NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM648766 Query DataSets for GSM648766
Status Public on Aug 01, 2011
Title 60 Min Treated Cy3 vs. Control Cy5 Rep. 2
Sample type RNA
 
Channel 1
Source name Streptococcus mutans, untreated, 60 min
Organism Streptococcus mutans UA159
Characteristics treatment: untreated
cell type: biofilm
genotype: wildtype
time point: 60 min
Treatment protocol biofilm cells were treated with 0.25 µg/ml carolacton, control wells without treatment
Growth protocol biofilms were grown in THBS medium for 3.5 hours (initial OD600 = 0.05) in 24 well polystyrene plates (Greiner, Germany), than the medium was exchanged against fresh THBS supplemented with and without carolacton (0.25 µg/ml)
Extracted molecule total RNA
Extraction protocol total RNA was extracted using the RNeasy Mini Kit (Qiagen, Germany)
Label Cy5
Label protocol RNA samples were labelled either with Cy3 or Cy5 using the ULS fluorescent labelling kit (Kreatech, Germany)
 
Channel 2
Source name Streptococcus mutans, treated, 60 min
Organism Streptococcus mutans UA159
Characteristics treatment: treated
cell type: biofilm
genotype: wildtype
time point: 60 min
Treatment protocol biofilm cells were treated with 0.25 µg/ml carolacton, control wells without treatment
Growth protocol biofilms were grown in THBS medium for 3.5 hours (initial OD600 = 0.05) in 24 well polystyrene plates (Greiner, Germany), than the medium was exchanged against fresh THBS supplemented with and without carolacton (0.25 µg/ml)
Extracted molecule total RNA
Extraction protocol total RNA was extracted using the RNeasy Mini Kit (Qiagen, Germany)
Label Cy3
Label protocol RNA samples were labelled either with Cy3 or Cy5 using the ULS fluorescent labelling kit (Kreatech, Germany)
 
 
Hybridization protocol 760 ng of each Cy3- and Cy5 labelled RNA was fracmented and hybridised to the microarray at 65°C for 16 h using the Agilent Hybridisation Chamber and Agilent Hybridisation Kit according to the manufacturer`s instructions.
Scan protocol the array was scanned using the Agilent DNA Microarray Scanner at 5 µm resolution and the raw data were extracted using Agilent Feature Extraction software (V9.5)
Description 60 Min DyeSwap 2/2, Repl. 2
Data processing The data were processed by Bioconductor packages written in R language (http://www.r-project.org). The linear models for microarray analysis (LIMMA) package was used for background correction, Loess normalisation of the two chanels of one array, quantile-normalisation between different arrays and identification of differentially expressed genes.
 
Submission date Jan 04, 2011
Last update date Aug 01, 2011
Contact name Michael Reck
E-mail(s) [email protected]
Organization name Helmholtz Centre for Infection Research
Department Microbial Communication
Street address Inhoffenstr. 7
City Braunschweig
ZIP/Postal code 38124
Country Germany
 
Platform ID GPL10540
Series (1)
GSE26441 Kinetic analysis of carolacton regulated genes

Data table header descriptions
ID_REF
VALUE Loess-normalized log2 ratio (treated/untreated)
INV_VALUE Loess-normalised log2 ratio (Cy5/Cy3)

Data table
ID_REF VALUE INV_VALUE
1 1.10717 -1.107165968
2 -0.168004 0.168003562
3 -0.00615264 0.006152637
4 -0.383782 0.383781895
5 -0.422498 0.422498041
6 0.211451 -0.211451414
7 -0.0939577 0.093957683
8 -0.257733 0.257733462
9 0.141512 -0.141512385
10 -0.145127 0.145127025
11 -0.057709 0.05770895
12 0.225067 -0.225067402
13 0.390598 -0.390598374
14 0.192324 -0.19232413
15 -0.473158 0.473158304
16 0.253492 -0.253491789
17 -0.0574332 0.05743319
18 -0.182376 0.182376254
19 0.568907 -0.568906841
20 -0.165982 0.165981946

Total number of rows: 15744

Table truncated, full table size 421 Kbytes.




Supplementary file Size Download File type/resource
GSM648766_60+Cy3vs.60-Cy5-II.txt.gz 4.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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