|
| Status |
Public on Mar 03, 2023 |
| Title |
sfl1Δ_biofilm_vs_ SN76_biofilm_rep1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
sfl1delta/sfl1delta
|
| Organism |
Candida albicans |
| Characteristics |
genotype: sfl1delta/sfl1delta
growth mode: biofilm
|
| Growth protocol |
For the transcriptomic profiling an individual colony of C. albicans SN76 and sfl1Δ/sfl1Δ strains was inoculated in SDB at 37 ºC with orbital agitation (120 rev/min) overnight and then re-inoculated (at 1x105 cel/ml) in 25 ml of RPMI at pH 4 and left to grow for 24h at 37ºC and 120 rev/min orbital shake, inside Erlenmeyer flaks and microtiter plates, in order to induce planktonic and biofilm growth, respectively.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The extraction of RNA from the cells was performed using the RiboPure – Yeast Kit (Life Technologies, CA), according to the manufacturer’s instructions.The concentration and purity of the extracted RNA were determined by spectrophotometry and its integrity was confirmed in an Agilent 2100 Bioanalyzer with an RNA 6000 Nano Assay (Agilent Technologies, CA).
|
| Label |
Cy5
|
| Label protocol |
cDNA synthesis, hybridization, and scanning were performed using the Agilent protocol for two-color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling v6.9 (Agilent Technologies), according to the manufacturer’s instructions. One hundred nanograms of total RNA of each strain were used to synthesize labeled cDNA (with Cyanine 3-CTP and cyanine 5-CTP), using Agilent T7 Promoter Primer and T7 RNA polymerase Blend (Agilent Technologies, Cat.5190–2305).
|
| |
|
| Channel 2 |
| Source name |
SN76
|
| Organism |
Candida albicans |
| Characteristics |
genotype: SN76
growth mode: biofilm
|
| Growth protocol |
For the transcriptomic profiling an individual colony of C. albicans SN76 and sfl1Δ/sfl1Δ strains was inoculated in SDB at 37 ºC with orbital agitation (120 rev/min) overnight and then re-inoculated (at 1x105 cel/ml) in 25 ml of RPMI at pH 4 and left to grow for 24h at 37ºC and 120 rev/min orbital shake, inside Erlenmeyer flaks and microtiter plates, in order to induce planktonic and biofilm growth, respectively.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The extraction of RNA from the cells was performed using the RiboPure – Yeast Kit (Life Technologies, CA), according to the manufacturer’s instructions.The concentration and purity of the extracted RNA were determined by spectrophotometry and its integrity was confirmed in an Agilent 2100 Bioanalyzer with an RNA 6000 Nano Assay (Agilent Technologies, CA).
|
| Label |
Cy3
|
| Label protocol |
cDNA synthesis, hybridization, and scanning were performed using the Agilent protocol for two-color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling v6.9 (Agilent Technologies), according to the manufacturer’s instructions. One hundred nanograms of total RNA of each strain were used to synthesize labeled cDNA (with Cyanine 3-CTP and cyanine 5-CTP), using Agilent T7 Promoter Primer and T7 RNA polymerase Blend (Agilent Technologies, Cat.5190–2305).
|
| |
|
| |
| Hybridization protocol |
Six hundred nanograms of labelled cDNA were hybridized in the microarray. Hybridizations were carried out using Agilent gasket slides in a rotating oven for 17 h at 65°C.
|
| Scan protocol |
Slides were then washed following manufacturer’s instructions and scanned in an Agilent G2565AA microarrays scanner. Probes signal values were extracted using Agilent Feature Extraction Software.
|
| Data processing |
Data were normalized using median centering of signal distribution with Biometric Research Branch BRB-Array tools v3.4.o software 36. Final statistical analysis was carried out using LIMMA package in MeV software (MultiExperiment Viewer 4.8.0) 36 with a cut-off p-value of 0.1.
|
| |
|
| Submission date |
Jun 15, 2022 |
| Last update date |
Mar 03, 2023 |
| Contact name |
Ana Soares |
| E-mail(s) |
ana.r.soares@ua.pt
|
| Organization name |
University of Aveiro
|
| Street address |
Campus de Santiago
|
| City |
Aveiro |
| ZIP/Postal code |
3810 |
| Country |
Portugal |
| |
|
| Platform ID |
GPL22275 |
| Series (1) |
| GSE206208 |
Transcriptomic regulation of acidic biofilms by Candida albicans Sfl1 |
|
