|
| Status |
Public on Jun 20, 2015 |
| Title |
Organotypic slices shRNF10 rep_1 |
| Sample type |
RNA |
| |
|
| Source name |
organotypic slices
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague-Dawley
tissue: organotypic hippocampal slice
age: grown for 14 days in vitro (DIV)
infection: shRNF10 at DIV3
|
| Treatment protocol |
Not applicable
|
| Growth protocol |
Hippocampal organotypic sliceswere prepared from P8 rat pups and grown for 14 days in vitro (DIV). Lentivirus infection was performed at DIV3.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Organotypic slices from both groups were manually identified as shRNF10 or scramble. Organotypic slices were freshly lyseted. Total RNA was obtained with trizol and nucleospin method
|
| Label |
Biotin
|
| Label protocol |
Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)
|
| |
|
| Hybridization protocol |
Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001
|
| Scan protocol |
Affymetrix Gene ChIP Scanner 3000 7G
|
| Description |
Organotypic hippocampal slices lentivirally infected with shRNF10
Sh_01
|
| Data processing |
Data handling was mainly done using TAC and Partek Genomic Suite software. The Robust MultichipAverage (RMA) method was employed to calculate probe set intensity. RMA is a robustmulti-chip average expression method that estimates the probe-level data from a set of chips:the perfect-match (PM) values are background-corrected, normalized and finally summarizedresulting in a set of expression measures.The identification of differentially expressed genes was addressed using FoldChange (FC) and ANOVA. For each experimental condition the probesets whose fold change are higher or equalthan 1.5 with an ANOVA unadjusted p-value lower than 0,05 are selected as significantlymodulated.
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| |
|
| Submission date |
May 27, 2015 |
| Last update date |
Jun 20, 2015 |
| Contact name |
Nico Mitro |
| E-mail(s) |
nico.mitro@unimi.it
|
| Phone |
00390250318344
|
| Organization name |
Università degli studi di Milano
|
| Department |
Pharmacological and biomolecular sciences
|
| Street address |
Via Balzaretti 9
|
| City |
Milan |
| State/province |
MI |
| ZIP/Postal code |
20133 |
| Country |
Italy |
| |
|
| Platform ID |
GPL11534 |
| Series (1) |
| GSE69267 |
Expression data from rat organotypic hippocampal slices lentivirally infected with shRNF10 or scramble construct |
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