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:
- Investigation description
- Sample and data relationship
- Raw data
- Processed data
- Array Design 1
- Array Design 2
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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