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===2 Step ppCapture + RCA modified FISSEQ=== *[[Matt:Experiments-FISSEQ|FISSEQ Experiments Page]] ====Probe/Primer Design==== *[[Matt:LabNotes/exonProbeDesign|Padlock Probe Design]] *[[Matt:LabNotes/2014-9-19|Suppressor oligos for COL1A1]] ====Probe Production and Testing==== *[[Matt:LabNotes/Probe Production and Capture|CustomArray Probe Production and Capture]] *[[Matt:LabNotes/2013-5-10|Agilent Probe Prep]] *[[Matt:LabNotes/2014-5-22|Agi26k0gap Probe Production]] *[[Matt:LabNotes/2014-6-11|Agi26k0gap Probe Production]] *[[Matt:LabNotes/2014-7-1|Agi26k0gap Probe Production]] *[[Matt:LabNotes/2014-8-15|Agi26k0gap Probe Production]] *[[Matt:LabNotes/2014-9-18|Agi26k0gap Probe Production]] *[[Matt:LabNotes/2013-8-20|CA12k Capture (MiSeq_130325) Analysis]] *[[Matt:LabNotes/2013-7-26#Analysis_of_HL152:_Representation_Bias_of_CA12k_Oligos_(Corrected)|CA12k End Sequencing (HL152_130524) Analysis]] *[[Matt:LabNotes/2013-7-26#Analysis_of_HL155:_Representation_Bias_of_Agi26k_Oligos_(Corrected)|Agi26k End Sequencing (HL155_130628) Analysis]] *[[Matt:LabNotes/2013-8-9#Quantifying_Errors_in_CA12k_and_Agi26k_Oligo_Pools_.28Ignoring_low_base_quality_substitution_errors.29|Quantifying Errors in CA12k and Agi26k Oligo Pools]] ===="Artificial" MALAT1 Rolony Experiments==== *[[Matt:LabNotes/2014-4-30|Making artificial MALAT1 rolonies (100nM template -> 10pM ppMALAT1)]] *[[Matt:LabNotes/2014-5-13|Making artificial MALAT1 rolonies (100nM template -> 100pM ppMALAT1)]] *[[Matt:LabNotes/2014-5-27#Artifical_Rolonies|Making artificial MALAT1 rolonies (100nM template -> 100pM ppMALAT1) trial with better cells]] *[[Matt:LabNotes/2014-5-7|ppMALAT1_dcProbe1 Capture of MALAT1 Rolonies +/- EDTA]] *[[Matt:LabNotes/2014-5-16|Detecting captured padlock probes]] *[[Matt:LabNotes/2014-9-6|Tertiary Rolony synthesis]] ====Ampligase Efficiency Test==== *[[Matt:LabNotes/2014-4-9|Ampligase Test First Try]] *[[Matt:LabNotes/2014-4-15|Ampligase Test Second Try]] *[[Matt:LabNotes/2014-5-16|Detecting ppMALAT1 Hybridization]] *[[Matt:LabNotes/2014-5-27#Exo_I.2FIII_Test|Testing Exo I/III Digestion of Hybridized Padlock Probes]] *[[Matt:LabNotes/2014-9-8|45C vs 60C Ampligase Incubation]] ====RT Primer Enrich mRNA -> cDNA==== *[[Matt:LabNotes/2014-5-14|Designing Hexamer RT Primer Enriched in Targeted mRNA]] *[[Matt:LabNotes/2014-6-9|Top48 RT Primer in vitro Validation shows UHRR has DNA contamination]] *[[Matt:LabNotes/2014-6-18|Repeat Top48 Hexamer RT Primer in vitro Validation]] *[[Matt:LabNotes/2014-7-14|Analyzing in vitro RNA-Seq with RT Primers]] *[[Matt:LabNotes/2014-7-30|Analyzing in vitro RNA-Seq with RT Primers continued]] *[[Matt:LabNotes/2014-8-1|Analyzing in vitro RNA-Seq with RT Primers continued]] *[[Matt:LabNotes/2014-9-5|qMDA confirms UHRR DNA contamination]] *[[Matt:LabNotes/2014-9-25|Top48 RT Primer in vitro Validation with purified UHRR]] *[[Matt:LabNotes/2014-10-31|RT Primer RNA-Seq Analysis]] ====FISSEQ Experiments==== *[[Matt:LabNotes/2014-10-6|Agi26k0gap + suppressor oligos & Agi26k20gap on PGP1f]] ====Decoding==== *[[Matt:LabNotes/2014-4-16|Decoding Partial Barcode (only 10 dye probes)]] *[[Matt:LabNotes/2014-8-20|First Full Decoding: PGP1F_Agi26k0gap with PISA Mask]]
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