|
| Status |
Public on Oct 01, 2014 |
| Title |
Adhered biofilm cells vs Mixed Reference 1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Adhered Biofilm (experiment 1)
|
| Organism |
Candida albicans |
| Characteristics |
source strain background: SC5314
strain: SN250
|
| Growth protocol |
C. albicans was grown in biofilms or in planktonic cultures at 30 deg or 37 deg in Spider media
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Ambion RiboPure Yeast RNA Kit (AM1926)
|
| Label |
Cy5
|
| Label protocol |
cDNA was synthesized from 8 mg total RNA using Superscript II Reverse Transcriptase (Invitrogen, 18064-014), according to the manufacturer’s instruction, and using a mixture of 0.5 mM 3:2 aminoally-dUTP (Ambion 8437):dNTPs. cDNA was dye coupled to either Cy3 or Cy5 (GE Healthcare PA23001 or PA25001)
|
| |
|
| Channel 2 |
| Source name |
Mixed reference pool#1: cDNA from 252016610046 - blocks 1 - 8
|
| Organism |
Candida albicans |
| Characteristics |
source strain background: SC5314
strain: SN250
|
| Growth protocol |
C. albicans was grown in biofilms or in planktonic cultures at 30 deg or 37 deg in Spider media
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Ambion RiboPure Yeast RNA Kit (AM1926)
|
| Label |
Cy3
|
| Label protocol |
cDNA was synthesized from 8 mg total RNA using Superscript II Reverse Transcriptase (Invitrogen, 18064-014), according to the manufacturer’s instruction, and using a mixture of 0.5 mM 3:2 aminoally-dUTP (Ambion 8437):dNTPs. cDNA was dye coupled to either Cy3 or Cy5 (GE Healthcare PA23001 or PA25001)
|
| |
|
| |
| Hybridization protocol |
0.4 mg Cy3-labelled cDNA and 0.4 mg Cy5-labelled cDNA were hybridized onto custom Agilent 8*15k microarrays (AMADID #020166)
|
| Scan protocol |
Scanned on a 4000B Axon Instrument Scanner
|
| Description |
252016610046-block 3
|
| Data processing |
Arrays were gridded with Gene Pix Pro software version 7, Lowess normalization was performed using a Goulphar script for R, Probes were collapsed to a median value using a custom java script
|
| |
|
| Submission date |
Sep 05, 2014 |
| Last update date |
Oct 01, 2014 |
| Contact name |
Emily Patricia Fox |
| E-mail(s) |
[email protected]
|
| Phone |
415-476-8097
|
| Organization name |
University of California, San Francisco
|
| Department |
Biochemistry and Biophysics
|
| Lab |
Alexander D. Johnson
|
| Street address |
600 16th Street, GH - N374
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143-2200 |
| Country |
USA |
| |
|
| Platform ID |
GPL13830 |
| Series (1) |
| GSE61143 |
C. albicans biofilm development |
|
