Matthew Cai: Difference between revisions

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>Mzcai
>Mzcai
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====Probe Prep====
====Probe Prep====
*[[Matt:LabNotes/2014-12-18|CA12k_Nov2014 Expansion PCR Test]]
*[[Matt:LabNotes/2014-12-18|CA12k_Nov2014 Expansion PCR Test]]
*[[Matt:LabNotes/2015-10-19|CA12k_Nov2014 V4 Expansion PCR]]


====Probe Production====
====Probe Production====
Line 125: Line 126:
*[[Matt:LabNotes/2015-5-18|V4 + suppv2 oligo Capture]]
*[[Matt:LabNotes/2015-5-18|V4 + suppv2 oligo Capture]]
*[[Matt:LabNotes/2015-7-12|V4 + suppv2 oligo Capture Sequencing Analysis]]
*[[Matt:LabNotes/2015-7-12|V4 + suppv2 oligo Capture Sequencing Analysis]]


====Dextran Sulfate + dcProbe====
====Dextran Sulfate + dcProbe====
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*[[Matt:LabNotes/2015-5-19|RNA-Seq not sensitive enough for small amounts of isolated RNA]]
*[[Matt:LabNotes/2015-5-19|RNA-Seq not sensitive enough for small amounts of isolated RNA]]
*[[Matt:LabNotes/2015-5-26|SMARTer_Seq]]
*[[Matt:LabNotes/2015-5-26|SMARTer_Seq]]
*[[]]
====Fiducial Beads====
*[[Matt:LabNotes/2015-8-3|Choosing buffer]]
*[[Matt:LabNotes/2015-8-4|DARTFISH BA8 with 1:500 Fiducial beads]]
*[[Matt:LabNotes/2015-8-13|BA8 with 1:2000 Fiducial beads]]


====VECTABOND====
*[[Matt:LabNotes/2015-9-25|Treat 50 coverslips and 20 slides]]
====DARTFISH BA8====
*[[Matt:LabNotes/2015-8-17|DARTFISH suppv2 BA8 with Fiducial beads failed because frozen/thawed PFA]]
*[[Matt:LabNotes/2015-8-18|DARTFISH suppv2 BA8 with Fiducial beads 0.3um z-stepsize 6 positions for 3D Decoding]]
*[[Matt:LabNotes/2015-9-2|Decode BA8 V4 Sample made by Hosuk with Fiducial beads 0.3um z-stepsize 4 positions for 3D Decoding]]
*[[Matt:LabNotes/2015-9-29|DARTFISH and FISSEQ on glass slides for Harvard to decode/sequence]]
*[[Matt:LabNotes/2015-10-7#FISSEQ_on_BA8_for_Harvard|FISSEQ on glass slide for Harvard to sequence]]
*[[Matt:LabNotes/2015-10-12|DARTFISH suppv2 BA8]]
*[[


====Regression Analysis====
====Regression Analysis====
Line 159: Line 175:
*[[Matt:LabNotes/2015-7-8|RNA FISH (CUX2 even and odd) in iNGN from Harvard]]
*[[Matt:LabNotes/2015-7-8|RNA FISH (CUX2 even and odd) in iNGN from Harvard]]
*[[Matt:LabNotes/2015-7-14|Improve dye coupling by repeating column purification]]
*[[Matt:LabNotes/2015-7-14|Improve dye coupling by repeating column purification]]
 
*[[Matt:LabNotes/2015-7-20|DARTFISH + suppv2 of motor neurons + RNA FISH (KIT,CUX2,SNAP25)]]
*[[Matt:LabNotes/2015-7-21|Design probes for 3 new genes (Never Ordered, switched to RNAscope instead)]]


===Mouse Embryo===
===Mouse Embryo===
Line 165: Line 182:
*[[Matt:LabNotes/2015-7-6|FISSEQ attempt 2 in whole mouse embryo]]
*[[Matt:LabNotes/2015-7-6|FISSEQ attempt 2 in whole mouse embryo]]
*[[Matt:LabNotes/2015-7-7|FISSEQ attempt 3 in whole mouse embryo]]
*[[Matt:LabNotes/2015-7-7|FISSEQ attempt 3 in whole mouse embryo]]
*[[Matt:LabNotes/2015-10-7#FISSEQ_on_Mouse_Embryo_Test|FISSEQ on mouse embryo section]]


==Protocols==
==Protocols==

Revision as of 02:16, 21 October 2015

Notebook

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

Regression Analysis

RNA FISH + DARTFISH in Cultured Neurons

Mouse Embryo

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)