Welcome to MTD: Microbial Transcriptome Database

General Information
Tools for Drawing Circular Transcriptome Maps
Tiling Microarray Probe Sets
Request Probe Sets
Direct RNA Labeling
HM-SVM Profiling
Transcriptome Data
Porphyromonas gingivalis W83
Tiling Array Profiles
View profiles
RNAseq Profiles
Transcriptome Viewer
JBrowse Transcriptome Viewer
Streptococcus mutans UA159
Tiling Array Profiles
View in Genome Viewer
View in Transcriptome Viewer
RNAseq Profiles
JBrowse Transcriptome Viewer
Supplemental Data
Høvik et al (2012) Comprehensive transcriptome analysis of the periodontopathogenic bacterium Porphyromonas gingivalis W83
Khan et al (2016) Comprehensive transcriptome profiles of Streptococcus mutans UA159 map core streptococcal competence genes
Khan et al (2017) A positive feedback loop mediated by Sigma X enhances expression of the streptococcal regulator ComR
Two important high-throughput technologies have recently emerged to revolutionize biological research. The first is the high-density microarray technology, which can print millions of probe spots on a single microarray slide using the in situ oligo synthesis method. This great probe capacity has been used for designing oligonucleotide probes covering an entire small genome or chromosome, or a continuous portion of larger genomes. These types of microarrays usually have the probes designed to closely tile on the genomic sequence and are known as genomic tiling microarrays. Genomic tiling microarrays have been used to study whole genome or chromosome transcription for various organisms including human. For smaller genomes such as those of prokaryotes, the capacity of the high-density tiling microarrays permits probe designs to densely cover the entire genomic sequence using only one microarray slide, making these tiling arrays particularly useful for studying the whole genome transcription of prokaryotes, i.e., the transcriptome.

The second important technology, high-throughput DNA sequencing, has evolved at an even quicker pace. Since the first available massively parallel DNA sequencing platform was announced in 2005, several more so-called next generation DNA sequencing technologies have already been commercialized. The three most commonly known systems are Roche 454, Illumina, and ABI SOLiD. Together they greatly reduce the cost and time for sequencing DNA and have been used in large scale and in-depth sequencing projects such as the Human Microbiome Project. Next generation sequencing platforms have also been applied in transcription studies for both eukaryotes and prokaryotes. Due to the advent of these high-throughput technologies, there has been an explosive discovery of novel RNAs from many organisms, including bacteria. These discoveries have shown that the transcription landscape of all organisms is more complicated than expected.

The goal of The Microbial Transcriptome Database (MTD) is to provide tools and information for studying the microbial transcriptome profiles, in particular the transcriptome data derived from the high-throughput technologies. Currently MTD provides a comprehensive and dynamic probe design pipeline for designing the genomic tiling array probe sets for all microbial genomic sequences. Probe sets for many microbial genomes can be downloaded and more genomes are being added to the probe design pipeline. MTD also accepts request for custom probe design with user specified genomes and array platforms. MTD also provides online tools and interfaces specifically designed for analyzing the transcriptome data.

MTD currently provides the following tools and information:
Tools for Analyzing RNAseq tracriptomic Data
 *Scripts for Generating Circular Transcriptome Maps from RNAseq Data
Perls scripts helpful for generating circular transcriptome maps, as shown in this publication by Hovik et al, 2012
 *Dynamic Transcriptome Viewer
MTD Transcriptomic Viewer is a convenient way to close-examine the RNAseq/Tiling-array transcriptome profiles at single nucleotide solution. [See example here]. Please contact us for custom-implementation of your data in the MTD Transcriptome Viewer.
Dynamic Tiling Array Probe Design
 *Genomic Tiling Microarray Probe Sets
Download oligonucleotide DNA probes designed by the pipeline described in the article "Dynamic probe selection for studying microbial transcriptome with high-density genomic tiling microarrays" (Hovik and Chen BMC Bioinformatics 2010, 11:82)
 *Request Additional Custom Tiling Array Probe Sets
Due to the intense computation time for designing the probes using our pipeline, more probe sets will be gradually made available for all NCBI microbial genomes. If a probe set is not yet available, users can request for a particular genome to be designed in the next queue. We also accept requests for designing probe sets with non-default parameters or for propriety genomes. Please contact us for more detail.
Direct RNA Labeling
 *Strand-specific transcriptome profiling with directly labeled RNA on genomic tiling microarrays
Conventional transcriptome profiling using microarrays involves reverse transcription, which converts RNA to cDNA. The cDNA is then labeled and hybridized to the probes on the arrays, thus the RNA signals are detected indirectly. Reverse transcription is known to generate artifactual cDNA, in particular the synthesis of second-strand cDNA, leading to false discovery of antisense RNA. We have developed an effective method using RNA that is directly labeled, thus by-passing the cDNA generation. Detail direct RNA labeling method is described in Yu, et al., BMC Molecular Biology 2011, 12:3.. )
Transcriptome profiling by HM-SVM
 * HM-SVM Algorithm
RNA expression signals detected by high-density genomic tiling microarrays contain comprehensive transcriptome information of the target organism. Current methods for determining the RNA transcription units are still computer-intense and lack the discriminative power. HM-SVM is an efficient and accurate method for analyzing transcriptome profiles. (Yu et al, Bioinformatics. 2010 26:1423-30)
 * Download HM-SVM
Download HM-SVM script and sample microarray data
Contributors: Khoi Nguyen, Wen-Han Yu, Hedda Hovik, Young Yi and Tsute Chen
Support: This project is supported by a grant from The National Institute of Dental and Craniofacial Research entitled - " Comprehensive transcriptome analysis for Porphyromonas gingivalis " (R21 DE018803-01A1).
Copyright 2007-2008 The Forsyth Institute
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