Rui:SingelCell RNAseq
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SCAP project[edit]
- SCAP website shared among UCSD/ILMN/Scripps, the main link [1] pwd:"24"
- Sample's link: Data center - under SCAP website, SingleCell, SingleCell!@34
- Libraries [2]
- Data: genome-miner.ucsd.edu:/media/Ext4T/KZ_Ext4T/RNAseq/
- RNAseq pipeline http://genome-tech.ucsd.edu/LabNotes/index.php/RNAseq_pipeline [3]
Background[edit]
- 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[edit]
- PCR based protocol
- IVT based protocol
- HRCA based protocol
- Nextera based protocol
- toto-TSO_RNAseq protocol
- toto-IVT_RNAseq protocol
QuickNotes[edit]
2014[edit]
- 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:
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2013[edit]
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2012[edit]
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2011[edit]
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