Matthew Cai
Notebook
2015
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2014
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2013
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Justin's Notebook
2015
name=Justin format=%name:JustinLabNotes/%year-%month-%day date=2015/01/01 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
150602_MiSeq: CA12kNov14suppv2_gDNA and CA12kNov14suppv2_cDNAdT
150623_MiSeq: CA12kNov14suppv2_cDNARan and CA12kNov14suppv2_NegCtrl
150616_MiSeq: SMART-Seq of whole BA8 tissue section
Probe Sets
CA12kNov2014_V4: 3,514 probes (150nt)
CA12kNov2014_V6: 3,514 probes (150nt) (RevComp of V4)
CA12kNov2014_V7: 2,486 probes (150nt)
CA12kNov2014_V8: 2,486 probes (150nt) (RevComp of V7)
CA12k: 12,355 probes (170nt)
Agi26k_0gap: 12,964 probes (193nt)
Agi26k_20gap: 13,179 probes (193nt)