The European Nucleotide Archive in 2017

Silvester, Nicole C.; Alako, Blaise T. F.; Amid, Clara; Cerdeño-Tárraga, Ana; Clarke, Laura; Cleland, Ian; Harrison, Peter W.; Jayathilaka, Suran; Kay, Simon; Keane, Thomas M.; Leinonen, Rasko; Xin, Liu; Martínez-Villacorta, Josué; Menchi, Manuela; Reddy, Kethi; Pakseresht, Nima; Rajan, Jeena; Rossello, Marc; Smirnov, Dmitriy; Toribio, Ana Luisa; Vaughan, David; Zalunin, Vadim; Cochrane, Guy

doi:10.1093/nar/gkx1125

Cited by 85 publications

(81 citation statements)

References 15 publications

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“…Sequencing data from single-cell human (accessions SRP011546 (Yan et al, 2013), SRP055810 (Blakeley et al, 2015), ERP012552 (Petropoulos et al, 2016)), and mouse (SRP110669 (Mohammed et al, 2017), SRP020490 (Deng et al, 2014)) embryo profiling studies were obtained from the European Nucleotide Archive (Silvester et al, 2018). Reads from each species dataset were aligned to human genome build GRCh38/hg38, common marmoset C_jacchus3.2.1, and mouse assembly GRCm38/mm10 with STAR 2.5.2b (Dobin et al, 2013) using the two-pass method for novel splice detection (Engström et al, 2013).…”

Section: Rna-seq Data Processingmentioning

confidence: 99%

Single-cell transcriptome analysis of human, marmoset and mouse embryos reveals common and divergent features of preimplantation development

Boroviak

Stirparo

Dietmann

et al. 2018

Preprint

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The mouse embryo is the canonical model for mammalian preimplantation development. Recent advances in single-cell profiling allow detailed analysis of embryogenesis in other eutherian species, including human, to distinguish conserved from divergent regulatory programs and signalling pathways in the rodent paradigm. Here, we identify and compare transcriptional features of human, marmoset and mouse embryos by single-cell RNA-seq. Zygotic genome activation correlates with the presence of Polycomb Repressive Complexes in all three species, while ribosome biogenesis emerges as a predominant attribute in primate embryos, supporting prolonged translation of maternally deposited RNAs. We find that transposable element expression signatures are species-, stage-and lineage-specific. The pluripotency network in the primate epiblast lacks certain regulators operative in mouse, but encompasses WNT components and genes associated with trophoblast specification. Sequential activation of GATA6, SOX17 and GATA4 markers of primitive endoderm identity is conserved in primates. Unexpectedly, OTX2 is also associated with primitive endoderm specification in human and nonhuman primate blastocysts. Our cross-species analysis demarcates both conserved and primate-specific features of preimplantation development and underscores the molecular adaptability of early mammalian embryogenesis.

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Section: Rna-seq Data Processingmentioning

confidence: 99%

Single-cell transcriptome analysis of human, marmoset and mouse embryos reveals common and divergent features of preimplantation development

Boroviak

Stirparo

Dietmann

et al. 2018

Preprint

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“…The QSs submitted to the running time experiments are based on two sources. Runtimes measures on the D652 dataset uses real world 16S rRNA bacterial amplicons retrieved from the Earth Microbiome Project (Thompson et al, 2017) via the European Nucleotide Archive (Silvester et al, 2018) and the help of custom scripts from github.com/biocore/emp/ . Only reads with length superior to 100bp were retained (max length 150bp).…”

Section: Methods Tested and Datasetsmentioning

confidence: 99%

Rapid alignment-free phylogenetic identification of metagenomic sequences

Linard

Swenson

Pardi

2018

Preprint

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Motivation:Taxonomic classification is at the core of environmental DNA analysis. When a phylogenetic tree can be built as a prior hypothesis to such classification, phylogenetic placement (PP) provides the most informative type of classification because each query sequence is assigned to its putative origin in the tree. This is useful whenever precision is sought (e.g. in diagnostics). However, likelihood-based PP algorithms struggle to scale with the ever increasing throughput of DNA sequencing. Results: We have developed RAPPAS (Rapid Alignment-free Phylogenetic Placement via Ancestral Sequences) which uses an alignment-free approach, removing the hurdle of query sequence alignment as a preliminary step to PP. Our approach relies on the precomputation of a database of k-mers that may be present with non-negligible probability in relatives of the reference sequences. The placement is performed by inspecting the stored phylogenetic origins of the k-mers in the query, and their probabilities. The database can be reused for the analysis of several different metagenomes. Experiments show that the first implementation of RAPPAS is already faster than competing likelihood-based PP algorithms, while keeping similar accuracy for short reads. RAPPAS scales PP for the era of routine metagenomic diagnostics. Availability: Program and sources freely available for download at gite.lirmm.fr/linard/RAPPAS.

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“…The reads were mapped to the coding sequences (CDS) with Kallisto 99 to obtain transcripts per million (TPM) gene expression values. Publicly available RNA-seq experiments were downloaded from ENA 100 . The CDSs were downloaded from Phytozome 1,101 .…”

Section: Estimating Gene Expression From Rna Sequencing Datamentioning

confidence: 99%

Expression atlas of Selaginella moellendorffii provides insights into the evolution of vasculature, secondary metabolism and roots

Ferrari

Shivhare

Hansen

et al. 2019

Preprint

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The lycophyte Selaginella moellendorffii represents early vascular plants and is studied to understand the evolution of higher plant traits such as the vasculature, leaves, stems, roots, and secondary metabolism. However, little is known about the gene expression and transcriptional coordination of Selaginella genes, which precludes us from understanding the evolution of transcriptional programs behind these traits. •Our updated database at conekt.plant.tools provides a unique resource to study the evolution of genes, gene families, transcriptomes, and functional gene modules in the Archaeplastida kingdom. Introduction:The lycophyte Selaginella moellendorffii is an important model organism for plant evolutionary studies and comparative genomics, as it represents lycophytes, a clade of one of the oldest still existing vascular plants on earth. It is characterised by adaxial sporangia, a root system (roots or rhizophores), a vasculature and leaf-like structures with a single vein, called microphylls. S. moellendorffii has a genome size of only about 100 Mbp, which is one of the smallest reported plant genomes 1 . Lycophytes appeared about 400 Myr ago during the Silurian period and were particularly abundant during the Devonian to mid-Carboniferous period, peaking around 310 Myr ago in Euramerican coal swamps 2 . During the Carboniferous period, many lycophytes were tall, fast-growing trees, and their remains now exist as coal. As 70% of the biomass responsible for the Bashkirian and Moscovian coal formations in Euramerica came from lycophytes 3 , they are an important source of fossil fuels. Despite their decreasing abundance at the end of the Carboniferous period, the impact of lycophytes on the climate was significant, as their role as carbon sinks most likely contributed to the dramatic decline in atmospheric CO 2 4 .Lycophytes produce spores for reproduction that are dispersed by wind and water. One means to increase spore dispersal and outcompete neighbors in light capture, and thus facilitate the colonization of land, is to increase the height of the sporophyte. This required the evolution of specialized vasculature (xylem and phloem) for the transport of nutrients, water, and various signaling molecules and the reinforcement of cell walls by lignification 5 . This lignification, in turn, was associated with the evolution of the phenylpropanoid metabolic pathway to synthesize and polymerize the heterogeneous aromatic lignin in the xylem cell walls 6 .To provide water and structural support to the larger sporophytes, land plants also evolved roots. Despite their morphological and evolutionary diversity, all roots have the capacity to acquire and transport water and nutrients, grow in a downward direction, and form branch roots, and they all possess a root cap (set of terminal protective cells), a root apical meristem (a self-sustaining stem cell population) and a radial organization of cell types (from outermost epidermis tissue to innermost vascular tissue). Root morphology in extant plants and fossil records...

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The European Nucleotide Archive in 2017

Cited by 85 publications

References 15 publications

Single-cell transcriptome analysis of human, marmoset and mouse embryos reveals common and divergent features of preimplantation development

Single-cell transcriptome analysis of human, marmoset and mouse embryos reveals common and divergent features of preimplantation development

Rapid alignment-free phylogenetic identification of metagenomic sequences

Expression atlas of Selaginella moellendorffii provides insights into the evolution of vasculature, secondary metabolism and roots

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