Daniel:Notebook/RNAFISH/2014-7-11: Difference between revisions
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>Djacobse (Created page with "=Probe Design= Back to Calendar ==Probe List== Rui sent me a list of genes to design probes for. Here it is: *GRIK4 Glutamate Recep...") |
>Djacobse No edit summary |
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*GAD2 glutamate decarboxylase 2 | *GAD2 glutamate decarboxylase 2 | ||
*CA10 carbonic anhydrase | *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) | |||
##[[Media:Geneseq_to_txt.txt|MATLAB script]] | |||
#Paste sequence into Stellaris website | |||
##Currently using 25 probes per gene | |||
#Copy/paste sequences into a .txt file |
Revision as of 19:34, 11 July 2014
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