Difference between revisions of "User:Karmella Haynes/Notebook/PcTF Genomics"

From OpenWetWare
Jump to: navigation, search
(Illumina ChIP-seq)
(fix raw html help text)
 
(35 intermediate revisions by one other user not shown)
Line 1: Line 1:
 +
< [http://openwetware.org/wiki/Haynes_Lab Haynes Lab OWW Home]
 +
 
{|{{table}} width="800"
 
{|{{table}} width="800"
 
|-
 
|-
Line 10: Line 12:
 
<!-- ## END search column  ## -->
 
<!-- ## END search column  ## -->
 
|-  
 
|-  
|colspan="2" style="background-color: #F2F2F2;" align="right"|[[{{FULLPAGENAME}}/Entry_Base|Customize your entry pages]] [[Help:Notebook/Project_Base/Customize_entry_page|<html><img src="/images/a/aa/Help.png" border="0" /></html>]]
+
|colspan="2" style="background-color: #F2F2F2;" align="right"|[[{{FULLPAGENAME}}/Entry_Base|Customize your entry pages]] [[Image:Help.png|frameless|link=Help:Notebook/Project_Base/Customize_entry_page]]
 
|-  
 
|-  
 
|colspan="2"|
 
|colspan="2"|
 
==Illumina ChIP-seq==
 
==Illumina ChIP-seq==
 +
* General Computing
 +
** [http://a2c2.asu.edu/how-to/get-started/# ASU Saguaro Computing Cluster a2c2] - login via the Mac Terminal, Command: ssh username@saguaro.fulton.asu.edu
 +
** a2c2 file transfer - [http://openwetware.org/wiki/User:Karmella_Haynes/Notebook/PcTF_Genomics/2014/04/02 04/02/14]
 
* ChIP DNA prep for Illumina:  
 
* ChIP DNA prep for Illumina:  
*  
+
** Experimental samples - [http://openwetware.org/wiki/User:Karmella_Haynes/Notebook/PcTF_Genomics/2011/12/13 12/13/11],  [http://openwetware.org/wiki/User:Karmella_Haynes/Notebook/PcTF_Genomics/2011/12/14 12/14/11], [http://openwetware.org/wiki/User:Karmella_Haynes/Notebook/PcTF_Genomics/2011/12/19 12/19/11]
 +
** Input DNA - [http://openwetware.org/wiki/User:Karmella_Haynes/Notebook/PcTF_Genomics/2013/01/25 01/25/13], [http://openwetware.org/wiki/User:Karmella_Haynes/Notebook/PcTF_Genomics/2013/04/04 4/04/13];
 +
* IP samples Fasta --> BAM files: Mark Teng from the Dinu lab (TGEN)
 +
* Input sample Fasta --> BAM file: Karthik Velmurugan on 5/16/13 (external hard drive)
 +
* Enrichment analysis (DNASTAR software)
 +
** MACS: BAM --> BED (peaks), done by Mark Teng [http://openwetware.org/wiki/User:Karmella_Haynes/Notebook/PcTF_Genomics/2012/05/16 05/16/12]
 +
** DNASTAR: BAM --> peaks/ enrichment histograms workflow [http://openwetware.org/wiki/User:Karmella_Haynes/Notebook/PcTF_Genomics/2012/12/13 12/13/2012]
 +
** DNASTAR: BAM --> wig files for UCSC browser workflow [http://openwetware.org/wiki/User:Karmella_Haynes/Notebook/PcTF_Genomics/2013/01/07 01/07/2013]
 +
** STAR: Sample BED vs. Input BED --> clean up false positive enrichment and filter out repeat-sequence hits [http://openwetware.org/wiki/User:Karmella_Haynes/Notebook/PcTF_Genomics/2014/02/10 02/10/2014]
 +
 
  
 
<br>
 
<br>
  
 
==Cell Type Study==
 
==Cell Type Study==
* Express PcTF (KAH126) in K-562 and SK-N-SH
+
* Carly Hom - Express PcTF (KAH126) in K-562 and SK-N-SH
 +
** K562 - TRIzol prep [http://openwetware.org/wiki/User:Karmella_Haynes/Notebook/PcTF_Genomics/2012/12/18 12/18/12]
 +
** SK-N-SH - TRIzol prep [http://openwetware.org/wiki/User:Karmella_Haynes/Notebook/PcTF_Genomics/2012/12/27 12/27/12]
 +
** U2OS TRIzol prep [http://openwetware.org/wiki/User:Karmella_Haynes/Notebook/PcTF_Genomics/2014/01/27 01/27/14]
 +
 
 +
 
 +
* Dr. Haynes - Quality control mCherry & GAPDH runs
 +
** K562 sets 1-3, SKNSH sets 1-3, U2OS sets 1-2  (1:1000 cDNA) [http://openwetware.org/wiki/User:Karmella_Haynes/Notebook/PcTF_Genomics/2014/05/16 5/16/14]
 +
** K562 sets 1-3, SKNSH sets 1-3, U2OS sets 1-2  (1:100 cDNA) [http://openwetware.org/wiki/User:Karmella_Haynes/Notebook/PcTF_Genomics/2014/05/16 5/16/14]
 +
 
 +
* Dr. Haynes - lentiviral transduction of PcTF's
 +
 
 +
==PcTF-Reporter Activation==
 +
* Measure range of PcTF expression in transiently transfected cells - flow cytometry, [http://openwetware.org/wiki/User:Karmella_Haynes/Notebook/PcTF_Genomics/2013/06/02 06/02/13]
 +
 
 +
 
 +
==Synthetic Repression==
 +
* Gal4-EED/luc staining experiments
 +
* Replacement of luc with CFP in Gal4EED/luc HEK293 cells
 +
 
  
  

Latest revision as of 16:45, 23 September 2017

< Haynes Lab OWW Home

<!-- sibboleth --><div id="lncal1" style="border:0px;"><div style="display:none;" id="id">lncal1</div><div style="display:none;" id="dtext">12/13/2011,12/14/2011,12/19/2011,05/16/2012,09/21/2012,10/23/2012,10/25/2012,10/29/2012,11/15/2012,12/01/2012,12/03/2012,12/12/2012,12/13/2012,12/18/2012,12/26/2012,12/27/2012,01/05/2013,01/06/2013,01/07/2013,01/25/2013,04/04/2013,06/02/2013,06/03/2013,06/10/2013,06/11/2013,06/12/2013,06/13/2013,06/14/2013,06/15/2013,06/18/2013,06/19/2013,06/26/2013,06/30/2013,07/04/2013,07/05/2013,07/06/2013,01/24/2014,01/27/2014,02/05/2014,02/10/2014,02/12/2014,02/13/2014,02/14/2014,03/17/2014,04/01/2014,04/02/2014,05/12/2014,05/14/2014,05/16/2014,05/19/2014,05/20/2014,05/21/2014,05/27/2014,05/29/2014,06/04/2014,07/23/2014,09/05/2014,09/07/2014,09/09/2014,09/10/2014,09/11/2014,09/22/2014,09/23/2014,09/24/2014,09/25/2014,09/30/2014,10/07/2014,10/08/2014,10/18/2014,11/10/2014,11/12/2014,11/14/2014,11/15/2014,11/16/2014,01/28/2015,02/03/2015,03/20/2015,06/25/2015,06/27/2015,08/12/2015,08/13/2015,08/14/2015,08/18/2015,10/20/2015</div><div style="display:none;" id="page">User:Karmella Haynes/Notebook/PcTF Genomics</div><div style="display:none;" id="fmt">yyyy/MM/dd</div><div style="display:none;" id="css">OWWNB</div><div style="display:none;" id="month"></div><div style="display:none;" id="year"></div><div style="display:none;" id="readonly">Y</div></div>

Owwnotebook icon.png <sitesearch>title=Search this Project</sitesearch>

Customize your entry pages Help.png

Illumina ChIP-seq

  • General Computing
  • ChIP DNA prep for Illumina:
  • IP samples Fasta --> BAM files: Mark Teng from the Dinu lab (TGEN)
  • Input sample Fasta --> BAM file: Karthik Velmurugan on 5/16/13 (external hard drive)
  • Enrichment analysis (DNASTAR software)
    • MACS: BAM --> BED (peaks), done by Mark Teng 05/16/12
    • DNASTAR: BAM --> peaks/ enrichment histograms workflow 12/13/2012
    • DNASTAR: BAM --> wig files for UCSC browser workflow 01/07/2013
    • STAR: Sample BED vs. Input BED --> clean up false positive enrichment and filter out repeat-sequence hits 02/10/2014



Cell Type Study

  • Carly Hom - Express PcTF (KAH126) in K-562 and SK-N-SH


  • Dr. Haynes - Quality control mCherry & GAPDH runs
    • K562 sets 1-3, SKNSH sets 1-3, U2OS sets 1-2 (1:1000 cDNA) 5/16/14
    • K562 sets 1-3, SKNSH sets 1-3, U2OS sets 1-2 (1:100 cDNA) 5/16/14
  • Dr. Haynes - lentiviral transduction of PcTF's

PcTF-Reporter Activation

  • Measure range of PcTF expression in transiently transfected cells - flow cytometry, 06/02/13


Synthetic Repression

  • Gal4-EED/luc staining experiments
  • Replacement of luc with CFP in Gal4EED/luc HEK293 cells


Recently Edited Notebook Pages