Samantha M. Hurndon Week 12: DNA Microarray project: Difference between revisions

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(New page: #Go to the ArrayExpress site for your data and select "view all available files". #Download the following files: #*Experiment ReadMe #*raw.zip #*processed.zip #*sdrf.xls #*Array ReadMe #*a...)
 
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#Go to the ArrayExpress site for your data and select "view all available files".
#Download the following files:
#*Experiment ReadMe
#*raw.zip
#*processed.zip
#*sdrf.xls
#*Array ReadMe
#*adf.xls
#Then upload these files to the OpenWetWare wiki and then link to them on your individual journal pages. Only one member of your group needs to upload them, then both partners can just link to the same file.
#From the methods section of your microarray paper, you need to figure out the following:
#From the methods section of your microarray paper, you need to figure out the following:
#*What samples did they collect and use for the microarray experiment?
#*What samples did they collect and use for the microarray experiment?
Line 19: Line 10:
#Using the sdrf.xls file, you need to then find the names of the files that correspond to the names of your samples from the paper. Make a list that says which file corresponds to which sample.
#Using the sdrf.xls file, you need to then find the names of the files that correspond to the names of your samples from the paper. Make a list that says which file corresponds to which sample.
#The instructor will then show you which columns of data to copy into a new Master spreadsheet. You will upload this spreadsheet to the wiki and then link to it from your journal page.
#The instructor will then show you which columns of data to copy into a new Master spreadsheet. You will upload this spreadsheet to the wiki and then link to it from your journal page.
===Link to all files from Douillard paper===
http://www.ebi.ac.uk/arrayexpress/files/E-BUGS-78
===Readme's===
*[[Media:E-BUGS-78.README.txt|Experiment E-BUGS-78]]
===Processed===
*[[Media:DBAD_32788.txt]]
*[[Media:DBAD_32789.txt]]
*[[Media:DBAD_32795.txt]]
*[[Media:E-BUGS-78-processed-data-1757476218.txt]]
*[[Media:E-BUGS-78-processed-data-1757476240.txt]]
*[[Media:E-BUGS-78-processed-data-1757476352.txt]]
===Raw===
*[[Media:MBAD_32054.txt]]
*[[Media:MBAD_32055.txt]]
*[[Media:MBAD_32056.txt]]
*[[Media:MBAD_32057.txt]]
*[[Media:MBAD_32058.txt]]
*[[Media:MBAD_32059.txt]]
*[[Media:MBAD_32062.txt]]
*[[Media:MBAD_32063.txt]]
*[[Media:MBAD_32064.txt]]
*[[Media:MBAD_32065.txt]]
*[[Media:MBAD_32066.txt]]
*[[Media:MBAD_32067.txt]]
*[[Media:MBAD_32068.txt]]
*[[Media:MBAD_32069.txt]]
*[[Media:MBAD_32070.txt]]
*[[Media:MBAD_32071.txt]]
*[[Media:MBAD_32074.txt]]
*[[Media:MBAD_32075.txt]]
*[[Media:MBAD_32080.txt]]
*[[Media:MBAD_32081.txt]]
*[[Media:MBAD_32084.txt]]
*[[Media:MBAD_32085.txt]]
===.sdrf.txt file===
*[[Media:E-BUGS-78.sdrf.txt]]
===Array Files===
*[[Media:A-BUGS-18.README.txt|Array A-BUGS-18]]
*[[Media:A-BUGS-18.adf.xls]]
===Cy5===
*hp0906KO total RNA (C1)
:[[Media:MBAD_32063.txt|MBAD_32063.txt]]
*CCUG17874 total RNA (C1)
:[[Media:MBAD_32085.txt|MBAD_32085.txt]]
*hp0906KO total RNA (B1)
:[[Media:MBAD_32065.txt|MBAD_32065.txt]]
*hp0906KO total RNA (A1)
:[[Media:MBAD_32067.txt|MBAD_32067.txt]]
*hp0958 KO total RNA (B1)
:[[Media:MBAD_32059.txt|MBAD_32059.txt]]
*hp0958 KO total RNA (A1)
:[[Media:MBAD_32057.txt|MBAD_32057.txt]]
*CCUG17874 total RNA (B1)
:[[Media:MBAD_32075.txt|MBAD_32075.txt]]
*CCUG17874 total RNA (A1)
:[[Media:MBAD_32081.txt|MBAD_32081.txt]]
*hp0958 KO total RNA (C1)
:[[Media:MBAD_32055.txt|MBAD_32055.txt]]
*CCUG17874 gDNA (B1)
:[[Media:MBAD_32069.txt|MBAD_32069.txt]]
*CCUG17874 gDNA (A1)__bugs.sgul.ac.uk:BuG@Sbase/BioSample:23772
:[[Media:MBAD_32081.txt|MBAD_32081.txt]]
===Cy3===
*CCUG17874 gDNA (A3)
:[[Media:MBAD_32062.txt|MBAD_32062.txt]]
*CCUG17874 gDNA (A3)__bugs.sgul.ac.uk:BuG@Sbase/BioSample:23768
:[[Media:MBAD_32084.txt|MBAD_32084.txt]]
*CCUG17874 gDNA (A2)
:[[Media:MBAD_32064.txt|MBAD_32064.txt]]
*CCUG17874 gDNA (A1)
:[[Media:MBAD_32067.txt|MBAD_32067.txt]]
*NCTC26695 gDNA (B1)
:[[Media:MBAD_32074.txt|MBAD_32074.txt]]
*CCUG17874 gDNA (A5)__bugs.sgul.ac.uk:BuG@Sbase/BioSample:23768
:[[Media:MBAD_32058.txt|MBAD_32058.txt]]
*NCTC26695 gDNA (A1)
:[[Media:MBAD_32070.txt|MBAD_32070.txt]]
*CCUG17874 gDNA (A4)__bugs.sgul.ac.uk:BuG@Sbase/BioSample:23768
:[[Media:MBAD_32056.txt|MBAD_32056.txt]]
*CCUG17874 gDNA (A2)__bugs.sgul.ac.uk:BuG@Sbase/BioSample:23768
:[[Media:MBAD_32068.txt|MBAD_32068.txt]]
*CCUG17874 gDNA (A1)__bugs.sgul.ac.uk:BuG@Sbase/BioSample:23768
:[[Media:MBAD_32080.txt|MBAD_32080.txt]]
*CCUG17874 gDNA (A6)__bugs.sgul.ac.uk:BuG@Sbase/BioSample:23768
:[[Media:MBAD_32054.txt|MBAD_32054.txt]]
===Hybridizations===
*Cy5 hp0906KO (C1) with Cy3 CCUG17874 (A3)              →  Hyb:32525
*Cy3 CCUG17874 (A3)-23856 with Cy5 CCUG17874 (C1)        →  Hyb:32519
*Cy5 hp0906KO (B1) with Cy3 CCUG17874 (A2)              →  Hyb:32524
*Cy3 CCUG17874 (A1) with Cy5 hp0906KO (A1)              →  Hyb:32523
*Cy5 CCUG17874 (B1) with Cy3 NCTC26695 (B1)              →  Hyb:32528
*Cy3 CCUG17874 (A5) with Cy5 hp0958 KO (B1)              →  Hyb:32521
*Cy3 NCTC26695 (A1) with Cy5 CCUG17874 (A1)              →  Hyb:32526
*Cy5 hp0958 KO (A1) with Cy3 CCUG17874 (A4)              →  Hyb:32520
*Cy3 CCUG17874 (A2)-23855 with Cy5 CCUG17874 (B2)-23817  →  Hyb:35218
*Cy3 CCUG17874 (A1)-23769 with Cy5 CCUG17874 (A1)-23814  →  Hyb:32517
*Cy3 CCUG17874 (A6) with Cy5 hp0958 KO (C1)              →  Hyb:32522
[[BIOL368/F11:Week_12]]

Revision as of 20:20, 24 November 2011

  1. From the methods section of your microarray paper, you need to figure out the following:
    • What samples did they collect and use for the microarray experiment?
    • How many microarray chips did they hybridize in the experiment?
    • Which samples were paired to hybridize on the chip?
    • Which was labeled red (Cy5)? Which was labeled green (Cy3)?
    • How many replicates did they perform of each type?
      • Biological replicates are made from entirely different biological samples.
      • Technical replicates are made when one biological sample is split at a particular stage in the procedure and then carried through to the end of the procedure.
  2. Record this information on your individual journal pages. If you have this from your journal outline, you can copy and paste it into your new journal page.
  3. Using the sdrf.xls file, you need to then find the names of the files that correspond to the names of your samples from the paper. Make a list that says which file corresponds to which sample.
  4. The instructor will then show you which columns of data to copy into a new Master spreadsheet. You will upload this spreadsheet to the wiki and then link to it from your journal page.

Link to all files from Douillard paper

http://www.ebi.ac.uk/arrayexpress/files/E-BUGS-78

Readme's

Processed

Raw

.sdrf.txt file

Array Files

Cy5

  • hp0906KO total RNA (C1)
MBAD_32063.txt
  • CCUG17874 total RNA (C1)
MBAD_32085.txt
  • hp0906KO total RNA (B1)
MBAD_32065.txt
  • hp0906KO total RNA (A1)
MBAD_32067.txt
  • hp0958 KO total RNA (B1)
MBAD_32059.txt
  • hp0958 KO total RNA (A1)
MBAD_32057.txt
  • CCUG17874 total RNA (B1)
MBAD_32075.txt
  • CCUG17874 total RNA (A1)
MBAD_32081.txt
  • hp0958 KO total RNA (C1)
MBAD_32055.txt
  • CCUG17874 gDNA (B1)
MBAD_32069.txt
  • CCUG17874 gDNA (A1)__bugs.sgul.ac.uk:BuG@Sbase/BioSample:23772
MBAD_32081.txt

Cy3

  • CCUG17874 gDNA (A3)
MBAD_32062.txt
  • CCUG17874 gDNA (A3)__bugs.sgul.ac.uk:BuG@Sbase/BioSample:23768
MBAD_32084.txt
  • CCUG17874 gDNA (A2)
MBAD_32064.txt
  • CCUG17874 gDNA (A1)
MBAD_32067.txt
  • NCTC26695 gDNA (B1)
MBAD_32074.txt
  • CCUG17874 gDNA (A5)__bugs.sgul.ac.uk:BuG@Sbase/BioSample:23768
MBAD_32058.txt
  • NCTC26695 gDNA (A1)
MBAD_32070.txt
  • CCUG17874 gDNA (A4)__bugs.sgul.ac.uk:BuG@Sbase/BioSample:23768
MBAD_32056.txt
  • CCUG17874 gDNA (A2)__bugs.sgul.ac.uk:BuG@Sbase/BioSample:23768
MBAD_32068.txt
  • CCUG17874 gDNA (A1)__bugs.sgul.ac.uk:BuG@Sbase/BioSample:23768
MBAD_32080.txt
  • CCUG17874 gDNA (A6)__bugs.sgul.ac.uk:BuG@Sbase/BioSample:23768
MBAD_32054.txt

Hybridizations

  • Cy5 hp0906KO (C1) with Cy3 CCUG17874 (A3) → Hyb:32525
  • Cy3 CCUG17874 (A3)-23856 with Cy5 CCUG17874 (C1) → Hyb:32519
  • Cy5 hp0906KO (B1) with Cy3 CCUG17874 (A2) → Hyb:32524
  • Cy3 CCUG17874 (A1) with Cy5 hp0906KO (A1) → Hyb:32523
  • Cy5 CCUG17874 (B1) with Cy3 NCTC26695 (B1) → Hyb:32528
  • Cy3 CCUG17874 (A5) with Cy5 hp0958 KO (B1) → Hyb:32521
  • Cy3 NCTC26695 (A1) with Cy5 CCUG17874 (A1) → Hyb:32526
  • Cy5 hp0958 KO (A1) with Cy3 CCUG17874 (A4) → Hyb:32520
  • Cy3 CCUG17874 (A2)-23855 with Cy5 CCUG17874 (B2)-23817 → Hyb:35218
  • Cy3 CCUG17874 (A1)-23769 with Cy5 CCUG17874 (A1)-23814 → Hyb:32517
  • Cy3 CCUG17874 (A6) with Cy5 hp0958 KO (C1) → Hyb:32522


BIOL368/F11:Week_12

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