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====Probe design==== *Strategy: Experimentally evaluate the capture efficiencies of 6,500 probes(or 13,000, depending on the minimal order allowed by Agilent), and pick the best ones. *Choice of genes: #Variable expression among different brain regions and cell types (based on published [http://www.nature.com/nature/journal/v489/n7416/full/nature11405.html ABI Brain Atlas data]). #Moderate abundance (too low: difficult to detect; too high: rolonies too crowded and difficult to resolve optically). #Avoid alternatively spliced exons. #Prioritizing genes used in [http://www.sciencedirect.com/science/article/pii/S0092867412003480 ABI ISH mapping]: Disease genes (383); Human cortical marker genes (167, 55 overlapped with disease genes). *Considerations: #Targeting RNA versus cDNA (RNA: one fewer step, more specific, efficiency could depends on secondary structure; DNA: one more step, can be immobilized, secondary structure could be less a problem); #Targeting nuclear transcripts versus cytoplasmic transcripts (space available for imaging, integration with single-cell toto-RNAseq data), nucleus versus cytoplasmic transcripts (based on the [http://www.nature.com/nature/journal/v489/n7414/full/nature11233.html ENCODE RNAseq paper]). #Targeting 3'-ends or random positions (affects how cDNAs are generated, poly-T primed or N6/9 primed); #Gap versus no gap (Specificity versus sensitivity); #Targeting single exons or across splice junctions (mature transcripts versus nascent transcripts or gDNA); *Constrains: #We can get only up to 240bp oligos from Agilent for now. #A minimal list of features on the probes: ##Amplification adaptors (36-44bp, depending on the probe prep protocol). ##Common linker (48bp for our standard linker sequence, need to be reduced significantly, which is fine since we will be doing RCA instead of PCR and only a short annealing region is enough) ##Decoding region (6x20bp=120bp) ##Capturing arms (40-50bp, need to set an upper limit) *First round probe design. **A list of [[Media:Gene-selection-top5k.xlsx|5333 genes]] were generated by Dr. Yun Zhu from Wei Wang's group based on the following criteria: ***Genes that show variable expression in the brain (based on PMID: 22996553). ***Genes included in the [http://www.cell.com/retrieve/pii/S0092867412003480 ABI's ISH data]. ***Genes present in both cytosol and nucleus (based on the [http://www.nature.com/nature/journal/v489/n7414/full/nature11233.htm ENCODE RNAseq paper]). **Matt selected up to 5 candidate regions per gene for probe design. One set of probes was designed with a gap size of 20bp. A second set has no gap. ***[[Media:outputFile_20gap.txt|Raw probe sequences (20bp gaps)]]. ***[[Media:outputFile_0gap.txt|Raw probe sequences (0bp gaps)]]. **I wrote [[Media:filter_probes.txt|a script]] to filter the probes to keep: ***Up to 5 probes per gene. ***All genes with names like "LOCxxxx" or "CxxOrfxxxx" are excluded because they are poorly annotated. **I then double-checked these probes by mapping to the human genome and reference mRNA sequences using NovoAlign. All probes that were not mapped to the refMrna, or were mapped to more than one location in the genome are excluded. [[Media:probes2fasta.txt|./probes2fasta.pl]] < outputFile_0gap_filtered.txt > outputFile_0gap_filtered.fasta [[Media:probes2fasta.txt|./probes2fasta.pl]] < outputFile_20gap_filtered.txt > outputFile_20gap_filtered.fasta /home/kunzhang/softwares/Novocraft/novocraft/novoalign -d /home/kunzhang/RNAseq/Data/CommonFiles/refMrna.ndx -f outputFile_0gap_filtered.fasta -F FA -r ALL > outputFile_0gap_filtered_novoalign_refMrna.out /home/kunzhang/softwares/Novocraft/novocraft/novoalign -d /home/kunzhang/softwares/Novocraft/novocraft/human_g1k_v37 -f outputFile_0gap_filtered.fasta -F FA -r ALL > outputFile_0gap_filtered_novoalign_human_g1k_v37.out & /home/kunzhang/softwares/Novocraft/novocraft/novoalign -d /home/kunzhang/RNAseq/Data/CommonFiles/refMrna.ndx -f outputFile_20gap_filtered.fasta -F FA -r ALL > outputFile_20gap_filtered_novoalign_refMrna.out /home/kunzhang/softwares/Novocraft/novocraft/novoalign -d /home/kunzhang/softwares/Novocraft/novocraft/human_g1k_v37 -f outputFile_20gap_filtered.fasta -F FA -r ALL > outputFile_20gap_filtered_novoalign_human_g1k_v37.out & *For 83 stem cell genes that no good probe was designed in the first pass, Matt repeat the probe design using mRNA sequences as the template. He generated two additional probe files, one for 20bp gaps, and one for 0bp gaps. I did the mapping to refMrna and human_g1k_v37.
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