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Compatibility of DMSO spotting buffers with Nexterion Slide E Epoxy-coated Microarray slides
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Compatibility of DMSO spotting buffers with Nexterion Slide E Epoxy-coated Microarray slides

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Compatibility of DMSO spotting buffers with SCHOTT Nexterion Epoxy-silane coated microarray slides. Effect of using different spotting pins and DMSO concentrations.

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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  • The complete labeling protocol as pdf is available upon request
    Lot-Numbers of dyes used:
    Dye 3E08-03158
    Dye 5E06-04115
    Cy3311839
    Cy5311840
    Alexa 55502E2-1
    Alexa 64702E1-1
  • spotting buffers from second test
    all combinations of DMSO, SSC and 0.05% or 0.1% SDS precipitated and could not be tested
  • spotting buffers from second test
    all combinations of DMSO, SSC and 0.05% or 0.1% SDS precipitated and could not be tested
  • selected spotting buffers from first test
  • selected spotting buffers from first test
    CTAB = cetyl- trimethylammonium bromide
  • spotting buffers from second test
    all combinations of DMSO, SSC and 0.05% or 0.1% SDS precipitated and could not be tested
  • spotting buffers from second test
    all combinations of DMSO, SSC and 0.05% or 0.1% SDS precipitated and could not be tested
  • selected spotting buffers from first test
  • selected spotting buffers from first test
    CTAB = cetyl- trimethylammonium bromide
  • * further tests are ongoing
  • Transcript

    • 1. November 2004DMSO Spotting BufferMicroarray 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
    • 2. 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
    • 3. 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
    • 4. 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
    • 5. 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
    • 6. 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% SDS Spot 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
    • 7. 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
    • 8. 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
    • 9. November 2004DMSO Spotting BufferMicroarray Solution SCHOTT Jenaer Glas GmbH Results aQu K2801 Pin 30% DMSO 30% DMSO 3x SSC spot 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
    • 10. 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% SDS Spot 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
    • 11. 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
    • 12. 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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