November 2004 DMSO Spotting Buffer Microarray Solution SCHOTT Jenaer Glas GmbH Final Report DMSO Spotting Buffers on Slide E Norman Rahnis, Kornelia Kuhn, Katrin Steinmetzer Application Support/R&D Microarray Solutions Schott Jenaer Glas GmbH
Compatibility of DMSO spotting buffers with Nexterion Slide E Epoxy-coated Microarray slides
Dec 05, 2014
Compatibility of DMSO spotting buffers with SCHOTT Nexterion Epoxy-silane coated microarray slides. Effect of using different spotting pins and DMSO concentrations.
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November 2004DMSO Spotting BufferMicroarray Solution
SCHOTT Jenaer Glas GmbH
Final ReportDMSO Spotting Buffers on Slide E
Norman Rahnis, Kornelia Kuhn, Katrin Steinmetzer
Application Support/R&D
Microarray Solutions
Schott Jenaer Glas GmbH
November 2004DMSO Spotting BufferMicroarray Solution
SCHOTT Jenaer Glas GmbH
Spotting Solution
Components DMSO, SSC, phosphate buffer, SDS
Slides Nexterion Slide E
Probes 70mer (from E. coli Genome Oligo Set Version 1.0) 10 µM
Spotting QArray Mini, 22°C, 45% RH, SMP3 pin (Telechem), aQu Split Pin K2801 (diameter 150 µm)
Target total RNA (E.coli) was used to synthesize aa-cDNA, the coupling of NHS-ester-dyes (Nexterion Dye3 and Dye5) was performed
with a standard protocol derived from a Cy3/Cy5 labeling protocol,
Hybridization Tecan Hybridization Station HS4800, in 5xSSC, 0.1% SDS, 0.1 mg/ml herring sperm DNA, 50% formamide, 42°C, 16 hrs
Scanning Affymetrix Array Scanner 428
Analysis IconoClust
Experimental Details
November 2004DMSO Spotting BufferMicroarray Solution
SCHOTT Jenaer Glas GmbH
....some remarks
the following images show results after hybridization
blue spots mean lower signal, green spots mean higher signals
suitable buffers were highlighted in red
spot diameter was only determined for good spots
November 2004DMSO Spotting BufferMicroarray Solution
SCHOTT Jenaer Glas GmbH
Results SMP3 Pin 50% DMSO
50% DMSO 3x SSC
50% DMSO 1.5x SSC, spot diameter 70 µm
50% DMSO 150 mM PP, 0.1% SDS
50% DMSO 150 mM PP, 0.05% SDS
50% DMSO 150 mM PP
50% DMSO
November 2004DMSO Spotting BufferMicroarray Solution
SCHOTT Jenaer Glas GmbH
Results SMP3 Pin 30% DMSO
30% DMSO 3x SSC
30% DMSO 1.5x SSC,spot diameter 70 µm
30% DMSO 150 mM PP, 0.1% SDS
30% DMSO 150 mM PP, 0.05% SDS
30% DMSO 150 mM PP
30% DMSO
November 2004DMSO Spotting BufferMicroarray Solution
SCHOTT Jenaer Glas GmbH
Results SMP3 Pin
25% DMSO 0.005% SDS
50% DMSO 1.5x SSC, 0.005% SDS,spot diameter 60-70 µm
25% DMSO 1.5xSSC, 0.005% SDSSpot diameter 90 µm
50% DMSO 75 mM PP
best results were obtained when combining DMSO with SSC and with or without SDS (but only for f.c. SDS of 0.005%, higher concentrations lead to precipitation)
a combination of DMSO, phosphate buffer and SDS does not work
further tests with additional combinations of DMSO, SSC and other detergents will be tested
November 2004DMSO Spotting BufferMicroarray Solution
SCHOTT Jenaer Glas GmbH
Results SMP3 Pin
50% DMSO 2x SSC
best results were obtained when combining DMSO with SSC and with or without detergents
spot sizes range between 100 and 140 µm
similar results were obtained with 30% DMSO
50% DMSO 1.5x SSC, 0.025% CTAB
50% DMSO 1.5x SSC, 0.025% Triton X100
50% DMSO 2.5x SSC
50% DMSO 1.5x SSC, 0.005% SDS
November 2004DMSO Spotting BufferMicroarray Solution
SCHOTT Jenaer Glas GmbH
Results aQu K2801 Pin 50% DMSO
50% DMSO 3x SSC
50% DMSO 1.5x SSC
50% DMSO 150 mM PP, 0.1% SDS
50% DMSO 150 mM PP, 0.05% SDS
50% DMSO 150 mM PP
50% DMSO
no suitable buffer combinations
November 2004DMSO Spotting BufferMicroarray Solution
SCHOTT Jenaer Glas GmbH
Results aQu K2801 Pin 30% DMSO
30% DMSO 3x SSCspot diameter 360 µm
30% DMSO 1.5x SSC,spot diameter 90 µm
30% DMSO 150 mM PP, 0.1% SDS
30% DMSO 150 mM PP, 0.05% SDS
30% DMSO 150 mM PP
30% DMSO
30% DMSO with 1.5x SSC gives good results, further SSC-concentrations will be tested
November 2004DMSO Spotting BufferMicroarray Solution
SCHOTT Jenaer Glas GmbH
Results aQu K2801 Pin
25% DMSO 0.005% SDS
50% DMSO 1.5x SSC, 0.005% SDS,spot diameter 110 µm
25% DMSO 1.5xSSC, 0.005% SDSSpot diameter 160 µm
50% DMSO 75 mM PP
best results were obtained when combining DMSO with SSC and with or without SDS (but only for f.c. SDS of 0.005%, higher concentrations lead to precipitation)
a combination of DMSO, phosphate buffer and SDS does not work
further tests with additional combinations of DMSO, SSC and other detergents will be tested
November 2004DMSO Spotting BufferMicroarray Solution
SCHOTT Jenaer Glas GmbH
Results aQu K2801 Pin
50% DMSO 1.5x SSC, 0.025% CTAB
50% DMSO 1.5x SSC, 0.025% Triton X100
50% DMSO 2.5x SSC
50% DMSO 2x SSC
best results were obtained when combining DMSO with SSC and with or without detergents
spot sizes range between 100 and 140 µm
similar results were obtained with 30% DMSO
50% DMSO 1.5x SSC, 0.005% SDS
November 2004DMSO Spotting BufferMicroarray Solution
SCHOTT Jenaer Glas GmbH
Summary
50 (30%) DMSO in water usually gives very small spots on Slide E (approximately 60 µm)
addition of SSC (f.c. 1.5x to 2.5x) with or without detergent (f.c. 0.005% to 0.025%) gives good spot morphology and size
spot size can be increased by increasing SSC concentration and/or adding detergent
50(30)% DMSO is not compatible with Next Spot or phosphate buffer (150 mM f.c. phosphate buffer), addition of detergent does not improve spot morphology*
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