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 99: Line 113:
====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 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====
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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]]
*[[Matt:LabNotes/2015-10-20|DARTFISH w/&w/o suppv2 BA8 with Fiducial]]
*[[Matt:LabNotes/2015-10-29|DARTFISH suppv2 BA8 90sec 0.01% pepsin]]


====Validate with RNAscope BA8====
*[[Matt:LabNotes/2015-11-6|RNAscope of BA8: RELN, SLC17A7, PDE1A, OLFM1]]
*[[Matt:LabNotes/2015-11-11|20X DARTFISH Imaging of 'DARTFISH suppv2 BA8 90sec 0.01% pepsin' Tile]]
*[[Matt:LabNotes/2015-11-15|20X DARTFISH Analysis of 'DARTFISH suppv2 BA8 90sec 0.01% pepsin' Tile]]
*[[Matt:LabNotes/2015-12-11|20X DARTFISH DE & Subpopulation Analysis]]


====Regression Analysis====
====Regression Analysis====
Line 159: Line 198:
*[[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===
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*[[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 Try 1]]
*[[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==
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*[[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 190: 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