Matthew Cai

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Notebook[edit]

2017[edit]

<calendar> name=Matt format=%name:LabNotes/%year-%month-%day date=2017/01/01 view=oneyear </calendar>

2016[edit]

<calendar> name=Matt format=%name:LabNotes/%year-%month-%day date=2016/01/01 view=oneyear </calendar>

2015[edit]

<calendar> name=Matt format=%name:LabNotes/%year-%month-%day date=2015/01/01 view=oneyear </calendar>

2014[edit]

<calendar> name=Matt format=%name:LabNotes/%year-%month-%day date=2014/01/01 view=oneyear </calendar>

2013[edit]

<calendar> name=Matt format=%name:LabNotes/%year-%month-%day date=2013/01/01 view=oneyear </calendar>

Justin's Notebook[edit]

2015[edit]

<calendar> name=Matt format=%name:JustinLabNotes/%year-%month-%day date=2015/01/01 view=oneyear </calendar>

Projects[edit]

2 Step ppCapture + RCA modified FISSEQ[edit]

Probe/Primer Design[edit]

Probe Production and Testing[edit]

"Artificial" MALAT1 Rolony Experiments[edit]

Ampligase Efficiency Test[edit]

RT Primer Enrich mRNA -> cDNA[edit]

FISSEQ Experiments[edit]

Decoding[edit]


DARTFISH[edit]

Probe Design[edit]

Probe Prep[edit]

Probe Production[edit]

In vitro Capture[edit]

Dextran Sulfate + dcProbe[edit]

NGS of Rolonies[edit]

RNA-Seq of BA8[edit]

Fiducial Beads[edit]

VECTABOND[edit]

DARTFISH BA8[edit]

Validate with RNAscope BA8[edit]

Regression Analysis[edit]

RNA FISH + DARTFISH in Cultured Neurons[edit]

Mouse Embryo[edit]

Mouse Brain[edit]

SplintR in vitro Testing Additives ie Formamide[edit]

Image & Seq[edit]

Protocols[edit]

Sequencing Runs[edit]

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[edit]

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)
21 Decoding Probes