|
| Status |
Public on Apr 29, 2018 |
| Title |
PNET_p53_Rb_rep2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
AdCre-induced PNET, Rb/p53 background
|
| Organism |
Mus musculus |
| Characteristics |
tissue: PNET
developmental stage: young adult mouse
background strain: C57 BL/6 and FVB mixed background
genotype: p53/Rb codeletion
|
| Treatment protocol |
Combinations of the conditional konck-out RbLoxP/LoxP, p53LoxP/LoxP,and PtenLoxP/LoxP,all in a ROSA26loxP/loxP background was achieved using adenovirus expressing Cre recombinase. The injection of adenovirus in relation to bregma was anterior 0mm; lateral 0.5mm and ventral 2.5mm. Injections were administered with a Hamilton syringe 1701RN and 26G needle.
|
| Growth protocol |
The total RNA in this study is directly extracted from frozen tumour tissue. Tumours were directly dissected from fresh brain. Before RNA extraction, the samples were stored in -80°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA used for microarray was extracted from frozen tumours using TRIzol method.
|
| Label |
Hy3
|
| Label protocol |
MiRNAs from 600ng of total RNA were labelled with Hy3 or Hy5 fluorophores according to manufacturer’s protocol (miRCURY LNA microRNA Hi-Power Labelling kit, Exiqon) by Exiqon company
|
| |
|
| Channel 2 |
| Source name |
Reference RNA
|
| Organism |
Mus musculus |
| Characteristics |
sample type: a pool of RNA consisting of equal amounts of each individual sample in this study
|
| Treatment protocol |
Combinations of the conditional konck-out RbLoxP/LoxP, p53LoxP/LoxP,and PtenLoxP/LoxP,all in a ROSA26loxP/loxP background was achieved using adenovirus expressing Cre recombinase. The injection of adenovirus in relation to bregma was anterior 0mm; lateral 0.5mm and ventral 2.5mm. Injections were administered with a Hamilton syringe 1701RN and 26G needle.
|
| Growth protocol |
The total RNA in this study is directly extracted from frozen tumour tissue. Tumours were directly dissected from fresh brain. Before RNA extraction, the samples were stored in -80°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA used for microarray was extracted from frozen tumours using TRIzol method.
|
| Label |
Hy5
|
| Label protocol |
MiRNAs from 600ng of total RNA were labelled with Hy3 or Hy5 fluorophores according to manufacturer’s protocol (miRCURY LNA microRNA Hi-Power Labelling kit, Exiqon) by Exiqon company
|
| |
|
| |
| Hybridization protocol |
Pair-wise RNA samples labelled with Hy3 or Hy5 dye were hybridized to the miRCURY LNA microRNA Array 7 (Exiqon), 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 LNA™ microRNA Array Instruction manual using a Tecan HS4800 hybridization station (Tecan, Austria).
|
| Scan protocol |
Microarray slides were scanned using Agilent G2565BA Microarray Scanner System (Agilent Technologies, USA).
|
| Description |
Sample name: PNET2893
|
| Data processing |
Images were quantified using ImaGene 9 (Exiqon, Denmark). The quantified signals were background corrected (Normexp with offset value 10, see Ritchie et al. 2007) and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm. The file normalized_data.txt contains the normalized log2 ratio (Hy3/Hy5) representing test/reference. The gal file "lot35016-35016_mmu-and-related-vira_from_mb200.gal" contains the miRNA IDs for each probe number.
|
| |
|
| Submission date |
Jun 15, 2017 |
| Last update date |
Apr 29, 2018 |
| Contact name |
Sebastian Brandner |
| E-mail(s) |
s.brandner@ucl.ac.uk
|
| Organization name |
University College London
|
| Department |
Institute of Neurology
|
| Street address |
Queen square house, UCL Institute of Neurology
|
| City |
London |
| State/province |
State... |
| ZIP/Postal code |
WC1N 3BG |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL17107 |
| Series (1) |
| GSE100065 |
The differential expression of miRNA between murine glioma and PNET |
|
