NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2515593 Query DataSets for GSM2515593
Status Public on Mar 01, 2017
Title strain T73, time point 96h, replicate 3
Sample type RNA
 
Channel 1
Source name strain T73, time point 96h, replicate 3
Organism Saccharomyces cerevisiae
Characteristics strain: T73
time point: 96 h
Growth protocol Fermentations in synthetic agave must at 28 ºC
Extracted molecule total RNA
Extraction protocol RNA extraction method was based on consecutive treatments with phenol-tris, phenol-chloroform (5:1) and chloroform-isoamyl alcohol (24:1) and a final precipitation with ethanol and sodium acetate (Garcia-Martinez et al., 2004).
Label Cy5
Label protocol 2-4 ug of total RNA was linearly amplified using the Low RNA Input Fluorescent Linear Amplification kit (Agilent Technologies™, Ca, USA). 2-3 ug of amplified cRNA was used as template for cDNA synthesis. cDNA was marked indirectly with “SuperScript™ Indirect cDNA Labeling System” (Invitrogen™, SanDiego, CA).
The fluorophores used were Cy3 and Cy5 mono-reactiveDye (Amersham GE Healthcare™, Amersham UK) and dye incorporation was monitored by a Nanodrop spectrophotometer.
 
Channel 2
Source name sample mix
Organism Saccharomyces cerevisiae
Characteristics strain: mixed
time point: 96 h
Growth protocol Fermentations in synthetic agave must at 28 ºC
Extracted molecule total RNA
Extraction protocol RNA extraction method was based on consecutive treatments with phenol-tris, phenol-chloroform (5:1) and chloroform-isoamyl alcohol (24:1) and a final precipitation with ethanol and sodium acetate (Garcia-Martinez et al., 2004).
Label Cy3
Label protocol 2-4 ug of total RNA was linearly amplified using the Low RNA Input Fluorescent Linear Amplification kit (Agilent Technologies™, Ca, USA). 2-3 ug of amplified cRNA was used as template for cDNA synthesis. cDNA was marked indirectly with “SuperScript™ Indirect cDNA Labeling System” (Invitrogen™, SanDiego, CA).
The fluorophores used were Cy3 and Cy5 mono-reactiveDye (Amersham GE Healthcare™, Amersham UK) and dye incorporation was monitored by a Nanodrop spectrophotometer.
 
 
Hybridization protocol A mixture of 200 to 300 pmol of the two samples labelled was concentrated in a Concentrator Plus (Eppendorf™, Hamburg, Germany). Competitive hybridization was performed in hybridization chambers AHC (ArrayIt Corporation, CA, USA) at 42°C overnight. (Prehybridization solution contained 3X SSC, 0.1% SDS and 0.1 mg/ml BSA; hybridization solution
contained 5X SSC, 0.1% SDS and 0.1 mg/ml of salmon DNA. Microarrays were washed manually with different solutions containing different SSC 20X and SDS 10% concentrations (Sol.1: 2X SSC-0.1% SDS; Sol.2: 0.1X SSC-0.1% SDS; Sol.3: 0.1 SSC; Sol4: 0.01X SSC).
Scan protocol Signal intensities of Cy3 and Cy5 were acquired with an Axon GenePix 4100A scanner (Molecular devices, CA, USA) using GenePix Pro v.6.1 software, at a resolution of 10 μm.
Description Biological replicate three of three
Data processing Raw data with a global background subtraction were generated from GenePix pro 6.0. Analyses were done using Acuity 4.0 software (Molecular Devices, CA, USA).The individual data sets were normalized to a log2 ratio value of 1. After lowess normalization, data were filtered to remove spots flagged as not found.
Only spots with at least two replicates were considered. Finally, replicates were combined and their medians were calculated.
Genes with a two-fold log2 ratio values were considered to be significantly expressed.
 
Submission date Feb 28, 2017
Last update date Mar 01, 2017
Contact name Roberto Pérez
E-mail(s) rober@iata.csic.es
Phone 0034963900022
Organization name Centro Superior de Investigaciones Científicas
Street address Av Agustín Escardino 7
City Paterna
State/province Valencia
ZIP/Postal code 46980
Country Spain
 
Platform ID GPL23130
Series (1)
GSE95507 Agave strain vs wine strain

Data table header descriptions
ID_REF
VALUE normalized log Cy5/Cy3

Data table
ID_REF VALUE
YAL001C -0.553
YAL002W -1.364
YAL003W 0.795
YAL004W 0.194
YAL005C 0.193
YAL007C 0.728
YAL008W -0.481
YAL009W -0.245
YAL010C 0.708
YAL011W 2.34
YAL012W 2.68
YAL013W 0.018
YAL014C -0.058
YAL015C 0.697
YAL016W 0.327
YAL017W -0.861
YAL018C -0.413
YAL019W 0.134
YAL020C -0.629
YAL021C -0.398

Total number of rows: 6257

Table truncated, full table size 87 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap