Matthew Cai: Difference between revisions

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>Mzcai
>Mzcai
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*[[Matt:LabNotes/2016-8-17|FISSEQ tests of 3 pepsin incubation times: Attempt 1]]
*[[Matt:LabNotes/2016-8-17|FISSEQ tests of 3 pepsin incubation times: Attempt 1]]
*[[Matt:LabNotes/2016-8-18|FISSEQ tests of 3 pepsin incubation times: Attempt 2]]
*[[Matt:LabNotes/2016-8-18|FISSEQ tests of 3 pepsin incubation times: Attempt 2]]
===Image & Seq===
*[[Matt:LabNotes/2017-6-1|1st Try]]
*[[Matt:LabNotes/2017-6-8|2nd Try: Vary number of cycles]]
*[[Matt:LabNotes/2017-6-13|3rd Try: USER]]
*[[Matt:LabNotes/2017-6-14|4th Try: USER]]
*[[Matt:LabNotes/2017-6-27|5th Try: USER, 45C Annealing, with Magnet]]


==Protocols==
==Protocols==

Revision as of 02:16, 12 July 2017

Notebook

2017

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

2016

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

2015

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

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>

Justin's Notebook

2015

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

Projects

2 Step ppCapture + RCA modified FISSEQ

Probe/Primer Design

Probe Production and Testing

"Artificial" MALAT1 Rolony Experiments

Ampligase Efficiency Test

RT Primer Enrich mRNA -> cDNA

FISSEQ Experiments

Decoding


DARTFISH

Probe Design

Probe Prep

Probe Production

In vitro Capture

Dextran Sulfate + dcProbe

NGS of Rolonies

RNA-Seq of BA8

Fiducial Beads

VECTABOND

DARTFISH BA8

Validate with RNAscope BA8

Regression Analysis

RNA FISH + DARTFISH in Cultured Neurons

Mouse Embryo

Mouse Brain

Image & Seq

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)
21 Decoding Probes