Effect of Detergent Concentration and Type when printing on Epoxy Coated NEXTERION® Slide E29.07.2011
Experimental Details§ Microarray Slide: NEXTERION® Slide E§ Probe:            10 µM oligonucleotides, 70 mer in NEXTERION®...
Signal Intensity – Detergent Concentration                                                                                ...
Spot Diameter – Detergent Concentration                                                                                   ...
SDS – Spot MorphologyDiameter (mean)            280µm        285µm    269µm   244µm    204µm   165µm    146µm      98µmDia...
Sarcosyl – Spot MorphologyDiameter (mean)            248µm        261µm    263µm   248µm    227µm   181µm    136µm      91...
Triton X-100 – Spot MorphologyDiameter (mean)            126µm        124µm    127µm   123µm    114µm   105µm    104µm    ...
Tween 20 – Spot MorphologyDiameter (mean)             95µm        96µm     122µm   139µm    121µm   111µm    112µm     100...
Results and Conclusions§ The best results in this test were obtained with:            - NEXTERION® Spot with Triton X-100 ...
Additional Information:           www.us.schott.com/nexterion© SCHOTT Technical Glass Solutions GmbH                 Page 10
Upcoming SlideShare
Loading in …5
×

Effect of Detergent Concentration and Type when printing on Epoxy Coated NEXTERION® Slide E

1,215 views

Published on

Effect of Detergent Concentration and Type when printing oligo microarrays on Epoxy Coated NEXTERION® Slide E

Published in: Technology, Business
0 Comments
0 Likes
Statistics
Notes
  • Be the first to comment

  • Be the first to like this

No Downloads
Views
Total views
1,215
On SlideShare
0
From Embeds
0
Number of Embeds
4
Actions
Shares
0
Downloads
10
Comments
0
Likes
0
Embeds 0
No embeds

No notes for slide

Effect of Detergent Concentration and Type when printing on Epoxy Coated NEXTERION® Slide E

  1. 1. Effect of Detergent Concentration and Type when printing on Epoxy Coated NEXTERION® Slide E29.07.2011
  2. 2. Experimental Details§ Microarray Slide: NEXTERION® Slide E§ Probe: 10 µM oligonucleotides, 70 mer in NEXTERION® Spot with varying detergent types / detergent concentrations§ Printing Method: Contact printing, SMP3 pins (Genetix QArray mini) at 47.2 % rH; 22.1 °C§ Immobilization: 30 min humidity chamber, 90% rH, RT; afterwards at ambient§ Target: 10 nM complementary oligonucleotides, 24 mer§ Hybridization: Automated hyb station (Tecan HS4800)§ Scanning: 532 nm, 140 gain, 10 µm scan resolution (Tecan LS400 reloaded)§ Data Analysis: Array-Pro Analyzer (Media Cybernetics, Inc.) © SCHOTT Technical Glass Solutions GmbH Page 2
  3. 3. Signal Intensity – Detergent Concentration NEXTERION® Spot - Signal Intensity vs. Detergent Concentration 50000 probe: 10µM oligo 70mer 45000 40000 35000 30000Intensity [rfu] 25000 20000 15000 10000 5000 0 0.0025% 0.0025% 0.0025% 0.0025% 0.015% 0.005% 0.015% 0.005% 0.015% 0.005% 0.015% 0.005% 0.00125% 0.00125% 0.00125% 0.00125% 0.04% 0.03% 0.02% 0.01% 0.04% 0.03% 0.02% 0.01% 0.04% 0.03% 0.02% 0.01% 0.04% 0.03% 0.02% 0.01% © SCHOTT Technical Glass Solutions GmbH Page 3 Tween 20 Triton X-100 Sarcosyl SDS
  4. 4. Spot Diameter – Detergent Concentration NEXTERION® Spot - Spot Diameter vs. Detergent Concentration 350 probe: 10µM oligo 70mer 300 250Spot Diameter [µm] 200 150 100 50 0 0.0025% 0.0025% 0.0025% 0.0025% 0.015% 0.005% 0.015% 0.005% 0.015% 0.005% 0.015% 0.005% 0.00125% 0.00125% 0.00125% 0.00125% 0.04% 0.03% 0.02% 0.01% 0.04% 0.03% 0.02% 0.01% 0.04% 0.03% 0.02% 0.01% 0.04% 0.03% 0.02% 0.01% © SCHOTT Technical Glass Solutions GmbH Tween 20 Triton X-100 Sarcosyl SDS Page 4
  5. 5. SDS – Spot MorphologyDiameter (mean) 280µm 285µm 269µm 244µm 204µm 165µm 146µm 98µmDiameter (max) 309µm 375µm 343µm 313µm 287µm 260µm 241µm 143µmDiameter (min) 254µm 250µm 242µm 218µm 173µm 112µm 80µm 66µmDiameter (Diff. max-min) 55µm 125µm 101µm 95µm 114µm 148µm 161µm 77µm 0.04% 0.03% 0.02% 0.015% 0.01% 0.005% 0.0025% 0.00125% © SCHOTT Technical Glass Solutions GmbH Page 5
  6. 6. Sarcosyl – Spot MorphologyDiameter (mean) 248µm 261µm 263µm 248µm 227µm 181µm 136µm 91µmDiameter (max) 262µm 320µm 323µm 309µm 329µm 307µm 194µm 140µmDiameter (min) 241µm 238µm 247µm 222µm 192µm 108µm 66µm 62µmDiameter (Diff. max-min) 21µm 82µm 76µm 87µm 137µm 199µm 128µm 78µm 0.04% 0.03% 0.02% 0.015% 0.01% 0.005% 0.0025% 0.00125% © SCHOTT Technical Glass Solutions GmbH Page 6
  7. 7. Triton X-100 – Spot MorphologyDiameter (mean) 126µm 124µm 127µm 123µm 114µm 105µm 104µm 95µmDiameter (max) 142µm 140µm 144µm 143µm 155µm 185µm 170µm 144µmDiameter (min) 109µm 107µm 116µm 112µm 97µm 77µm 66µm 61µmDiameter (Diff. max-min) 33µm 33µm 28µm 31µm 58µm 108µm 104µm 83µm 0.04% 0.03% 0.02% 0.015% 0.01% 0.005% 0.0025% 0.00125% © SCHOTT Technical Glass Solutions GmbH Page 7
  8. 8. Tween 20 – Spot MorphologyDiameter (mean) 95µm 96µm 122µm 139µm 121µm 111µm 112µm 100µmDiameter (max) 106µm 142µm 169µm 187µm 151µm 169µm 200µm 158µmDiameter (min) 84µm 80µm 92µm 108µm 101µm 88µm 80µm 68µmDiameter (Diff. max-min) 22µm 62µm 77µm 79µm 50µm 81µm 120µm 90µm 0.04% 0.03% 0.02% 0.015% 0.01% 0.005% 0.0025% 0.00125% © SCHOTT Technical Glass Solutions GmbH Page 8
  9. 9. Results and Conclusions§ The best results in this test were obtained with: - NEXTERION® Spot with Triton X-100 - Concentration range of 0.015% - 0.04% - Uniform spot intensity / shape / diameter - Lowest difference between minimal and maximal spot diameter (at good spot morphology)§ Spot size and signal intensity are influenced by the detergent concentration and type used in NEXTERION® Spot print buffer.§ Lower detergent concentrations generates non-uniform spot size.§ With increased detergent concentration there is an increased risk of irregular spot shapes / poor spot morphologies increases.§ Optimal detergent type and concentration must be determined empirically, taking into account; coating, probe type, probe concentration, immobilization and spotting method. © SCHOTT Technical Glass Solutions GmbH Page 9
  10. 10. Additional Information: www.us.schott.com/nexterion© SCHOTT Technical Glass Solutions GmbH Page 10

×