|
| Status |
Public on Mar 11, 2013 |
| Title |
CgSTB5OE - repeat 3 - mAdbID:112910 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Cg84 Control_Cy3
|
| Organism |
Nakaseomyces glabratus |
| Characteristics |
strain: Cg84
genotype/variation: wild type
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol Sample Extraction Protocol
Total RNA was isolated by using Trizol (Invitrogen, Carlsbad, CA) and the RNeasy MiniElute cleanup kit (Qiagen, Valencia, CA).
|
| Label |
cy3
|
| Label protocol |
Cy3 Sample Labeling Protocol
Total RNA was reverse transcribed to cDNA to incorporate the fluorescent Cy3-dUTP (GE Health Care, Piscataway, NJ).
|
| |
|
| Channel 2 |
| Source name |
CgSTB5OE_Cy5
|
| Organism |
Nakaseomyces glabratus |
| Characteristics |
strain background: Cg84u (uracil auxotroph of Cg84)
strain: CgSTB5OE
genotype/variation: CgSTB5 overexpression
|
| Treatment protocol |
The 84u/stb5 mutant (Cgstb5delta) was generated as follows. The S. cerevisiae URA3 gene replaced the CAGL0I02552g ORF in the 84u strain. Transformants were selected on MIN media, and CAGL0I02552g deletion was confirmed by southern blot. Subsequently, CgSTB5 was sequence confirmed, digested with BamH1 and EcoR1 (both New England Biosciences), and ligated (Rapid DNA Ligation Kit , Roche Diagnostics, Germany) into pGRB2.2 (pGRB2.2/STB5) for overexpression in the C. glabrata 84u strain (CgSTB5OE).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol Sample Extraction Protocol
Total RNA was isolated by using Trizol (Invitrogen, Carlsbad, CA) and the RNeasy MiniElute cleanup kit (Qiagen, Valencia, CA).
|
| Label |
cy5
|
| Label protocol |
Cy5 Sample Labeling Protocol
Total RNA was reverse transcribed to cDNA to incorporate the fluorescent Cy5-dUTP (GE Health Care, Piscataway, NJ).
|
| |
|
| |
| Hybridization protocol |
Agilent Hybridization
According to the manufacture's recommended protocol (Two-Color Microarray-Based Gene Expression Analysis, Agilent).
|
| Scan protocol |
Scan_MicronsPerPixelX: 5
Scan_MicronsPerPixelY: 5
Scan_ScannerName: Agilent Technologies Scanner G2505C US45103101
|
| Description |
mAdb experiment ID: 112910
|
| Data processing |
CgSTB5OE Data Processing Protocol
Calculation Method: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software. Spot values were normalized using the default linear-lowess normalization. Default Ratio: ChanB/ChanA (Cy5/Cy3); Signal calculation: Agilent FE Processed Signals; Any Features designated Control were excluded; Normalization method: None (Using Agilent FE Processed Signals); Spot Filter Options: Both Chan A and Chan B Percentage of Target Pixels Saturated <= 50% AND Both Chan A and Chan B Signal >= 10 Override other Chan A & B criteria and Include if Chan A Signal >= 1000 OR Chan B Signal >= 1000 Signal Values were floored at 50 (ChanA and ChanB); Data was extracted and aligned by the Inventory Well ID Within array multiple occurrences of Well ID were reduced to a single instance by selecting the Median Value.
FeatureExtractor_Version: 10.7.3.1
Protocol_Name: GE2_107_Sep09 (Read Only)
|
| |
|
| Submission date |
Apr 05, 2012 |
| Last update date |
Mar 11, 2013 |
| Contact name |
Jason A Noble |
| E-mail(s) |
noblej2@mail.nih.gov
|
| Phone |
301-4968956
|
| Organization name |
National Institutes of Health
|
| Department |
NIAID
|
| Lab |
Clinical Mycology
|
| Street address |
10 Center Drive, Building 10, Room 11N228
|
| City |
Bethesda |
| State/province |
Maryland |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL10325 |
| Series (1) |
| GSE37071 |
The Candida glabrata transcription factor Stb5p is a negative regulator of ATP-binding cassette transporters |
|
