Rui:SingelCell RNAseq: Difference between revisions
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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== | ==Background== | ||
* Goal: the smallest functional unit; the exact quantity; full-length RNAs; sense vs anti-sense; all classes; at single-base resolution | * Goal: the smallest functional unit; the exact quantity; full-length RNAs; sense vs anti-sense; all classes; at single-base resolution | ||
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*[[Rui:HRCA based protocol|HRCA based protocol]] | *[[Rui:HRCA based protocol|HRCA based protocol]] | ||
*[[Rui:Nextera based protocol|Nextera based protocol]] | *[[Rui:Nextera based protocol|Nextera based protocol]] | ||
*[[Rui: | *[[Rui:toto-TSO_RNAseq protocol|toto-TSO_RNAseq protocol]] | ||
*[[Rui:toto-IVT_RNAseq protocol|toto-IVT_RNAseq protocol]] | |||
* | |||
==QuickNotes== | ==QuickNotes== | ||
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*[[Rui:IVT note|IVT note]] | *[[Rui:IVT note|IVT note]] | ||
*[[Rui:HRCA note|HRCA 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== | ==2012== | ||
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view=oneyear | view=oneyear | ||
</calendar> | </calendar> | ||
==2011== | ==2011== |
Latest revision as of 06:14, 13 October 2014
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:
<calendar> name=Rui:LabNotes/SingleCell format=%name/%year-%month-%day date=2014/10/1 view=oneyear </calendar>
2013[edit]
<calendar> name=Rui:LabNotes/SingleCell format=%name/%year-%month-%day date=2013/10/1 view=oneyear </calendar>
2012[edit]
<calendar> name=Rui:LabNotes/SingleCell format=%name/%year-%month-%day date=2012/10/1 view=oneyear </calendar>
2011[edit]
<calendar> name=Rui:LabNotes/SingleCell format=%name/%year-%month-%day date=2011/10/1 view=oneyear </calendar>