User:Karmella Haynes/Notebook/PcTF Genomics

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(Illumina ChIP-seq)
(Cell Type Study)
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==Illumina ChIP-seq==
==Illumina ChIP-seq==
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* General Computing
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** [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
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** 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]
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** Input DNA - [http://openwetware.org/wiki/User:Karmella_Haynes/Notebook/PcTF_Genomics/2013/01/25 01/25/13]
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** 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];
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* Fasta --> BAM files: Mark Teng from the Dinu lab (TGEN)
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* IP samples Fasta --> BAM files: Mark Teng from the Dinu lab (TGEN)
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* Input sample Fasta --> BAM file: Karthik Velmurugan on 5/16/13 (external hard drive)
* Enrichment analysis (DNASTAR software)
* Enrichment analysis (DNASTAR software)
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** 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 --> 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]
** DNASTAR: BAM --> wig files for UCSC browser workflow [http://openwetware.org/wiki/User:Karmella_Haynes/Notebook/PcTF_Genomics/2013/01/07 01/07/2013]
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** K562 - TRIzol prep [http://openwetware.org/wiki/User:Karmella_Haynes/Notebook/PcTF_Genomics/2012/12/18 12/18/12]
** 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]
** SK-N-SH - TRIzol prep [http://openwetware.org/wiki/User:Karmella_Haynes/Notebook/PcTF_Genomics/2012/12/27 12/27/12]
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** U2OS TriZOL prep
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** U2OS TRIzol prep [http://openwetware.org/wiki/User:Karmella_Haynes/Notebook/PcTF_Genomics/2014/01/27 01/27/14]
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* Dr. Haynes - Quality control mCherry & GAPDH runs
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** 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]
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** 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]
==PcTF-Reporter Activation==
==PcTF-Reporter Activation==

Revision as of 13:50, 4 June 2014

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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

PcTF-Reporter Activation

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


Synthetic Repression

  • Gal4-EED/luc staining experiments


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