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














  • 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

  • On the binding of aminoalkyl adenylates to isoleucyl-tRNA synthetase from Escherichia coli MRE 600.

    abstract::The binding of nine aminoalkyl adenylates to isoleucyl-tRNA synthetase from Escherichia coli MRE 600 was measured and compared with the binding of the cognate amino acids. It was found that they bind rather tightly to the enzyme, the Kd's ranging from 3.1.10(-4) M with glycinol-AMP ester to 3.7.10(-9) M with L-isoleuc...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Flossdorf J,Marutzky R,Messer K,Kula MR

    更新日期:1977-03-01 00:00:00

  • Systematic analysis of enzymatic DNA polymerization using oligo-DNA templates and triphosphate analogs involving 2',4'-bridged nucleosides.

    abstract::In order to systematically analyze the effects of nucleoside modification of sugar moieties in DNA polymerase reactions, we synthesized 16 modified templates containing 2',4'-bridged nucleotides and three types of 2',4'-bridged nucleoside-5'-triphospates with different bridging structures. Among the five types of ther...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Kuwahara M,Obika S,Nagashima J,Ohta Y,Suto Y,Ozaki H,Sawai H,Imanishi T

    更新日期:2008-08-01 00:00:00

  • The conformational landscape of transcription intermediates involved in the regulation of the ZMP-sensing riboswitch from Thermosinus carboxydivorans.

    abstract::Recently, prokaryotic riboswitches have been identified that regulate transcription in response to change of the concentration of secondary messengers. The ZMP (5-Aminoimidazole-4-carboxamide ribonucleotide (AICAR))-sensing riboswitch from Thermosinus carboxydivorans is a transcriptional ON-switch that is involved in ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Binas O,Schamber T,Schwalbe H

    更新日期:2020-07-09 00:00:00

  • Conserved elements containing NF-E2 and tandem GATA binding sites are required for erythroid-specific chromatin structure reorganization within the human beta-globin locus control region.

    abstract::Proper expression of the genes of the human beta-globin gene locus requires the associated locus control region (LCR). Structurally, the LCR is defined by the presence of four domains of erythroid-specific chromatin structure. These domains, which have been characterized as DNase I hypersensitive sites (HSs), comprise...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Pomerantz O,Goodwin AJ,Joyce T,Lowrey CH

    更新日期:1998-12-15 00:00:00

  • Complete nucleotide sequence of the Escherichia coli recB gene.

    abstract::The complete nucleotide sequence of the Escherichia coli recB gene which encodes a subunit of the ATP-dependent DNase, Exonuclease V, has been determined. The proposed coding region for the RecB protein is 3543 nucleotides long and would encode a polypeptide of 1180 amino acids with a calculated molecular weight of 13...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Finch PW,Storey A,Chapman KE,Brown K,Hickson ID,Emmerson PT

    更新日期:1986-11-11 00:00:00

  • ADAR2 A-->I editing: site selectivity and editing efficiency are separate events.

    abstract::ADAR enzymes, adenosine deaminases that act on RNA, form a family of RNA editing enzymes that convert adenosine to inosine within RNA that is completely or largely double-stranded. Site-selective A-->I editing has been detected at specific sites within a few structured pre-mRNAs of metazoans. We have analyzed the edit...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Källman AM,Sahlin M,Ohman M

    更新日期:2003-08-15 00:00:00

  • DNA polymerase I and a protein complex bind specifically to E. coli palindromic unit highly repetitive DNA: implications for bacterial chromosome organization.

    abstract::Starting from a crude E. coli extract, two activities which specifically protect highly repetitive bacterial DNA sequences (called PU for Palindromic Unit or REP for Repetitive Extragenic Palindromic sequence) against a digestion with Exonuclease III have been purified. We show that one of these activities is due to t...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Gilson E,Perrin D,Hofnung M

    更新日期:1990-07-11 00:00:00

  • The siRNA suppressor RTL1 is redox-regulated through glutathionylation of a conserved cysteine in the double-stranded-RNA-binding domain.

    abstract::RNase III enzymes cleave double stranded (ds)RNA. This is an essential step for regulating the processing of mRNA, rRNA, snoRNA and other small RNAs, including siRNA and miRNA. Arabidopsis thaliana encodes nine RNase III: four DICER-LIKE (DCL) and five RNASE THREE LIKE (RTL). To better understand the molecular functio...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Charbonnel C,Niazi AK,Elvira-Matelot E,Nowak E,Zytnicki M,de Bures A,Jobet E,Opsomer A,Shamandi N,Nowotny M,Carapito C,Reichheld JP,Vaucheret H,Sáez-Vásquez J

    更新日期:2017-11-16 00:00:00

  • Primary structure, developmentally regulated expression and potential duplication of the zebrafish homeobox gene ZF-21.

    abstract::We report the molecular cloning and characterization of a cDNA derived from a zebrafish gene (ZF-21) related to the mouse homeobox containing gene Hox2.1. Interesting information about the differential conservation of various domains was gained from comparisons between the putative protein sequences from ZF-21 (275 am...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Njølstad PR,Molven A,Hordvik I,Apold J,Fjose A

    更新日期:1988-10-11 00:00:00

  • Cell stress and translational inhibitors transiently increase the abundance of mammalian SINE transcripts.

    abstract::The abundance of Alu RNA is transiently increased by heat shock in human cell lines. This effect is specific to Alu repeats among Pol III transcribed genes, since the abundance of 7SL, 7SK, 5S and U6 RNAs is essentially unaffected by heat shock. The rapid induction of Alu expression precedes the heat shock induction o...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Liu WM,Chu WM,Choudary PV,Schmid CW

    更新日期:1995-05-25 00:00:00

  • Vienna-PTM web server: a toolkit for MD simulations of protein post-translational modifications.

    abstract::Post-translational modifications (PTMs) play a key role in numerous cellular processes by directly affecting structure, dynamics and interaction networks of target proteins. Despite their importance, our understanding of protein PTMs at the atomistic level is still largely incomplete. Molecular dynamics (MD) simulatio...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Margreitter C,Petrov D,Zagrovic B

    更新日期:2013-07-01 00:00:00

  • Serial analysis of mutation spectra (SAMS): a new approach for the determination of mutation spectra of site-specific DNA damage and their sequence dependence.

    abstract::Many mutations occur as a result of DNA synthesis past the site of DNA damage by DNA damage bypass polymerases. The frequency and types of mutations not only depend on the nature of the damage, but also on the sequence context, as revealed from analysis of mutation spectra of DNA exposed to mutagens. Herein we report ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Fang H,Taylor JS

    更新日期:2008-10-01 00:00:00

  • Quantitation of RNA editing substrates, products and potential intermediates: implications for developmental regulation.

    abstract::Kinetoplast mitochondrial RNA editing is the developmentally regulated post-transcriptional process of uridine insertion and deletion in mRNAs directed by short guide RNAs (gRNAs), which creates functional mRNAs. Two mechanisms are proposed: transesterification which predicts gRNA/mRNA chimeric intermediates, and enzy...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Riley GR,Myler PJ,Stuart K

    更新日期:1995-02-25 00:00:00

  • Biochemical and electron microscope analyses of the DNA reverse transcripts present in the virus-like particles of the yeast transposon Ty1. Identification of a second origin of Ty1DNA plus strand synthesis.

    abstract::Transposition of Saccharomyces cerevisiae Ty1 retroelements has been shown to involve reverse transcription in intracytoplasmic virus-like particles (Ty-VLPs). Ty DNA present in the particles specified by Ty1-H3 element was found to consist of the full-length genomic DNA as well as incomplete cDNAs mainly of plus pola...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Pochart P,Agoutin B,Rousset S,Chanet R,Doroszkiewicz V,Heyman T

    更新日期:1993-07-25 00:00:00

  • The structural integrity exerted by N-terminal pyroglutamate is crucial for the cytotoxicity of frog ribonuclease from Rana pipiens.

    abstract::Onconase, a cytotoxic ribonuclease from Rana pipiens, possesses pyroglutamate (Pyr) at the N-terminus and has a substrate preference for uridine-guanine (UG). To identify residues responsible for onconase's cytotoxicity, we cloned the rpr gene from genomic DNA and expressed it in Escherichia coli BL21(DE3). The recomb...

    journal_title:Nucleic acids research

    pub_type: 评论,杂志文章


    authors: Liao YD,Wang SC,Leu YJ,Wang CF,Chang ST,Hong YT,Pan YR,Chen C

    更新日期:2003-09-15 00:00:00

  • A new minor groove binding asymmetric cyanine reporter dye for real-time PCR.

    abstract::The minor groove binding asymmetric cyanine dye 4-[(3-methyl-6-(benzothiazol-2-yl)-2,3-dihydro- (benzo-1,3-thiazole)-2-methylidene)]-1-methyl-pyridin ium iodide (BEBO) is tested as sequence non- specific label in real-time PCR. The fluorescence intensity of BEBO increases upon binding to double-stranded DNA allowing e...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Bengtsson M,Karlsson HJ,Westman G,Kubista M

    更新日期:2003-04-15 00:00:00

  • Structural analysis of an RNA molecule involved in replication control of plasmid R1.

    abstract::The replication control circuit of the FII plasmids R1, R100 and R6-5 involves a small untranslated RNA molecule of about 93 nucleotides. This RNA, designated CopA RNA in plasmid R1, acts in vivo as a post-transcriptional inhibitor of the expression of the RepA protein whose synthesis is required for each round of pla...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Gerhart E,Wagner H,Nordström K

    更新日期:1986-03-25 00:00:00

  • PubMeth: a cancer methylation database combining text-mining and expert annotation.

    abstract::Epigenetics, and more specifically DNA methylation is a fast evolving research area. In almost every cancer type, each month new publications confirm the differentiated regulation of specific genes due to methylation and mention the discovery of novel methylation markers. Therefore, it would be extremely useful to hav...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Ongenaert M,Van Neste L,De Meyer T,Menschaert G,Bekaert S,Van Criekinge W

    更新日期:2008-01-01 00:00:00

  • The RNA helicase RHAU (DHX36) unwinds a G4-quadruplex in human telomerase RNA and promotes the formation of the P1 helix template boundary.

    abstract::Human telomerase RNA (hTR) contains several guanine tracts at its 5'-end that can form a G4-quadruplex structure. Previous evidence suggests that a G4-quadruplex within this region disrupts the formation of an important structure within hTR known as the P1 helix, a critical element in defining the template boundary fo...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Booy EP,Meier M,Okun N,Novakowski SK,Xiong S,Stetefeld J,McKenna SA

    更新日期:2012-05-01 00:00:00

  • Mutations in the RNA polymerase recognition sequence of the Klebsiella pneumoniae nifH promoter permitting transcriptional activation in the absence of NifA binding to upstream activator sequences.

    abstract::Positive control of the wild-type Klebsiella pneumoniae nifH promoter by the NifA protein requires that NifA is bound at the upstream activator sequence (UAS). By introducing base substitutions at -15 to -17 in the RNA polymerase recognition sequence of the nifH promoter, positive control by a form of NifA unable to b...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Buck M,Cannon W

    更新日期:1989-04-11 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

  • Molecular evolution of protein-RNA mimicry as a mechanism for translational control.

    abstract::Elongation factor P (EF-P) is a conserved ribosome-binding protein that structurally mimics tRNA to enable the synthesis of peptides containing motifs that otherwise would induce translational stalling, including polyproline. In many bacteria, EF-P function requires post-translational modification with (R)-β-lysine by...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Katz A,Solden L,Zou SB,Navarre WW,Ibba M

    更新日期:2014-03-01 00:00:00

  • HSCARG, a novel regulator of H2A ubiquitination by downregulating PRC1 ubiquitin E3 ligase activity, is essential for cell proliferation.

    abstract::Histone H2A ubiquitination plays critical roles in transcriptional repression and deoxyribonucleic acid (DNA) damage response. More attention has been focused on ubiquitin E3 ligases of H2A, however, less is known about the negative regulators of H2A ubiquitination. Here we identified HSCARG as a new negative regulato...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Hu B,Li S,Zhang X,Zheng X

    更新日期:2014-05-01 00:00:00

  • A homogeneous nucleic acid hybridization assay based on strand displacement.

    abstract::A homogeneous nucleic acid hybridization assay which is conducted in solution and requires no separation steps is described. The assay is based on the concept of strand displacement. In the strand displacement assay, an RNA "signal strand" is hybridized within a larger DNA strand termed the "probe strand", which is, i...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Vary CP

    更新日期:1987-09-11 00:00:00

  • Programmable gene regulation for metabolic engineering using decoy transcription factor binding sites.

    abstract::Transcription factor decoy binding sites are short DNA sequences that can titrate a transcription factor away from its natural binding site, therefore regulating gene expression. In this study, we harness synthetic transcription factor decoy systems to regulate gene expression for metabolic pathways in Escherichia col...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Wang T,Tague N,Whelan SA,Dunlop MJ

    更新日期:2021-01-25 00:00:00

  • Precursors to 16S and 23S ribosomal RNA from a ribonuclear III-strain of Escherichia coli contain intact RNase III processing sites.

    abstract::Escherichia coli cells lacking the ribosomal RNA processing enzyme RNase III do no excise the normal RNA precursors p16a (17S) and p23a from nascent rRNA transcripts. These cells produce, instead, slightly larger p16b and p23b precursors. Digestion of p16b or p23b rRNA with RNases A plus T1 yields double-stranded frag...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Gegenheimer P,Apirion D

    更新日期:1980-04-25 00:00:00

  • High frequency vector-mediated transformation and gene replacement in Tetrahymena.

    abstract::Recently, we developed a mass DNA-mediated transformation technique for the ciliated protozoan Tetrahymena thermophila that introduces transforming DNA by electroporation into conjugating cells. Other studies demonstrated that a neomycin resistance gene flanked by Tetrahymena H4-I gene regulatory sequences transformed...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Gaertig J,Gu L,Hai B,Gorovsky MA

    更新日期:1994-12-11 00:00:00

  • Snap-to-it probes: chelate-constrained nucleobase oligomers with enhanced binding specificity.

    abstract::We describe snap-to-it probes, a novel probe technology to enhance the hybridization specificity of natural and unnatural nucleic acid oligomers using a simple and readily introduced structural motif. Snap-to-it probes were prepared from peptide nucleic acid (PNA) oligomers by modifying each terminus with a coordinati...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Morgan JR,Lyon RP,Maeda DY,Zebala JA

    更新日期:2008-06-01 00:00:00

  • Atlas of Genetics and Cytogenetics in Oncology and Haematology, year 2003.

    abstract::The 'Atlas of Genetics and Cytogenetics in Oncology and Haematology' ( contains concise and updated cards on genes involved in cancer, cytogenetics and clinical entities in oncology, and cancer-prone diseases, a portal towards genetics/cancer, and teaching materials in gen...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Huret JL,Dessen P,Bernheim A

    更新日期:2003-01-01 00:00:00