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Sample GSM229990 Query DataSets for GSM229990
Status Public on Jul 01, 2008
Title HHO1_delta_25_degrees_vs_Wild_type_25_degrees
Sample type RNA
 
Channel 1
Source name HHO1 delta grown at 25 degrees C.
Organism Saccharomyces cerevisiae
Characteristics Euroscarf strain Y02125 (Mat alpha, his3 delta 1, leu2 delta 0, met15 delta 0, ura3 delta 0, YPL127C::kanMx4)
Growth protocol Cells were grown at 25 degrees C in YPAD medium to 0D600 0.5 with agitation.
Extracted molecule total RNA
Extraction protocol Hot phenol
Label Cy3
Label protocol Total RNA was amplified and fluorescently labeled using the Agilent Technologies Low Input Linear Amplification Kit (part number 5184-3523) following the protocol described in the kit manual.
 
Channel 2
Source name Wild type grown at 25 degrees C.
Organism Saccharomyces cerevisiae
Characteristics Euroscarf strain BY4741 (Mat alpha, his3 delta 1, leu2 delta 0, met15 delta 0, ura3 delta 0)
Growth protocol Cells were grown at 25 degrees C in YPAD medium to 0D600 0.5 with agitation.
Extracted molecule total RNA
Extraction protocol Hot phenol
Label Cy5
Label protocol Total RNA was amplified and fluorescently labeled using the Agilent Technologies Low Input Linear Amplification Kit (part number 5184-3523) following the protocol described in the kit manual.
 
 
Hybridization protocol For each hybridization, 750 ng of cyanine 3- and 750 ng of cyanine 5-labeled cRNA were fragmented and hybridized to an Agilent Technologies Yeast (V2) Gene Expression Microarray (part number G4140B), using the Agilent Gene Expression hybridization kit (part number 5188-5242) as described in the manual.
Scan protocol All microarrays were scanned using Agilent's dual laser DNA microarray scanner G2505B. The data were then extracted from images by using Feature Extraction 9.1 software (Agilent Technologies).
Description Yeast were grown at 25 degrees C.
Data processing The R 2.4 software and the LIMMA package from the Bioconductor project (http://www.bioconductor.org ) were used to normalize the microarray data using VSN normalization. VALUES presented as log 2 ratio (mu25/wt25).
 
Submission date Sep 17, 2007
Last update date Aug 14, 2011
Contact name Don Jay Katcoff
E-mail(s) katcoff@mail.biu.ac.il
Phone +972-3-531-8248
Fax +972-3-738-4097
Organization name Bar Ilan University
Department Life Sciences
Street address Ramat Gan
City Ramat Gan
ZIP/Postal code 52900
Country Israel
 
Platform ID GPL2883
Series (1)
GSE9095 Yeast linker histone HHO1p effect on transcription before and after heat shock

Data table header descriptions
ID_REF
VALUE log 2 of ratio (mu25/wt25)

Data table
ID_REF VALUE
1 0.120066762
2 0.233186471
3 0.418435043
4 0.018129159
5 0.006365454
6 -0.102215382
7 -0.13127726
8 1.128867059
9 -0.154335975
10 0.458914699
11 0.373697329
12 -0.259145512
13 0.162291309
14 -0.136013254
15 -1.671048376
16 -0.186734471
17 -0.112542538
18 0.110820884
19 0.265875735
20 0.977281178

Total number of rows: 10789

Table truncated, full table size 183 Kbytes.




Supplementary file Size Download File type/resource
GSM229990.txt.gz 2.7 Mb (ftp)(http) TXT
Processed data included within Sample table

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