Immobilized probe and glass surface chemistry as variables in microarray fabrication
© Hessner et al; licensee BioMed Central Ltd. 2004
Received: 02 June 2004
Accepted: 04 August 2004
Published: 04 August 2004
Global gene expression studies with microarrays can offer biological insights never before possible. However, the technology possesses many sources of technical variability that are an obstacle to obtaining high quality data sets. Since spotted microarrays offer design/content flexibility and potential cost savings over commercial systems, we have developed prehybridization quality control strategies for spotted cDNA and oligonucleotide arrays. These approaches utilize a third fluorescent dye (fluorescein) to monitor key fabrication variables, such as print/spot morphology, DNA retention, and background arising from probe redistributed during blocking. Here, our labeled cDNA array platform is used to study, 1) compression of array data using known input ratios of Arabidopsis in vitro transcripts and arrayed serial dilutions of homologous probes; 2) how curing time of in-house poly-L-lysine coated slides impacts probe retention capacity; and 3) the retention characteristics of 13 commercially available surfaces.
When array element fluorescein intensity drops below 5,000 RFU/pixel, gene expression measurements become increasingly compressed, thereby validating this value as a prehybridization quality control threshold. We observe that the DNA retention capacity of in-house poly-L-lysine slides decreases rapidly over time (~50% reduction between 3 and 12 weeks post-coating; p < 0.0002) and that there are considerable differences in retention characteristics among commercially available poly-L-lysine and amino silane-coated slides.
High DNA retention rates are necessary for accurate gene expression measurements. Therefore, an understanding of the characteristics and optimization of protocols to an array surface are prerequisites to fabrication of high quality arrays.
The generation of reliable gene expression data with cDNA microarrays requires fabrication of quality arrays. This task encompasses the amplification of adequate amounts of concentrated PCR product for use as probe from the cDNA clone, followed by ordered arraying of the probes onto coated glass slides. The glass slide is a key variable in either spotted cDNA or oligonucleotide array fabrication since it must possess: 1) a uniform surface that yields spots of consistent shape and size, 2) low background fluorescence, and 3) high DNA retention capacity. Since the array is clearly a source of experimental variability, we have developed a novel three-color array approach where it is possible to directly visualize either cDNA or oligonucleotide arrays prior to hybridization [1–3]. For cDNA arrays, the probes are easily tagged with a third, Cy3/Cy5 compatible, fluorescent dye (fluorescein) during amplification. After purification of PCR products, which includes removal of unincorporated oligonucleotide primer, the detected fluorescein fluorescence represents deposited cDNA probe on the array. This three-color approach allows for assessment of slide fabrication independent of hybridization, thereby enabling 1) direct visualization of array/element morphology, 2) quantification of probe deposition and retention on the slide surface and 3) ultimately a means for array quality control prior to hybridization.
By labeling the array itself with a third color, we have observed that arrays fabricated together are not equivalent in terms of a number of measurable physical parameters, including the amount of DNA probe deposited and retained and the amount of background arising from probe solublized and re-deposited during post-processing. In prior studies, we observed that these pre-hybridization array-based variables play a direct and significant relationship in replicate consistency, and that microarray data quality can be improved through prehybridization slide selection based upon these quality parameters [1, 2]. As a result of these studies, we identified putative slide acceptance criteria: array fluorescein mean element intensity >5000 RFU/pixel, coefficient of variation (CV) in intensity <10%, mean signal to noise score (signal/signal + noise; S/S+N) >0.85, and CV in spot size <20%. In this report, using known input ratios of in vitro transcript we experimentally correlate the quantity of support bound probe to measured expression ratios, in order to validate our quality control threshold for array acceptance. We then utilize our three-color array platform to evaluate the characteristics of in-house prepared poly-L-lysine coated slides and 13 additional commercially available coating surfaces, in terms of background auto-fluorescence, spot morphology, and DNA retention.
Results and Discussion
The relationship between support bound probe and measured ratio reliability
It has been assumed that the amount of cDNA probe deposited and retained on the array surface would have a nominal effect on observed differential expression ratios due to the competitive nature of two channel fluorescent hybridizations ; however this assumption has been shown to be false [1, 5]. Yue et al., using unlabeled Saccharomyces cerevisiae probes and complementary Cy5 and Cy3 labeled cDNA targets derived from in vitro transcripts, indirectly demonstrated this by printing yeast probes at increasingly dilute concentrations (<50 ng/ul) and observed elimination of the measured dynamic range to where input transcript ratios of 30:1 or 1:30 were both detected as output ratios close to 1:1, illustrating that limiting bound probe results in an underestimation or failure to detect differential gene expression .
Impact of poly-L-lysine cure-time on DNA retention capacity
Clearly, the amount of immobilized probe on the coated glass surface is a critical array fabrication variable, therefore factors that affect the amount of retention characteristics, such as surface chemistry, probe concentration, spotting buffer, spotting conditions, cross-linking and blocking conditions are important to understand. Protocols for coating glass microscope slides with poly-L-lysine are readily available on-line and reasonably simple to perform (for example: http://cmgm.stanford.edu/pbrown/protocols/; http://www.agac.umn.edu/microarray/protocols; http://microarray.swmed.edu). Although most available protocols are quite similar, some recommend the curing of slides for two weeks prior to spotting, while others state that coated slides are not stable for extended periods of time and recommend not printing onto slides that are greater than 4 months old. To investigate slide coating age as a potential variable in retention capacity, we fabricated more than 1,000 rat cDNA arrays (18,000 element/slide) using in-house poly-L-lysine coated slides ranging in age from 3 to 12 weeks. These slides were coated in 26 independent sessions and utilized over 12 different print runs. After printing all arrays were post-processed  and imaged under standardized conditions as previously described [1, 2].
Investigation of probe retention characteristics of commercially available coated slides
Given the potential time-dependent variability of in-house prepared poly-L-lysine coated slides, we investigated the retention characteristics of commercially available coated slides. Our objective was to identify a surface with consistently higher retention characteristics than our "fresh" in-house slides without having to change the spotting buffer (1.5 M betaine/5% DMSO) or the nonaqueous post-processing protocol [1, 2, 9], since these methods were previously found to yield high quality results on poly-L-lysine coated slides prepared in-house. We obtained examples of 13 different vendor-supplied slides for evaluation that possessed either poly-L-lysine, aminosilane, or undisclosed surface chemistries. Prior to printing, background auto-fluorescence in the fluorescein, Cy3, and Cy5 channels was evaluated. Fluorescein auto-fluorescence was observed on all poly-L-lysine slides except for those produced in-house, as well as 6 of the aminosilane slides (Asper Biotech, Corning, Erie Scientific, Genetix, Telechem), and the proprietary surface from Full Moon Biosciences. Cy3 auto-fluorescence was observed on all 3 commercial poly-L-lysine slides but not those prepared in-house, however none was observed on any of the aminosilane slides. Insignificant background in the Cy5 channel was only observed on 2 commercial poly-L-lysine slides (Electron Microscopy Sciences, Polysciences Inc.).
Retention Studies on Commercial Coated Slide Surfaces
RFU/Pixel deposited × 103
RFU/pixel retained × 103
Electron Microscopy Sciences
Corning Ultra GAPS
Corning GAPS II
Telechem Super Amine
Full Moon Biosystems
It has been reported that the amount of UV irradiation may be an important array fabrication variable since the amount of hybridization signal from spotted 70-mer oligonucleotides has been found to be dependent on the amount of cross-linking . In this previous report, different optimal cross-linking intensities for attachment of spotted 70-mer oligonucleotides were observed for different slide coating chemistries (poly-L-lysine, aldehyde, aminosilane, epoxide) ; furthermore, different cross-linking optima for probe attachment were also observed for slides with the same or similar slide chemistry from different vendors. This variable was not explored in our evaluation of vendor-supplied surfaces and may account for some of the performance differences observed. The report by Wang et al.,  prompted us to revisit this parameter for our in-house slides and we have observed approximately 20% better DNA retention by increasing the UV cross-linking energy from 60 mJ/cm2 to 200 mJ/cm2 independent of coated slide lot.
Fabrication of high quality spotted arrays is a daunting task possessing a high number of variables. The vendor supplied slides tested here were done so under conditions that have been optimized for our in-house prepared poly-L-lysine coated slides, although our optimized protocol is not drastically different than those used by other laboratories nor drastically different from any of the vendor provided protocols. Our observations, as well as the observations of others, suggest that optimization of ones protocol to a surface chemistry is an essential first step to generating reliable global gene expression measurements using in-house spotted microarrays.
A sequence-verified human library (Research Genetics, Huntsville, AL), consisting of 41,472 clones or a 36,000 clone rat cDNA library obtained from the University of Iowa was used as a source of probe DNA. Cultures were grown in 150 ul Terrific Broth (Sigma, St. Louis, MO) supplemented with 100 mg/ml ampicillin in 384 deep-well plates (Matrix Technologies, Hudson, NH) sealed with air pore tape sheets (Qiagen, Valencia, CA) and incubated with agitation for 14–16 hr. Clone inserts were amplified in duplicate in 384-well format from 0.5 ul bacterial culture or from 0.5 ul purified plasmid (controls only) using 0.26 μM of each vector primer (SK865 5'-fluorescein-GTC CGT ATG TTG TGT GGA A-3' and SK536: 5'-fluorescein-GCG AAA GGG GGA TGT GCT G-3' ) (Sigma-Genosys, The Woodlands, TX) in a 20 μl reaction consisting of 10 mM Tris-HCl pH8.3, 3.0 mM MgCl2, 50 mM KCl, 0.2 mM each dNTP (Amersham, Piscataway, NJ), 1 M betaine [11, 12], and 0.50 U Taq polymerase (Roche, Indianapolis IN). Reactions were amplified with a touchdown thermal profile consisting of 94°C for 5 min; 20 cycles of 94°C for 1 min, 60°C for 1 min (minus 0.5° per cycle), 72°C for 1 min; and 15 cycles of 94°C for 5 min; 20 cycles 94°C for 1 min, 55°C for 1 min, 72°C for 1 min; terminated with a 7 min hold at 72° [13–15]. PCR reactions were analyzed for single products by 1% agarose gel electrophoresis. Products from replicate plates were pooled and then purified by size exclusion filtration using the Multiscreen 384 PCR filter plates (Millipore, Bedford, MA). Forty wells of each 384-well probe plate were quantified by the PicoGreen assay (Molecular Probes, Eugene, OR) according to the manufacturers instructions. After quantification, all plates were dried down, and reconstituted at 125 ng/μl in 3% DMSO/1.5 M betaine. It has been shown that betaine normalizes base pair stability differences, increases solution viscosity, reduces evaporation rates , and enhances probe binding to surfaces such as poly-L-lysine or aminosilane [1, 9]. We have observed higher probe retention at much lower DNA concentrations (150–200 ng/ul) in the presence of betaine versus the typically required 4–500 ng/ul when using conventional printing solutions [2, 3].
Arabidopsis thaliana PCR product and in vitro transcript were purchased from Stratagene (La Jolla, CA) as part of the SpotReport®-10 Array Validation System. Arabidopsis thaliana PCR product was cloned into the pCRII vector using the TA cloning kit (Invitrogen, Carlsbad CA) and fluorescein-labeled PCR products for photosystem I chlorophyll a/b-binding protein, RUBISCO activase, ribulose-1,5-biphosphate carboxylase/oxygenase, lipid transfer protein 6 lipid transfer protein 5, papain-type cysteine endopeptidase, root cap 1, and triosphophate isomerase were generated using vector-specific primers essentially as described above. Products were purified, quantified, and a 1:2 dilution series (200 ng/ul to 12.5 ng/ul) was prepared and printed in duplicate onto each array.
Poly-L-lysine coated slides were prepared in-house as previously described  on Corning (Corning, NY) pre-cleaned 75 × 25 mm glass micro slides. Nine different commercially available aminosilane coated slides (Apogent Discoveries, Waltham, MA; Asper Biotech, Redwood City, CA; Bioslide Technologies, Walnut, CA; Corning Inc, Corning NY; Erie Scientific, Portsmouth, NH; Genetix, St. James, NY; Sigma, St. Louis, MO; Telechem International Inc, Sunnyvale, CA) and 3 different commercially available poly-L-lysine coated slides (Cel-Associates, Pearland, TX; Electron Microscopy Sciences, Fort Washington, PA; Polysciences Inc., Warrington, PA) were obtained for evaluation. Additionally, slides coated with a proprietary chemistry (Full Moon Biosystems, Sunnyvale, CA) were obtained. Microarrays possessing a density of 9,600 human probes/slide were printed onto coated slides using a GeneMachines Omni Grid printer (San Carlos, CA) with 16 Telechem International SMP3 pins (Sunnyvale, CA) at 40% humidity and 22°C. To control pin contact force and duration, the instrument was set with the following Z motion parameters, velocity: 7 cm/sec, acceleration: 100 cm/sec2, deceleration: 100 cm/sec2. All slides were post-processed using the previously described non-aqueous protocol  using 60 mJ/cm2 UV cross-linking energy. This protocol has yielded more favorable fluorescein post-blocking signal-to-noise values (signal/signal+noise; S/S+N) as compared to blocking in aqueous solutions. Image files on all slides were collected prior to printing to establish background fluorescence (fluorescein, Cy3 and Cy5), after printing (fluorescein), and after blocking (fluorescein), with a ScanArray 5000 (GSI Lumonics, Billerica, MA). Array image files were analyzed with the Matarray software [7, 8, 17].
Isolation of mRNA, labeling, and hybridization were performed as described previously http://cmgm.stanford.edu/pbrown/mguide/index.html. Known input ratios of photosystem I chlorophyll a/b-binding protein (30:1); RUBISCO activase (10:1); ribulose-1,5-biphosphate carboxylase/oxygenase (5:1); lipid transfer protein 6 (1:1); 0.7 lipid transfer protein 5 (1:1); papain-type cysteine endopeptidase (1:5); root cap 1 (1:10); and triosphophate isomerase (1:30) were spiked into Cy3 and Cy5 RNA labeling reactions, respectively. After hybridization, arrays were scanned with a ScanArray 5000 (GSI Lumonics, Billerica, MA) and image files were obtained. Again, array image files were analyzed with the Matarray software [7, 8, 17].
M.J.H is supported by a National Institute of Biomedical Imaging and Bioengineering Grant (EB001421) and by a special fund from the Children's Hospital of Wisconsin Foundation.
- Hessner MJ, Wang X, Khan S, Meyer L, Schlicht M, Tackes J, Datta MW, Jacob HJ, Ghosh S: Use of a three-color cDNA microarray platform to measure and control support-bound probe for improved data quality and reproducibility. Nucleic Acids Res. 2003, 31: e60-10.1093/nar/gng059.PubMed CentralView ArticlePubMedGoogle Scholar
- Hessner MJ, Wang X, Hulse K, Meyer L, Wu Y, Nye S, Guo SW, Ghosh S: Three color cDNA microarrays: quantitative assessment through the use of fluorescein-labeled probes. Nucleic Acids Res. 2003, 31: e14-10.1093/nar/gng014.PubMed CentralView ArticlePubMedGoogle Scholar
- Hessner MJ, Singh VK, Wang X, Khan S, Tschannen MR, Zahrt TC: Utilization of a labeled tracking oligonucleotide for visualization and quality control of spotted 70-mer arrays. BMC Genomics. 2004, 5: 12-10.1186/1471-2164-5-12.PubMed CentralView ArticlePubMedGoogle Scholar
- Winzeler EA, Schena M, Davis RW: Fluorescence-based expression monitoring using microarrays. Methods Enzymol. 1999, 306: 3-18. 10.1016/S0076-6879(99)06003-6.View ArticlePubMedGoogle Scholar
- Yue H, Eastman PS, Wang BB, Minor J, Doctolero MH, Nuttall RL, Stack R, Becker JW, Montgomery JR, Vainer M, Johnston R: An evaluation of the performance of cDNA microarrays for detecting changes in global mRNA expression. Nucleic Acids Res. 2001, 29: E41-41. 10.1093/nar/29.8.e41.PubMed CentralView ArticlePubMedGoogle Scholar
- MacMurray AJ, Moralejo DH, Kwitek AE, Rutledge EA, Van Yserloo B, Gohlke P, Speros SJ, Snyder B, Schaefer J, Bieg S, Jiang J, Ettinger RA, Fuller J, Daniels TL, Pettersson A, Orlebeke K, Birren B, Jacob HJ, Lander ES, Lernmark A: Lymphopenia in the BB Rat Model of Type 1 Diabetes is Due to a Mutation in a Novel Immune-Associated Nucleotide (Ian)-Related Gene. Genome Res. 2002, 12: 1029-1039. 10.1101/gr.412702.PubMed CentralView ArticlePubMedGoogle Scholar
- Wang X, Ghosh S, Guo S-W: Quantitative quality control in microarray image processing and data acquisition. Nucleic Acids Research. 2001, 29: E75-82. 10.1093/nar/29.15.e75.PubMed CentralView ArticlePubMedGoogle Scholar
- Wang X, Hessner MJ, Wu Y, Pati N, Ghosh S: Quantitative quality control in microarray experiments and the application in data filtering, normalization and false positive rate prediction. Bioinformatics. 2003, 19: 1341-1347. 10.1093/bioinformatics/btg154.View ArticlePubMedGoogle Scholar
- Diehl F, Grahlmann S, Beier M, Hoheisel J: Manufacturing DNA microarrays of high spot homogeneity and reduced background signal. Nucleic Acids Research. 2001, 29: e38-10.1093/nar/29.7.e38.PubMed CentralView ArticlePubMedGoogle Scholar
- Wang HY, Malek RL, Kwitek AE, Greene AS, Luu TV, Behbahani B, Frank B, Quackenbush J, Lee NH: Assessing unmodified 70-mer oligonucleotide probe performance on glass-slide microarrays. Genome Biol. 2003, 4: R5-10.1186/gb-2003-4-1-r5.PubMed CentralView ArticlePubMedGoogle Scholar
- Rees W, Yager T, Korte J, Von Hippel P: Betaine can eliminate the base pair composition dependence of DNA melting. Biochemistry. 1993, 32: 137-144. 10.1021/bi00052a019.View ArticlePubMedGoogle Scholar
- Henke W, Herdel K, Jung K, Schnorr D, Loening S: Betaine improves the PCR amplification of GC-rich sequences. Nucleic Acids Research. 1997, 25: 3957-3958. 10.1093/nar/25.19.3957.PubMed CentralView ArticlePubMedGoogle Scholar
- Don RH, Cox PT, Wainwright BJ, Baker K, Mattick JS: 'Touchdown' PCR to circumvent spurious priming during gene amplification. Nucleic Acids Res. 1991, 19: 4008-PubMed CentralView ArticlePubMedGoogle Scholar
- Hecker KH, Roux KH: High and low annealing temperatures increase both specificity and yield in touchdown and stepdown PCR. Biotechniques. 1996, 20: 478-485.PubMedGoogle Scholar
- Roux KH, Hecker KH: One-step optimization using touchdown and stepdown PCR. Methods Mol Biol. 1997, 67: 39-45.PubMedGoogle Scholar
- Eisen M, Brown P: DNA arrays for analysis of gene expression. Methods in Enzymology. 1999, 303: 179-205. 10.1016/S0076-6879(99)03014-1.View ArticlePubMedGoogle Scholar
- Wang X, Jiang N, Feng X, Xie Y, Tonellato P, Ghosh S, Hessner MJ: A novel approach for high quality microarray processing using third-dye array visualization technology. IEEE Transactions on Nanoscience. 2003, 2: 193-201. 10.1109/TNB.2003.816233.View ArticleGoogle Scholar
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