Daniel:Notebook/RNAFISH/2014-7-11
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Probe Design
Probe List
Rui sent me a list of genes to design probes for. Here it is:
- GRIK4 Glutamate Receptor, IK-4
- GPC6 HS glypican -coreceptor for growth factors
- ERBB4 ERBB4
- GRIK1 Glutamate receptor, IK-1
- DNER Notch-like grow factor receptor
- DCC netrin 1 receptor
- POU6F2 POU TF
- FOXP2 TF
- GAD1 glutamate decarboxylase 1
- GAD2 glutamate decarboxylase 2
- CA10 carbonic anhydrase
Workflow
- Identify genomic coordinates using UCSC genome browser, hg38
- Download the CDS Exon sequence using the tables tab of the genome browser
- Run MATLAB script that outputs only the sequence can also trim the sequence to 8kbp (Stellaris maximum)
- Paste sequence into Stellaris website
- Currently using 25 probes per gene
- Copy/paste sequences into a .txt file