We thank Anne de Jong and Siger Holsappel for help with the DNA microarrays slide production. Anne de Jong&#8217;s support for bioinformatics analysis is also appreciated. We also thank Jelle Slager for reviewing the paper. Muhammad Afzal and Irfan Manzoor are supported by the GC University, Faisalabad, Pakistan under the faculty development program of HEC Pakistan.

1. Preparation of Media, and Cell Culture
<ol>
	<li>Grow S. pneumoniae D39 wild-type strain21 as described previously11. Inoculate cells stored at -80&#160;oC in 10% glycerol (with 1/100 ratio in 50 ml sterile tubes) in 50 ml Chemically Defined Medium (CDM) with a final pH of 6.4 15, but omit L-serine from the amino acid mixture. 
	Note: two different CDMs were used; one containing a minimum concentration of L-serine (150 &#181;M) and the other containing a maxi...

<ol>
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J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=FIVA:+Functional+Information+Viewer+and+Analyzer+extracting+biological+knowledge+from+transcriptome+data+of+prokaryotes.">FIVA: Functional Information Viewer and Analyzer extracting biological knowledge from transcriptome data of prokaryotes.</a> Bioinforma. Oxf. Engl. 23, 1161-1163 (2007).</li><li>Blom, E. J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Prosecutor:+parameter-free+inference+of+gene+function+for+prokaryotes+using+DNA+microarray+data,+genomic+context+and+multiple+gene+annotation+sources.">Prosecutor: parameter-free inference of gene function for prokaryotes using DNA microarray data, genomic context and multiple gene annotation sources.</a> BMC Genomics. 9, 495 (2008).</li><li>Blom, E. J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=DISCLOSE+:+DISsection+of+CLusters+Obtained+by+SEries+of+transcriptome+data+using+functional+annotations+and+putative+transcription+factor+binding+sites.">DISCLOSE : DISsection of CLusters Obtained by SEries of transcriptome data using functional annotations and putative transcription factor binding sites.</a> BMC Bioinformatics. 9, 535 (2008).</li><li>Baerends, R. J. S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Genome2D:+a+visualization+tool+for+the+rapid+analysis+of+bacterial+transcriptome+data.">Genome2D: a visualization tool for the rapid analysis of bacterial transcriptome data.</a> Genome Biol. 5 (5), R37 (2004).</li><li>De Jong, A., Pietersma, H., Cordes, M., Kuipers, O. 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We describe a user-friendly protocol that can be applied to perform whole transcriptome analysis of bacteria. The key point about this particular technique is that the condition under which the cells are harvested will vary. After harvesting the cells and RNA isolation, this technique becomes equal for all types of bacterial samples and follows exactly identical steps and therefore, can be applied to any type of bacterial culture. The protocol is very simple and convenient and starts from RNA isolation. Our RNA isolation...

The study of the whole set of mRNA abundance (transcriptome) encoded by the genome of a unicellular organism or a eukaryotic cell at a specific time or under a specific condition, including gene overexpression or knock-out, is called transcriptomics. Transcriptomics allows us to observe to what extent genes are expressed under a particular condition at a time point X and gives us information about how strongly the genes are expressed relative to a reference.
A microarray is a two-dimensional array on a solid substrate (usually a glass slide or silicon thin-film cell) that can be used to assay large quantities of biological material using high-throughput screening, and miniaturized, multiplexed and parallel processing and detection methods. Microarrays come in various types, including DNA-microarrays, protein microarrays, peptide microarrays, tissue microarrays, antibody microarrays, cellular microarrays and others. A DNA microarray is basically an assembly of microscopic DNA spots fixed to a solid surface, usually glass. DNA microarrays are used to measure the expression levels of a gene or a set of genes simultaneously or to genotype multiple regions of a genome2,3. Picomoles (10-12 moles) of a probe are present within each DNA spot that represents a specific DNA sequence, also known as a reporter. The labelled mRNA molecules from the samples are called &#8216;targets&#8217;. Fluorophores are used to measure probe-target hybridization and detection of fluorophore-labelled targets determines the relative abundance of nucleic acid sequences in the target. A microarray experiment can accomplish multiple genetic tests in parallel because an array may contain tens of thousands of probes. The layout of a simple microarray experiment is shown in Figure 1. Recently, it was established in our and other labs that these arrays are reusable, which makes this technique quite cost-effective.
Different RNA isolation and purification techniques have been developed over the years including C-TAB, SDS and GT methods 4&#8211;8. Furthermore, several commercial kits are also available. For gene expression high quality RNA is very important. Therefore, the RNA isolation methods are modified to get a maximum quantity of RNA. Similarly, the steps for cDNA preparation and labelling of cDNA are minimized. Normalization of data after scanning is also performed efficiently by using in-house built software packages and tools9.
Streptococcus pneumoniae is a Gram-positive human pathogen that colonizes the nasopharynx and is the cause of multiple infections such as pneumonia, sepsis, otitis media and meningitis10. The bacterium can utilize a wide variety of the nutrients required for growth and survival 11,12. A number of studies have been carried out on the pneumococcal nitrogen metabolism and regulation emphasizing the importance of amino acids and their role in virulence13,14. In this study, the transcriptomic response of S. pneumoniae to changing concentrations of L-serine, an amino acid abundantly present in the human blood plasma, is reported using DNA microarrays. The transcriptomic response of S. pneumoniae grown in a minimum concentration of L-serine (150 &#181;M) was compared to that grown in a maximum concentration (10 mM) of serine. Chemically defined medium (CDM or minimal medium)15 was used for this study to control the concentration of serine. The focus of this study is to make this technique user-friendly and to provide different tools for data normalization and analysis. Therefore, a number of tools were developed for analysis and data interpretation. FIVA (Functional Information Viewer and Analyzer) provides a platform for processing information contained in clusters of genes having similar gene expression patterns and for constructing functional profiles16. PROSECUTOR is another software package that facilitates the identification of putative functions and annotations of genes 17. By making use of clustering methods, DISCLOSE provides a DNA binding site detection algorithm. Cis-regulatory motifs of genes can be projected by using this algorithm 18. Genome2D offers a Windows-based platform for visualization and analysis of transcriptome data by offering different color ranges to characterize the changes in gene expression levels on a genome map19. The PePPER webserver offers, in addition to the all-in-one analysis method, a toolbox for mining for regulons, promoters and transcription factor binding sites 20. Full annotation of intergenic regions in a bacterial genome can be achieved by using this package. Biologists can greatly benefit from PePPER as it offers them a platform for designing experiments so that the hypothesized information can be confirmed in vitro20. These software packages contribute significantly to the microarray analysis as most of them are freely available and make data normalization and analysis very reliable.

<table border="0" cellpadding="0" cellspacing="0">
	<tbody>
		<tr>
			<td>Acid phenol</td>
			<td>SigmaAldrich</td>
			<td>P4682</td>
			<td></td>
		</tr>
		<tr>
			<td>Roche RNA isolation kit</td>
			<td>Roche Applied Science</td>
			<td>11828665001</td>
			<td></td>
		</tr>
		<tr>
			<td>Glass beads</td>
			<td></td>
			<td>105015</td>
			<td></td>
		</tr>
		<tr>
			<td>Chloroform</td>
			<td>Boom</td>
			<td>92013505.1000.</td>
			<td></td>
		</tr>
		<tr>
			<td>IAA</td>
			<td></td>
			<td>106630</td>
			<td></td>
		</tr>
		<tr>
			<td>Nanodrop</td>
			<td>Nanodrop</td>
			<td>ND-100</td>
			<td></td>
		</tr>
		<tr>
			<td>Agilent BioAnalyser</td>
			<td>Agilent</td>
			<td>G2940CA</td>
			<td></td>
		</tr>
		<tr>
			<td>Superscript III</td>
			<td>Life technologies Invitrogen</td>
			<td>18080044</td>
			<td></td>
		</tr>
		<tr>
			<td>AA-dUTP</td>
			<td>Life technologies Invitrogen</td>
			<td>AM8439</td>
			<td></td>
		</tr>
		<tr>
			<td>DDT</td>
			<td>Life technologies Invitrogen</td>
			<td>18080044</td>
			<td></td>
		</tr>
		<tr>
			<td>First Strand buffer</td>
			<td>Life technologies Invitrogen</td>
			<td>18080044</td>
			<td></td>
		</tr>
		<tr>
			<td>NaOH</td>
			<td>SigmaAldrich</td>
			<td>S8045-1KG</td>
			<td></td>
		</tr>
		<tr>
			<td>HEPES</td>
			<td>SigmaAldrich</td>
			<td>H4034-500G</td>
			<td></td>
		</tr>
		<tr>
			<td>DyLight-550</td>
			<td>Thermoscientiffic</td>
			<td>62262</td>
			<td></td>
		</tr>
		<tr>
			<td>DyLight-650</td>
			<td>Thermoscientiffic</td>
			<td>62265</td>
			<td></td>
		</tr>
		<tr>
			<td>SHY Buffer</td>
			<td>SigmaAldrich</td>
			<td>H7033-125ML</td>
			<td></td>
		</tr>
		<tr>
			<td>Speedvac cooler</td>
			<td>Eppendorf</td>
			<td>RUGNE3140</td>
			<td>Speedvac concentrator plus</td>
		</tr>
		<tr>
			<td>Hybridization oven</td>
			<td>Grant Boekel</td>
			<td>Iso-20</td>
			<td></td>
		</tr>
		<tr>
			<td>Lifter-slips</td>
			<td>Erie Scientific</td>
			<td>25x60I-M-5439</td>
			<td></td>
		</tr>
		<tr>
			<td>Wipe</td>
			<td>KIMTECH</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>SDS</td>
			<td>SigmaAldrich</td>
			<td>L3771-100g</td>
			<td></td>
		</tr>
		<tr>
			<td>SSC</td>
			<td>SigmaAldrich</td>
			<td>W302600-1KG-K</td>
			<td></td>
		</tr>
		<tr>
			<td>Genpix autoloader 4200A1</td>
			<td>MSD analytical technologies</td>
			<td></td>
			<td>Microarray scanner</td>
		</tr>
		<tr>
			<td>Sodium bicarbonate</td>
			<td>SigmaAldrich</td>
			<td>104766</td>
			<td></td>
		</tr>
	</tbody>
</table>

a fast and reliable pipeline for bacterial transcriptome analysis case study: serine-dependent gene regulation in streptococcus pneumoniae

Gene expression and its regulation are very important to understand the behavior of cells under different conditions. Various techniques are used nowadays to study gene expression, but most are limited in terms of providing an overall picture of the expression of the whole transcriptome. DNA microarrays offer a fast and economic research technology, which gives a full overview of global gene expression and have a vast number of applications including identification of novel genes and transcription factor binding sites, characterization of transcriptional activity of the cells and also help in analyzing thousands of genes (in a single experiment). In the present study, the conditions for bacterial transcriptome analysis from cell harvest to DNA microarray analysis have been optimized. Taking into account the time, costs and accuracy of the experiments, this technology platform proves to be very useful and universally applicabale for studying bacterial transcriptomes. Here, we perform DNA microarray analysis with Streptococcus pneumoniae as a case-study by comparing the transcriptional responses of S. pneumoniae grown in the presence of varying L-serine concentrations in the medium. Total RNA was isolated by using a Macaloid method using an RNA isolation kit and the quality of RNA was checked by using an RNA quality check kit. cDNA was prepared using reverse transcriptase and the cDNA samples were labelled using one of two amine-reactive fluorescent dyes. Homemade DNA microarray slides were used for hybridization of the labelled cDNA samples and microarray data were analyzed by using a cDNA microarray data pre-processing framework (Microprep). Finally, Cyber-T was used to analyze the data generated using Microprep for the identification of statistically significant differentially expressed genes. Furthermore, in-house built software packages (PePPER, FIVA, DISCLOSE, PROSECUTOR, Genome2D) were used to analyze data.

RNA, cDNA isolations and analysis
L-serine is one of the essential amino acids and its concentration in human blood plasma varies from 60-150 &#181;M in children and adults. Its role in the biosynthesis of purines and pyrimidines highlights its importance in metabolism and it is a precursor to several amino acids (glycine, cysteine and tryptophan). To study the impact of L-serine on the whole transcriptome of S. pneumoniae D39 wild-type strain, microarray analysis of ...

Watch this Scientific Journal Video about A Fast and Reliable Pipeline for Bacterial Transcriptome Analysis Case study: Serine-dependent Gene Regulation in Streptococcus pneumoniae at JoVE.com

A Fast and Reliable Pipeline for Bacterial Transcriptome Analysis Case study: Serine-dependent Gene Regulation in Streptococcus pneumoniae

This manuscript describes the use of state-of-the-art technology provided by DNA-microarrays. Microarrays provide an overview of the transcriptomic changes in bacteria incurred under a specific condition. Moreover, we highlight the ease by which large amounts of data can be analyzed by using convenient in-house developed software packages.

A Fast and Reliable Pipeline for Bacterial Transcriptome Analysis Case study: Serine-dependent Gene Regulation in Streptococcus pneumoniae

Gene expression and its regulation are very important to understand the behavior of cells under different conditions. Various techniques are used nowadays ...

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10.2K vistas.  University of Groningen. This manuscript describes the use of state-of-the-art technology provided by DNA-microarrays. Microarrays provide an overview of the transcriptomic changes in bacteria incurred under a specific condition. Moreover, we highlight the ease by which large amounts of data can be analyzed by using convenient in-house developed software packages. 