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===DARTFISH=== *[[Matt:LabNotes/2014-9-2|Barcoding Scheme]] ====Probe Design==== *[[Matt:LabNotes/2014-9-17|Gene selection]] *[[Matt:LabNotes/2014-10-9|Design New Padlock Probe Set]] *[[Matt:LabNotes/2014-10-30|ppDesigner on 450 genes]] *[[Matt:LabNotes/2014-11-1|ppDesigner on new genelist]] *[[Matt:LabNotes/2014-11-10|ppDesigner on new genelist + contigs to meet 12,000 oligo requirement]] *[[Matt:LabNotes/2014-11-19|Final Padlock Probe Design: CA12k_Nov2014]] ====Probe Prep==== *[[Matt:LabNotes/2014-12-18|CA12k_Nov2014 Expansion PCR Test]] *[[Matt:LabNotes/2015-10-19|CA12k_Nov2014 V4 Expansion PCR]] ====Probe Production==== *[[Matt:LabNotes/2015-1-5|CA12k_Nov2014 V4 and V7 Probe Production]] *[[Matt:LabNotes/2015-1-13|CA12k_Nov2014 V7 Probe Production]] *[[Matt:LabNotes/2015-1-15|CA12k_Nov2014 V4 Probe Production]] *[[Matt:LabNotes/2015-1-26|CA12k_Nov2014 V6 and V8 Probe Production]] *[[Matt:LabNotes/2015-2-2|CA12k_Nov2014 V4 Probe Production]] *[[Matt:LabNotes/2015-2-5|CA12k_Nov2014 V7 Probe Production]] *[[Matt:LabNotes/2015-2-28|CA12k_Nov2014 V4 Probe Production]] *[[Matt:LabNotes/2015-3-25|CA12k_Nov2014 V4 Probe Production]] *[[Matt:LabNotes/2015-5-5|CA12k_Nov2014 V4 Probe Production]] *[[Matt:LabNotes/2015-5-11|CA12k_Nov2014 V4 Probe Production]] *[[Matt:LabNotes/2015-6-3|CA12k_Nov2014 V4 Probe Production]] *[[Matt:LabNotes/2015-6-29|CA12k_Nov2014 V4 Probe Production]] *[[Matt:LabNotes/2015-5-11|CA12k_Nov2014 V4 Probe Production]] ====In vitro Capture==== *[[Matt:LabNotes/2015-1-12|UHRR cDNA synthesis]] *[[Matt:LabNotes/2015-1-21|V4 and V7 Capture]] *[[Matt:LabNotes/2015-3-19|V4 Capture Sequencing Analysis + Design 39 suppressor oligos]] *[[Matt:LabNotes/2015-4-8|V7 Capture Sequencing Analysis]] *[[Matt:LabNotes/2015-4-28|V4 + supp oligo Capture]] *[[Matt:LabNotes/2015-5-8|V4 + supp oligo Capture Sequencing Analysis]] *[[Matt:LabNotes/2015-5-15|BA8 cDNA synthesis]] *[[Matt:LabNotes/2015-5-18|V4 + suppv2 oligo Capture]] *[[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==== *[[Matt:LabNotes/2015-3-12|Dextran sulfate to improve fluorescence intensity distribution -> bimodal]] ====NGS of Rolonies==== *[[Matt:LabNotes/2015-3-14|Primer design]] *[[Matt:LabNotes/2015-3-31|Amplify rolonies via slide PCR Experiment]] *[[Matt:LabNotes/2015-4-13|Sequencing alignment and analysis]] ====RNA-Seq of BA8==== *[[Matt:LabNotes/2015-5-19|RNA-Seq not sensitive enough for small amounts of isolated RNA]] *[[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==== *[[Matt:LabNotes/2015-4-8#Regression_Analysis|Px-px decoding of DARTFISH PGP1f & BA8]] *[[Matt:LabNotes/2015-4-14|Try normalize DARTFISH with in vitro cDNA capture]] *[[Matt:LabNotes/2015-4-15|Spearman's rank correlation]] *[[Matt:LabNotes/2015-5-14|V4 + supp oligos normalized vs HBRR/UHRR]] *[[]]
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