Rui:SingelCell RNAseq: Difference between revisions
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==2014== | ==2014== | ||
* Reference RNA data analysis: | |||
* The first 1000 single-nucleus data workflow: | |||
* The pipeline: | |||
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==2013== | ==2013== |
Revision as of 02:54, 22 July 2014
SCAP project
- 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
- 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
- PCR based protocol
- IVT based protocol
- HRCA based protocol
- Nextera based protocol
- toto-TSO_RNAseq protocol
- toto-IVT_RNAseq protocol
QuickNotes
2014
- Reference RNA data analysis:
- The first 1000 single-nucleus data workflow:
- 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>