|
| Status |
Public on Feb 12, 2015 |
| Title |
NAC RNAi replicate 1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
cytosolic ribosomes
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: SS104, sterile mutant
age: day 3 adult
vector: NAC RNAi
|
| Treatment protocol |
RNAi was performed by feeding bacteria producing dsRNA, start of RNAi treatment was in the L2/L3 larval stage
|
| Growth protocol |
Worms were grown at 25°C (non-permissive temperature) in liquid culture
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with Qiagen RNeasy Mini Kit according to manufacturer's instructions
|
| Label |
cy3
|
| Label protocol |
50 ng RNA were labelled according to Oaklabs standard protocol
|
| |
|
| Channel 2 |
| Source name |
ER-attached ribosomes
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: SS104, sterile mutant
age: day 3 adult
vector: NAC RNAi
|
| Treatment protocol |
RNAi was performed by feeding bacteria producing dsRNA, start of RNAi treatment was in the L2/L3 larval stage
|
| Growth protocol |
Worms were grown at 25°C (non-permissive temperature) in liquid culture
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with Qiagen RNeasy Mini Kit according to manufacturer's instructions
|
| Label |
Cy5
|
| Label protocol |
50 ng RNA were labelled according to Oaklabs standard protocol
|
| |
|
| |
| Hybridization protocol |
hybridization was performed by Oaklabs according to their standard protocol
|
| Scan protocol |
scanning was performed by Oaklabs according to their standard protocol
|
| Description |
Biological replicate 1 of 4. NAC RNAi
|
| Data processing |
Create two files specifying what experimental samples are to be found in what data-file CYT refers to the measured cytosolic fraction, ER refers to the measured membrane-associated fraction (predominantly Endoplasmic Reticulum) Empty_vector (ev) is the control experiment, RNAi_vector (RNAi) is the experiments in which the genes of interest were knocked down by RNAi. Read the data into 'R' using read.maimages ('limma' package) commands: RAWev <- read.maimages(targetsev, path="./", source="agilent.median") RAWrnai <- read.maimages(targetsrnai, path="./", source="agilent.median"). Normalize this data within each array using the 'loess' normalization implemented in the 'limma' package commands: LOESSev <- normalizeWithinArrays(RAWev, method="loess") LOESSrnai <- normalizeWithinArrays(RAWrnai, method="loess"). Lastly write the data to the files 'MAev.Rfile' (normalized empty_vector experiment data) and 'MArnai.Rfile' (normalized RNAi-experiment data).
|
| |
|
| Submission date |
Dec 05, 2014 |
| Last update date |
Feb 12, 2015 |
| Contact name |
Tancred Frickey |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Konstanz
|
| Department |
Biology
|
| Lab |
Applied Bioinformatics
|
| Street address |
Universitaetsstr. 10
|
| City |
Konstanz |
| State/province |
BW |
| ZIP/Postal code |
78464 |
| Country |
Germany |
| |
|
| Platform ID |
GPL19516 |
| Series (1) |
| GSE63928 |
C. elegans (strain SS104, sterile mutant) Control vs. NAC RNAi |
|
