2026-05-13T09:05:20Z https://ena2pansimple.gfbio.org/oai/

oai:ena2pansimple.gfbio.org:PRJDA18705 2021-10-07

An emerging zoonotic agent isolated from fish, cattle and humans ENA European Nucleotide Archive Dataset insdc:PRJDA18705 Lactococcus garvieae ATCC 49156. This strain is being sequenced for comparative genome analysis. en https://www.ebi.ac.uk/ena/browser/view/PRJDA18705 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA18707 2021-10-07

An emerging zoonotic agent isolated from fish, cattle, and humans ENA European Nucleotide Archive Dataset insdc:PRJDA18707 Lactococcus garvieae Lg2. This strain is being sequenced for comparative genome analysis. en https://www.ebi.ac.uk/ena/browser/view/PRJDA18707 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA19951 2021-10-07

Antibiotic-producing soil bacterium ENA European Nucleotide Archive Dataset insdc:PRJDA19951 Kitasatospora setae KM-6054. Kitasatospora setae KM-6054 (NBRC 14216, ATCC 33774, DSM 43861) was isolated from soil in Japan and will provide information on the production and regulation of the antibiotics setamycin and bafilomycin B1. en https://www.ebi.ac.uk/ena/browser/view/PRJDA19951 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA20085 2021-10-07

Antibiotic producing bacterium ENA European Nucleotide Archive Dataset insdc:PRJDA20085 Streptomyces griseus NBRC 13350. This strain will be used for comparative analysis. en https://www.ebi.ac.uk/ena/browser/view/PRJDA20085 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA20209 2021-10-07

Bacterium associated with meat and sheep, goat and cattle milk ENA European Nucleotide Archive Dataset insdc:PRJDA20209 Macrococcus caseolyticus JCSC5402. This methicillin-resistant strain was isolated from animal meat in a supermarket. en https://www.ebi.ac.uk/ena/browser/view/PRJDA20209 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA20217 2021-10-07

Whole Genome Shotgun (WGS) sequence of the Bombyx mori genome, based on a collaboration between Southwest Agricultural University, China and the National Institute of Agrobiological Sciences, Japan ENA European Nucleotide Archive Dataset insdc:PRJDA20217 The international silkworm genome sequencing consortium is a joint collaboration of the National Institute of Agrobiological Sciences (NIAS) in Japan and the Southwest University in Chongqing City, China. The consortium has integrated the two independent whole genome shotgun (WGS) assemblies originally published in 2004 (<a href="http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&id=46810265">BAAB00000000</a> and <a href="http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&id=54109712">AADK00000000</a>), resulting in a single high-quality WGS assembly with approximately 10x coverage of the Bombyx mori genome (<a href="http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&id=186680507">BABH00000000</a>). Genome browsers are available at <a href="http://sgp.dna.affrc.go.jp/KAIKO/index.html">KAIKObase</a> and <a href="http://silkworm.genomics.org.cn/">SilkDB</a>. Scaffolds have been assembled into 28 linkage groups based on previously published linkage mapping (<a href="http://www.ncbi.nlm.nih.gov/pubmed/18226216?dopt=Abstract">Yamamoto K et al. 2008</a>), and are available for browsing at KAIKObase. en https://www.ebi.ac.uk/ena/browser/view/PRJDA20217 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA20361 2021-10-07

Methane-producing strain isolated from a rice paddy ENA European Nucleotide Archive Dataset insdc:PRJDA20361 Methanocella paludicola SANAE. This strain was isolated in Japan from rice paddy samples. en https://www.ebi.ac.uk/ena/browser/view/PRJDA20361 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA20395 2021-10-07

Bioremediation microorganism ENA European Nucleotide Archive Dataset insdc:PRJDA20395 Rhodococcus erythropolis PR4 (NBRC 100887). Rhodococcus erythropolis PR4 (NBRC 100887) was isolated from Pacific Ocean seawater. It has the enzymes necessary for the degradation of different alkanes, such as pristane. PR4 shows tolerance to hydrocarbons and it is capable of producing several compounds with medical, industrial, and nutritional applications such as beta-carotenes (i.e. astaxanthin) and fatty acid-containing extracellular polysaccharides (i.e. mucoidan). PR4 strain harbors one linear plasmid, pREL1 and two circular plasmids, pREC1 and pREC2, all with sequence similarities to other Rhodococcus plasmids. Plasmid pREL1 harbors metal-resistance and alkane-degradation genes. Plasmid pREC1 encodes for a complete set of beta-oxidation enzymes of fatty acids. en https://www.ebi.ac.uk/ena/browser/view/PRJDA20395 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA28997 2021-10-07

Clinical isolate ENA European Nucleotide Archive Dataset insdc:PRJDA28997 Streptococcus mutans NN2025. This strain is a clinical serotype c strain isolated in Japan in 2002. en https://www.ebi.ac.uk/ena/browser/view/PRJDA28997 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA31129 2021-10-07

Strain for comparative analysis ENA European Nucleotide Archive Dataset insdc:PRJDA31129 Acetobacter pasteurianus NBRC3283-01. This strain will be used for comparative analysis. en https://www.ebi.ac.uk/ena/browser/view/PRJDA31129 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA31131 2021-10-07

Strain for comparative analysis ENA European Nucleotide Archive Dataset insdc:PRJDA31131 Acetobacter pasteurianus NBRC3283-03. This strain will be used for comparative analysis. en https://www.ebi.ac.uk/ena/browser/view/PRJDA31131 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA31133 2021-10-07

Strain for comparative analysis ENA European Nucleotide Archive Dataset insdc:PRJDA31133 Acetobacter pasteurianus NBRC3283-07. This strain will be used for comparative analysis. en https://www.ebi.ac.uk/ena/browser/view/PRJDA31133 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA31135 2021-10-07

Strain for comparative analysis ENA European Nucleotide Archive Dataset insdc:PRJDA31135 Acetobacter pasteurianus NBRC3283-22. This strain will be used for comparative analysis. en https://www.ebi.ac.uk/ena/browser/view/PRJDA31135 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA31137 2021-10-07

Strain for comparative analysis ENA European Nucleotide Archive Dataset insdc:PRJDA31137 Acetobacter pasteurianus NBRC3283-26. This strain will be used for comparative analysis. en https://www.ebi.ac.uk/ena/browser/view/PRJDA31137 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA31139 2021-10-07

Strain for comparative analysis ENA European Nucleotide Archive Dataset insdc:PRJDA31139 Acetobacter pasteurianus NBRC3283-32. This strain will be used for comparative analysis. en https://www.ebi.ac.uk/ena/browser/view/PRJDA31139 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA31141 2021-10-07

Strain for comparative analysis ENA European Nucleotide Archive Dataset insdc:PRJDA31141 Acetobacter pasteurianus NBRC3283-01_42. This strain will be used for comparative analysis. en https://www.ebi.ac.uk/ena/browser/view/PRJDA31141 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA31211 2021-10-07

This strain is being sequenced for comparative genome analysis ENA European Nucleotide Archive Dataset insdc:PRJDA31211 Mycobacterium bovis BCG str. Tokyo 172. This strain is being sequenced for comparative genome analysis. en https://www.ebi.ac.uk/ena/browser/view/PRJDA31211 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA32047 2021-10-07

This strain will be used for comparative genome analysis ENA European Nucleotide Archive Dataset insdc:PRJDA32047 Bifidobacterium longum subsp. longum JCM 1217. This strain will be used for comparative genome analysis. en https://www.ebi.ac.uk/ena/browser/view/PRJDA32047 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA32049 2021-10-07

This strain will be used for comparative genome analysis ENA European Nucleotide Archive Dataset insdc:PRJDA32049 Bifidobacterium longum subsp. infantis JCM 1222. This strain will be used for comparative genome analysis. en https://www.ebi.ac.uk/ena/browser/view/PRJDA32049 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA32051 2021-10-07

This strain will be used for comparative genome analysis ENA European Nucleotide Archive Dataset insdc:PRJDA32051 Bifidobacterium longum subsp. infantis 157F-NC. This strain will be used for comparative genome analysis. en https://www.ebi.ac.uk/ena/browser/view/PRJDA32051 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA32509 2021-10-07

Enterohemorrhagic strain ENA European Nucleotide Archive Dataset insdc:PRJDA32509 Escherichia coli O26:H11 str. 11368. Escherichia coli O26:H11 str. 11368 is a human enterohemorrhagic E. coli which attaches to and effaces cells in the large intestine. The identifier O26:H11 refers to the serotype of EHEC, and reflects the specific antigenic markers found on the surface of the cell. This strain will be used for comparative analysis with other pathogenic and nonpathogenic E. coli. en https://www.ebi.ac.uk/ena/browser/view/PRJDA32509 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA32511 2021-10-07

This strain will be used for comparative genome analysis ENA European Nucleotide Archive Dataset insdc:PRJDA32511 Escherichia coli O103:H2 str. 12009. An enterohemorrhagic E. coli (EHEC) strain. This strain will be used for comparative genome analysis. en https://www.ebi.ac.uk/ena/browser/view/PRJDA32511 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA32513 2021-10-07

This strain will be used for comparative genome analysis ENA European Nucleotide Archive Dataset insdc:PRJDA32513 Escherichia coli O111:H- str. 11128. An enterohemorrhagic E. coli (EHEC) strain. This strain will be used for comparative genome analysis. en https://www.ebi.ac.uk/ena/browser/view/PRJDA32513 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA32551 2021-10-07

Plant growth promoting bacterium ENA European Nucleotide Archive Dataset insdc:PRJDA32551 Azospirillum sp. B510. Azospirillum sp. B510 was isolated from rice in Japan and will be used for comparative analysis with other plant growth promoting bacteria. en https://www.ebi.ac.uk/ena/browser/view/PRJDA32551 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA33133 2021-10-07

Human hepatocellular carcinoma Hep G2 cell line transcriptome ENA European Nucleotide Archive Dataset insdc:PRJDA33133 This experiment was made on total RNA extracted from cultured HepG2 cells. The human hepatocellular carcinoma Hep G2 (ATCC No. HB-8065) is a reference cell line that has been used in many transcriptome analysis. en https://www.ebi.ac.uk/ena/browser/view/PRJDA33133 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA33271 2021-10-07

Involved in the production of caproic acid. ENA European Nucleotide Archive Dataset insdc:PRJDA33271 Clostridium kluyveri NBRC 12016. Clostridium kluyveri NBRC 12016 (DSM 555) is being sequenced for comparative genome analysis. en https://www.ebi.ac.uk/ena/browser/view/PRJDA33271 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA33425 2021-10-07

Toxoplasma gondii ENA European Nucleotide Archive Dataset insdc:PRJDA33425 en https://www.ebi.ac.uk/ena/browser/view/PRJDA33425 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA33427 2021-10-07

Cryptosporidium parvum ENA European Nucleotide Archive Dataset insdc:PRJDA33427 en https://www.ebi.ac.uk/ena/browser/view/PRJDA33427 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA33429 2021-10-07

Plasmodium yoelii ENA European Nucleotide Archive Dataset insdc:PRJDA33429 en https://www.ebi.ac.uk/ena/browser/view/PRJDA33429 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA33431 2021-10-07

Plasmodium falciparum transcriptome project ENA European Nucleotide Archive Dataset insdc:PRJDA33431 A collection of over 11,400 full-length cDNAs covering 1375 (25%) of the estimated number of the entire 5409 parasite genes exists and can be found in the <a href="http://fullmal.hgc.jp/index_ajax.html">Malaria Full-Length cDNA database</a>. en https://www.ebi.ac.uk/ena/browser/view/PRJDA33431 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA33433 2021-10-07

Plasmodium vivax ENA European Nucleotide Archive Dataset insdc:PRJDA33433 en https://www.ebi.ac.uk/ena/browser/view/PRJDA33433 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA33435 2021-10-07

Babesia bovis ENA European Nucleotide Archive Dataset insdc:PRJDA33435 en https://www.ebi.ac.uk/ena/browser/view/PRJDA33435 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA33437 2021-10-07

Plasmodium berghei ENA European Nucleotide Archive Dataset insdc:PRJDA33437 en https://www.ebi.ac.uk/ena/browser/view/PRJDA33437 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA33439 2021-10-07

Anopheles stephensi transcriptome project ENA European Nucleotide Archive Dataset insdc:PRJDA33439 This transcriptome project is being performed at the University of Tokyo, Department of Medical Genome Sciences. en https://www.ebi.ac.uk/ena/browser/view/PRJDA33439 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA33441 2021-10-07

Glossina morsitans transcriptome project ENA European Nucleotide Archive Dataset insdc:PRJDA33441 en https://www.ebi.ac.uk/ena/browser/view/PRJDA33441 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA33443 2021-10-07

This strain will be used for comparative genome analysis ENA European Nucleotide Archive Dataset insdc:PRJDA33443 Streptococcus intermedius JTH08. This strain will be used for comparative genome analysis. en https://www.ebi.ac.uk/ena/browser/view/PRJDA33443 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA33445 2021-10-07

Vancomycin susceptible strain ENA European Nucleotide Archive Dataset insdc:PRJDA33445 Staphylococcus aureus subsp. aureus str. Mu50-omega. Staphylococcus aureus subsp. aureus str. Mu50-omega is a vancomycin susceptible strain and will be used for comparative analysis with other Staphylococcus aureus strains. en https://www.ebi.ac.uk/ena/browser/view/PRJDA33445 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA34063 2021-10-07

Methanococcus maripaludis KA1 genome sequencing ENA European Nucleotide Archive Dataset insdc:PRJDA34063 This strain will be used for comparative analysis. en https://www.ebi.ac.uk/ena/browser/view/PRJDA34063 2014-10-01

oai:ena2pansimple.gfbio.org:PRJDA34065 2021-10-07

Methanococcus maripaludis OS7 genome sequencing ENA European Nucleotide Archive Dataset insdc:PRJDA34065 This strain will be used for comparative analysis. en https://www.ebi.ac.uk/ena/browser/view/PRJDA34065 2014-10-01

oai:ena2pansimple.gfbio.org:PRJDA34131 2021-10-07

This strain will be used for comparative genome analysis ENA European Nucleotide Archive Dataset insdc:PRJDA34131 Hydrogenobacter thermophilus TK-6. This strain will be used for comparative genome analysis. en https://www.ebi.ac.uk/ena/browser/view/PRJDA34131 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA34711 2021-10-07

Streptococcus dysgalactiae subsp. equisimilis RE378 genome sequencing ENA European Nucleotide Archive Dataset insdc:PRJDA34711 en https://www.ebi.ac.uk/ena/browser/view/PRJDA34711 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA34739 2021-10-07

Shewanella violacea DSS12 Genome sequencing ENA European Nucleotide Archive Dataset insdc:PRJDA34739 Shewanella violacea DSS12. Shewanella violacea DSS12 was isolated from mud, taken at a depth of 5110 m, from the Ryukyu Trench in the Philippine Sea. Shewanella violacea DSS12 will be used to study the adaptations necessary for growth at high pressures and low temperatures. en https://www.ebi.ac.uk/ena/browser/view/PRJDA34739 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA34839 2021-10-07

Rhodococcus opacus B4 genome sequencing project ENA European Nucleotide Archive Dataset insdc:PRJDA34839 Rhodococcus opacus B4. This is a benzene-tolerant strain. This strain will be used for comparative genome analysis. en https://www.ebi.ac.uk/ena/browser/view/PRJDA34839 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA40637 2021-10-07

Lactobacillus rhamnosus GG strain ATCC 53103 genome sequencing project ENA European Nucleotide Archive Dataset insdc:PRJDA40637 Lactobacillus rhamnosus GG ATCC 53103. This strain was isolated from healthly human intestinal flora. It is one of the most widely used probiotics. en https://www.ebi.ac.uk/ena/browser/view/PRJDA40637 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA41121 2021-10-07

human epigenomics sequencing project of breast cancer and normal cell lines ENA European Nucleotide Archive Dataset insdc:PRJDA41121 Human breast cancer/normal cell lines (HMC18, HMEC, Hs578T, MCF7, MDAMB231, MDAMB453, MRKnu1, SKBR3, T47D) en https://www.ebi.ac.uk/ena/browser/view/PRJDA41121 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA42489 2021-10-07

Thermus phage YS40 genome sequencing project. ENA European Nucleotide Archive Dataset insdc:PRJDA42489 This registration was done by DDBJ submission staff instead of submitters. Please keep confidential for this registration. en https://www.ebi.ac.uk/ena/browser/view/PRJDA42489 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA42491 2021-10-07

Thermus phage TMA genome sequencing project. ENA European Nucleotide Archive Dataset insdc:PRJDA42491 This registration was done by DDBJ submission staff instead of submitters. Please keep confidential for this registration. en https://www.ebi.ac.uk/ena/browser/view/PRJDA42491 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA42805 2021-10-07

Comparative Genomics of Bacillus anthracis ENA European Nucleotide Archive Dataset insdc:PRJDA42805 Whole SNPs analysis among B. anthracis strains. BA103 isolated from bovine in Japan in 1991. BA104 isolated from swine in Japan in 1982 en https://www.ebi.ac.uk/ena/browser/view/PRJDA42805 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA43375 2021-10-07

Streptococcus salivarius HT9R genome sequencing project. ENA European Nucleotide Archive Dataset insdc:PRJDA43375 Streptococcus salivarius HT9R. Streptococcus salivarius HT9R is a member of the oral streptococci group and will be used for comparative analysis with other Streptococcus species. en https://www.ebi.ac.uk/ena/browser/view/PRJDA43375 2015-02-04

oai:ena2pansimple.gfbio.org:PRJDA43743 2021-10-07

Sequencing muscle short RNAs (16-40nt) to investigate possible regulation of myogenesis phenotypes. ENA European Nucleotide Archive Dataset insdc:PRJDA43743 Short RNAs (sRNAs) originating in pseudogenes and retrotransposons have been demonstrated to function as trans-regulatory elements in mammals. It followed therefore that the observed myogenesis phenotypes may have been caused by the perturbation of LINE-1 derived and/or other sRNAs, which are known to affect numerous cellular processes including differentiation. We therefore sequenced 2.1 million 16-40nt sRNAs from C2C12 muscle cells from one of the broadly used mouse strains. en https://www.ebi.ac.uk/ena/browser/view/PRJDA43743 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA45827 2021-10-07

Saccharomyces cerevisiae strain kyokai no. 7 genome sequencing project ENA European Nucleotide Archive Dataset insdc:PRJDA45827 en https://www.ebi.ac.uk/ena/browser/view/PRJDA45827 2014-05-31

oai:ena2pansimple.gfbio.org:PRJDA45949 2021-10-07

Rattus norvegicus transcriptome project ENA European Nucleotide Archive Dataset insdc:PRJDA45949 Rattus norvegicus is an important animal model in biology and medicine, in particular neuroscience. en https://www.ebi.ac.uk/ena/browser/view/PRJDA45949 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA46243 2021-10-07

Metatranscriptomic Analysis for Eukaryotic Functional Genes in Forest Soil ENA European Nucleotide Archive Dataset insdc:PRJDA46243 For the extraction of environmental RNA after enrichment with wheat bran and avicel, the sample was collected from the forest humic soil in the site of AIST. A forest soil in the site of AIST Tsukuba, Japan (36.06N 140.17E). The extraction of total RNA and the purification of polyadenylated eukaryotic mRNA from the enriched soil sample were used to commercially available kit, respectively. The synthesized cDNA sample from the purified mRNA was outsourced to Dragon Genomics Center for 454 GS FLX sequencing. The aim of this study is the exploration of the novel eukaryotic functional genes from an environmental sample using metatranscriptomic approach. This method is widely applicable to the provision of novel eukaryotic enzymes and proteins of potential industrial or medical use. en https://www.ebi.ac.uk/ena/browser/view/PRJDA46243 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA46247 2021-10-07

Ciona intestinalis transcriptome project ENA European Nucleotide Archive Dataset insdc:PRJDA46247 In mammals, CpG islands are good markers of genes because they are often linked to promoters. Genomic stretches with high frequencies of G+C and the CpG dinucleotide are observed in mammals and other vertebrates, although their contents vary considerably among species. CpG islands generally escape DNA methylation and tend to occur in the promoters of widely expressed genes. Another class of promoter has lower G+C and CpG contents, and is thought to be involved in the spatiotemporal regulation of gene expression. Invertebrates are reported to have a single class of promoter, with high-frequency CpG dinucleotides, suggesting that this is the original type of promoter. However, the limited annotation of invertebrate genes has impeded the large-scale analysis of their promoters. To determine the origins of the two classes of vertebrate promoters, we chose Ciona intestinalis, an invertebrate that is evolutionarily close to the vertebrates, and identified its transcription start sites genomewide in mid-tailbud-stage embryos using a next-generation sequencer. We observed high G+C and CpG contents around the transcription start sites, but their levels in the promoters and background sequences differed much less than in mammals. The CpG-rich stretches were also fairly restricted, so they were more similar to mammalian CpG-poor promoters than to CpG island promoters. From these data, we infer that CpG islands are not sufficiently ancient to be found in invertebrates. They probably appeared early in vertebrate evolution via some active mechanism and have since been maintained as part of vertebrate promoters. en https://www.ebi.ac.uk/ena/browser/view/PRJDA46247 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA46487 2021-10-07

Comprehensive analysis of salinity stress inducible genes in Oryza sativa ENA European Nucleotide Archive Dataset insdc:PRJDA46487 Illumina mRNA-seq analysis was performed to detect salinity stress inducible genes in Oryza sativa L. ssp. japonica cv. Nipponbare. Seeds of rice were germinated at 28o C in a sterilized germination tray. The seedlings had been grown for 7 days at 28o degrees C. Total RNA were extracted from shoots and roots under normal and 1 hr after salinity stress (150 mM NaCl solution). The expression profiles among four samples were compared to find rice salinity stress inducible genes. This work was supported by a grant from the Ministry of Agriculture, Forestry and Fisheries of Japan (Genomics for Agricultural Innovation, RTR-0001). en https://www.ebi.ac.uk/ena/browser/view/PRJDA46487 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA47577 2021-10-07

Mus musculus ENA European Nucleotide Archive Dataset insdc:PRJDA47577 We analyzed the genome wide incorporation of H3.3 in mouse cell lines. The enrichment of H3.3 was found at transcriptional start sites in myogenic genes. en https://www.ebi.ac.uk/ena/browser/view/PRJDA47577 2013-06-27

oai:ena2pansimple.gfbio.org:PRJDA47927 2021-10-07

Hevea brasiliensis subsp. brasiliensis strain:clone RRIM 600 Transcriptome or Gene expression ENA European Nucleotide Archive Dataset insdc:PRJDA47927 Hevea brasiliensis is the major economic crop as a source of natural rubber production. However, limited information of genomic resource and the lack of molecular markers developed for this plant species hinder breeding programs for crop improvement. To gain a better understanding of the rubber tree genome, we generated Expressed Sequence Tags (ESTs) and developed microsatellite markers from the transcriptome of H. brasiliensis leaf. We have sequenced 2,265,782 reads from the using 454 pyrosequencing technology. After clustering and assembly, a total of 214,013 unique sequences, comprising 32,633 contigs and 181,380 singlets, were generated. Gene annotation revealed that 49% shared sequence similarity with proteins in the Genbank non-redundant protein database. Functional categorization was performed by mapping against Gene Ontology (GO). We also identified 43,865 loci microsatellites from the data set. en https://www.ebi.ac.uk/ena/browser/view/PRJDA47927 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA48009 2021-10-07

Mus musculus epigenomics project ENA European Nucleotide Archive Dataset insdc:PRJDA48009 C2C12 myoblasts and NIH3T3 derived cell B22 en https://www.ebi.ac.uk/ena/browser/view/PRJDA48009 2013-06-27

oai:ena2pansimple.gfbio.org:PRJDA48395 2021-10-07

Whole genome resequencing for Bos taurus, Kuchinoshima-Ushi breed ENA European Nucleotide Archive Dataset insdc:PRJDA48395 Whole genome analysis of Japanese native cattle (Bos taurus) 'Kuchinoshima-Ushi' en https://www.ebi.ac.uk/ena/browser/view/PRJDA48395 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA48573 2021-10-07

Mixia osmundae IAM 14324 genome sequencing ENA European Nucleotide Archive Dataset insdc:PRJDA48573 en https://www.ebi.ac.uk/ena/browser/view/PRJDA48573 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA48645 2021-10-07

Bombyx mori transcriptome sequencing project ENA European Nucleotide Archive Dataset insdc:PRJDA48645 Total RNAs were prepared using Trizol reagent (Invitrogen) according to the manufacturer's protocol. Total RNA (10 ug) was loaded onto a 15% denaturing polyacrylamide gel containing 10 M urea, electrophoresed, and then stained with SYBRGold (Invitrogen). Signals were visualized using LAS-1000 film (Fujifilm). Small RNA libraries were constructed using a Small RNA cloning kit (Takara). DNA sequencing was performed using the Solexa genetic analysis system (Illumina) (Bently, 2006). One nano-gram of the prepared cDNA was used for the sequencing reactions with the Illumina GA. 10,000-15,000 clusters were generated per 'tile' and 36 cycles of the sequencing reactions were performed. The protocols of the cluster generation and sequence reactions were according to the manufacturer's instructions. Solexa sequencing generated reads of up to 36 nucleotides in length. cell line/type' 1:Wild type strain p50T, day 4 pupal ovary (called 'OV' in this study) 2:Wild type strain p50T, day 4 pupal testis (called 'TE' in this study) 3:Sex-limited yellow(T(W:2)Y-Abe; called 'LY' in this study) , day 4 pupal ovary 4:Mandarina W, (called 'MW' in this study), day 4 pupal ovary 5:DfZ-DfW (called 'without Fem', WF in this study), day 4 pupal testis en https://www.ebi.ac.uk/ena/browser/view/PRJDA48645 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA50447 2021-10-07

Homo sapiens ENA European Nucleotide Archive Dataset insdc:PRJDA50447 Genomic DNA from exons on chromosome X and whole genomic DNA of human cell line GM18940, and those from chromosome 21 and Y of human cell line GM130B en https://www.ebi.ac.uk/ena/browser/view/PRJDA50447 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA50789 2021-10-07

Botryococcus braunii BOT22 transcriptome project ENA European Nucleotide Archive Dataset insdc:PRJDA50789 We employed the 454 pyrosequencing technique to analyze the transcriptome of Botryococcus braunii (strain BOT22), which biosynthesizes terpenoid hydrocarbons resembling petroleum. en https://www.ebi.ac.uk/ena/browser/view/PRJDA50789 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA50791 2021-10-07

Botryococcus braunii BOT88-2 transcriptome project ENA European Nucleotide Archive Dataset insdc:PRJDA50791 454 pyrosequencing technique was used to analyze the transcriptome of Botryococcus braunii (strain BOT88-2), which biosynthesizes liquid hydrocarbons resembling petroleum via the very long-chain fatty acid biosynthesis pathway. en https://www.ebi.ac.uk/ena/browser/view/PRJDA50791 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA51189 2021-10-07

Francisella tularensis subsp. tularensis multi-isolate project ENA European Nucleotide Archive Dataset insdc:PRJDA51189 F. tularensis SCHU cultured confluently for 3 days on Chocolate II agar (BD) from glycerol stock was suspended with saline. The SCHU passage 0 (P0) clone 3 was isolated from this bacterial suspension. Three C57BL/6J mice were inoculated with 10^6 CFU/0.1 ml of above bacterial suspension. When mice showed the severe clinical signs or alive at 4 days after inoculation, three mice were sacrificed and their spleens were collected. The pool of spleen homogenate was plated on Chocolate II agar (BD) and then first passage F. tularensis SCHU were grown for 3days. The bacterial suspension was prepared with saline and then mice inoculated with this suspension were sacrificed. The nine times in vivo passages were carried out. Mice were inoculated with 10^8 to 10^9 CFU of SCHU in passage 2 to 5 because low amount of SCHU cannot produce the successive generations of SCHU in early passages. In contrast, mice were inoculated with 10^5 CFU of SCHU in passage 6 to 9. Since the increasing pathogenicities were observed during serial in vivo passage, SCHU P5 clone 3 and P9 clone 1 were isolated from pools of spleen homogenate at five and nine passages, respectively. In this study, SCHU P0 clone 3, SCHU P5 clone 3 and SCHU P9 clone 1 were named as SCHU P0, P5 and P9, respectively. en https://www.ebi.ac.uk/ena/browser/view/PRJDA51189 2014-04-09

oai:ena2pansimple.gfbio.org:PRJDA51407 2021-10-07

Homo sapiens THP-1 cell transcriptome project ENA European Nucleotide Archive Dataset insdc:PRJDA51407 Knockdown of 4 transcription factors in the THP-1 cell line followed up by CAGE technology. en https://www.ebi.ac.uk/ena/browser/view/PRJDA51407 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA51427 2021-10-07

Mus musculus neural stem cell transcriptome project ENA European Nucleotide Archive Dataset insdc:PRJDA51427 Transcriptome dynamics were evaluated in neural stem cells (NSCs) with different contexts by RNA-Seq. 1. NSCs allowed to differentiate for 7 days in culture dish. 2. NSCs engrafted into naïve spinal cord and isolated at 7 days after transplantation. 3. NSCs immediately engrafted into injured spinal cord and isolated at 7 days after transplantation. 4. Pre-transplantation NSCs. The striatum of green mouse on embryonic day 14 was dissociated, and passaged 2 times in media hormone mix supplemented with EGF, FGF-2 and B28. en https://www.ebi.ac.uk/ena/browser/view/PRJDA51427 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA51437 2021-10-07

Oryzias latipes Hd-rR Genome sequencing project ENA European Nucleotide Archive Dataset insdc:PRJDA51437 Medaka Hd-rR genome en https://www.ebi.ac.uk/ena/browser/view/PRJDA51437 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA51679 2021-10-07

Giardia intestinalis assemblage A, isolate AS175 genome sequencing project. ENA European Nucleotide Archive Dataset insdc:PRJDA51679 en https://www.ebi.ac.uk/ena/browser/view/PRJDA51679 2014-05-31

oai:ena2pansimple.gfbio.org:PRJDA51849 2021-10-07

Escherichia coli K-12 Transcriptome project ENA European Nucleotide Archive Dataset insdc:PRJDA51849 First, Escherichia coli cells were grown to late exponential phase (O.D.600 = 0.76) in modified M63 medium. Then, low molecular weight RNAs (<200 nt) were isolated from the cultured cells using mirVana miRNA Isolation Kit (Ambion). cDNA library was built from the RNA sample ligated with both 5' and 3' end specific RNA adapters for determining direction of each transcript. The cDNA library was deep sequenced by Illumina/Solexa 1G Genome Analyzer system. en https://www.ebi.ac.uk/ena/browser/view/PRJDA51849 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA51895 2021-10-07

Homo sapiens HapMap sample ID NA18943 Genome sequencing ENA European Nucleotide Archive Dataset insdc:PRJDA51895 HapMap-JPT NA18943 lymphoblastoid cell line. en https://www.ebi.ac.uk/ena/browser/view/PRJDA51895 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA52077 2021-10-07

Escherichia coli DH1 Genome sequencing project ENA European Nucleotide Archive Dataset insdc:PRJDA52077 Please refer to the following web page for source information; http://www.shigen.nig.ac.jp/ecoli/strain/nbrpStrainDetailAction.do?strainId=998 en https://www.ebi.ac.uk/ena/browser/view/PRJDA52077 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA52649 2021-10-07

Acetobacter aceti NBRC 14818 genome sequencing project ENA European Nucleotide Archive Dataset insdc:PRJDA52649 en https://www.ebi.ac.uk/ena/browser/view/PRJDA52649 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA52835 2021-10-07

Trichosporon asahii JCM 2466 ENA European Nucleotide Archive Dataset insdc:PRJDA52835 en https://www.ebi.ac.uk/ena/browser/view/PRJDA52835 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA63201 2021-10-07

Homo sapiens epigenomics ENA European Nucleotide Archive Dataset insdc:PRJDA63201 genomic DNA and mRNA from Hela cells To analyzed transcriptional regulation in Hela cells, we performed RNASeq and ChIPSeq using monoclonal antibodies which react Ser2P or Ser5P of RNAP2 specifically. Our result revealed that the state of transcribing RNAP2 can be divided three categories. This implies how to control serial mRNA expression by RNAP2. en https://www.ebi.ac.uk/ena/browser/view/PRJDA63201 2013-06-27

oai:ena2pansimple.gfbio.org:PRJDA63647 2021-10-07

Corynebacterium ulcerans 0102 Genome sequencing project ENA European Nucleotide Archive Dataset insdc:PRJDA63647 This strain will be used for comparative genome analysis. en https://www.ebi.ac.uk/ena/browser/view/PRJDA63647 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA65233 2021-10-07

Kluyveromyces marxianus DMKU3-1042 genome sequencing ENA European Nucleotide Archive Dataset insdc:PRJDA65233 en https://www.ebi.ac.uk/ena/browser/view/PRJDA65233 2014-01-15

oai:ena2pansimple.gfbio.org:PRJDA65427 2021-10-07

Exploring Bacterial Diversity of the Abyssal Seafloor in the East Sea, Korea ENA European Nucleotide Archive Dataset insdc:PRJDA65427 DNA from Surface Sediment (2269m and 1880m depth) in East Sea, Korea en https://www.ebi.ac.uk/ena/browser/view/PRJDA65427 2014-08-05

oai:ena2pansimple.gfbio.org:PRJDA66657 2021-10-07

Lagenaria siceraria strain:hangzhou gourd Genome sequencing ENA European Nucleotide Archive Dataset insdc:PRJDA66657 Genome of Lagenaria siceraria is being sequenced at the Zhejiang Academy of Agricultural Sciences. en https://www.ebi.ac.uk/ena/browser/view/PRJDA66657 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA66727 2021-10-07

Candidatus Arthromitus sp. SFB-mouse-Japan Genome sequencing project ENA European Nucleotide Archive Dataset insdc:PRJDA66727 en https://www.ebi.ac.uk/ena/browser/view/PRJDA66727 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA66755 2021-10-07

Porphyromonas gingivalis TDC60 genome sequencing project ENA European Nucleotide Archive Dataset insdc:PRJDA66755 en https://www.ebi.ac.uk/ena/browser/view/PRJDA66755 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA66833 2021-10-07

Pandalus latirostris Transcriptome project ENA European Nucleotide Archive Dataset insdc:PRJDA66833 Total RNA of Hokkai Shrimp, Pandalus latirostris, was extracted from ovary of five individuals of mature female. Samples were collected from two populations; Lake Notoro and Notsuke Bay in Hokkaido, Japan. Total RNA was pooled in each population. en https://www.ebi.ac.uk/ena/browser/view/PRJDA66833 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA66971 2021-10-07

Aspergillus kawachii IFO4308 genome sequencing ENA European Nucleotide Archive Dataset insdc:PRJDA66971 en https://www.ebi.ac.uk/ena/browser/view/PRJDA66971 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA67081 2021-10-07

Synechocystis sp. PCC 6803 Genome sequencing project ENA European Nucleotide Archive Dataset insdc:PRJDA67081 en https://www.ebi.ac.uk/ena/browser/view/PRJDA67081 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA67163 2021-10-07

Oryza sativa Japonica Group strain:Hitomebore Genome sequencing and assembly ENA European Nucleotide Archive Dataset insdc:PRJDA67163 Oryza sativa Japonica Group Hitomebore Genome sequencing project en https://www.ebi.ac.uk/ena/browser/view/PRJDA67163 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA67291 2021-10-07

Sorghum bicolor strain:Moench BTx623 Transcriptome or Gene expression ENA European Nucleotide Archive Dataset insdc:PRJDA67291 Total RNAs were extracted from shoot of Sorghum bicolor (L.) Moench BTx623 at the 7-8 leaf stage before and 7 days after inoculation of Bipolaris sorghicola isolate BC-24 (MAFF number 511379). en https://www.ebi.ac.uk/ena/browser/view/PRJDA67291 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA67327 2021-10-07

Calophyllum inophyllum Transcriptome or Gene expression ENA European Nucleotide Archive Dataset insdc:PRJDA67327 Several-year-old seedlings naturally grown in Bonin Island were used for RNA extraction. Inner bark, current year twigs and terminal buds were cut and frozen in liquid nitrogen, ground using mortar and pestle. Total RNA was extracted by the CTAB method (Le Provost et al., 2007), and contaminated DNA was removed by SV total RNA isolation system (Promega, Madison, WI). en https://www.ebi.ac.uk/ena/browser/view/PRJDA67327 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA67329 2021-10-07

Elaeocarpus photiniifolius transcriptome project ENA European Nucleotide Archive Dataset insdc:PRJDA67329 Several-year-old seedlings of Elaeocarpus photiniaefolius, naturally grown in Bonin Island were used for RNA extraction. Inner bark, current year twigs and terminal buds were cut and frozen in liquid nitrogen, ground using mortar and pestle. Total RNA was extracted by the CTAB method (Le Provost et al., 2007), and contaminated DNA was removed by SV total RNA isolation system (Promega, Madison, WI). en https://www.ebi.ac.uk/ena/browser/view/PRJDA67329 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA67331 2021-10-07

Schima mertensiana transcriptome project ENA European Nucleotide Archive Dataset insdc:PRJDA67331 Several-year-old seedlings of Schima mertensiana, naturally grown in Bonin Island were used for RNA extraction. Inner bark, and current year twigs were cut and frozen in liquid nitrogen, ground using mortar and pestle. Total RNA was extracted by the CTAB method (Le Provost et al., 2007), and contaminated DNA was removed by SV total RNA isolation system (Promega, Madison, WI). en https://www.ebi.ac.uk/ena/browser/view/PRJDA67331 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA67835 2021-10-07

Candidatus Arthromitus sp. SFB-mouse-Yit genome sequencing project ENA European Nucleotide Archive Dataset insdc:PRJDA67835 en https://www.ebi.ac.uk/ena/browser/view/PRJDA67835 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA67837 2021-10-07

Candidatus Arthromitus sp. SFB-rat-Yit genome sequencing project ENA European Nucleotide Archive Dataset insdc:PRJDA67837 en https://www.ebi.ac.uk/ena/browser/view/PRJDA67837 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA68077 2021-10-07

Lactococcus lactis subsp. lactis IO-1 genome sequencing project ENA European Nucleotide Archive Dataset insdc:PRJDA68077 Lactococcus lactis subsp. lactis IO-1. This strain will be used for comparative genome analysis. en https://www.ebi.ac.uk/ena/browser/view/PRJDA68077 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA68079 2021-10-07

Leuconostoc carnosum KCTC 3525 genome sequencing project ENA European Nucleotide Archive Dataset insdc:PRJDA68079 Leuconostoc carnosum KCTC 3525. This strain will be used for comparative genome analysis. en https://www.ebi.ac.uk/ena/browser/view/PRJDA68079 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA68081 2021-10-07

Lactobacillus malefermentans KCTC 3548 genome sequencing project ENA European Nucleotide Archive Dataset insdc:PRJDA68081 Lactobacillus malefermentans KCTC 3548. This strain is used for comparative genome analysis. en https://www.ebi.ac.uk/ena/browser/view/PRJDA68081 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA68083 2021-10-07

Lactobacillus suebicus KCTC 3549 genome sequencing project ENA European Nucleotide Archive Dataset insdc:PRJDA68083 Lactobacillus suebicus KCTC 3549. This strain will be used for comparative genome analysis. en https://www.ebi.ac.uk/ena/browser/view/PRJDA68083 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA68085 2021-10-07

Lactobacillus mali KCTC 3596 genome sequencing project ENA European Nucleotide Archive Dataset insdc:PRJDA68085 Lactobacillus mali KCTC 3596. This strain will be used for comparative genome analysis. en https://www.ebi.ac.uk/ena/browser/view/PRJDA68085 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA68087 2021-10-07

Lactobacillus zeae KCTC 3804 genome sequencing project ENA European Nucleotide Archive Dataset insdc:PRJDA68087 Lactobacillus zeae KCTC 3804. This strain will be used for comparative genome analysis. en https://www.ebi.ac.uk/ena/browser/view/PRJDA68087 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA68089 2021-10-07

Lactobacillus versmoldensis KCTC 3814 genome sequencing project ENA European Nucleotide Archive Dataset insdc:PRJDA68089 Lactobacillus versmoldensis KCTC 3814. This strain will be used for comparative genome analysis. en https://www.ebi.ac.uk/ena/browser/view/PRJDA68089 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA68091 2021-10-07

Lactobacillus acidipiscis KCTC 13900 genome sequencing project ENA European Nucleotide Archive Dataset insdc:PRJDA68091 Lactobacillus acidipiscis KCTC 13900. This strain will be used for comparative genome analysis. en https://www.ebi.ac.uk/ena/browser/view/PRJDA68091 2013-05-31

oai:ena2pansimple.gfbio.org:PRJDA68269 2021-10-07

Canis lupus familiaris Transcriptome project ENA European Nucleotide Archive Dataset insdc:PRJDA68269 Transcriptomes of the heart left ventricle muscles of a normal control dog and a congestive heart failure dog. en https://www.ebi.ac.uk/ena/browser/view/PRJDA68269 2013-05-31 106f27c0-b3f0-4278-b11e-2bf71f14c716