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

From OpenWetWare
Jump to: navigation, search
(Illumina ChIP-seq)
(Illumina ChIP-seq)
Line 21: Line 21:
 
* 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]; BAM file was created by Karthik Velmurugan on 5/16/13 (external hard drive)
+
** 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]; BAM file was created by Karthik Velmurugan on 5/16/13 (external hard drive)
 
* Fasta --> BAM files: Mark Teng from the Dinu lab (TGEN)
 
* Fasta --> BAM files: Mark Teng from the Dinu lab (TGEN)
 
* Enrichment analysis (DNASTAR software)
 
* Enrichment analysis (DNASTAR software)

Revision as of 14:40, 3 April 2014

< 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 <html><img src="/images/a/aa/Help.png" border="0" /></html>

Illumina ChIP-seq

  • General Computing
  • ChIP DNA prep for Illumina:
  • Fasta --> BAM files: Mark Teng from the Dinu lab (TGEN)
  • 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

PcTF-Reporter Activation

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


Synthetic Repression

  • Gal4-EED/luc staining experiments


Recent changes

19 October 2017

     13:51 

(Upload log). .

[Thorntca‎; Shae M. Diaz‎]

     

13:51

. . Shae M. Diaz (talk | contribs) uploaded File:BME100ShaeD.JPG

     

13:17

. . Thorntca (talk | contribs) uploaded File:2Dgel.png.jpg

     13:50  Klenow Assembly Method: Seamless cloning‎ (diff | hist) . . (+105). . David M.D. Bailey (talk | contribs) (The Klenow Assembly Method (KAM) for the seamless cloning of overlapping double stranded DNA fragments: Very cheap alternative to the Gibson Assembly)

     13:22 

User:Thorntca‎‎ (8 changes | history) . . (+529). . [Thorntca‎ (8×)]

     

13:22

(cur | prev) . . (+145). . Thorntca (talk | contribs)

     

13:19

(cur | prev) . . (+17). . Thorntca (talk | contribs)

     

13:19

(cur | prev) . . (+4). . Thorntca (talk | contribs)

     

13:18

(cur | prev) . . (+30). . Thorntca (talk | contribs)

     

13:16

(cur | prev) . . (+417). . Thorntca (talk | contribs)

     

12:52

(cur | prev) . . (+12). . Thorntca (talk | contribs)

     

12:51

(cur | prev) . . (-5). . Thorntca (talk | contribs)

     

12:51

(cur | prev) . . (-91). . Thorntca (talk | contribs)

     12:27 

User:Madeline.churchill‎‎ (2 changes | history) . . (+302). . [Madeline.churchill‎ (2×)]

     

12:27

(cur | prev) . . (0). . Madeline.churchill (talk | contribs) (TZAP protein controls telomere Trimming process)

     

12:27

(cur | prev) . . (+302). . Madeline.churchill (talk | contribs) (Madeline Churchill's Discussion Page)

     12:15  CONJ606:Materials‎ (diff | hist) . . (+319). . Weinjule (talk | contribs) (Papers)
     10:53  User:Peteral‎ (diff | hist) . . (+728). . Peteral (talk | contribs) (Alec's Discussion Questions)
     09:17  BioMicroCenter:BIG meeting‎ (diff | hist) . . (+19). . George W Bell (talk | contribs) (2017-2018 academic year)
     07:06 (User creation log) . . User account Newfish (talk | contribs) was created by Yar (talk | contribs) and password was sent by email ‎

     04:10 

BioMicroCenter:BioinfoClasses‎‎ (3 changes | history) . . (+132). . [Charlie Whittaker‎ (3×)]

     

04:10

(cur | prev) . . (+9). . Charlie Whittaker (talk | contribs) (Teaching Schedule)

     

04:09

(cur | prev) . . (0). . Charlie Whittaker (talk | contribs) (Teaching Schedule)

     

04:08

(cur | prev) . . (+123). . Charlie Whittaker (talk | contribs) (Teaching Schedule)

     03:36  User:Timothee Flutre‎ (diff | hist) . . (+146). . Timothee Flutre (talk | contribs) (add contrib breedR and SO)

 m   02:27 

How to write a research paper‎‎ (2 changes | history) . . (+91). . [Formand‎ (2×)]

 m   

02:27

(cur | prev) . . (-1). . Formand (talk | contribs) (External links)

 m   

02:24

(cur | prev) . . (+92). . Formand (talk | contribs) (External links)

18 October 2017

     19:09  BME100 f2017:Group10 W0800 L4‎ (diff | hist) . . (+1). . Osvaldo J Pagan (talk | contribs)

     15:56 

BME100 f2017:Group8 W1030 L4‎‎ (2 changes | history) . . (+426). . [Jennifer L. Brodsky‎; Jacob Tomas Harrison Haye‎]

     

15:56

(cur | prev) . . (+409). . Jennifer L. Brodsky (talk | contribs) (Research and Development)

     

14:17

(cur | prev) . . (+17). . Jacob Tomas Harrison Haye (talk | contribs) (SNP Information & Primer Design)

     15:20  BME100 f2017:Group7 W0800 L4‎ (diff | hist) . . (-4). . Miguel R. Almanza Lopez (talk | contribs) (OUR TEAM)

     15:16 

(Upload log). .

[Miguel R. Almanza Lopez‎; Kaifu Chen‎ (2×); Jacob Tomas Harrison Haye‎ (4×); Alivia Ankrum‎ (4×)]

     

15:16

. . Miguel R. Almanza Lopez (talk | contribs) uploaded File:MralPoopy.jpg

     

14:39

. . Kaifu Chen (talk | contribs) uploaded File:Jcm.jpg

     

14:38

. . Kaifu Chen (talk | contribs) uploaded File:Wgy.jpg

     

14:25

. . Jacob Tomas Harrison Haye (talk | contribs) uploaded a new version of File:DNA4.jpg

     

14:25

. . Jacob Tomas Harrison Haye (talk | contribs) uploaded a new version of File:DNA4.jpg

     

14:22

. . Jacob Tomas Harrison Haye (talk | contribs) uploaded a new version of File:DNA3.jpg

     

14:18

. . Jacob Tomas Harrison Haye (talk | contribs) uploaded File:DNA4.jpg

     

14:18

. . Alivia Ankrum (talk | contribs) uploaded File:Badg12.png

     

14:10

. . Alivia Ankrum (talk | contribs) uploaded a new version of File:Goodresultsg12.png

     

14:07

. . Alivia Ankrum (talk | contribs) uploaded File:Goodresultsg12.png

     

14:06

. . Alivia Ankrum (talk | contribs) uploaded a new version of File:Screenshot1.png

     14:40 

BME100 f2017:Group1 W1030 L4‎‎ (8 changes | history) . . (+503). . [Emily A. Hanzlick‎; Abby E. Krell‎ (7×)]

     

14:40

(cur | prev) . . (+33). . Abby E. Krell (talk | contribs) (Protocol)

     

14:39

(cur | prev) . . (+28). . Abby E. Krell (talk | contribs) (Protocol)

     

14:38

(cur | prev) . . (+220). . Abby E. Krell (talk | contribs) (Protocol)

     

14:35

(cur | prev) . . (+178). . Abby E. Krell (talk | contribs) (Protocol)

     

14:32

(cur | prev) . . (+4). . Abby E. Krell (talk | contribs) (Research and Development)

     

14:32

(cur | prev) . . (0). . Abby E. Krell (talk | contribs) (Research and Development)

     

14:30

(cur | prev) . . (+17). . Abby E. Krell (talk | contribs) (Protocol)

     

14:01

(cur | prev) . . (+23). . Emily A. Hanzlick (talk | contribs) (Research and Development)

     14:19 

BME100 f2017:Group12 W1030 L4‎‎ (4 changes | history) . . (+68). . [Alivia Ankrum‎ (4×)]

     

14:19

(cur | prev) . . (0). . Alivia Ankrum (talk | contribs) (SNP Information & Primer Design)

     

14:19

(cur | prev) . . (+30). . Alivia Ankrum (talk | contribs) (SNP Information & Primer Design)

     

14:14

(cur | prev) . . (0). . Alivia Ankrum (talk | contribs) (SNP Information & Primer Design)

     

14:13

(cur | prev) . . (+38). . Alivia Ankrum (talk | contribs) (SNP Information & Primer Design)