OpenTein: a database of digital whole-slide images of stem cell-derived teratomas.


:Human stem cells are promising sources for regenerative therapy. To ensure safety of future therapeutic applications, the differentiation potency of stem cells has to be tested and be widely opened to the public. The potency is generally assessed by teratoma formation comprising differentiated cells from all three germ layers, and the teratomas can be inspected through high-quality digital images. The teratoma assay, however, lacks consistency in transplantation protocols and even in interpretation, which needs community-based efforts for improving the assay quality. Here, we have developed a novel database OpenTein (Open Teratoma Investigation, to archive and freely distribute high-resolution whole-slide images and relevant records. OpenTein has been designed as a searchable, zoomable and annotatable web-based repository system. We have deposited 468 images of teratomas derived by our transplantation of human stem cells, and users can freely access and process such digital teratoma images. Approximately, the current version of OpenTein responds within 11.2 min for processing 2.03 gigapixel teratoma images. Our system offers valuable tools and resources in the new era of stem cell biology.


Nucleic Acids Res


Nucleic acids research


Park SJ,Komiyama Y,Suemori H,Umezawa A,Nakai K




Has Abstract


2016-01-04 00:00:00














  • Contributions of discrete tRNA(Ser) domains to aminoacylation by E.coli seryl-tRNA synthetase: a kinetic analysis using model RNA substrates.

    abstract::The aminoacylation kinetics of T7 transcripts representing defined regions of Escherichia coli serine tRNAs were determined using purified E.coli seryl-tRNA synthetase (SerRS) and the kinetic values were used to estimate the relative contribution of various tRNA(Ser) domains to recognition by SerRS. The analysis revea...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Sampson JR,Saks ME

    更新日期:1993-09-25 00:00:00

  • Efficient reamplification of differential display products by transient ligation and thermal asymmetric PCR.

    abstract::A new method for specific reamplification of DDRT-PCR products is presented. After transient ligation of the primary DDRT-PCR fragments into a T-vector, the cDNAs of interest were reamplified by hemi-nested PCR and thermally asymmetric cycles. In contrast to the originally described protocol, this method of reamplific...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Bonnet S,Prévot G,Bourgouin C

    更新日期:1998-02-15 00:00:00

  • IEDB-AR: immune epitope database-analysis resource in 2019.

    abstract::The Immune Epitope Database Analysis Resource (IEDB-AR, is a companion website to the IEDB that provides computational tools focused on the prediction and analysis of B and T cell epitopes. All of the tools are freely available through the public website and many are also available through a RE...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Dhanda SK,Mahajan S,Paul S,Yan Z,Kim H,Jespersen MC,Jurtz V,Andreatta M,Greenbaum JA,Marcatili P,Sette A,Nielsen M,Peters B

    更新日期:2019-07-02 00:00:00

  • Tumor-associated mutations of rat mitochondrial transfer RNA genes.

    abstract::Mitochondrial DNA is a sensitive target of chemical carcinogens (Backer and Weinstein (1980) Science 209, 297-299), suggesting that mutations of the mitochondrial genome occur in tumor cells. We examined this point by comparing mitochondrial DNA sequences in four rat tumors with those of normal rat liver. Some novel m...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Taira M,Yoshida E,Kobayashi M,Yaginuma K,Koike K

    更新日期:1983-03-25 00:00:00

  • Cation and sequence effects on stability of intermolecular pyrimidine-purine-purine triplex.

    abstract::A differential effect is found of various bivalent cations (Ba2+, Ca2+, Mg2+, Cd2+, Co2+, Mn2+, Ni2+, Zn2+ and Hg2+) on stability of intermolecular Py-Pu-Pu triplex with different sequence of base triads. Ca2+, Mg2+, Cd2+, Co2+, Mn2+, Ni2+ and Zn2+ do stabilize the d(C)n d(G)n d(G)n triplex whereas Ba2+ and Hg2+ do no...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Malkov VA,Voloshin ON,Soyfer VN,Frank-Kamenetskii MD

    更新日期:1993-02-11 00:00:00

  • Systematic design and functional analysis of artificial microRNAs.

    abstract::Unlike short interfering RNAs (siRNAs), which are commonly designed to repress a single messenger RNA (mRNA) target through perfect base pairing, microRNAs (miRNAs) are endogenous small RNAs that have evolved to concurrently repress multiple mRNA targets through imperfect complementarity. MicroRNA target recognition i...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Arroyo JD,Gallichotte EN,Tewari M

    更新日期:2014-05-01 00:00:00

  • DAP-like kinase interacts with the rat homolog of Schizosaccharomyces pombe CDC5 protein, a factor involved in pre-mRNA splicing and required for G2/M phase transition.

    abstract::DAP-like kinase (Dlk, also termed ZIP kinase) is a leucine zipper-containing serine/threonine-specific protein kinase with as yet unknown biological function(s). Interaction partners so far identified are either transcription factors or proteins that can support or counteract apoptosis. Thus, Dlk might be involved in ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Engemann H,Heinzel V,Page G,Preuss U,Scheidtmann KH

    更新日期:2002-03-15 00:00:00

  • PomBase 2015: updates to the fission yeast database.

    abstract::PomBase ( is the model organism database for the fission yeast Schizosaccharomyces pombe. PomBase provides a central hub for the fission yeast community, supporting both exploratory and hypothesis-driven research. It provides users easy access to data ranging from the sequence level, to molecula...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: McDowall MD,Harris MA,Lock A,Rutherford K,Staines DM,Bähler J,Kersey PJ,Oliver SG,Wood V

    更新日期:2015-01-01 00:00:00

  • pre-miRNA profiles obtained through application of locked nucleic acids and deep sequencing reveals complex 5'/3' arm variation including concomitant cleavage and polyuridylation patterns.

    abstract::Recent research hints at an underappreciated complexity in pre-miRNA processing and regulation. Global profiling of pre-miRNA and its potential to increase understanding of the pre-miRNA landscape is impeded by overlap with highly expressed classes of other non coding (nc) RNA. Here, we present a data set excluding th...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Burroughs AM,Kawano M,Ando Y,Daub CO,Hayashizaki Y

    更新日期:2012-02-01 00:00:00

  • DEG: a database of essential genes.

    abstract::Essential genes are genes that are indispensable to support cellular life. These genes constitute a minimal gene set required for a living cell. We have constructed a Database of Essential Genes (DEG), which contains all the essential genes that are currently available. The functions encoded by essential genes are con...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Zhang R,Ou HY,Zhang CT

    更新日期:2004-01-01 00:00:00

  • The output of the tRNA modification pathways controlled by the Escherichia coli MnmEG and MnmC enzymes depends on the growth conditions and the tRNA species.

    abstract::In Escherichia coli, the MnmEG complex modifies transfer RNAs (tRNAs) decoding NNA/NNG codons. MnmEG catalyzes two different modification reactions, which add an aminomethyl (nm) or carboxymethylaminomethyl (cmnm) group to position 5 of the anticodon wobble uridine using ammonium or glycine, respectively. In tRNA(cmnm...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Moukadiri I,Garzón MJ,Björk GR,Armengod ME

    更新日期:2014-02-01 00:00:00

  • Monoclonal antibody-based, selective isolation of DNA fragments containing an alkylated base to be quantified in defined gene sequences.

    abstract::We have established a sensitive, monoclonal antibody (Mab)-based procedure permitting the selective enrichment of sequences containing the miscoding alkylation product O6-ethylguanine (O6-EtGua) from mammalian DNA. H5 rat hepatoma cells were reacted with the N-nitroso carcinogen N-ethyl-N-nitrosourea in vitro, to give...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Hochleitner K,Thomale J,Nikitin AYu,Rajewsky MF

    更新日期:1991-08-25 00:00:00

  • Rfam: annotating non-coding RNAs in complete genomes.

    abstract::Rfam is a comprehensive collection of non-coding RNA (ncRNA) families, represented by multiple sequence alignments and profile stochastic context-free grammars. Rfam aims to facilitate the identification and classification of new members of known sequence families, and distributes annotation of ncRNAs in over 200 comp...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Griffiths-Jones S,Moxon S,Marshall M,Khanna A,Eddy SR,Bateman A

    更新日期:2005-01-01 00:00:00

  • NAIMA: target amplification strategy allowing quantitative on-chip detection of GMOs.

    abstract::We have developed a novel multiplex quantitative DNA-based target amplification method suitable for sensitive, specific and quantitative detection on microarray. This new method named NASBA Implemented Microarray Analysis (NAIMA) was applied to GMO detection in food and feed, but its application can be extended to all...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Morisset D,Dobnik D,Hamels S,Zel J,Gruden K

    更新日期:2008-10-01 00:00:00

  • Target specificity of neuronal RNA-binding protein, Mel-N1: direct binding to the 3' untranslated region of its own mRNA.

    abstract::We have identified cDNAs encoding Mel-N1, the mouse homologue of a human nervous system-specific RNA-binding protein, Hel-N1. Two major mRNA transcripts of Mel-N1 were detected predominantly in the adult mouse brain by Northern blot analysis. To gain insight into the RNA binding specificity of Mel-N1, we performed ite...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Abe R,Yamamoto K,Sakamoto H

    更新日期:1996-06-01 00:00:00

  • SETDB1, HP1 and SUV39 promote repositioning of 53BP1 to extend resection during homologous recombination in G2 cells.

    abstract::Recent studies have shown that homologous recombination (HR) requires chromatin repression as well as relaxation at DNA double strand breaks (DSBs). HP1 and SUV39H1/2 are repressive factors essential for HR. Here, we identify SETDB1 as an additional compacting factor promoting HR. Depletion of HP1, SUV39, SETDB1 or BR...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Alagoz M,Katsuki Y,Ogiwara H,Ogi T,Shibata A,Kakarougkas A,Jeggo P

    更新日期:2015-09-18 00:00:00

  • Structure and possible function of a G-quadruplex in the long terminal repeat of the proviral HIV-1 genome.

    abstract::The long terminal repeat (LTR) of the proviral human immunodeficiency virus (HIV)-1 genome is integral to virus transcription and host cell infection. The guanine-rich U3 region within the LTR promoter, previously shown to form G-quadruplex structures, represents an attractive target to inhibit HIV transcription and r...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: De Nicola B,Lech CJ,Heddi B,Regmi S,Frasson I,Perrone R,Richter SN,Phan AT

    更新日期:2016-07-27 00:00:00

  • Intercalation of ethidium bromide into a triple-stranded oligonucleotide.

    abstract::We have examined the ability of a cationic planar chromophore, ethidium bromide, to intercalate into a short, defined triple helix. Using UV absorption, fluorescence spectroscopy and a gel retardation assay we demonstrate that ethidium bromide is able to bind to a triple helix with a lower affinity than to the corresp...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Mergny JL,Collier D,Rougée M,Montenay-Garestier T,Hélène C

    更新日期:1991-04-11 00:00:00

  • Human testis expresses a specific poly(A)-binding protein.

    abstract::In testis mRNA stability and translation initiation are extensively under the control of poly(A)-binding proteins (PABP). Here we have cloned a new human testis-specific PABP (PABP3) of 631 amino acids (70.1 kDa) with 92.5% identical residues to the ubiquitous PABP1. A northern blot of multiple human tissues hybridise...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Féral C,Guellaën G,Pawlak A

    更新日期:2001-05-01 00:00:00

  • Observations on template-specific conditions for DNA synthesis by avian myeloblastosis virus DNA polymerase.

    abstract::The effects of Mg++, Mn++, and KCl addition, individually and in combination, on the rate of DNA- and RNA-primed DNA synthesis by avian myeloblastosis virus DNA polymerase (reverse transcriptase) using a variety of natural and synthetic template-primer combinations were examined. Optimal divalent cation concentrations...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Marcus SL,Modak MJ

    更新日期:1976-06-01 00:00:00

  • Transferring the purine 2-amino group from guanines to adenines in DNA changes the sequence-specific binding of antibiotics.

    abstract::The proposition that the 2-amino group of guanine plays a critical role in determining how antibiotics recognise their binding sites in DNA has been tested by relocating it, using tyrT DNA derivative molecules substituted with inosine plus 2,6-diaminopurine (DAP). Irrespective of their mode of interaction with DNA, su...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Bailly C,Waring MJ

    更新日期:1995-03-25 00:00:00

  • Bipartite pattern discovery by entropy minimization-based multiple local alignment.

    abstract::Many multimeric transcription factors recognize DNA sequence patterns by cooperatively binding to bipartite elements composed of half sites separated by a flexible spacer. We developed a novel bipartite algorithm, bipartite pattern discovery (Bipad), which produces a mathematical model based on information maximizatio...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Bi C,Rogan PK

    更新日期:2004-09-23 00:00:00

  • Complementation of the DNA repair-deficient swi10 mutant of fission yeast by the human ERCC1 gene.

    abstract::In human cells DNA damage caused by UV light is mainly repaired by the nucleotide excision repair pathway. This mechanism involves dual incisions on both sides of the damage catalyzed by two nucleases. In mammalian cells XPG cleaves 3' of the DNA lesion while the ERCC1-XPF complex makes the 5' incision. The amino acid...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Rödel C,Jupitz T,Schmidt H

    更新日期:1997-07-15 00:00:00

  • Cloning and expression of cDNA encoding mouse tyrosinase.

    abstract::We have isolated a pigment cell-specific cDNA clone from a B16 mouse melanoma cDNA library by differential hybridization. The mRNA of isolated cDNA is highly expressed in B16 melanoma cells and in black mouse (C57BL/6) skin, but is not detectable in mouse neuroblastoma cells nor in K1735 mouse amelanotic melanoma cell...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Shibahara S,Tomita Y,Sakakura T,Nager C,Chaudhuri B,Müller R

    更新日期:1986-03-25 00:00:00

  • COXPRESdb in 2015: coexpression database for animal species by DNA-microarray and RNAseq-based expression data with multiple quality assessment systems.

    abstract::The COXPRESdb ( provides gene coexpression relationships for animal species. Here, we report the updates of the database, mainly focusing on the following two points. For the first point, we added RNAseq-based gene coexpression data for three species (human, mouse and fly), and largely increased th...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Okamura Y,Aoki Y,Obayashi T,Tadaka S,Ito S,Narise T,Kinoshita K

    更新日期:2015-01-01 00:00:00

  • PreCisIon: PREdiction of CIS-regulatory elements improved by gene's positION.

    abstract::Conventional approaches to predict transcriptional regulatory interactions usually rely on the definition of a shared motif sequence on the target genes of a transcription factor (TF). These efforts have been frustrated by the limited availability and accuracy of TF binding site motifs, usually represented as position...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Elati M,Nicolle R,Junier I,Fernández D,Fekih R,Font J,Képès F

    更新日期:2013-02-01 00:00:00

  • The genome portal of the Department of Energy Joint Genome Institute.

    abstract::The Department of Energy (DOE) Joint Genome Institute (JGI) is a national user facility with massive-scale DNA sequencing and analysis capabilities dedicated to advancing genomics for bioenergy and environmental applications. Beyond generating tens of trillions of DNA bases annually, the Institute develops and maintai...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Grigoriev IV,Nordberg H,Shabalov I,Aerts A,Cantor M,Goodstein D,Kuo A,Minovitsky S,Nikitin R,Ohm RA,Otillar R,Poliakov A,Ratnere I,Riley R,Smirnova T,Rokhsar D,Dubchak I

    更新日期:2012-01-01 00:00:00

  • RNA binding candidates for human ADAR3 from substrates of a gain of function mutant expressed in neuronal cells.

    abstract::Human ADAR3 is a catalytically inactive member of the Adenosine Deaminase Acting on RNA (ADAR) protein family, whose active members catalyze A-to-I RNA editing in metazoans. Until now, the reasons for the catalytic incapability of ADAR3 has not been defined and its biological function rarely explored. Yet, its exclusi...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Wang Y,Chung DH,Monteleone LR,Li J,Chiang Y,Toney MD,Beal PA

    更新日期:2019-11-18 00:00:00

  • Nucleotide sequence from the coding region of rabbit beta-globin messenger RNA.

    abstract::A sequence of 89 nucleotides from rabbit beta-globin mRNA has been determined and is shown to code for residues 107 to 137 of the beta-globin protein. In addition, a sequence heterogeneity has been identified within this 89 nucleotide long sequence which corresponds to a known polymorphic variant of rabbit beta-globin...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Proudfoot NJ

    更新日期:1976-07-01 00:00:00

  • Atlas of Genetics and Cytogenetics in Oncology and Haematology, updated.

    abstract::The 'Atlas of Genetics and Cytogenetics in Oncology and Haematology' ( is an Internet database aimed at genes involved in cancer, cytogenetics and clinical entities in cancer, and cancer-prone diseases. It presents information in concise and updated reviews (cards) or long...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Huret JL,Dessen P,Bernheim A

    更新日期:2001-01-01 00:00:00