Data Files for Selected Publications

The following publications analyze large data sets that we made available to everybody interested in the raw data.  Windows XP may not open the downloaded files due to security reasons.  Right-click on the downloaded file, choose Properties and on the General tab press “Unblock” button.

Evaluation of Gel-Pad Oligonucleotide Microarray Technology Using Artificial Neural Networks

Pozhitkov, A., Chernov, B., Yershov, G. and Noble, P.A. (2005), Appl. Environ. Microbiol., 71, 8663–8676.

Microsoft Access database: Download

 

Grid placement effect (see Fig. 10 in the paper).  Excel files contain raw data, data processed according to the Fotin et al method as well as images on how sampling grid was applied.  To locate the chart, see Chart1 worksheet.  The file containing data for the Oligonucleotide1 target is exactly what was used to make Fig 10.  Stacks of raw images can be provided upon request.

Target

Label

File

Oligonucleotide1

Oregon Green

oligo_target1.xls

Oligonucleotide2

Oregon Green

oligo_target2.xls

RNA1

Cy3

rna_target1.xls

RNA2

Lissamine-Rhodamine

rna_target2.xls

Tests of rRNA Hybridization to Microarrays Suggest that Hybridization Characteristics of Oligonucleotide Probes for Species Discrimination Cannot Be Predicted

Pozhitkov, A., Noble, P.A., Domazet-Loso, T., Nolte, A., Sonnennberg, R., Staehler, P., Beier, M. and Tautz, D. (2006) Nucleic Acids Research, 34(9):e66.

Microsoft Access database: Download

Supplementary material

Microsoft Access database: Download

Development of a statistically robust quantification method for microorganisms in mixtures using oligonucleotide microarrays

Pozhitkov, A., Bailey, K.D. and Noble P.A. (2007) Journal of Microbiological Methods, In Press, Accepted Manuscript, Available online 10 May 2007,

Microsoft Access database: Download

Comment on discrimination of shifts in soil microbial communities using nonequilibrium thermal dissociation and gel pad array technology.

Pozhitkov,A. and Noble,P.A. (2007) Environmental Science and Technology,  41, 1797-1798. 10.1021/es062479m

Figure 1 in the paper correspond to the last row (RNA2) in the above table under “Evaluation of Gel-Pad Oligonucleotide Microarray Technology Using Artificial Neural Networks”.  See also other files for the grid-displacement effect.

Revision of the Nonequilibrium Thermal Dissociation and Stringent Washing Approaches For Identification of Mixed Nucleic Acid Targets by Microarrays

Pozhitkov, A., Stedtfeld,R.D., Hashsham, S.A., and Noble, P.A. (2007)  Nucleic Acids Research, 35(9):e70.

Microsoft Access database: Download

Concentration-dependency of nonequilibrium thermal dissociation curves in complex target samples

Pozhitkov, A., Rule, R.A., Stedtfeld, R.G., Hashsham, S.A. and Noble, P.A.  (2008) Journal of Microbiological Methods. doi: 10.1016/j.mimet.2008.03.010.

 

Full database (MS Access file)

Download

Theoretical vs. actual curves, pure target

Download

Pure target, comparison of array batches

Download

Comparison of 1, 5 and 10% mixtures

Download

Comparison of pure target with 10% mixture 

Download

Comparison of pure target with bioreactor background (0% mixture)

Download

Simultaneous quantification of multiple nucleic acid targets in complex rRNA mixtures using high density microarrays and nonspecific hybridization as a source of information.

Pozhitkov, A.E., Nies, G., Kleinhenz, B., Tautz, D. and Noble, P.A.  (2008) Journal of Microbiological Methods, In press

 

Full database (MS Access file)

Download

Use of hidden correlations in short oligonucleotide array data are insufficient for accurate quantification of nucleic acid targets in complex target mixtures

Rebecca A. Rule, Alex E. Pozhitkov, and Peter A. Noble (2008)

All supplements are archived in a single ZIP file. Click here to download.

#

Description

File Name

1

Document describing how to use Sup2.xls to determine gamma

Sup1.doc

2

Excel file used to fit gamma

Sup2.xls

3

Document describing how to use Sup4.xls to determine d and h

Sup3.doc

4

Excel file used to determine d and h

Sup4.xls

5

Document describing how to use Sup6.xls to analyze the 1st Latin square data set

Sup5.doc

6

Excel file used to analyze the 1st Latin square data set

Sup6.xls

7

Excel file used to analyze the 2nd Latin square data set

Sup7.xls

8

Document describing how to use Sup9.xls to analyze the 1st Latin square data set using PM

Sup8.doc

9

Excel file used to analyze the 1st Latin square data set using PM

Sup9.xls

10

Excel file used to analyze the 2nd Latin square data set using PM

Sup10.xls

11

Excel file used to analyze the 1st Latin square data set using a 5th Order Polynomial for beta

Sup11.xls

12

Excel file used to analyze the 2nd Latin square data set using a 5th Order Polynomial for beta

Sup12.xls

13

Excel file used to analyze the 1st Latin square data set using PM & a 5th Order Polynomial for beta

Sup13.xls

14

Excel file used to analyze the 2nd Latin square data set using PM & a 5th Order Polynomial for beta

Sup14.xls

15

Excel file used to analyze Tot Y vs. Sig Intensity for the 1st Latin square data set

Sup15.xls

16

Excel file used to analyze Tot Y vs. Sig Intensity for the 2nd Latin square data set

Sup16.xls

17

Excel file used to analyze Tot Y vs. Sig Intensity for the 1st Latin square data set using PM

Sup17.xls

18

Excel file used to analyze Tot Y vs. Sig Intensity for the 2nd Latin square data set using PM

Sup18.xls

Erratum

We have found several errors in our publication.  Please click here to download the erratum file.