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Sample GSM189565 Query DataSets for GSM189565
Status Public on May 17, 2007
Title Fig 1C: cdc28-4 (A2594) chem RNA
Sample type RNA
 
Channel 1
Source name F20 4/4/06 (2587, wt) RNA
Organism Saccharomyces cerevisiae
Characteristics Strain Name : wt (A2587)
Biomaterial provider Cheryl Christianson, Dunham Lab, Princeton University
Extracted molecule total RNA
Extraction protocol Description : Filters were incubated for 1 hour at 65oC in lysis buffer (10 mM EDTA, 0.5% SDS, and 10 mM Tris, pH 7.5) and acid phenol. The aqueous phase was further extracted twice with an equal volume of chloroform using phase lock gel (Eppendorf). Total RNA was then ethanol precipitated and further purified over RNeasy columns (Qiagen). RNA quality was checked using the Bioanalyzer RNA Nano kit.
Label Cy3
Label protocol Description : 325 ng was used for microarray labeling with the Agilent Low RNA Input Fluorescent Linear Amplification Kit. Reactions were performed as directed except using half the recommended reaction volume and one quarter the recommended Cy-CTP amount. Dye incorporation and yield were measured with a Nanodrop spectrophotometer.
 
Channel 2
Source name F22 4/4/06 (2594) RNA
Organism Saccharomyces cerevisiae
Characteristics Strain Name : cdc28-4 (A2594)
Biomaterial provider Cheryl Christianson, Dunham Lab, Princeton University
Growth protocol Description : ATR Sixfors fermenters were modified for use as chemostats. Chemostat cultures were run at 30oC at a working volume of 300 mls, mixed at 400 rpm, and sparged at 5 standard liters per minute with humidified and filter-sterilized air. The dilution rate was set to 0.17 volumes/hour. Cultures were run in phosphate limited minimal defined medium containing the following (per liter): 100 mg calcium chloride, 100 mg sodium chloride, 500 mg magnesium sulfate, 5 g ammonium sulfate, 1 g potassium chloride, 500 mg boric acid, 40 mg copper sulfate, 100 mg potassium iodide, 200 mg ferric chloride, 400 mg manganese sulfate, 200 mg sodium molybdate, 400 mg zinc sulfate, 1 mg biotin, 200 mg calcium pantothenate, 1 mg folic acid, 1 mg inositol, 200 mg niacin, 100 mg p-aminobenzoic acid, 200 mg pyridoxine, 100 mg riboflavin, 200 mg thiamine, 50 mg adenine, 50 mg tryptophan, 20 mg uracil, 100 mg lysine, 20 mg methionine, 100 mg leucine, 100 mg G418, and 5 g glucose. Chemostats were inoculated with 1 ml overnight culture grown in chemostat media. Cultures were maintained in batch for 24 hours, at which time the media flow was switched on. Cultures were sampled daily for cell density by Coulter count, klett, and absorbance, and were considered to be in steady state when all parameters measurements were the same for two consecutive measurements, which occurred 4 days after inoculation for all cultures. 100 ml of cultures were harvested by vacuum filtration, flash-frozen in liquid nitrogen, and stored at ?80oC until RNA extraction.
Extracted molecule total RNA
Extraction protocol Description : Filters were incubated for 1 hour at 65oC in lysis buffer (10 mM EDTA, 0.5% SDS, and 10 mM Tris, pH 7.5) and acid phenol. The aqueous phase was further extracted twice with an equal volume of chloroform using phase lock gel (Eppendorf). Total RNA was then ethanol precipitated and further purified over RNeasy columns (Qiagen). RNA quality was checked using the Bioanalyzer RNA Nano kit.
Label Cy5
Label protocol Description : 325 ng was used for microarray labeling with the Agilent Low RNA Input Fluorescent Linear Amplification Kit. Reactions were performed as directed except using half the recommended reaction volume and one quarter the recommended Cy-CTP amount. Dye incorporation and yield were measured with a Nanodrop spectrophotometer.
 
 
Hybridization protocol Description : Equal masses of differentially labeled control and sample cRNA were combined such that each sample contained at least 2.5 pmol dye. Samples were mixed with control targets, fragmented, combined with hybridization buffer, and applied to a microarray consisting of 60mer probes for each yeast open reading frame (Agilent). Microarrays were rotated at 60?C for 17 hours in a hybridization oven (Agilent). Arrays were then washed according to the Agilent SSPE wash protocol, and scanned on an Agilent scanner.
Scan protocol Pixel Size : 10
Scan Date : 2006-04-18
Scan Time : 10:06:27
Scanner Make : Agilent Technologies Scanner
Scanner Model : G2505B
Scanning software : ChipScan
Scanning software version : A.6.3.1
Description former name: AA 2594 (cdc28-4) chemostat RNA
Data processing Extraction Software : Agilent Feature Extractor
Extraction Software Version : A.7.5.1
Datafile type : Agilent result file
 
Submission date May 15, 2007
Last update date May 16, 2007
Contact name Maitreya J. Dunham
E-mail(s) maitreya@uw.edu
Phone 206-543-2338
Organization name University of Washington
Department Genome Sciences
Lab Dunham Lab
Street address Foege Building, S403B, Box 355065
City Seattle
State/province WA
ZIP/Postal code 98195-5065
Country USA
 
Platform ID GPL2883
Series (1)
GSE7812 Effects of aneuploidy on cellular physiology and cell division in haploid yeast.

Data table header descriptions
ID_REF Uniquely identifies feature/spot in array layout.
VALUE log(base 2) (R_PROCESSED_SIGNAL/G_PROCESSED_SIGNAL)
R_PROCESSED_SIGNAL The propagated feature signal in the red channel, used for computation of log ratio
G_PROCESSED_SIGNAL The propagated feature signal in the green channel, used for computation of log ratio
R_MEAN_SIGNAL Mean foreground intensity Ch 2.
G_MEAN_SIGNAL Mean foreground intensity Ch 1.

Data table
ID_REF VALUE R_PROCESSED_SIGNAL G_PROCESSED_SIGNAL R_MEAN_SIGNAL G_MEAN_SIGNAL
1 -6.644 135.9441 55567.11 59.29508 5845.016
2 0 22.46457 22.49494 27.30189 29.81132
3 .15 2881.167 2596.578 681.7797 301.4576
4 -.121 560.0484 609.0339 154.5246 93.93443
5 -.271 1270.271 1532.8 314.2143 191.4286
6 .425 60.86109 45.33109 43.25424 34.0678
7 -.334 36.64444 46.18845 37.47368 34.17544
8 1.016 700.8618 346.5479 187 65.93548
9 -.271 1699.345 2050.905 411.7419 245.5323
10 -.174 6016.801 6789.845 1450.918 711.2459
11 .439 2599.66 1917.035 615.7037 231
12 -.242 2508.2 2966.256 597.8246 339.8421
13 .326 167.9653 134.0051 69.42623 42.60656
14 .405 13295.96 10040.77 3251.534 1012.466
15 1.006 59.50092 29.62933 43.4 32.26667
16 .021 2145.569 2114.724 513.2679 251.8393
17 -.561 29.12737 42.9711 36.33929 33.64286
18 -.387 5603.22 7328.233 1353.895 765.0526
19 .19 10042.23 8805.643 2445.433 897.8833
20 -.022 57.15057 58.01325 43.38182 35.01818

Total number of rows: 10789

Table truncated, full table size 477 Kbytes.




Supplementary file Size Download File type/resource
GSM189565.txt.gz 2.4 Mb (ftp)(http) TXT
Processed data included within Sample table

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