The sequence read archive: explosive growth of sequencing data

Kodama, Yuichi; Shumway, Martin; Leinonen, Rasko

doi:10.1093/nar/gkr854

Cited by 846 publications

(694 citation statements)

References 8 publications

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“…To evaluate the prevalence and abundance of miBC members in gut microbiota, other host-derived ecosystems and environmental samples, we used an integrated metagenomic platform developed in-house and used in previous work (www.imngs.org) 16,57. All 16S rRNA gene amplicon studies available in the SRA 58 were extracted and organized in samplespecific databases. The IMNGS build 1510 used in the present study contained a total of 55,073 samples, including 6,001 and 11,705 from the mouse and human gut, respectively.…”

Section: Methodsmentioning

confidence: 99%

The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota

et al. 2016

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Intestinal bacteria influence mammalian physiology, but many types of bacteria are still uncharacterized. Moreover, reference strains of mouse gut bacteria are not easily available, although mouse models are extensively used in medical research. These are major limitations for the investigation of intestinal microbiomes and their interactions with diet and host. It is thus important to study in detail the diversity and functions of gut microbiota members, including those colonizing the mouse intestine. To address these issues, we aimed at establishing the Mouse Intestinal Bacterial Collection (miBC), a public repository of bacterial strains and associated genomes from the mouse gut, and studied host-specificity of colonization and sequence-based relevance of the resource. The collection includes several strains representing novel species, genera and even one family. Genomic analyses showed that certain species are specific to the mouse intestine and that a minimal consortium of 18 strains covered 50-75% of the known functional potential of metagenomes. The present work will sustain future research on microbiota-host interactions in health and disease, as it will facilitate targeted colonization and molecular studies. The resource is available at www.dsmz.de/miBC.

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Section: Methodsmentioning

confidence: 99%

The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota

et al. 2016

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“…Furthermore, in January 2012, 11,768 sets of Illumina raw reads with assigned species were downloaded from the NCBI Sequence Reads Archive (SRA [http://www.ncbi.nlm.nih.gov/sra]) (22). A total of 10,517 of these had been sequenced by the Illumina Genome Analyzer II sequencer, while the remaining 1,251 had been sequenced by the Illumina HiSeq 2000 sequencer.…”

Section: Data Set (I) Training Datamentioning

confidence: 99%

Benchmarking of Methods for Genomic Taxonomy

et al. 2014

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One of the first issues that emerges when a prokaryotic organism of interest is encountered is the question of what it is-that is, which species it is. The 16S rRNA gene formed the basis of the first method for sequence-based taxonomy and has had a tremendous impact on the field of microbiology. Nevertheless, the method has been found to have a number of shortcomings. In the current study, we trained and benchmarked five methods for whole-genome sequence-based prokaryotic species identification on a common data set of complete genomes: (i) SpeciesFinder, which is based on the complete 16S rRNA gene; (ii) Reads2Type that searches for species-specific 50-mers in either the 16S rRNA gene or the gyrB gene (for the Enterobacteraceae family); (iii) the ribosomal multilocus sequence typing (rMLST) method that samples up to 53 ribosomal genes; (iv) TaxonomyFinder, which is based on species-specific functional protein domain profiles; and finally (v) KmerFinder, which examines the number of cooccurring k-mers (substrings of k nucleotides in DNA sequence data). The performances of the methods were subsequently evaluated on three data sets of short sequence reads or draft genomes from public databases. In total, the evaluation sets constituted sequence data from more than 11,000 isolates covering 159 genera and 243 species. Our results indicate that methods that sample only chromosomal, core genes have difficulties in distinguishing closely related species which only recently diverged. The KmerFinder method had the overall highest accuracy and correctly identified from 93% to 97% of the isolates in the evaluations sets.

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“…The RNA-Seq expression compendium was built with public data sets from the National Center for Biotechnology Information's Sequence Read Archive (SRA; Kodama et al, 2012). The compendium contains gene-level expression values for 40 manually selected samples (Supplemental Table S5) of different treatment and tissue combinations.…”

Section: Rna-seq Compendiummentioning

confidence: 99%

A Collection of Conserved Noncoding Sequences to Study Gene Regulation in Flowering Plants

Velde

Bel²,

Vaneechoutte³

et al. 2016

Plant Physiol.

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Transcription factors (TFs) regulate gene expression by binding cis-regulatory elements, of which the identification remains an ongoing challenge owing to the prevalence of large numbers of nonfunctional TF binding sites. Powerful comparative genomics methods, such as phylogenetic footprinting, can be used for the detection of conserved noncoding sequences (CNSs), which are functionally constrained and can greatly help in reducing the number of false-positive elements. In this study, we applied a phylogenetic footprinting approach for the identification of CNSs in 10 dicot plants, yielding 1,032,291 CNSs associated with 243,187 genes. To annotate CNSs with TF binding sites, we made use of binding site information for 642 TFs originating from 35 TF families in Arabidopsis (Arabidopsis thaliana). In three species, the identified CNSs were evaluated using TF chromatin immunoprecipitation sequencing data, resulting in significant overlap for the majority of data sets. To identify ultraconserved CNSs, we included genomes of additional plant families and identified 715 binding sites for 501 genes conserved in dicots, monocots, mosses, and green algae. Additionally, we found that genes that are part of conserved mini-regulons have a higher coherence in their expression profile than other divergent gene pairs. All identified CNSs were integrated in the PLAZA 3.0 Dicots comparative genomics platform (http://bioinformatics.psb.ugent.be/plaza/versions/plaza_v3_dicots/) together with new functionalities facilitating the exploration of conserved cis-regulatory elements and their associated genes. The availability of this data set in a user-friendly platform enables the exploration of functional noncoding DNA to study gene regulation in a variety of plant species, including crops.

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The sequence read archive: explosive growth of sequencing data

Cited by 846 publications

References 8 publications

The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota

The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota

Benchmarking of Methods for Genomic Taxonomy

A Collection of Conserved Noncoding Sequences to Study Gene Regulation in Flowering Plants

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