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

From OpenWetWare
Jump to: navigation, search
(Cell Type Study)
(fix raw html help text)
 
(27 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]
 
** 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]
+
** 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];
* Fasta --> BAM files: Mark Teng from the Dinu lab (TGEN)
+
* 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)
 
* Enrichment analysis (DNASTAR software)
** BAM --> peaks/ enrichment histograms workflow [http://openwetware.org/wiki/User:Karmella_Haynes/Notebook/PcTF_Genomics/2012/12/13 12/13/2012]
+
** MACS: BAM --> BED (peaks), done by Mark Teng [http://openwetware.org/wiki/User:Karmella_Haynes/Notebook/PcTF_Genomics/2012/05/16 05/16/12]
** BAM --> wig files for UCSC browser workflow [http://openwetware.org/wiki/User:Karmella_Haynes/Notebook/PcTF_Genomics/2013/01/07 01/07/2013]
+
** 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]
  
  
Line 27: Line 35:
 
==Cell Type Study==
 
==Cell Type Study==
 
* Carly Hom - 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 17:45, 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


Recent changes

26 September 2017

     11:27 

BME100 f2017:Group7 W1030 L3‎‎ (2 changes | history) . . (+1,888). . [Sarah R. Brady‎ (2×)]

     

11:27

(cur | prev) . . (+946). . Sarah R. Brady (talk | contribs) (Experimental Design of Own Device)

     

11:10

(cur | prev) . . (+942). . Sarah R. Brady (talk | contribs) (Design Flaws and Recommendations)

N    11:26 

BME100 f2017:Group3 W1030 L3‎‎ (6 changes | history) . . (+2,680). . [Blake A. McCal‎ (6×)]

     

11:26

(cur | prev) . . (-1). . Blake A. McCal (talk | contribs) (Inferential Stats)

     

11:26

(cur | prev) . . (+199). . Blake A. McCal (talk | contribs) (Inferential Stats)

     

11:24

(cur | prev) . . (+29). . Blake A. McCal (talk | contribs) (Descriptive Stats and Graph)

     

11:23

(cur | prev) . . (+165). . Blake A. McCal (talk | contribs) (Descriptive Stats and Graph)

     

10:54

(cur | prev) . . (-176). . Blake A. McCal (talk | contribs) (LAB 1 WRITE-UP)

N    

10:27

(cur | prev) . . (+2,464). . Blake A. McCal (talk | contribs) (Created page with "{|{{table}} width="800" |- |style="background-color: #EEE"|128px<span style="font-size:22px;"> BME 100 Fall 2017</span> |style="background-color...")

     11:02  CAMRI:iLab‎ (diff | hist) . . (-4). . Lacey Berry (talk | contribs) (Problems)
     10:59  Template:CAMRI Navigation Bar‎ (diff | hist) . . (-137). . Michael S Beauchamp (talk | contribs)

     10:58 

Beauchamp‎‎ (11 changes | history) . . (+19). . [Michael S Beauchamp‎ (11×)]

     

10:58

(cur | prev) . . (+5). . Michael S Beauchamp (talk | contribs)

     

10:58

(cur | prev) . . (-5). . Michael S Beauchamp (talk | contribs)

     

10:57

(cur | prev) . . (+5). . Michael S Beauchamp (talk | contribs)

     

10:57

(cur | prev) . . (+10). . Michael S Beauchamp (talk | contribs)

     

10:57

(cur | prev) . . (0). . Michael S Beauchamp (talk | contribs)

     

10:45

(cur | prev) . . (+4). . Michael S Beauchamp (talk | contribs)

     

10:45

(cur | prev) . . (0). . Michael S Beauchamp (talk | contribs)

     

10:44

(cur | prev) . . (+2). . Michael S Beauchamp (talk | contribs)

     

10:41

(cur | prev) . . (+231). . Michael S Beauchamp (talk | contribs)

     

10:41

(cur | prev) . . (-231). . Michael S Beauchamp (talk | contribs)

     

10:40

(cur | prev) . . (-2). . Michael S Beauchamp (talk | contribs)

     10:55 

CTR:Notebook/Migrant/2016/09/19‎‎ (2 changes | history) . . (+106). . [Vinh T. Le‎ (2×)]

     

10:55

(cur | prev) . . (+71). . Vinh T. Le (talk | contribs) (Silvereye)

     

10:55

(cur | prev) . . (+35). . Vinh T. Le (talk | contribs) (Silvereye)

     10:47  Template:Beauchamp Lab Notebook Navigation Bar‎ (diff | hist) . . (-137). . Michael S Beauchamp (talk | contribs)

     10:43 

BME100 f2017:Group8 W1030 L3‎‎ (7 changes | history) . . (+2,378). . [Jennifer L. Brodsky‎ (7×)]

     

10:43

(cur | prev) . . (+246). . Jennifer L. Brodsky (talk | contribs) (Experimental Design of Own Device)

     

10:40

(cur | prev) . . (+255). . Jennifer L. Brodsky (talk | contribs) (Experimental Design of Own Device)

     

10:40

(cur | prev) . . (+512). . Jennifer L. Brodsky (talk | contribs) (Experimental Design of Own Device)

     

10:38

(cur | prev) . . (+370). . Jennifer L. Brodsky (talk | contribs) (Experimental Design of Own Device)

     

10:33

(cur | prev) . . (+24). . Jennifer L. Brodsky (talk | contribs) (Experimental Design of Own Device)

     

10:29

(cur | prev) . . (+2). . Jennifer L. Brodsky (talk | contribs) (Experimental Design of Own Device)

     

10:28

(cur | prev) . . (+969). . Jennifer L. Brodsky (talk | contribs) (Experimental Design of Own Device)

     10:42 (Move log) . . Yar (talk | contribs) moved page Template:Extension DPL to Template:Not Extension Not DPL without leaving a redirect ‎(unbreak)
     10:42  Template:Beauchamp Navigation Bar‎ (diff | hist) . . (-137). . Michael S Beauchamp (talk | contribs)

     10:34 

(Upload log). .

[Jennifer L. Brodsky‎ (2×)]

     

10:34

. . Jennifer L. Brodsky (talk | contribs) uploaded a new version of File:Energy.jpg

     

10:34

. . Jennifer L. Brodsky (talk | contribs) uploaded File:Energy.jpg

N    10:23 

Nbtest‎‎ (4 changes | history) . . (+70). . [Yar‎ (4×)]

     

10:23

(cur | prev) . . (-30). . Yar (talk | contribs) (whoa)

     

10:23

(cur | prev) . . (-114). . Yar (talk | contribs) (simpler)

     

10:18

(cur | prev) . . (+61). . Yar (talk | contribs) (inspect vars)

N    

10:17

(cur | prev) . . (+153). . Yar (talk | contribs) (testing dpl)

N    10:15  Template:Extension DPL‎ (diff | hist) . . (+252). . Yar (talk | contribs) (maybe this will solve permission issues for some bizarre reason)
N    09:45  CTR:Notebook/Migrant/2017/09/12‎ (diff | hist) . . (+950). . Vinh T. Le (talk | contribs) (Autocreate 2017/09/12 Entry for CTR:Notebook/Migrant)
 m   09:35  Li Lab:People‎ (diff | hist) . . (+1). . Wei Li Bcm (talk | contribs)

     09:21 

(User creation log). .

[Yar‎ (3×)]

     

09:21

. . User account Calacalu (talk | contribs) was created by Yar (talk | contribs) and password was sent by email ‎

     

09:21

. . User account Wagroves (talk | contribs) was created by Yar (talk | contribs) and password was sent by email ‎

     

09:03

. . User account Merman (talk | contribs) was created by Yar (talk | contribs) and password was sent by email ‎

N    09:13 

User:Merman‎‎ (2 changes | history) . . (+32). . [Merman‎ (2×)]

     

09:13

(cur | prev) . . (+23). . Merman (talk | contribs) (test link)

N    

09:09

(cur | prev) . . (+9). . Merman (talk | contribs) (testing no captcha)

     08:42  Hoatlin:BMB seminar series 2017-2018‎ (diff | hist) . . (-75). . Maureen E. Hoatlin (talk | contribs) (Seminar Schedule 2017-2018)