BIOL368/F14:Isabel Gonzaga Week 12

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Getting to Know Your Microarray Data

The ArrayExpress site for the Voskuil et al. (2003) article was accessed and the following files were downloaded and uploaded onto Lionshare:


Based on the methods section of the paper:

  • What samples did they collect and use for the microarray experiment?
    • Mtb 1254 exposed to 50μM DETA/NO for 40 minutes
    • Mtb 1254 control condition
    • Mtb H37Rv exposed to 0.2% O2 for 2 hours (hypoxia)
    • Mtb H37Rv at 4 days gradual adaptation and low O2 (dormancy)
    • Mtb exposed to 5μM DETA/NO for 40 minutes
    • Mtb exposed to 50μM DETA/NO for 40 minutes
    • Mtb exposed to 500μM DETA/NO for 40 minutes
    • Mtb exposed to 1000μM DETA/NO for 40 minutes
    • Mtb exposed to 5000μM DETA/NO for 40 minutes
    • Mtb exposed to 500μM DETA/NO for 0 minutes
    • Mtb exposed to 500μM DETA/NO for 10 minutes
    • Mtb exposed to 500μM DETA/NO for 20 minutes
    • Mtb exposed to 500μM DETA/NO for 40 minutes
    • Mtb exposed to 500μM DETA/NO for 60 minutes
    • Mtb exposed to 500μM DETA/NO for 2 hours
    • Mtb exposed to 500μM DETA/NO for 8 hours
    • Mtb exposed to 500μM DETA/NO for 16 hours
    • Mtb exposed to 500μM DETA/NO for 24 hours + 40 minutes with additional NO pulse
    • Mtb exposed to 50μM DETA/NO for 40 minutes
    • Mtb exposed to 50μM KCN for 40 minutes
    • Mtb exposed to 50μM KCN + DETA/NO for 40 minutes
    • Mtb exposed to 2 hour hypoxia
    • Mtb exposed to 500μM KCN + 2 hour hypoxia
    • Mtb exposed to 0μM DETA/NO at low aeration
    • Mtb exposed to 1μM DETA/NO at low aeration
    • Mtb exposed to 5μM DETA/NO at low aeration
    • Mtb exposed to 10μM DETA/NO at low aeration
    • Mtb exposed to 50 μM DETA/NO at low aeration
    • Mtb exposed to 0μM DETA/NO at high aeration
    • Mtb exposed to 1μM DETA/NO at high aeration
    • Mtb exposed to 5μM DETA/NO at high aeration
    • Mtb exposed to 10μM DETA/NO at high aeration
    • Mtb exposed to 50 μM DETA/NO at high aeration
  • How many microarray chips did they hybridize in the experiment? 131 chips
  • Which samples were paired to hybridize on the chip?
    • Mtb 1254 control / Mtb 1254 exposed to 50μM DETA/NO for 40 minutes
    • Mtb H37Rv control / Mtb H37Rv exposed to 0.2% O2 for 2 hours (hypoxia)
    • Mtb H37Rv control / Mtb H37Rv at 4 days gradual adaptation and low O2 (dormancy)
    • Mtb 1254 control / Mtb 1254 exposed to 5μM DETA/NO for 40 minutes
    • Mtb 1254 control / Mtb 1254 exposed to 50μM DETA/NO for 40 minutes
    • Mtb 1254 control / Mtb 1254 exposed to 500μM DETA/NO for 40 minutes
    • Mtb 1254 control / Mtb 1254 exposed to 1000μM DETA/NO for 40 minutes
    • Mtb 1254 control / Mtb 1254 exposed to 5000μM DETA/NO for 40 minutes
    • Mtb exposed to 500μM DETA/NO for 0 minutes / Mtb exposed to 500μM DETA/NO for 10 minutes
    • Mtb exposed to 500μM DETA/NO for 0 minutes / Mtb exposed to 500μM DETA/NO for 20 minutes
    • Mtb exposed to 500μM DETA/NO for 0 minutes / Mtb exposed to 500μM DETA/NO for 40 minutes
    • Mtb exposed to 500μM DETA/NO for 0 minutes / Mtb exposed to 500μM DETA/NO for 60 minutes
    • Mtb exposed to 500μM DETA/NO for 0 minutes / Mtb exposed to 500μM DETA/NO for 2 hours
    • Mtb exposed to 500μM DETA/NO for 0 minutes / Mtb exposed to 500μM DETA/NO for 8 hours
    • Mtb exposed to 500μM DETA/NO for 0 minutes / Mtb exposed to 500μM DETA/NO for 16 hours
    • Mtb exposed to 500μM DETA/NO for 0 minutes / Mtb exposed to 500μM DETA/NO for 24 hours + 40 minutes with additional NO pulse
    • Mtb 1254 control / Mtb exposed to 50μM DETA/NO for 40 minutes
    • Mtb 1254 control / Mtb exposed to 50μM KCN for 40 minutes
    • Mtb 1254 control / Mtb exposed to 50μM KCN + DETA/NO for 40 minutes
    • Mtb 1254 control / Mtb exposed to 2 hour hypoxia
    • Mtb 1254 control / Mtb exposed to 500μM KCN + 2 hour hypoxia
    • Mtb exposed to 0μM DETA/NO at low aeration / Mtb exposed to 1μM DETA/NO at low aeration
    • Mtb exposed to 0μM DETA/NO at low aeration / Mtb exposed to 5μM DETA/NO at low aeration
    • Mtb exposed to 0μM DETA/NO at low aeration / Mtb exposed to 10μM DETA/NO at low aeration
    • Mtb exposed to 0μM DETA/NO at low aeration / Mtb exposed to 50 μM DETA/NO at low aeration
    • Mtb exposed to 0μM DETA/NO at high aeration / Mtb exposed to 1μM DETA/NO at high aeration
    • Mtb exposed to 0μM DETA/NO at high aeration / Mtb exposed to 5μM DETA/NO at high aeration
    • Mtb exposed to 0μM DETA/NO at high aeration / Mtb exposed to 10μM DETA/NO at high aeration
    • Mtb exposed to 0μM DETA/NO at high aeration / Mtb exposed to 50 μM DETA/NO at high aeration
  • Which was labeled red (Cy5)? Which was labeled green (Cy3)?
    • The control samples were labeled green with Cy3 with experimental samples labeled red with Cy5
  • How many replicates did they perform of each type?
    • For all experiments, they performed 3 biological replicates with 2 technical replicates for a total of 6 replicates per type
    • For the experiments in Figure 2, they performed 2 biological replicates with 4 technical replicates

Using the .sdrf.txt file, I determined which files corresponded to the samples used in Figure 1
MTB strain 1254 0.05mM DETA/NO for 40 min

Condition Extract Name and Label Data File
Cy3 Control treatment GSM886377 LE 1 GSM886377_sample_table.txt
Cy5 0.05mM DETA/NO for 40 min GSM886377 LE 2 GSM886377_sample_table.txt
Cy3 Control treatment GSM886320 LE 1 GSM886320_sample_table.txt
Cy5 0.05mM DETA/NO for 40 min GSM886320 LE 2 GSM886320_sample_table.txt
Cy3 Control treatment GSM886253 LE 1 GSM886253_sample_table.txt
Cy5 0.05mM DETA/NO for 40 min GSM886253 LE 2 GSM886253_sample_table.txt
Cy3 Control treatment GSM886327 LE 1 GSM886327_sample_table.txt
Cy5 0.05mM DETA/NO for 40 min GSM886327 LE 2 GSM886327_sample_table.txt
Cy3 Control treatment GSM886295 LE 1 GSM886295_sample_table.txt
Cy5 0.05mM DETA/NO for 40 min GSM886295 LE 2 GSM886295_sample_table.txt
Cy3 Control treatment GSM886347 LE 1 GSM886347_sample_table.txt
Cy5 0.05mM DETA/NO for 40 min GSM886347 LE 2 GSM886347_sample_table.txt
Cy3 Control treatment GSM886364 LE 1 GSM886364_sample_table.txt
Cy5 0.05mM DETA/NO for 40 min GSM886364 LE 2 GSM886364_sample_table.txt




Hypoxia Condition: 2 hr to 0.2% O2

Condition Extract Name and Label Data File
Cy3 Control treatment GSM886332 LE 1 GSM886332_sample_table.txt
Cy5 1254 HypoxiaGP 2h GSM886332 LE 2 GSM886332_sample_table.txt
Cy3 Control treatment GSM886273 LE 1 GSM886273_sample_table.txt
Cy5 1254 HypoxiaGP 2h GSM886273 LE 2 GSM886273_sample_table.txt
Cy3 Control treatment GSM886373 LE 1 GSM886373_sample_table.txt
Cy5 GasPak 2h 1256 GSM886373 LE 2 GSM886373_sample_table.txt




Dormancy condition: Mtb H37Rv Day 4 gradual adaptation

Condition Extract Name and Label Data File
Cy3 Control treatment GSM886248 LE 1 GSM886248_sample_table.txt
Cy5 NRP (Wayne Growth)/4 days GSM886248 LE 2 GSM886248_sample_table.txt
Cy3 Control treatment GSM886348 LE 1 GSM886348_sample_table.txt
Cy5 NRP (Wayne Growth)/4 days GSM886348 LE 2 GSM886348_sample_table.txt
Cy3 Control treatment GSM886264 LE 1 GSM886264_sample_table.txt
Cy5 NRP (Wayne Growth)/4 days GSM886264 LE 2 GSM886264_sample_table.txt
Cy3 Control treatment GSM886355 LE 1 GSM886355_sample_table.txt
Cy5 NRP (Wayne Growth)/4 days GSM886355 LE 2 GSM886355_sample_table.txt
Cy3 Control treatment GSM886294 LE 1 GSM886294_sample_table.txt
Cy5 NRP (Wayne Growth)/4 days GSM886294 LE 2 GSM886294_sample_table.txt
Cy3 Control treatment GSM886339 LE 1 GSM886339_sample_table.txt
Cy5 NRP (Wayne Growth)/4 days GSM886339 LE 2 GSM886339_sample_table.txt



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