Matthew Cai: Difference between revisions

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==Notebook==
==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 ===
=== 2015 ===
<calendar>
<calendar>
Line 126: Line 140:
*[[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]]
*[[Matt:LabNotes/2017-5-4|Agi15kFeb2017 V4 SplintR Capture with 20% Formamide]]
*[[Matt:LabNotes/2017-6-19|Agi15kFeb2017 V4 SplintR Capture with 5% Formamide and 10% DMF]]


====Dextran Sulfate + dcProbe====
====Dextran Sulfate + dcProbe====
Line 191: Line 207:
*[[Matt:LabNotes/2015-10-7#FISSEQ_on_Mouse_Embryo_Test|FISSEQ on mouse embryo section Try 1]]
*[[Matt:LabNotes/2015-10-7#FISSEQ_on_Mouse_Embryo_Test|FISSEQ on mouse embryo section Try 1]]
*[[Matt:LabNotes/2015-12-14|FISSEQ on mouse embryo section Try 2]]
*[[Matt:LabNotes/2015-12-14|FISSEQ on mouse embryo section Try 2]]
*[[Matt:LabNotes/2016-3-8|FISSEQ attempt 4 in whole mouse embryo]]
*[[Matt:LabNotes/2016-5-17|FISSEQ attempt 5 in whole mouse embryo]]
*[[Matt:LabNotes/2016-6-15|FISSEQ attempt 6 in whole mouse embryo]]
*[[Matt:LabNotes/2016-7-19|FISSEQ attempt 7 with PACT/CLARITY in whole mouse embryo]]
*[[Matt:LabNotes/2016-9-28|FISSEQ attempt 8 with Focus Clear]]
===Mouse Brain===
*[[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]]
===SplintR in vitro Testing Additives ie Formamide===
*[[Matt:LabNotes/2017-4-22|1st Try]]
*[[Matt:LabNotes/2017-5-8|2nd Try: ET SSB + 10% Formamide]]
*[[Matt:LabNotes/2017-5-15|3rd Try]]
*[[Matt:LabNotes/2017-5-19|4th Try]]
*[[Matt:LabNotes/2017-5-22|5th Try]]
*[[Matt:LabNotes/2017-6-7|6th Try: DMF, DMSO, Betaine]]
*[[Matt:LabNotes/2017-5-4|Agi15kFeb2017 V4 SplintR Capture with 20% Formamide]]
*[[Matt:LabNotes/2017-6-19|Agi15kFeb2017 V4 SplintR Capture with 5% Formamide and 10% DMF]]
===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==
Line 196: Line 238:
*[[Matt:LabNotes/Bead Purification Protocol|Bead Purification Protocol]]
*[[Matt:LabNotes/Bead Purification Protocol|Bead Purification Protocol]]
*[[Matt:LabNotes/Qubit Protocol|Qubit Protocol]]
*[[Matt:LabNotes/Qubit Protocol|Qubit Protocol]]
 
*[[Matt:LabNotes/Polyacrylamide Gel Protocol|Polyacrylamide Gel Protocol]]
*[[Hosuk:LabNotes/2014-3-24|CircLigase II Buffer]]
*[[Matt:LabNotes/2014-2-19|BF "Skeleton" Image]]
*[[Matt:LabNotes/2014-2-19|BF "Skeleton" Image]]


Line 216: Line 259:
CA12k: 12,355 probes (170nt)<br>
CA12k: 12,355 probes (170nt)<br>
Agi26k_0gap:  12,964 probes (193nt) <br>
Agi26k_0gap:  12,964 probes (193nt) <br>
Agi26k_20gap: 13,179 probes (193nt)
Agi26k_20gap: 13,179 probes (193nt) <br>
[[Matt:LabNotes/dcProbes7x3 |21 Decoding Probes]]

Latest revision as of 02:48, 12 July 2017

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