Matthew Cai: Difference between revisions
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*[[Matt:LabNotes/exonProbeDesign|Padlock Probe Design]] | *[[Matt:LabNotes/exonProbeDesign|Padlock Probe Design]] | ||
*[[Matt:LabNotes/2014-5-14|Designing Hexamer RT Primer Enriched in Targeted mRNA]] | *[[Matt:LabNotes/2014-5-14|Designing Hexamer RT Primer Enriched in Targeted mRNA]] | ||
*[[Matt:LabNotes/2014-7-14|Analyzing in vitro RNA-Seq with RT Primers]] | |||
====Probe Production and Testing==== | ====Probe Production and Testing==== |
Revision as of 16:27, 29 July 2014
Notebook
2014
<calendar> name=Matt format=%name:LabNotes/%year-%month-%day date=2014/01/01 view=oneyear </calendar>
2013
<calendar> name=Matt format=%name:LabNotes/%year-%month-%day date=2013/01/01 view=oneyear </calendar>
Projects
in Situ Sequencing
Probe/Primer Design
- Padlock Probe Design
- Designing Hexamer RT Primer Enriched in Targeted mRNA
- Analyzing in vitro RNA-Seq with RT Primers
Probe Production and Testing
- CustomArray Probe Production and Capture
- Agilent Probe Prep
- CA12k Capture (MiSeq_130325) Analysis
- CA12k End Sequencing (HL152_130524) Analysis
- Agi26k End Sequencing (HL155_130628) Analysis
- Quantifying Errors in CA12k and Agi26k Oligo Pools
Rolony Experiments
- Making artificial MALAT1 rolonies (100nM template -> 10pM ppMALAT1)
- Making artificial MALAT1 rolonies (100nM template -> 100pM ppMALAT1)
- Making artificial MALAT1 rolonies (100nM template -> 100pM ppMALAT1) trial with better cells
- ppMALAT1_dcProbe1 Capture of MALAT1 Rolonies +/- EDTA
Ampligase Efficiency Test
- Ampligase Test First Try
- Ampligase Test Second Try
- Detecting ppMALAT1 Hybridization
- Testing Exo I/III Digestion of Hybridized Padlock Probes
Decoding
Protocols
Sequencing Runs
130325_MiSeq: CA12k capture of gDNA, cDNAwRNase, and cDNA-RNase
130524_HL152 (Lane 2, unassigned): CA12k oligos
130628_HL155 (Lane 3, Indx 10 & 12): Agi26k_0gap and Agi26k_20gap oligos
130729_MiSeq: Agi26k_0gap and Agi26k_20gap capture of gDNA and cDNA
131220_HL162 (Lane 1, unassigned): PhiX Control
Probe Sets
CA12k: 12,355 probes (170nt)
Agi26k_0gap: 12,964 probes (193nt)
Agi26k_20gap: 13,179 probes (193nt)