
+32 4 366 25 74
|
| Organization name |
CHU Liege
|
| Department |
Medical Oncology
|
| Lab |
Human Genetics
|
| Street address |
rue de l'hopital, 1
|
| City |
Liège |
| State/province |
Liège |
| ZIP/Postal code |
4000 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL15644 |
| Series (1) |
| GSE38443 |
Identification of microRNA landscape of inflammation-induced colorectal carcinogenesis |
|
