Rui:SingelCell RNAseq: Difference between revisions

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==SCAP project==
==SCAP project==
* Main link [http://genome-tech.ucsd.edu/SCAP/index.php/Main_Page]
* 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]
* Libraries [http://genome-tech.ucsd.edu/LabNotes/index.php/Rui:RNAseq-libraries]
* Data: genome-miner.ucsd.edu:/media/Ext4T/KZ_Ext4T/RNAseq/
* Data: genome-miner.ucsd.edu:/media/Ext4T/KZ_Ext4T/RNAseq/
* Haiyang's link [http://tabit.ucsd.edu/fetchers/genemodel/test/www/html/sdec/brwtrk.php]
* RNAseq pipeline http://genome-tech.ucsd.edu/LabNotes/index.php/RNAseq_pipeline [http://genome-tech.ucsd.edu/LabNotes/index.php/RNAseq_pipeline]


==Background==
==Background==
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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:totoRNAseq protocol|totoRNAseq protocol]]
*[[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==
==2013==

Latest revision as of 06:14, 13 October 2014

SCAP project[edit]

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:
  1. Single cell and cell lysis
  2. 1st cDNA synthesis and free primer removal
  3. 2nd cDNA synthesis: A-tailing vs random
  4. Amplification: PCR or IVT
  5. QC and clone

Protocols[edit]

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>