|
| Status |
Public on May 05, 2018 |
| Title |
Pnt RNAi rep1 |
| Sample type |
RNA |
| |
|
| Source name |
CNS tissue from nsybGal4/Pnt RNAi larvae
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: CNS tissue from nsybGal4/Pnt RNAi larvae
genotype/variation: nsybGal4/Pnt RNAi
|
| Treatment protocol |
One control and five experimental genotypes were used: Control (nsybGal4/+), Experimental group 1: TFAM3M (nsybGal4>UAS-TFAM3M), Experimental group 2: Pnt RNAi (nsybGal4>UAS-Pnt RNAi #JF02227), Experimental group 3: Aop RNAi (nsybGal4>UAS-Aop RNAi #3166R1), Experimental group 4: TFAM3M, Pnt RNAi (nsybGal4>UAS-TFAM3M, UAS-Pnt RNAi #JF02227), Experimental group 5: TFAM3M, Aop RNAi (nsybGal4>UAS-TFAM3M, UAS-Aop RNAi #3166R1).
|
| Growth protocol |
Larvae were grown on standard fly food at 25 degrees.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For the microarray analysis the complete CNS from 20 wandering third instar larvae were dissected in PBS and placed into PBS on ice and then transferred into 100ul of lysis buffer from the Absolutely RNA Microprep kit (Stratagene) and vortexed for 5 seconds. Total RNA was then prepared using this kit. For each genotype RNA samples were prepared in triplicate and stored at -80oC.
|
| Label |
biotin
|
| Label protocol |
10ng of RNA per genotype was converted into labelled cDNA with the Nugen Ovation V2 protocol (NuGEN Technologies Inc.)
|
| |
|
| Hybridization protocol |
7mg of labelled cDNA was hybridised to Affymetrix Drosophila genome v2 GeneChips
|
| Scan protocol |
Genechips were washed, stained (GeneChip® Fluidics Station 450) and scanned (GeneChip Scanner 3000 7G) according to manufacturer’s instructions (Nugen Technologies Inc & Affymetrix)
|
| Description |
Gene expression data from CNS with Pnt knock-down in neurons
|
| Data processing |
Data was processed using a MAS5.0 algorithm and analysed using the Transcriptome Analysis Console (ThermoFisher) using gene level differential expression analysis. Means were calculated using Tukey's Bi-weight average algorithm and differential expression between groups was calculated using un-paired one way one way analysis of variance (ANOVA). A statistical cutoff of p<0.05 was used and a fold change cutoff of ±1.5 fold were used.
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| |
|
| Submission date |
May 04, 2018 |
| Last update date |
May 05, 2018 |
| Contact name |
Joseph M. Bateman |
| E-mail(s) |
[email protected]
|
| Phone |
2078488144
|
| Organization name |
King's College London
|
| Street address |
Guy's campus
|
| City |
London |
| State/province |
(Click to Select US State) |
| ZIP/Postal code |
SE1 1UL |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL1322 |
| Series (1) |
| GSE114054 |
Drosophila CNS mitochondrial dysfunction with Ras/MAPK inhibition microarray |
|
