|
| Status |
Public on Nov 20, 2018 |
| Title |
CRZ2_4h_rep1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Untreated control, grown in YPD medium during 4h
|
| Organism |
Candida albicans |
| Characteristics |
strain/background: C90
genotype/variation: homozygous crz2-/- deletion and CIp-PTET-CRZ5
treatment: none
time point: 4h
|
| Treatment protocol |
See growth protocol.
|
| Growth protocol |
For the CRZ2_2h, CRZ2_4h and TETp microarray experiments (Samples 1-6 and 19-22), total RNA was extracted from 3 independently-generated crz2Δ/crz2Δ strains carrying the PTET-CRZ2 fusion (samples 1-6) or the PTET empty vector (samples 19-22), pre-grown overnight in 10 ml YPD at 30ºC then diluted in fresh YPD medium supplemented or not with 40 µg.mL−1 doxycycline to an OD600 nm of 0.3 and re-grown for 2 (samples 1-3) and 4 (samples 4-6 and 19-22) hours. For the WT vs. crz2Δ/Δ and the Norm > Hyp shift microarray experiments (samples 7-12 and 13-18, respectively), strains CEC369 (wild-type) and C90 (crz2Δ/Δ) were grown overnight in 10 ml YPD at 30ºC, then diluted to an OD600 nm of 0.16 in 250-ml flasks containing 50 ml of YPD medium. The flasks were incubated in a BBL GasPak anaerobic jar at 37°C for 24 h without shaking (Hypoxia 37ºC) or in a 30ºC-incubator for 24h under vigorous shaking (Normoxia, 30ºC).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the hot phenol method as described in Znaidi et al. (2013) PLoS Pathogens 9: e1003519.
|
| Label |
Cy3
|
| Label protocol |
First-strand cDNA synthesis and Cy5/Cy3 labeling from 20 µg total RNA was performed using the Superscript III indirect cDNA labeling system (Invitrogen).
|
| |
|
| Channel 2 |
| Source name |
Dox-treated at a concentration of 40 µg/mL in YPD medium for 4h
|
| Organism |
Candida albicans |
| Characteristics |
strain/background: C90
genotype/variation: homozygous crz2-/- deletion and CIp-PTET-CRZ5
treatment: doxycycline
time point: 4h
|
| Treatment protocol |
See growth protocol.
|
| Growth protocol |
For the CRZ2_2h, CRZ2_4h and TETp microarray experiments (Samples 1-6 and 19-22), total RNA was extracted from 3 independently-generated crz2Δ/crz2Δ strains carrying the PTET-CRZ2 fusion (samples 1-6) or the PTET empty vector (samples 19-22), pre-grown overnight in 10 ml YPD at 30ºC then diluted in fresh YPD medium supplemented or not with 40 µg.mL−1 doxycycline to an OD600 nm of 0.3 and re-grown for 2 (samples 1-3) and 4 (samples 4-6 and 19-22) hours. For the WT vs. crz2Δ/Δ and the Norm > Hyp shift microarray experiments (samples 7-12 and 13-18, respectively), strains CEC369 (wild-type) and C90 (crz2Δ/Δ) were grown overnight in 10 ml YPD at 30ºC, then diluted to an OD600 nm of 0.16 in 250-ml flasks containing 50 ml of YPD medium. The flasks were incubated in a BBL GasPak anaerobic jar at 37°C for 24 h without shaking (Hypoxia 37ºC) or in a 30ºC-incubator for 24h under vigorous shaking (Normoxia, 30ºC).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the hot phenol method as described in Znaidi et al. (2013) PLoS Pathogens 9: e1003519.
|
| Label |
Cy5
|
| Label protocol |
First-strand cDNA synthesis and Cy5/Cy3 labeling from 20 µg total RNA was performed using the Superscript III indirect cDNA labeling system (Invitrogen).
|
| |
|
| |
| Hybridization protocol |
Gene Expression Hybridization Kit (Cat# 5188-5242) from Agilent Technologies was used to prepare 50 µl of purified labeled samples as recommended by the manufacturer, followed by hybridization to the Agilent-026869 array.
|
| Scan protocol |
Images of Cy5 and Cy3 fluorescence were generated by scanning the expression arrays using an Axon Autoloader 4200AL scanner (Molecular Devices, Downington, PA). Images were analyzed with the GenePix Pro 6.1.0.2 software (Molecular Devices, Downington, PA).
|
| Description |
Sample 4
|
| Data processing |
GenePix Results (GPR) files were imported into the Arraypipe 2.0 for spot filtering, background subtraction (limma normexp BG correction) and Lowess global normalization of signal intensities.
|
| |
|
| Submission date |
Mar 24, 2015 |
| Last update date |
Oct 20, 2020 |
| Contact name |
Sadri ZNAIDI |
| E-mail(s) |
sadri.znaidi@gmail.com
|
| Organization name |
Institut Pasteur
|
| Department |
Mycology Department
|
| Lab |
Fungal Biology and Pathogenicity
|
| Street address |
25 rue du Docteur Roux
|
| City |
Paris |
| ZIP/Postal code |
75015 |
| Country |
France |
| |
|
| Platform ID |
GPL19932 |
| Series (2) |
| GSE67226 |
Genome-wide expression profiling of Candida albicans transcription factor Crz2p |
| GSE67235 |
Systematic gene overexpression in Candida albicans identifies a regulator of early adaptation to the mammalian gut |
|
