|
| Status |
Public on Apr 13, 2021 |
| Title |
C. albicans SN250 Biofilm Growth in Spider Replicate 1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
SN250 spider biofilm
|
| Organism |
Candida albicans |
| Characteristics |
media: Spider
growth: biofilm
|
| Treatment protocol |
See Nobile et al. Cell 2012
|
| Growth protocol |
Cultures for the extraction of total RNA under biofilm growth conditions were performed on biofilms grown on the bottom of 6-well polystyrene plates for 48 hours at 37°C and 200 rpm as previously described (Nobile et al. 2012). The media used was Spider 1% glucose, Spider and RPMI 1% glucose. Planktonic cultures for total RNA were grown in the same media by inoculating with cells from an overnight 30°C YPD culture to an OD600 of 0.05. Cultures were then grown in flasks at 37°C with shaking at 225 rpm until they reached an OD600 of 1.0.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated and reverse transcribed as previously described (Nobile et al. 2012). Additionally, reverse transcription reactions were performed on either individual samples or on RNA in which an equivalent amount of each RNA sample was pooled.
|
| Label |
Cy5
|
| Label protocol |
cDNA was dried and resuspended in 5 μL 0.1 M sodium bicarbonate. An equivalent volume of Cy3 (pool) or Cy5 (individual) dye (Amersham) was added (dyes were resuspended in 60 μL of DMSO) and the reaction incubated at 65° for 20 minutes in the dark. Labeled cDNAs were purified using a Clean and Concentrator -5 kit (Zymo Research).
|
| |
|
| Channel 2 |
| Source name |
pooled reference
|
| Organism |
Candida albicans |
| Characteristics |
tag: pooled reference
|
| Treatment protocol |
See Nobile et al. Cell 2012
|
| Growth protocol |
Cultures for the extraction of total RNA under biofilm growth conditions were performed on biofilms grown on the bottom of 6-well polystyrene plates for 48 hours at 37°C and 200 rpm as previously described (Nobile et al. 2012). The media used was Spider 1% glucose, Spider and RPMI 1% glucose. Planktonic cultures for total RNA were grown in the same media by inoculating with cells from an overnight 30°C YPD culture to an OD600 of 0.05. Cultures were then grown in flasks at 37°C with shaking at 225 rpm until they reached an OD600 of 1.0.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated and reverse transcribed as previously described (Nobile et al. 2012). Additionally, reverse transcription reactions were performed on either individual samples or on RNA in which an equivalent amount of each RNA sample was pooled.
|
| Label |
Cy3
|
| Label protocol |
cDNA was dried and resuspended in 5 μL 0.1 M sodium bicarbonate. An equivalent volume of Cy3 (pool) or Cy5 (individual) dye (Amersham) was added (dyes were resuspended in 60 μL of DMSO) and the reaction incubated at 65° for 20 minutes in the dark. Labeled cDNAs were purified using a Clean and Concentrator -5 kit (Zymo Research).
|
| |
|
| |
| Hybridization protocol |
Equal amounts of the Cy3 and Cy5 labeled cDNA hybridized to the array overnight, as described in the Agilent protocol. Following hybridization, the arrays were washed as specified by Agilent.
|
| Scan protocol |
Arrays were scanned at 5 μm, averaging 2 lines, with an Axon GenePix 4000A scanner.
|
| Description |
sn250-sp-biofilm-1
|
| Data processing |
Arrays were gridded using GenePix Pro version 5.1. Global Lowess normalization analysis was performed for each array using a Goulphar script (The R Foundation for Statistical Computing). Normalized data was collapsed first by averaging the result for all duplicate probes and finally by taking the median of the probes for each ORF. Data was transformed as described for each experiment. Note that comparisons between arrays can only be made if they share a pooled reference (Ch2)
|
| |
|
| Submission date |
Nov 03, 2020 |
| Last update date |
Apr 17, 2021 |
| Contact name |
Eugenio Mancera |
| E-mail(s) |
[email protected]
|
| Organization name |
Cinvestav
|
| Department |
Ingenieria Genetica
|
| Street address |
Km. 9.6 Libramiento Norte Carretera Irapuato-Leon
|
| City |
Irapuato |
| State/province |
Guanajuato |
| ZIP/Postal code |
36824 |
| Country |
Mexico |
| |
|
| Platform ID |
GPL16243 |
| Series (2) |
| GSE160782 |
Gene Expression Arrays comparing C. albicans SN250 during planktonic and biofilm growth in different media |
| GSE160783 |
Evolution of biofilm formation in Candida |
|
