|
| Status |
Public on May 13, 2011 |
| Title |
Wild-type control 3 |
| Sample type |
RNA |
| |
|
| Source name |
WT_3
|
| Organism |
Mus musculus |
| Characteristics |
genotype: Wild-type
tissue: brain amygdala
genetic background: C57BL/6
|
| Growth protocol |
Experiments were performed on three-month old wild-type (C57BL/6) or neuropsin-/- mice backcrossed to C57BL/6 for 12 generations. Animals were housed three to five per cage in a colony room with a 12 hour light/dark cycle (lights on at 7AM) with ad libitum access to commercial chow and tap water. The experiments were approved by the UK Home Office and the UoL Ethical Committee.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Amygdalae tissue have been submerged in RNAlater solution (Qiagen) and stored at -20°C until RNA purification. Total RNA was extracted using RNeasy Lipid Tissue Mini Kit (Qiagen) as per manufacturer's instructions. The rybosomal fraction of RNA was significantly reduced with RiboMinus Kit (Invitrogen) and the RNA integrity has been verified by electrophoresis using Agilent Bioanalyser 2100.
|
| Label |
biotin
|
| Label protocol |
1 ug of total RNA was processed using a ribosomal RNA reduction step (RiboMinus Kit, Invitrogen) and labeled according to the Whole Transcriptome Sense Kit (Affymetrix).
|
| |
|
| Hybridization protocol |
Hybridization protocol 10 ug of fragmented cRNA was hybridized to each array for 17 hours at 45°C with rotation at 60rpm according to the Affymetrix standard protocol.
|
| Scan protocol |
Mouse Exon 1.0 ST Affymetrix arrays were scanned using the GeneChip Scanner 3000.
|
| Description |
RMA expression value derived from Expression Console software
|
| Data processing |
Microarray data were initially processed using GeneChip Operating Software. DTT data were transferred by Transfer Tool software (Affymetrix). Chip quality and raw microarray data pre-processing were performed according to the Affymetrix guidelines using Expression Console software. The following parameters were checked on the arrays: mean signal, mean background signal and comparison of signal values from the positive controls to the negative. After background subtraction, the data were processed using RMA (All: RMA-Sketch) method and quantile normalization.
|
| |
|
| Submission date |
Feb 04, 2011 |
| Last update date |
May 13, 2011 |
| Contact name |
Marcin Piechota |
| E-mail(s) |
marpiech@if-pan.krakow.pl
|
| Phone |
(+4812) 6623328
|
| Organization name |
Institute of Pharmacology PAS
|
| Department |
Molecular Neuropharmacology
|
| Street address |
Smetna 12
|
| City |
Krakow |
| ZIP/Postal code |
31-343 |
| Country |
Poland |
| |
|
| Platform ID |
GPL6193 |
| Series (1) |
| GSE27088 |
The comparison of gene expression profile in the amygdalae between the wild-type and neuropsin knock-out mice |
|
