cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3803709.v1
title: PR2 rRNA gene database

description: The Protist Ribosomal Reference database (PR<sup>2</sup>) provides a unique access to eukaryotic small sub-unit (SSU) ribosomal RNA and DNA sequences, with curated taxonomy. The database mainly consists of nuclear-encoded protistan sequences. However, metazoans, land plants, macrosporic fungi and eukaryotic organelles (mitochondrion, plastid and others) are also included because they are useful for the analysis of high-troughput sequencing data sets. Introns and putative chimeric sequences have been also carefully checked. Taxonomic assignation of sequences consists of eight unique taxonomic fields.<br><br><b>Files</b><br><br>The files provided are for use with Qiime or Mothur. Four files are provided.<br>* <b>pr2....fasta</b> contains all sequences in fasta format<br>* <b>pr2....tax</b> contains the taxonomy of each sequence<br>* <b>PR2 version notes.docx</b> contains the revision history<br>* <b>PR2 versions.xls</b> is a condensed list of the different versions<br><br><b>Current version</b> : 4.2 based on GenBank 203<br><br><b>Contributors<br><br></b>- Tristan Biard<br>- Margot Tragin<br>- Bente Edvardsen<br> <br><b>References</b><br>Guillou, L., Bachar, D., Audic, S., Bass, D., Berney, C., Bittner, L., Boutte, C. et al. 2013. The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy. <i>Nucleic Acids Res.</i> 41:D597–604.Edvardsen, B., Egge, E.S. & Vaulot, D. 2016. Diversity and distribution of haptophytes revealed by environmental sequencing and metabarcoding – a review. <i>Perspect. Phycol.</i> in press.Tragin, M., Lopes dos Santos, A., Christen, R. & Vaulot, D. 2016. Diversity and ecology of green microalgae in marine systems: an overview based on 18S rRNA gene sequences. <i>Perspect. Phycol.</i> in press. <br><br><br>
DOI: 10.6084/m9.figshare.3803709.v3
title: Protist Ribosomal Reference database (PR2) - SSU rRNA gene database

description: The Protist Ribosomal Reference database (PR<sup>2</sup>) provides a unique access to eukaryotic small sub-unit (SSU) ribosomal RNA and DNA sequences, with curated taxonomy. The database mainly consists of nuclear-encoded protistan sequences. However, metazoans, land plants, macrosporic fungi and eukaryotic organelles (mitochondrion, plastid and others) are also included because they are useful for the analysis of high-troughput sequencing data sets. Introns and putative chimeric sequences have been also carefully checked. Taxonomic assignation of sequences consists of eight unique taxonomic fields.<br><br><b>Files</b><br><br>The files provided are for use with Qiime or Mothur. Four files are provided.<br>* <b>pr2....fasta</b> contains all sequences in fasta format<br>* <b>pr2....tax</b> contains the taxonomy of each sequence<br>* <b>PR2 version notes.docx</b> contains the revision history<br>* <b>PR2 versions.xls</b> is a condensed list of the different versions<br><br><b>Current version</b> : 4.3 based on GenBank 203<br><br><b>Contact<br><br></b>Laure GUILLOU and Daniel VAULOT<br>DIPO team, Plankton Group, UMR 7144 CNRS-UPMC<br>Station Biologique,<br>Place G. Tessier<br>29680 Roscoff FRANCE<br>email: vaulot@sb-roscoff.fr<br><br><b>Contributors<br><br></b>- Tristan Biard<br>- Margot Tragin<br>- Bente Edvardsen<br> <br><b>References</b><br>Guillou, L., Bachar, D., Audic, S., Bass, D., Berney, C., Bittner, L., Boutte, C. et al. 2013. The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy. <i>Nucleic Acids Res.</i> 41:D597–604.Edvardsen, B., Egge, E.S. & Vaulot, D. 2016. Diversity and distribution of haptophytes revealed by environmental sequencing and metabarcoding – a review. <i>Perspect. Phycol.</i> in press.Tragin, M., Lopes dos Santos, A., Christen, R. & Vaulot, D. 2016. Diversity and ecology of green microalgae in marine systems: an overview based on 18S rRNA gene sequences. <i>Perspect. Phycol.</i> in press. <br><br><br>
DOI: 10.5519/qd.8yf8fl8c
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (10 records)
DOI: 10.6084/m9.figshare.3803709.v7
title: Protist Ribosomal Reference database (PR2) - SSU rRNA gene database - flat files for mothur

description: The Protist Ribosomal Reference database (PR<sup>2</sup>) provides a unique access to eukaryotic small sub-unit (SSU) ribosomal RNA and DNA sequences, with curated taxonomy. The database mainly consists of nuclear-encoded protistan sequences. However, metazoans, land plants, macrosporic fungi and eukaryotic organelles (mitochondrion, plastid and others) are also included because they are useful for the analysis of high-troughput sequencing data sets. Introns and putative chimeric sequences have been also carefully checked. Taxonomic assignation of sequences consists of eight unique taxonomic fields.<br><br>The original web site (http://ssu-rrna.org/pr2) is currently out and we are proposing updated version of PR2 as flat files to use for annotating metabarcodes.<br><br><b>Files</b><br><br>The files provided are for use with Qiime or Mothur. Four files are provided.<br>* <b>pr2....fasta</b> contains all sequences in fasta format<br>* <b>pr2....tax</b> contains the taxonomy of each sequence<br>* <b>PR2 version notes.docx</b> contains the revision history<br>* <b>PR2 versions.xls</b> is a condensed list of the different versions<br><br><b>Current version</b> : 4.5 based on GenBank 203<br><b>Last update</b> : 17 January 2017<br><br><b>Notes<br></b>- Qiime can only use 7 taxonomical levels<b><br><br>Contact<br><br></b>Laure GUILLOU and Daniel VAULOT<br>DIPO team, Plankton Group, UMR 7144 CNRS-UPMC<br>Station Biologique,<br>Place G. Tessier<br>29680 Roscoff FRANCE<br>email: vaulot@sb-roscoff.fr<br><br><b>Contributors<br><br></b>- Tristan Biard<br>- Margot Tragin<br>- Bente Edvardsen<br> <br><b>References</b><br>Guillou, L., Bachar, D., Audic, S., Bass, D., Berney, C., Bittner, L., Boutte, C. et al. 2013. The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy. <i>Nucleic Acids Res.</i> 41:D597–604.Edvardsen, B., Egge, E.S. & Vaulot, D. 2016. Diversity and distribution of haptophytes revealed by environmental sequencing and metabarcoding – a review. <i>Perspect. Phycol.</i> in press.Tragin, M., Lopes dos Santos, A., Christen, R. & Vaulot, D. 2016. Diversity and ecology of green microalgae in marine systems: an overview based on 18S rRNA gene sequences. <i>Perspect. Phycol.</i> in press. <br><br><br>
DOI: 10.6084/m9.figshare.3803709.v8
title: Protist Ribosomal Reference database (PR2) - SSU rRNA gene database - flat files for mothur

description: The Protist Ribosomal Reference database (PR<sup>2</sup>) provides a unique access to eukaryotic small sub-unit (SSU) ribosomal RNA and DNA sequences, with curated taxonomy. The database mainly consists of nuclear-encoded protistan sequences. However, metazoans, land plants, macrosporic fungi and eukaryotic organelles (mitochondrion, plastid and others) are also included because they are useful for the analysis of high-troughput sequencing data sets. Introns and putative chimeric sequences have been also carefully checked. Taxonomic assignation of sequences consists of eight unique taxonomic fields.<br><br>The original web site (http://ssu-rrna.org/pr2) is currently out and we are proposing updated version of PR2 as flat files to use for annotating metabarcodes.<br><br><b>Files</b><br><br>The files provided are for use with Qiime or Mothur. Four files are provided.<br>* <b>pr2....fasta</b> contains all sequences in fasta format<br>* <b>pr2....tax</b> contains the taxonomy of each sequence<br>* <b>PR2 version notes.docx</b> contains the revision history<br>* <b>PR2 versions.xls</b> is a condensed list of the different versions<br><br><b>Current version</b> : 4.5 based on GenBank 203<br><b>Last update</b> : 17 January 2017<br><br><b>Notes<br></b>- Qiime can only use 7 taxonomical levels<b><br><br>Contact<br><br></b>Laure GUILLOU and Daniel VAULOT<br>DIPO team, Plankton Group, UMR 7144 CNRS-UPMC<br>Station Biologique,<br>Place G. Tessier<br>29680 Roscoff FRANCE<br>email: vaulot@sb-roscoff.fr<br><br><b>Contributors<br><br></b>- Tristan Biard<br>- Margot Tragin<br>- Bente Edvardsen<br> <br><b>References</b><br>Guillou, L., Bachar, D., Audic, S., Bass, D., Berney, C., Bittner, L., Boutte, C. et al. 2013. The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy. <i>Nucleic Acids Res.</i> 41:D597–604.Edvardsen, B., Egge, E.S. & Vaulot, D. 2016. Diversity and distribution of haptophytes revealed by environmental sequencing and metabarcoding – a review. <i>Perspect. Phycol.</i> in press.Tragin, M., Lopes dos Santos, A., Christen, R. & Vaulot, D. 2016. Diversity and ecology of green microalgae in marine systems: an overview based on 18S rRNA gene sequences. <i>Perspect. Phycol.</i> in press. <br><br><br>
DOI: 10.6084/m9.figshare.3803709.v9
title: Protist Ribosomal Reference database (PR2) - SSU rRNA gene database - flat files for mothur

description: The Protist Ribosomal Reference database (PR<sup>2</sup>) provides a unique access to eukaryotic small sub-unit (SSU) ribosomal RNA and DNA sequences, with curated taxonomy. The database mainly consists of nuclear-encoded protistan sequences. However, metazoans, land plants, macrosporic fungi and eukaryotic organelles (mitochondrion, plastid and others) are also included because they are useful for the analysis of high-troughput sequencing data sets. Introns and putative chimeric sequences have been also carefully checked. Taxonomic assignation of sequences consists of eight unique taxonomic fields.<br><br>The original web site (http://ssu-rrna.org/pr2) is currently out and we are proposing updated version of PR2 as flat files to use for annotating metabarcodes.<br><br><b>Files</b><br><br>The files provided are for use with Qiime or Mothur. Four files are provided.<br>* <b>pr2....fasta</b> contains all sequences in fasta format<br>* <b>pr2....tax</b> contains the taxonomy of each sequence<br>* <b>PR2 version notes.docx</b> contains the revision history<br>* <b>PR2 versions.xls</b> is a condensed list of the different versions<br><br><b>Current version</b> : 4.5 based on GenBank 203<br><b>Last update</b> : 17 January 2017<br><br><b>Notes<br></b>- Qiime can only use 7 taxonomical levels<b><br><br>Contact<br><br></b>Laure GUILLOU and Daniel VAULOT<br>DIPO team, Plankton Group, UMR 7144 CNRS-UPMC<br>Station Biologique,<br>Place G. Tessier<br>29680 Roscoff FRANCE<br>email: vaulot@sb-roscoff.fr<br><br><b>Contributors<br><br></b>- Tristan Biard<br>- Margot Tragin<br>- Bente Edvardsen<br> <br><b>References</b><br>Guillou, L., Bachar, D., Audic, S., Bass, D., Berney, C., Bittner, L., Boutte, C. et al. 2013. The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy. <i>Nucleic Acids Res.</i> 41:D597–604.Edvardsen, B., Egge, E.S. & Vaulot, D. 2016. Diversity and distribution of haptophytes revealed by environmental sequencing and metabarcoding – a review. <i>Perspect. Phycol.</i> in press.Tragin, M., Lopes dos Santos, A., Christen, R. & Vaulot, D. 2016. Diversity and ecology of green microalgae in marine systems: an overview based on 18S rRNA gene sequences. <i>Perspect. Phycol.</i> in press. <br><br><br>
DOI: 10.6084/m9.figshare.3803709.v11
title: Protist Ribosomal Reference database (PR2) - SSU rRNA gene database - flat files for mothur

description: The Protist Ribosomal Reference database (PR<sup>2</sup>) provides a unique access to eukaryotic small sub-unit (SSU) ribosomal RNA and DNA sequences, with curated taxonomy. The database mainly consists of nuclear-encoded protistan sequences. However, metazoans, land plants, macrosporic fungi and eukaryotic organelles (mitochondrion, plastid and others) are also included because they are useful for the analysis of high-troughput sequencing data sets. Introns and putative chimeric sequences have been also carefully checked. Taxonomic assignation of sequences consists of eight unique taxonomic fields.<br><br>The original web site (http://ssu-rrna.org/pr2) is currently out and we are proposing updated version of PR2 as flat files to use for annotating metabarcodes.<br><br><b>Files</b><br><br><b>- pr2_gb203_version_4.x.zip</b> contains two files for use with Qiime or Mothur.<br> * <b>pr2....fasta</b> contains all sequences in fasta format with the accession in the description line<br> * <b>pr2....tax</b> contains the taxonomy of each sequence separated from the accession number by a tabulation<br><br><b>- pr2_gb203_version_4.x.for_BLAST.zip</b> contains one fasta file with the accession number of the sequence and its taxonomy on the description line. It is suitable to build a local database for BLAST search<br><br>- <b>PR2 version notes.docx</b> contains the revision history<br><br>- <b>PR2 versions.xls</b> is a condensed list of the different versions<br><br><b>Current version</b> : 4.5 based on GenBank 203<br><b>Last update</b> : 17 January 2017<br><br><b>Notes<br></b>- Qiime can only use 7 taxonomical levels<b><br><br>Contact<br><br></b>Laure GUILLOU and Daniel VAULOT<br>DIPO team, Plankton Group, UMR 7144 CNRS-UPMC<br>Station Biologique,<br>Place G. Tessier<br>29680 Roscoff FRANCE<br>email: vaulot@sb-roscoff.fr<br><br><b>Contributors<br><br></b>- Tristan Biard<br>- Margot Tragin<br>- Bente Edvardsen<br> <br><b>References</b><br>Guillou, L., Bachar, D., Audic, S., Bass, D., Berney, C., Bittner, L., Boutte, C. et al. 2013. The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy. <i>Nucleic Acids Res.</i> 41:D597–604.Edvardsen, B., Egge, E.S. & Vaulot, D. 2016. Diversity and distribution of haptophytes revealed by environmental sequencing and metabarcoding – a review. <i>Perspect. Phycol.</i> in press.Tragin, M., Lopes dos Santos, A., Christen, R. & Vaulot, D. 2016. Diversity and ecology of green microalgae in marine systems: an overview based on 18S rRNA gene sequences. <i>Perspect. Phycol.</i> in press. <br><br><br>
DOI: 10.6084/m9.figshare.3803688.v1
title: PolyamideFiles.zip

description: Supporting material for:<br>Multiscale molecular simulations of the formation and structure of polyamide membranes created by interfacial polymerization <br>Jordan Muscatello, Erich A. Müller, Arash A. Mostofi, and Adrian P. Sutton<br>Paper submitted to J. Memb. Sci. (2016) <br>Large scale molecular simulations to model the formation of polyamide membranes have been carried out using a procedure that mimics experimental interfacial polymer- ization of trimesoyl chloride (TMC) and metaphenylene diamine (MPD) monomers. A coarse-grained representation of the monomers has been developed to facilitate these simulations, which captures essential features of the stereochemistry of the monomers and of amide bonding between them. Atomic models of the membranes are recreated from the final coarse-grained representations.<br><br>This data set includes both the programs needed to recreate the data and final atomistic configurations (LAMMPS) for the membranes described in the original publication.<br>
DOI: 10.6084/m9.figshare.3803646
title: Involvement of Rho GAP GRAF1 in maintenance of epithelial phenotype

description: Adhesion of epithelial cell to each other and to extracellular matrix, as well as cell migration ability and cytoskeleton organization undergo significant alterations in the course of neoplastic transformation, but regulatory mechanisms involved in these processes are not fully understood. Here, we studied the role of a Rho GAP protein GRAF1 (<i>G</i>TPase <i>R</i>egulator <i>A</i>ssociated with <i>F</i>ocal adhesion kinase-<i>1</i>) in the regulation of the epithelial phenotype in cells of breast derived, non-malignant, MCF10A cell line. GRAF1 was shown to be localized to cell-cell junctions, and its depletion resulted in accelerated cell migration velocity, elongation of the cells and cell colonies, impaired monolayer integrity and significant disruption of desmosomes with a loss of associated keratin filaments. These processes were accompanied by formation of larger focal adhesions, an increased number of contractile actin stress fibers, reduction in epithelial markers and increase in mesenchymal markers such as epithelial-mesenchymal transition (EMT)-specific transcription factors Snail-1 and Snail-2, as well as N-cadherin, and vimentin. Moreover, unlike control cells, GRAF1 knocked-down cells demonstrated anchorage-independent growth in soft agar. GRAF1 expression in several highly invasive breast cancer cell lines was low, as compared to the non-malignant MCF10A cells, while overexpressing of GRAF1 in the malignant BT-549 cell line led to a decrease of mesenchymal markers, especially the Snail-1 and 2. Altogether, our analysis suggests that GRAF1 plays a role in the maintenance of normal epithelial phenotype and its depletion leads to an EMT-like process that might be involved in neoplastic transformation.
DOI: 10.6084/m9.figshare.3803646.v1
title: Involvement of Rho GAP GRAF1 in maintenance of epithelial phenotype

description: Adhesion of epithelial cell to each other and to extracellular matrix, as well as cell migration ability and cytoskeleton organization undergo significant alterations in the course of neoplastic transformation, but regulatory mechanisms involved in these processes are not fully understood. Here, we studied the role of a Rho GAP protein GRAF1 (<i>G</i>TPase <i>R</i>egulator <i>A</i>ssociated with <i>F</i>ocal adhesion kinase-<i>1</i>) in the regulation of the epithelial phenotype in cells of breast derived, non-malignant, MCF10A cell line. GRAF1 was shown to be localized to cell-cell junctions, and its depletion resulted in accelerated cell migration velocity, elongation of the cells and cell colonies, impaired monolayer integrity and significant disruption of desmosomes with a loss of associated keratin filaments. These processes were accompanied by formation of larger focal adhesions, an increased number of contractile actin stress fibers, reduction in epithelial markers and increase in mesenchymal markers such as epithelial-mesenchymal transition (EMT)-specific transcription factors Snail-1 and Snail-2, as well as N-cadherin, and vimentin. Moreover, unlike control cells, GRAF1 knocked-down cells demonstrated anchorage-independent growth in soft agar. GRAF1 expression in several highly invasive breast cancer cell lines was low, as compared to the non-malignant MCF10A cells, while overexpressing of GRAF1 in the malignant BT-549 cell line led to a decrease of mesenchymal markers, especially the Snail-1 and 2. Altogether, our analysis suggests that GRAF1 plays a role in the maintenance of normal epithelial phenotype and its depletion leads to an EMT-like process that might be involved in neoplastic transformation.
DOI: 10.6084/m9.figshare.3803589
title: Perturbation of the molecular clockwork in the SCN of non-obese diabetic mice prior to diabetes onset

description: Circadian disruption is associated with the development of diabetes. Non-obese diabetic (NOD) mice show abnormal diurnal profiles in energy balance and locomotor activity suggesting circadian misalignment. Therefore, we analyzed cFos and mPER1 as markers for rhythmic neuronal activity within the suprachiasmatic nucleus (SCN) of wildtype (WT) and non-diabetic (nNOD) as well as acutely diabetic NOD (dNOD) mice. cFos levels show a day/night difference in both WT and nNOD but not in dNOD. mPER1 levels did not show a day/night difference in both nNOD and dNOD. This suggests that disruption of SCN rhythmicity in NOD mice precedes the actual onset of diabetes.
DOI: 10.6084/m9.figshare.3803589.v1
title: Perturbation of the molecular clockwork in the SCN of non-obese diabetic mice prior to diabetes onset

description: Circadian disruption is associated with the development of diabetes. Non-obese diabetic (NOD) mice show abnormal diurnal profiles in energy balance and locomotor activity suggesting circadian misalignment. Therefore, we analyzed cFos and mPER1 as markers for rhythmic neuronal activity within the suprachiasmatic nucleus (SCN) of wildtype (WT) and non-diabetic (nNOD) as well as acutely diabetic NOD (dNOD) mice. cFos levels show a day/night difference in both WT and nNOD but not in dNOD. mPER1 levels did not show a day/night difference in both nNOD and dNOD. This suggests that disruption of SCN rhythmicity in NOD mice precedes the actual onset of diabetes.
DOI: 10.6084/m9.figshare.3803448
title: confinement_MLwin.xlsx

description: Data shows number of fish on each thermal chamber. we have 3 groups of 12 fish per treatment. Treatments are control vs confinement event (15min in a net under water). Recordings are each 30min for 10 secs during first and last 4hours.
DOI: 10.6084/m9.figshare.3803448.v1
title: confinement_MLwin.xlsx

description: Data shows number of fish on each thermal chamber. we have 3 groups of 12 fish per treatment. Treatments are control vs confinement event (15min in a net under water). Recordings are each 30min for 10 secs during first and last 4hours.