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Series GSE970 Query DataSets for GSE970
Status Public on Dec 08, 2004
Title Glucose dependent cell size is regulated by novel GPCR system
Organism Saccharomyces cerevisiae
Experiment type Expression profiling by array
Summary Experiment design
Type of experiment: Gene expression profiling analysis of S.cerevisiae W303-1a.
Experimental factor: genetic variation (WT, gpr1 and gpa2 mutant strains).
Number of hybridizations: 6. Single-colour labeling was performed for each sample.
Sample preparation:
Total RNA was prepared using FastRNA Pro Red Kit (BIO 101 Systems) according to the manufacturers' instructions.

Labeling protocol
10 µg of total RNA was reverse transcribed using the SuperScript Choice system for cDNA synthesis (Life Technologies) according to the protocol recommended by Affymetrix. The oligonucleotide used for priming was 5’-ggccagtgaattgtaatacgactcactatagggaggcgg-(t)24-3’ (Genset Oligo). Double-stranded cDNA was cleaned by phenol:chloroform extraction and the aqueous phase removed by centrifugation through Phase-lock Gel (Eppendorf). In vitro transcription was performed on 1 µg of cDNA using the Enzo BioArray High Yield RNA transcript labelling kit (Enzo Diagnostics). The cRNA was cleaned using RNAeasy clean-up columns (Qiagen). The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.

Hybridization protocol
10 µg of fragmented cRNA were hybridised (45°C, 16 hours). Hybridization was controled by use of the GeneChip™ Eukaryotic Hybridization Control Kit (Affymetrix). Washing and staining was performed in a Fluidics Station 400 (Affymetrix) using the protocol EukGE-WS2v4.

Measurement data, specifications and data processing
Scanning was performed in an Affymetrix GeneChip scanner. Chip analysis was performed using the Affymetrix Microarray Suite v5.
Changes in gene expression were assessed by looking for concordant changes between all replicates using a signed Wilcoxon rank test. The “change” p-value threshold was < 0.025 for increase and > 0.975 for decrease.

Array design
Microarray analysis was performed using YGS98 GeneChips™ oligonucleotide arrays (Affymetrix #900256) representing approximately 6000 ORFs. Sequences and GenBank accession numbers of all probe sets are available at the Affymetrix home page http://www.affymetrix.com/index.affx.

Keywords: ordered
 
 
Contributor(s) Tamaki H, Shirahige K, Yun C, Shinozaki M, Mizutani T, Tsuzuki T, Takagi Y, Kodama Y, Kumagai H
Citation(s) 15743410
Submission date Jan 16, 2004
Last update date Jul 01, 2016
Contact name Katsuhiko Shirahige
E-mail(s) kshirahi@iam.u-tokyo.ac.jp
Phone +81-3-5842-0756
Fax +81-3-5842-0757
URL http://www.iam.u-tokyo.ac.jp/chromosomeinformatics/
Organization name The University of Tokyo
Department Research Center for Epigenetic Disease
Lab Laboratory of Genome Structure and Function
Street address 1-1-1 Yayoi
City Bunkyo-ku
State/province Tokyo
ZIP/Postal code 113-0032
Country Japan
 
Platforms (1)
GPL90 [YG_S98] Affymetrix Yeast Genome S98 Array
Samples (6)
GSM15273 Expression profile of gpa2 deletion mutant (1)
GSM15275 Expression profile of gpa2 deletion mutant (2)
GSM15277 Expression profile of gpr1 deletion mutant (1)
Relations
BioProject PRJNA88007

Comparison analysis table header descriptions
ID_REF
VALUE1 gpa2 deletion mutant (1st) compaired with Wild (1)
Signal Log Ratio1
Change1
Change p-value1
VALUE2 gpa2 deletion mutant (1st) compaired with Wild (2)
Signal Log Ratio2
Change2
Change p-value2
VALUE3 gpa2 deletion mutant (2nd) compaired with Wild (1)
Signal Log Ratio3
Change3
Change p-value3
VALUE4 gpa2 deletion mutant (2nd) compaired with Wild (2)
Signal Log Ratio4
Change4
Change p-value4
VALUE5 gpr1 deletion mutant (1st) compared with Wild (1)
Signal Log Ratio5
Change5
Change p-value5
VALUE6 gpr1 deletion mutant (1st) compared with Wild (2)
Signal Log Ratio6
Change6
Change p-value6
VALUE7 gpr1 deletion mutant (2nd) compared with Wild (1)
Signal Log Ratio7
Change7
Change p-value7
VALUE8 gpr1 deletion mutant (2nd) compared with Wild (2)
Signal Log Ratio8
Change8
Change p-value8
Description Description

Data table
ID_REF VALUE1 Signal Log Ratio1 Change1 Change p-value1 VALUE2 Signal Log Ratio2 Change2 Change p-value2 VALUE3 Signal Log Ratio3 Change3 Change p-value3 VALUE4 Signal Log Ratio4 Change4 Change p-value4 VALUE5 Signal Log Ratio5 Change5 Change p-value5 VALUE6 Signal Log Ratio6 Change6 Change p-value6 VALUE7 Signal Log Ratio7 Change7 Change p-value7 VALUE8 Signal Log Ratio8 Change8 Change p-value8 Description
AFFX-MurIL2_at 19.2 -2.6 NC 0.988444 14.5 0.6 NC 0.016847 15.2 -2.6 D 0.999528 11.5 0.6 NC 0.085186 14.3 -3 D 0.999372 10.8 0 NC 0.081072 26.5 -2.6 D 0.99917 20 0.6 NC 0.011969 M16762 Mouse interleukin 2 (IL-2) gene, exon 4
AFFX-MurIL10_at 5.5 -0.3 D 0.999208 4.2 0.3 NC 0.255069 6.8 0.1 NC 0.981996 5.2 0.7 NC 0.147222 5.1 -0.2 NC 0.314233 3.8 0.4 I 0.000029 5.2 -0.1 D 0.99917 4 0.5 NC 0.198553 M37897 Mouse interleukin 10 mRNA, complete cds
AFFX-MurIL4_at 9.6 0 NC 0.819644 7.3 0.9 NC 0.014228 4.1 0.2 NC 0.90385 3.1 1.1 NC 0.1535 1.6 -0.3 NC 0.873379 1.2 0.3 NC 0.010392 3.2 0.2 NC 0.924814 2.4 1.4 NC 0.049137 M25892 Mus musculus interleukin 4 (Il-4) mRNA, complete cds
AFFX-MurFAS_at 52.2 -0.1 NC 0.666446 39.4 4.1 NC 0.008064 2.4 -3.1 NC 0.992228 1.8 1 NC 0.17338 14.7 -1.9 NC 0.993552 11.1 2 NC 0.093878 9 -2.1 NC 0.942098 6.8 1.8 NC 0.022602 M83649 Mus musculus Fas antigen mRNA, complete cds
AFFX-BioB-5_at 662.1 -0.1 NC 0.993048 499.4 -0.2 D 0.999278 859.9 0.1 NC 0.5 648.6 0.1 NC 0.5 878.4 0.1 NC 0.5 662.6 -0.1 NC 0.5 810.1 0.1 NC 0.5 611 0 NC 0.651657 J04423 E coli bioB gene biotin synthetase (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-BioB-M_at 633.8 -0.1 NC 0.991936 478.1 -0.1 NC 0.843296 944.4 0.3 NC 0.5 712.4 0.3 NC 0.057902 704.3 0.2 NC 0.016292 531.3 0.2 NC 0.004741 697.8 0.1 NC 0.5 526.3 0.1 NC 0.5 J04423 E coli bioB gene biotin synthetase (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-BioB-3_at 567.9 -0.1 NC 0.99682 428.3 -0.1 NC 0.790016 892.6 0.2 NC 0.5 673.3 0.1 NC 0.5 895.5 0.2 NC 0.213878 675.4 0.1 NC 0.183909 689.9 0.1 NC 0.5 520.4 0.1 NC 0.5 J04423 E coli bioB gene biotin synthetase (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-BioC-5_at 1115.5 -0.2 D 0.99886 841.5 -0.2 NC 0.836757 1548.4 0.2 NC 0.5 1167.9 0.2 NC 0.163243 1307 0.1 NC 0.5 985.9 0.1 NC 0.051933 1355.9 0.1 NC 0.5 1022.8 0.1 NC 0.5 J04423 E coli bioC protein (-5 and -3 represent transcript regions 5 prime and 3 prime respectively)
AFFX-BioC-3_at 861.4 -0.1 NC 0.90385 649.8 -0.1 NC 0.801447 1076.5 0.3 NC 0.5 812 0.1 NC 0.5 1223.8 0.2 NC 0.233971 923.1 0.2 NC 0.054853 1135.3 0.2 NC 0.5 856.3 0.1 NC 0.5 J04423 E coli bioC protein (-5 and -3 represent transcript regions 5 prime and 3 prime respectively)
AFFX-BioDn-5_at 735.5 -0.3 D 0.999996 554.8 0.1 NC 0.5 944.4 -0.2 D 0.997989 712.4 0.2 NC 0.5 993 0 NC 0.5 749 0.3 I 0.000002 890.6 -0.3 D 1 671.7 0 NC 0.5 J04423 E coli bioD gene dethiobiotin synthetase (-5 and -3 represent transcript regions 5 prime and 3 prime respectively)
AFFX-BioDn-3_at 8212.5 0 NC 0.5 6194.7 0 NC 0.5 9770.1 0.1 NC 0.5 7369.6 0.1 NC 0.5 7898.9 0 NC 0.5 5958.1 0 NC 0.306825 9552.7 0.1 NC 0.5 7205.6 0.1 NC 0.5 J04423 E coli bioD gene dethiobiotin synthetase (-5 and -3 represent transcript regions 5 prime and 3 prime respectively)
AFFX-CreX-5_at 14226.9 -0.4 D 0.99977 10731.3 0.2 NC 0.5 14047.3 -0.3 D 0.999913 10595.9 0.2 NC 0.462519 15454.8 0 NC 0.5 11657.6 0.4 I 0.000003 15315.9 -0.1 D 0.999613 11552.8 0.4 I 0.000051 X03453 Bacteriophage P1 cre recombinase protein (-5 and -3 represent transcript regions 5 prime and 3 prime respectively)
AFFX-CreX-3_at 23444.5 -0.2 D 0.999753 17684.2 0.3 I 0.002343 18332.6 -0.3 D 0.999981 13828.3 0.1 NC 0.5 20416.5 0.1 NC 0.5 15400.2 0.5 I 0.000002 23591 -0.1 D 0.999338 17794.7 0.3 NC 0.020557 X03453 Bacteriophage P1 cre recombinase protein (-5 and -3 represent transcript regions 5 prime and 3 prime respectively)
AFFX-BioB-5_st 99 2.5 NC 0.446538 74.7 1.7 NC 0.5 113.1 2 NC 0.5 85.3 1.5 NC 0.977398 102.5 1.9 NC 0.5 77.3 1.5 NC 0.5 70.2 2.3 NC 0.049137 53 1.7 NC 0.404412 J04423 E coli bioB gene biotin synthetase (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-BioB-M_st 31.3 0.2 NC 0.5 23.6 0 NC 0.558771 26 0 NC 0.5 19.6 -0.2 NC 0.881563 28.2 -0.1 NC 0.5 21.3 -0.1 NC 0.5 40.2 0.5 NC 0.5 30.3 0.4 NC 0.5 J04423 E coli bioB gene biotin synthetase (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-BioB-3_st 25 0.3 NC 0.5 18.8 -0.1 NC 0.986716 31.8 0.2 NC 0.558771 24 -0.2 NC 0.994247 30.6 0.1 NC 0.446538 23.1 -0.3 NC 0.790016 24.9 0.6 NC 0.373502 18.8 0.3 NC 0.5 J04423 E coli bioB gene biotin synthetase (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-BioC-5_st 55.4 0 NC 0.5 41.8 -0.1 NC 0.937277 171.4 0.6 NC 0.621396 129.3 0.4 NC 0.761888 57.4 0 NC 0.5 43.3 -0.3 NC 0.86481 81.3 0.5 NC 0.118437 61.3 0.4 NC 0.5 J04423 E coli bioC protein (-5 and -3 represent transcript regions 5 prime and 3 prime respectively)
AFFX-BioC-3_st 55.7 0.9 NC 0.300066 42 0.7 NC 0.5 7.6 0.1 NC 0.5 5.7 -0.2 NC 0.833421 29.5 0 NC 0.5 22.2 0 NC 0.5 19.2 0.5 NC 0.031805 14.5 0.4 NC 0.348343 J04423 E coli bioC protein (-5 and -3 represent transcript regions 5 prime and 3 prime respectively)
AFFX-BioDn-5_st 118.8 0.1 NC 0.5 89.6 0.2 NC 0.5 107 0 NC 0.521439 80.7 0 NC 0.774189 143.4 0 NC 0.5 108.2 -0.2 NC 0.680982 105.9 0.3 NC 0.661544 79.9 0.1 NC 0.5 J04423 E coli bioD gene dethiobiotin synthetase (-5 and -3 represent transcript regions 5 prime and 3 prime respectively)
AFFX-BioDn-3_st 136.1 1.3 NC 0.5 102.7 1.5 NC 0.5 200.5 1.7 NC 0.5 151.3 2.8 NC 0.5 175.2 1.3 NC 0.5 132.2 1.8 NC 0.5 88.1 0.8 NC 0.5 66.5 1.6 NC 0.5 J04423 E coli bioD gene dethiobiotin synthetase (-5 and -3 represent transcript regions 5 prime and 3 prime respectively)

Total number of rows: 9335

Table truncated, full table size 2191 Kbytes.




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Supplementary file Size Download File type/resource
GSE970_RAW.tar 13.0 Mb (http)(custom) TAR (of CEL)

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