|
| Status |
Public on Sep 20, 2011 |
| Title |
TRA1 vs. tra1_SRR3413_L3733A (array 3) |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Cy3: CY2706(TRA1::Tn10LUK with 1980(myc9-TRA1-YCplac111))
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
Yeast cells were grown in YP media containing 2% glucose to an A600=2.0.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was performed as described in Mutiu AI, and Brandl CJ (2005) RNA isolation from yeast using silica matrices. J Biomol Tech 16:316-317.
|
| Label |
Cy3
|
| Label protocol |
Labeling was performed at MOgene LC (St. Louis, MO). Total RNA from yeast was amplified using Agilent's low input linear amplification kit according to the process outlined by the manufacturer (Agilent Technologies). 1-5ug of amplified target cRNA was labeled using the Micromax kit (PerkinElmer, Inc.). The labeled material was passed through a zymo RNA Clean-up Kit-5 column (Zymo Research Corp., CA) to remove un-incorporated label and eluted in 15-20ul of RNase-free water (Ambion, Inc.). All of the labeling and post-labeling procedures were conducted in an ozone-free environment to ensure the integrity of the label.
|
| |
|
| Channel 2 |
| Source name |
Cy5: CY3015(TRA1::Tn10LUK with IB157(myc9-tra1_SRR3413_L3733A-YCplac111))
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
Yeast cells were grown in YP media containing 2% glucose to an A600=2.0.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was performed as described in Mutiu AI, and Brandl CJ (2005) RNA isolation from yeast using silica matrices. J Biomol Tech 16:316-317.
|
| Label |
Cy5
|
| Label protocol |
Labeling was performed at MOgene LC (St. Louis, MO). Total RNA from yeast was amplified using Agilent's low input linear amplification kit according to the process outlined by the manufacturer (Agilent Technologies). 1-5ug of amplified target cRNA was labeled using the Micromax kit (PerkinElmer, Inc.). The labeled material was passed through a zymo RNA Clean-up Kit-5 column (Zymo Research Corp., CA) to remove un-incorporated label and eluted in 15-20ul of RNase-free water (Ambion, Inc.). All of the labeling and post-labeling procedures were conducted in an ozone-free environment to ensure the integrity of the label.
|
| |
|
| |
| Hybridization protocol |
Hybridization was performed at MOgene LC (St. Louis, MO). Labeled material was fragmented according to the protocol described in the Agilent processing manual and hybridized overnight with the array in a rotating oven at 60 degrees Celsius in an ozone-free environment. Wash conditions used were as outlined in the Agilent processing manual.
|
| Scan protocol |
Scanning was performed at MOgene LC (St. Louis, MO) using an Agilent scanner.
|
| Description |
Experiment was performed to analyze the effects of the tra1_SRR3413_L3733A allele on gene expression. This array is one of three replicates including one dye-swap.
|
| Data processing |
Data processing was performed at MOgene LC (St. Louis, MO). Feature extraction, normalization and background subtraction of reported values were performed using Agilent software.
|
| |
|
| Submission date |
Nov 11, 2008 |
| Last update date |
Sep 20, 2011 |
| Contact name |
Christopher Brandl |
| Organization name |
University of Western Ontario
|
| Department |
Biochemistry
|
| Lab |
Brandl
|
| Street address |
1151 Richmond St.
|
| City |
London |
| State/province |
Ontario |
| ZIP/Postal code |
N6A 5C1 |
| Country |
Canada |
| |
|
| Platform ID |
GPL7542 |
| Series (1) |
| GSE13561 |
Transcriptional Control by the FATC Domain of Saccharomyces cerevisiae Tra1 |
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