Samantha M. Hurndon Week 12: DNA Microarray project

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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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Revision as of 20:47, 16 November 2011

  1. Go to the ArrayExpress site for your data and select "view all available files".
  2. Download the following files:
    • Experiment ReadMe
    • raw.zip
    • processed.zip
    • sdrf.xls
    • Array ReadMe
    • adf.xls
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
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