Matt:LabNotes/2015-7-21
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Design 3 New RNA FISH Probes for Validating DARTFISH in Motor Neurons[edit]
- Current RNA FISH probes don't include a high expression gene in Sebastian's motor neurons
- Based on DARTFISH and RNA-Seq data
- See 'Sum' sheet
- Based on DARTFISH and RNA-Seq data
Pick 3 new genes that validate DARTFISH[edit]
- Validate normalization method can properly characterize true gene expression
- Pick only genes with >10 DARTFISH raw count in 8 positions (see above data link)
- High DARTFISH raw count and high DARTFISH normalized value
- KIF5C: #3 in raw count and #7 in gDNA normalized value
- High DARTFISH raw count and low DARTFISH normalized value
- PHKB: #15 in raw count and #77 in gDNA normalized value
- Low DARTFISH raw count and high DARTFISH normalized value
- OLFM1: #78 in raw count and #12 in gDNA normalized value
mRNA coding sequence[edit]
- Find using UCSC Genome Browser 'UCSC Genes' track to pick shortest transcript variant that shares as many exons with other variants
KIF5C[edit]
- Picked short transcript at 3' end
Description: Homo sapiens kinesin family member 5C (KIF5C), mRNA. mRNA sequence from here Transcript (Including UTRs)
Position: chr2:149,856,449-149,883,273 Size: 26,825 Total Exon Count: 7 Strand: +
Coding Region
Position: chr2:149,856,881-149,868,190 Size: 11,310 Coding Exon Count: 6
PHKB[edit]
- Picked short transcript at 3' end
Description: Homo sapiens phosphorylase kinase, beta (PHKB), transcript variant 2, mRNA. mRNA sequence from here Transcript (Including UTRs)
Position: chr16:47,699,183-47,735,434 Size: 36,252 Total Exon Count: 7 Strand: +
Coding Region
Position: chr16:47,699,794-47,733,277 Size: 33,484 Coding Exon Count: 7
OLFM1[edit]
- Picked 2nd to shortest transcript that has 3' end
Description: Homo sapiens olfactomedin 1 (OLFM1), transcript variant 1, mRNA. mRNA sequence from here Transcript (Including UTRs)
Position: chr9:137,979,817-138,013,030 Size: 33,214 Total Exon Count: 6 Strand: +
Coding Region
Position: chr9:137,979,836-138,012,024 Size: 32,189 Coding Exon Count: 6
Stellaris® Probe Designer version 4.1[edit]
- Account: mzcai (pswd same as labnotes)
- Sequences saved in shopping cart
- Design parameters:
- Organism: human
- Masking level: 5
- Max number of probes: 48
- Probe length: 20
- Min spacing: 2