cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5258/soton/d2779
title: Dataset in support of the University of Southampton Doctoral Thesis: Identifying antibiotic precursors by screening genetically encoded cyclic peptide libraries by Leonie Windeln

description: Dataset in support of the University of Southampton Doctoral Thesis: Identifying antibiotic precursors by screening genetically encoded cyclic peptide libraries by Leonie Windeln.

The data contains growth curves of E. coli in response to cyclic peptide exposure and cyclic peptide production via arabinose-dependent expression. As well as synthetic peptide testing data. Further, this dataset contains Sanger and next generation sequencing results and their analysis for the purpose of quality control, cyclic peptide identification and target identification. 

There are 5 power point presentations that hold the original main figures of the thesis. Sanger sequencing contains screenshots and figures of the data generated via sanger sequencing throughout the thesis. Characterisation of naïve libraries holds the information and figures about the naïve libraries in detail. Patterns drop out contains all figures about the drop out and is complemented by the two excel sheets focussed drop out sx5 summary and raw data patterns dropout as well as the prism file SFX4 focussed dropout barchart. Synthetic compound testing contains the files for growth curves and original images of testing the synthetic compounds. Target ID contains all data relevant to target identification. 

The data was collected via different experimental methods (growth curves of E.coli, NGS, WGS, Sanger sequencing, SPPS, RTqPCR) that are detailed in the thesis, which is also included as a word and pdf document. 

Licence:
CC BY NC ND

Related projects/Funders:
MSD funded
Grant: EP/R513325/1
DOI: 10.6084/m9.figshare.11984724
title: Additional file 1 of Genome-wide identification of long noncoding RNAs and their competing endogenous RNA networks involved in the odontogenic differentiation of human dental pulp stem cells

description: Additional file 1: Table S1. The expression profiles of upregulated lncRNAs in differentiated and undifferentiated hDPSCs. (XLS 72 kb)
DOI: 10.6084/m9.figshare.11984724.v1
title: Additional file 1 of Genome-wide identification of long noncoding RNAs and their competing endogenous RNA networks involved in the odontogenic differentiation of human dental pulp stem cells

description: Additional file 1: Table S1. The expression profiles of upregulated lncRNAs in differentiated and undifferentiated hDPSCs. (XLS 72 kb)
DOI: 10.6084/m9.figshare.11984739
title: Additional file 3 of Genome-wide identification of long noncoding RNAs and their competing endogenous RNA networks involved in the odontogenic differentiation of human dental pulp stem cells

description: Additional file 3: Table S3. The expression profiles of upregulated miRNAs in differentiated and undifferentiated hDPSCs. (XLS 33 kb)
DOI: 10.6084/m9.figshare.11984739.v1
title: Additional file 3 of Genome-wide identification of long noncoding RNAs and their competing endogenous RNA networks involved in the odontogenic differentiation of human dental pulp stem cells

description: Additional file 3: Table S3. The expression profiles of upregulated miRNAs in differentiated and undifferentiated hDPSCs. (XLS 33 kb)
DOI: 10.6084/m9.figshare.11984730
title: Additional file 2 of Genome-wide identification of long noncoding RNAs and their competing endogenous RNA networks involved in the odontogenic differentiation of human dental pulp stem cells

description: Additional file 2: Table S2. The expression profiles of downregulated lncRNAs in differentiated and undifferentiated hDPSCs. (XLS 119 kb)
DOI: 10.6084/m9.figshare.11984730.v1
title: Additional file 2 of Genome-wide identification of long noncoding RNAs and their competing endogenous RNA networks involved in the odontogenic differentiation of human dental pulp stem cells

description: Additional file 2: Table S2. The expression profiles of downregulated lncRNAs in differentiated and undifferentiated hDPSCs. (XLS 119 kb)
DOI: 10.6084/m9.figshare.11984748
title: Additional file 4 of Genome-wide identification of long noncoding RNAs and their competing endogenous RNA networks involved in the odontogenic differentiation of human dental pulp stem cells

description: Additional file 4: Table S4. The expression profiles of downregulated miRNAs in differentiated and undifferentiated hDPSCs. (XLS 63 kb)
DOI: 10.6084/m9.figshare.11984748.v1
title: Additional file 4 of Genome-wide identification of long noncoding RNAs and their competing endogenous RNA networks involved in the odontogenic differentiation of human dental pulp stem cells

description: Additional file 4: Table S4. The expression profiles of downregulated miRNAs in differentiated and undifferentiated hDPSCs. (XLS 63 kb)
DOI: 10.6084/m9.figshare.11984754
title: Additional file 5 of Genome-wide identification of long noncoding RNAs and their competing endogenous RNA networks involved in the odontogenic differentiation of human dental pulp stem cells

description: Additional file 5: Table S5. The expression profiles of upregulated mRNAs in differentiated and undifferentiated hDPSCs. (XLS 88 kb)
DOI: 10.6084/m9.figshare.11984754.v1
title: Additional file 5 of Genome-wide identification of long noncoding RNAs and their competing endogenous RNA networks involved in the odontogenic differentiation of human dental pulp stem cells

description: Additional file 5: Table S5. The expression profiles of upregulated mRNAs in differentiated and undifferentiated hDPSCs. (XLS 88 kb)
DOI: 10.6084/m9.figshare.11984763
title: Additional file 6 of Genome-wide identification of long noncoding RNAs and their competing endogenous RNA networks involved in the odontogenic differentiation of human dental pulp stem cells

description: Additional file 6: Table S6. The expression profiles of downregulated mRNAs in differentiated and undifferentiated hDPSCs. (XLS 108 kb)
DOI: 10.6084/m9.figshare.11984763.v1
title: Additional file 6 of Genome-wide identification of long noncoding RNAs and their competing endogenous RNA networks involved in the odontogenic differentiation of human dental pulp stem cells

description: Additional file 6: Table S6. The expression profiles of downregulated mRNAs in differentiated and undifferentiated hDPSCs. (XLS 108 kb)
DOI: 10.6084/m9.figshare.7790522
title: Additional file 13: of 2C-ChIP: measuring chromatin immunoprecipitation signal from defined genomic regions with deep sequencing

description: 5C datasets. This folder contains the read count-normalized 5C data in matrix format (.txt) of all the 5C samples produced for this study. These files can be uploaded directly to the 3DG browser (my5C; http://3DG.umassmed.edu ). 5C dataset 1. 5C analysis of the HOXA cluster region in untreated (0 h) NT2-D1 (set B). 5C dataset 2. 5C analysis of the HOXA cluster region in RA-treated (6 h) NT2-D1 (set B). 5C dataset 3. 5C analysis of the HOXA cluster region in RA-treated (3d) NT2-D1 (set B). 5C dataset 4. 5C analysis of the HOXA cluster region in RA-treated (7d) NT2-D1 (set B). 5C dataset 5. 5C analysis of the HOXA cluster region in control (siGFP) NT2-D1 cells induced with RA for 5 days. 5C dataset 6. 5C analysis of the HOXA cluster region in test (siAS2) NT2-D1 cells induced with RA for 5 days. (CPGZ 22 kb)
DOI: 10.6084/m9.figshare.7790522.v1
title: Additional file 13: of 2C-ChIP: measuring chromatin immunoprecipitation signal from defined genomic regions with deep sequencing

description: 5C datasets. This folder contains the read count-normalized 5C data in matrix format (.txt) of all the 5C samples produced for this study. These files can be uploaded directly to the 3DG browser (my5C; http://3DG.umassmed.edu ). 5C dataset 1. 5C analysis of the HOXA cluster region in untreated (0 h) NT2-D1 (set B). 5C dataset 2. 5C analysis of the HOXA cluster region in RA-treated (6 h) NT2-D1 (set B). 5C dataset 3. 5C analysis of the HOXA cluster region in RA-treated (3d) NT2-D1 (set B). 5C dataset 4. 5C analysis of the HOXA cluster region in RA-treated (7d) NT2-D1 (set B). 5C dataset 5. 5C analysis of the HOXA cluster region in control (siGFP) NT2-D1 cells induced with RA for 5 days. 5C dataset 6. 5C analysis of the HOXA cluster region in test (siAS2) NT2-D1 cells induced with RA for 5 days. (CPGZ 22 kb)
DOI: 10.6084/m9.figshare.21946300
title: Preparation and performance of magnetic zirconium-iron oxide nanoparticles loaded on palygorskite in the adsorption of phosphate from water

description: Magnetic zirconium-iron oxide nanoparticles loaded on palygorskite as a low-cost adsorbent was produced by one-step co precipitation technique and its properties for phosphate adsorption were overall investigated. The Brunauer Emmett Teller (BET) specific surface area analysis, scanning electron microscopy (SEM), thermo gravimetric analysis (TGA), Fourier transform infrared spectroscopy (FTIR), X-ray diffraction (XRD) and X-ray photoelectron spectroscopy (XPS) were used to characterize the adsorbent and evaluate the adsorption interactions. The influences of pH, ionic strength and coexisting ions on phosphate adsorption were measured with a discussion of the adsorption mechanism. Results indicated that no very noticeable changes on the surface properties, structure and phosphate adsorption capacity be found for the magnetic zirconium-iron oxide nanoparticles loaded on palygorskite or not. The adsorption kinetics fitted to the pseudo-second-order model and adsorption isotherm followed Langmuir equation and Dubinin-Radushkevich equation. The phosphate adsorption was slightly affected by ionic strength and highly dependent on pH, i.e. increasing pH sharply restrained adsorption under neutral and alkaline conditions. The surface OH groups in the adsorbent processed an important role in adsorption and the adsorption mechanism conformed to ion exchange and complex. The adsorbent could be conveniently regenerated and effectively reused.
DOI: 10.6084/m9.figshare.21946300.v1
title: Preparation and performance of magnetic zirconium-iron oxide nanoparticles loaded on palygorskite in the adsorption of phosphate from water

description: Magnetic zirconium-iron oxide nanoparticles loaded on palygorskite as a low-cost adsorbent was produced by one-step co precipitation technique and its properties for phosphate adsorption were overall investigated. The Brunauer Emmett Teller (BET) specific surface area analysis, scanning electron microscopy (SEM), thermo gravimetric analysis (TGA), Fourier transform infrared spectroscopy (FTIR), X-ray diffraction (XRD) and X-ray photoelectron spectroscopy (XPS) were used to characterize the adsorbent and evaluate the adsorption interactions. The influences of pH, ionic strength and coexisting ions on phosphate adsorption were measured with a discussion of the adsorption mechanism. Results indicated that no very noticeable changes on the surface properties, structure and phosphate adsorption capacity be found for the magnetic zirconium-iron oxide nanoparticles loaded on palygorskite or not. The adsorption kinetics fitted to the pseudo-second-order model and adsorption isotherm followed Langmuir equation and Dubinin-Radushkevich equation. The phosphate adsorption was slightly affected by ionic strength and highly dependent on pH, i.e. increasing pH sharply restrained adsorption under neutral and alkaline conditions. The surface OH groups in the adsorbent processed an important role in adsorption and the adsorption mechanism conformed to ion exchange and complex. The adsorbent could be conveniently regenerated and effectively reused.
DOI: 10.6084/m9.figshare.7790525
title: Additional file 14: of 2C-ChIP: measuring chromatin immunoprecipitation signal from defined genomic regions with deep sequencing

description: Table S6. List of primer sequences used for chromatin conformation capture carbon copy (5C). (XLSX 10 kb)
DOI: 10.6084/m9.figshare.7790525.v1
title: Additional file 14: of 2C-ChIP: measuring chromatin immunoprecipitation signal from defined genomic regions with deep sequencing

description: Table S6. List of primer sequences used for chromatin conformation capture carbon copy (5C). (XLSX 10 kb)
DOI: 10.6084/m9.figshare.7790540
title: Additional file 1: of 2C-ChIP: measuring chromatin immunoprecipitation signal from defined genomic regions with deep sequencing

description: Table S1. HOXA and lncRNA gene expression in NT2-D1 cells before and after a 3-day treatment with retinoic acid (RA; 10 micromolar) as measured by RT-qPCR. This table contains steady-state mRNA quantifications from at least 3 independent PCRs in two biological replicates. (XLSX 14 kb)
DOI: 10.15468/9cgs2u
title: Données animation Natura 2000 et Espace Naturel Sensible - Amélioration des connaissances des lépidoptères et mesures de gestion des espèces à enjeux

description: Inventaires ciblés de 4 rhopalocères à enjeux
DOI: 10.15468/63h3jz
title: Mycological Reports. Part 2

description: This is the second part of the planned series of publications that will include data on new localities of macrofungi identified by members of the Polish Mycological Society's Fungal Diversity and Conservation Section. These studies aim to broaden the knowledge about the current distribution of fungi in Poland. The current dataset presents data on 228 new sites of 163 species of macrofungi (16 species of Ascomycota and 147 species of Basidiomycota). These dataset refers to following paper: https://kp.org.pl/images/pp/artyku%C5%82y_od_2019/4_2022_XXXIII_4/Domian%20et%20al_2022_Obserwacje%20mykologiczne.pdf
DOI: 10.15468/df6484
title: projet centrale photovoltaïque de Selongey - Reptiles - Inventaire non protocolé

description: Listes des reptiles observés dans le cadre des prospections de terrain réalisées au niveau de l'aire d'étude du projet photovoltaïque de Selongey (21)
DOI: 10.15468/n3gx7j
title: Projet de parc éolien de Bois Chantret-Bois Chantret - insectes

description: Liste des insectes observés dans le cadre des prospections de terrain réalisées au niveau de l'aire d'étude immédiate du projet éolien
DOI: 10.15468/cv6ya3
title: Renouvellement de l'autorisation d'exploiter de la carrière de Villiers-sur-Seine-Inventaire mammifères terrestres

description: Inventaire non standardisé
DOI: 10.6084/m9.figshare.7790546
title: Additional file 2: of 2C-ChIP: measuring chromatin immunoprecipitation signal from defined genomic regions with deep sequencing

description: Table S2. List of primer sequences used to quantify gene expression by quantitative real-time polymerase chain reaction (RT-qPCR). (XLSX 11 kb)
DOI: 10.15468/fz2tkp
title: 30 - Inventaires mycologiques - Bourget du Lac 2016-2017

description: Bourget du Lac 2016-2017 / Acquisition de données d'inventaire de la fonge réalisé à la demande d'un commanditaire public
DOI: 10.6084/m9.figshare.7790546.v1
title: Additional file 2: of 2C-ChIP: measuring chromatin immunoprecipitation signal from defined genomic regions with deep sequencing

description: Table S2. List of primer sequences used to quantify gene expression by quantitative real-time polymerase chain reaction (RT-qPCR). (XLSX 11 kb)
DOI: 10.15468/6d23ar
title: Parc éolien du Haut Chemin [SUIVIS 2017,2018,2019,2020]-Chiroptères - Points d'écoute

description: Listes des chiroptères contactées grâce à des points d'écoute au niveau de l'aire d'étude du projet.
DOI: 10.15468/e5sws7
title: Projet d'aménagement de la ZAC Satory Ouest - Amphibiens - Inventaire non standardisé

description: Liste des amphibiens observés dans le cadre des prospections de terrain réalisées au niveau de l'aire d'étude du projet xxx
DOI: 10.15468/vaz84a
title: 2021_Conservatoire du littoral_2

description: 2020_CdL_Lacs_PACA:Conservatoire du littoral
DOI: 10.6084/m9.figshare.7790549
title: Additional file 3: of 2C-ChIP: measuring chromatin immunoprecipitation signal from defined genomic regions with deep sequencing

description: Table S3. List of primer sequences used to PCR-quantify DNA regions isolated by chromatin immunoprecipitation (ChIP-qPCR). (XLSX 10 kb)
DOI: 10.15468/xbpus2
title: Parc éolien de Bois de Bajouve - Données brutes activité de chiroptères

description: Données brutes d'activité de chiroptères recueilli dans la cadre de suivi post-implantation du parc éolien de Bois de Bajouve en 2019
DOI: 10.6084/m9.figshare.7790549.v1
title: Additional file 3: of 2C-ChIP: measuring chromatin immunoprecipitation signal from defined genomic regions with deep sequencing

description: Table S3. List of primer sequences used to PCR-quantify DNA regions isolated by chromatin immunoprecipitation (ChIP-qPCR). (XLSX 10 kb)
DOI: 10.6073/pasta/b9d82ebb94fcbed47d13371b538d72e0
title: Water transparency in the Laurentian Great Lakes

description: The Laurentian Great Lakes in the mid-east region of North America, is one of the largest freshwater ecosystems in the world. This data set contains limnological data, focusing on underwater transparency in this ecosystem and the surrounding region, beginning in 1999. Current water transparency data sets highlight the increase in offshore transparency measured by a deepening of average Secchi Disk depth since the invasion of the Dreissenid mussels. However, limited data exists on the Great Lakes to provide insight to the underwater optical environment of the offshore, nearshore, and surrounding water bodies of these lakes. These data illustrate the vertical underwater light environment with data from wavelengths of sunlight including photosynthetically active radiation (400 – 700 nm), UV-A radiation (320 - 400 nm) and UV-B radiation (290 - 320 nm). Understanding the depths to which these specific wavelengths of sunlight reach within a lake, as well as the substances within the lake that may influence the attenuation of sunlight can provide a picture of how habitats within the lake system have been impacted. This data set is a part of a continuous data collaboration among multiple research groups, and will be updated periodically as more data are made available. As such, this initial data set provides a snapshot of water transparency in the Great Lakes, and more sampling sites and years of data are forthcoming.
 The data here are contained in five files, including Data_GreatLakes.csv, SiteInformation_GreatLakes.csv, Methods_GreatLakes.csv, Project_GreatLakes, and Variables_GreatLakes. The main data are in Data_GreatLakes.csv. SiteInformation_GreatLakes.csv, Methods_GreatLakes.csv, Project_GreatLakes.csv, and Variables_GreatLakes.csv support the main data file with descriptions of the sampling sites, methods by which samples were processed, project and contact information for each data point, and descriptions of variables, respectively.
DOI: 10.15468/jb22p6
title: 2020_Pierrick GIRAUDET_1

description: 2020_GIRAUDET:Pierrick GIRAUDET
DOI: 10.15468/6ydwg6
title: ONF - Données issues d'études conventionnelles commandées par organismes exterieurs à l'ONF - MOA : Ministère de l'environnement - ONF - Inventaire chiroptère 2018-19 site NATURA 2000 S38

description: Données transmises à l'ONF dans le cadre d'études commandées par MOA axterieures à l'ONF
DOI: 10.6084/m9.figshare.7790558
title: Additional file 4: of 2C-ChIP: measuring chromatin immunoprecipitation signal from defined genomic regions with deep sequencing

description: Table S4. List of 2C-ChIP primer sequences used in this study. (XLSX 70 kb)
DOI: 10.6084/m9.figshare.7790558.v1
title: Additional file 4: of 2C-ChIP: measuring chromatin immunoprecipitation signal from defined genomic regions with deep sequencing

description: Table S4. List of 2C-ChIP primer sequences used in this study. (XLSX 70 kb)
DOI: 10.15468/ss63fk
title: Etude chiroptère du projet de parc éolien de Cheniers Energies

description: Inventaire Chiroptère avec dispositif SM2 bat
DOI: 10.15468/92ppsy
title: Suivi post-implantation du parc éolien de Cuxac-Cabardès en 2018/2019

description: Suivi de la mortalité des oiseaux et des chauves-souris Suivi en continu de l'activité des chiroptères à hauteur de nacelle
DOI: 10.15468/p79fgt
title: Parc solaire de Logelbach - Logelbach Oiseaux

description: Le parc solaire de Logelbach est prévu sur l'ancienne décharge de Ligibel. les données ci-jointes sont relatives aux observations dans le cadre de l'étude d'impact du permis de construire
DOI: 10.5281/zenodo.10721746
title: time course gene expression of atrial cardiomyocyte differentiation

description: atrial cardiomyocyte protocol was similar to that described by Cyganek et al. 2018
DOI: 10.5281/zenodo.10721747
title: time course gene expression of atrial cardiomyocyte differentiation

description: atrial cardiomyocyte protocol was similar to that described by Cyganek et al. 2018
DOI: 10.6084/m9.figshare.7790564
title: Additional file 5: of 2C-ChIP: measuring chromatin immunoprecipitation signal from defined genomic regions with deep sequencing

description: Table S5. List of primer sequences used to amplify 2C-ChIP libraries prior to deep sequencing on a PGMâ ˘ system (Thermo Fisher Scientific). (XLSX 54 kb)
DOI: 10.6084/m9.figshare.7790564.v1
title: Additional file 5: of 2C-ChIP: measuring chromatin immunoprecipitation signal from defined genomic regions with deep sequencing

description: Table S5. List of primer sequences used to amplify 2C-ChIP libraries prior to deep sequencing on a PGMâ ˘ system (Thermo Fisher Scientific). (XLSX 54 kb)
DOI: 10.15468/bg79rf
title: Partenariats avec les Parcs Naturels Régionaux - Données OPIE partenariats PNR

description: Jeu de données compilant les données recueillies par l'OPIE dans le cadre de ses actions avec les Pars naturels régionaux
DOI: 10.15468/72ytmh
title: krokar-predatory-invertebrates

description: This dataset consists of ground-dwelling predatory invertebrates (spiders, centipedes and ground-dwelling beetles) from Krokar virgin forest located on Borovec Mountain in SE Slovenia.
DOI: 10.15468/rkcyk5
title: Suivi post-implantation du parc éolien de Grand Bois en 2018 / 2019

description: Suivi de la mortalité des oiseaux et des chauves-souris
DOI: 10.15468/u75sbw
title: ABC de Saint Michel De Dèze - Atlas de la Biodiversité Communale sur la commune de St-Michel-de-Dèze

description: Jeu de données compilant les données saisies par l'OPIE lors de la réalisation des Atlas de la Biodiversité Communale sur la commune de St-Michel-de-Dèze
DOI: 10.15468/kfuqvj
title: Construction de l'Hôpital Paris-Saclay - Insectes - Inventaire non protocolé

description: Liste des insectes observées dans le cadre des prospections de terrain réalisées au niveau de l'aire d'étude du projet de Création du nouvel hôpital du GHNE au sein du plateau de Saclay (91)
DOI: 10.15468/4pysjr
title: Renouvellement de l'autorisation d'exploiter de la carrière de Villiers-sur-Seine-Inventaire insectes (lépidotères, orthoptères, odonates)

description: Inventaire non standardisé
DOI: 10.15468/hvca39
title: Renouvellement de l'autorisation d'exploiter de la carrière de Villiers-sur-Seine-inventaire reptiles

description: Inventaire non standardisé
DOI: 10.15468/s7uaxp
title: 2020_Communauté d'agglomération de la Riviera française_1

description: 2020_CARF_GEOECO:Communauté d'agglomération de la Riviera française
DOI: 10.15468/kpux67
title: SNC Ferme Eolienne La Grande Plaine - Chiroptères - Inventaire non protocolé

description: Liste des chiroptères observés dans le cadre des prospections de terrain réalisées au niveau de l'aire d'étude immédiate du projet éolien La Grande Plaine (51°
DOI: 10.15468/4796c9
title: Projet d'aménagement de la ZAC Satory Ouest - Insectes - Inventaire non standardisé - 2

description: Liste des insectes observés dans le cadre des prospections de terrain réalisées au niveau de l'aire d'étude du projet de la ZAC de Satory Ouest dans le cadre de l'établissement de l'état initial.