Microarray
From Wikionchus
Microarrays for gene expression profiling in Pristionchus pacificus.
Contents |
Designing Microarrays
Building Transcriptome
- Input 1: A gff file containing all the gene predictions
- Input 2: A gff file conatining all the ESTs (Sanger, 454 etc)
- Input 3: The fasta file for the supercontigs.
- Do: For each gene prediction, find all the overlapping ESTs. If one or more than one EST found, replace gene prediction gff lines with those of the ESTs. This will generate a new gff file.
- Based on this new gff, get fasta seuences of each transcritp from the supercontigs.fasta.
Designing probes for each transcript in the transcriptome
- This can be done by submitting the transcriptome to either Agilent's eArray tool [1] OR using the more customizable application Oligowiz. We prefer to use Oligowiz. For more details see the reference [2] and the OligoWiz homepage [3].
- Submit the final fasta to Oligowiz program. See specific commands at [4] and an example here: Oligowiz Commands.
Microarray manufacture : eArray
- Once all the probes have been designed using Oligowiz, upload them to Agilent's eArray website [5], and create a microarray design.
- Submit the microarray design for manufacture. Place an order. Wait 4-5 weeks!
Links
- Back to Pristionchus pacificus Protocols page.
External Links
- Agilent's Two-Color Microarray-Based Gene Expression (Quick Amp Labeling)Protocol: http://www.chem.agilent.com/en-US/Search/Library/_layouts/Agilent/PublicationSummary.aspx?whid=48835&liid=3785
- OligoWiz homepage: http://www.cbs.dtu.dk/services/OligoWiz/
- Agilent eArray website: https://earray.chem.agilent.com/earray/
