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==SCAP project== * SCAP website shared among UCSD/ILMN/Scripps, the main link [http://genome-tech.ucsd.edu/SCAP/index.php/Main_Page] pwd:"24" * Sample's link: Data center - under SCAP website, SingleCell, SingleCell!@34 * Libraries [http://genome-tech.ucsd.edu/LabNotes/index.php/Rui:RNAseq-libraries] * Data: genome-miner.ucsd.edu:/media/Ext4T/KZ_Ext4T/RNAseq/ * RNAseq pipeline http://genome-tech.ucsd.edu/LabNotes/index.php/RNAseq_pipeline [http://genome-tech.ucsd.edu/LabNotes/index.php/RNAseq_pipeline] ==Background== * Goal: the smallest functional unit; the exact quantity; full-length RNAs; sense vs anti-sense; all classes; at single-base resolution * Review papers: * Key papers: # Single cell and cell lysis # 1st cDNA synthesis and free primer removal # 2nd cDNA synthesis: A-tailing vs random # Amplification: PCR or IVT # QC and clone ==Protocols== *[[Rui:PCR based protocol|PCR based protocol]] *[[Rui:IVT based protocol|IVT based protocol]] *[[Rui:HRCA based protocol|HRCA based protocol]] *[[Rui:Nextera based protocol|Nextera based protocol]] *[[Rui:toto-TSO_RNAseq protocol|toto-TSO_RNAseq protocol]] *[[Rui:toto-IVT_RNAseq protocol|toto-IVT_RNAseq protocol]] ==QuickNotes== *[[Rui:PCR note|PCR note]] *[[Rui:IVT note|IVT note]] *[[Rui:HRCA note|HRCA note]] *[[Rui:10.10.13 discussion|10.10.13 discussion]] ==2014== * Reference RNA data analysis: * The first 1000 single-nucleus data workflow: 7.3; 7.4; 7.14; 8.7 * The bulk sample analysis: 7.9.14; 10.10.14 * The pipeline: <calendar> name=Rui:LabNotes/SingleCell format=%name/%year-%month-%day date=2014/10/1 view=oneyear </calendar> ==2013== <calendar> name=Rui:LabNotes/SingleCell format=%name/%year-%month-%day date=2013/10/1 view=oneyear </calendar> ==2012== <calendar> name=Rui:LabNotes/SingleCell format=%name/%year-%month-%day date=2012/10/1 view=oneyear </calendar> ==2011== <calendar> name=Rui:LabNotes/SingleCell format=%name/%year-%month-%day date=2011/10/1 view=oneyear </calendar>
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