cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.1594/pangaea.959031
title: Continuous thermosalinograph oceanography along RV METEOR cruise track M180

description: Underway temperature and salinity data was collected along the cruise track with two autonomous thermosalinograph (TSG) systems, each consisting of a SBE21 TSG together with a SBE38 Thermometer. Both systems worked independent from each other throughout the cruise. While temperature is taken at the water inlet in about 5 m depth, salinity is estimated within the interior TSG from conductivity and interior temperature. No correction against independent data was performed neither for temperature nor for salinity. Finally, TSG1 was chosen for publication. For details to all processing steps see Data Processing Report.
DOI: 10.6084/m9.figshare.29236728.v1
title: Systematic analysis of A-to-I RNA editing upon release of ADAR from the nucleolus

description: Adenosine-to-inosine (A-to-I) RNA editing, catalysed by two ADAR isoforms (p110 and p150) and ADARB1, is a critical regulatory step in gene expression. Intriguingly, the nucleolus is conspicuously rich in ADAR p110 and ADARB1, though the biological reason remains unclear. To investigate a putative role of nucleolar enrichment in ADAR, we released it gradually from the nucleolus into the nucleoplasm by treating cells briefly with low doses of actinomycin D, known to disassemble the nucleolus. Deep sequencing of the transcriptome revealed that as ADAR dissociated from the nucleolus, RNA editing increased significantly, with sharp rises in both the number of edited sites and editing frequency. This co-transcriptional editing, predominantly in intronic regions, was associated with disrupted pre-mRNA splicing, causing exon skipping and intron retention which remodelled gene expression. These findings suggest that the nucleolar localization of ADAR serves to restrain its activity, preventing excessive editing that could lead to splicing errors and cellular dysfunction.
DOI: 10.1594/pangaea.960974
title: Continuous thermosalinograph oceanography along RV METEOR cruise track M186/2

description: Underway temperature and salinity data was collected along the cruise track with two autonomous thermosalinograph (TSG) systems, each consisting of a SBE21 TSG together with a SBE38 Thermometer. Both systems worked independent from each other throughout the cruise. While temperature is taken at the water inlet in about 5 m depth, salinity is estimated within the interior TSG from conductivity and interior temperature. No correction against independent data was performed for temperature. Salinity was calibrated against independent water samples. Finally, TSG1 was chosen for publication. For details to all processing steps see Data Processing Report.
description: Salinity was calibrated independently against water samples from 5 m depth. Value added to TSG1 salinity data = 0.023904. Value added to TSG2 salinity data = 0.014440.
DOI: 10.1594/pangaea.961924
title: Master tracks in different resolutions of SONNE cruise SO296/1, Ensenada - Talcahuano, 2022-12-26 - 2023-01-18

description: Raw data acquired by position sensors on board RV SONNE during expedition SO296_1 were processed to receive a validated master track which can be used as reference of further expedition data. During SO296_1 the motion reference unit Kongsberg SeaTex AS MRU-5 combined with Kongsberg SeaTex AS Seapath 320 and two GPS receivers SAAB MGL-4 were used as navigation sensors. Data were downloaded from DAVIS SHIP data base (https://dship.bsh.de) with a resolution of 1 sec. Processing and evaluation of the data is outlined in the data processing report. Processed data are provided as a master track with 1 sec resolution derived from the position sensors' data selected by priority and a generalized track with a reduced set of the most significant positions of the master track.
description: This dataset contains the master track in 10 min resolution, for other resolutions please see "Further details" and "Other version" references.
DOI: 10.6084/m9.figshare.28023192
title: Identification of deleterious non-synonymous single nucleotide polymorphisms in the mRNA decay activator ZFP36L2

description: More than 4,000 single nucleotide polymorphisms (SNP) variants have been identified in the human <i>ZFP36L2</i> gene, however only a few have been studied in the context of protein function. The tandem zinc finger domain of ZFP36L2, an RNA binding protein, is the functional domain that binds to its target mRNAs. This protein/RNA interaction triggers mRNA degradation, controlling gene expression. We identified 32 non-synonymous SNPs (nsSNPs) in the tandem zinc finger domain of ZFP36L2 that could have possible deleterious impacts in humans. Using different bioinformatic strategies, we prioritized five among these 32 nsSNPs, namely rs375096815, rs1183688047, rs1214015428, rs1215671792 and rs920398592 to be validated. When we experimentally tested the functionality of these protein variants using gel shift assays, all five (Y154H, R160W, R184C, G204D, and C206F) resulted in a dramatic reduction in RNA binding compared to the WT protein. To understand the mechanistic effect of these variants on the protein/RNA interaction, we employed DUET, DynaMut and PyMOL to investigate structural changes in the protein. Additionally, we conducted Molecular Docking and Molecular Dynamics Simulations to fine tune the active behaviour of this biomolecular system at an atomic level. Our results propose atomic explanations for the impact of each of these five genetic variants identified.
DOI: 10.6084/m9.figshare.28023192.v1
title: Identification of deleterious non-synonymous single nucleotide polymorphisms in the mRNA decay activator ZFP36L2

description: More than 4,000 single nucleotide polymorphisms (SNP) variants have been identified in the human <i>ZFP36L2</i> gene, however only a few have been studied in the context of protein function. The tandem zinc finger domain of ZFP36L2, an RNA binding protein, is the functional domain that binds to its target mRNAs. This protein/RNA interaction triggers mRNA degradation, controlling gene expression. We identified 32 non-synonymous SNPs (nsSNPs) in the tandem zinc finger domain of ZFP36L2 that could have possible deleterious impacts in humans. Using different bioinformatic strategies, we prioritized five among these 32 nsSNPs, namely rs375096815, rs1183688047, rs1214015428, rs1215671792 and rs920398592 to be validated. When we experimentally tested the functionality of these protein variants using gel shift assays, all five (Y154H, R160W, R184C, G204D, and C206F) resulted in a dramatic reduction in RNA binding compared to the WT protein. To understand the mechanistic effect of these variants on the protein/RNA interaction, we employed DUET, DynaMut and PyMOL to investigate structural changes in the protein. Additionally, we conducted Molecular Docking and Molecular Dynamics Simulations to fine tune the active behaviour of this biomolecular system at an atomic level. Our results propose atomic explanations for the impact of each of these five genetic variants identified.
DOI: 10.1594/pangaea.961041
title: Master track of Eugen Seibold cruise ES21C02, Playa Blanca - Las Palmas de Gran Canaria, 2021-02-08 - 2021-02-09

description: This dataset contains the validated master track of the S/Y Eugen Seibold during expedition ES21C02, with a time resolution of about 10 seconds. This master track can be used as reference for further expedition data. For creating the master track, the 1-second resolution raw data acquired by the GPS position sensor on board S/Y Eugen Seibold were processed, averaging latitude and longitude within equidistant 10-second intervals. Quality control was performed visually and by checking the maximum speed calculated between neighbouring positions. In case of unrealistically high speeds, data points have been removed.
description: Details about the processing routine and the meaning of the quality flag are given in the Standard Operating Procedure (SOP). Cruise-specific remarks are given in the Data Processing Report (DPR).
DOI: 10.1594/pangaea.961050
title: Master track of Eugen Seibold cruise ES19C14, Ponta Delgada - Vigo, 2019-08-10 - 2019-08-17

description: This dataset contains the validated master track of the S/Y Eugen Seibold during expedition ES19C14, with a time resolution of about 10 seconds. This master track can be used as reference for further expedition data. For creating the master track, the 1-second resolution raw data acquired by the GPS position sensor on board S/Y Eugen Seibold were processed, averaging latitude and longitude within equidistant 10-second intervals. Quality control was performed visually and by checking the maximum speed calculated between neighbouring positions. In case of unrealistically high speeds, data points have been removed.
description: Details about the processing routine and the meaning of the quality flag are given in the Standard Operating Procedure (SOP). Cruise-specific remarks are given in the Data Processing Report (DPR).
DOI: 10.6084/m9.figshare.28638637
title: Sorafenib-associated translation reprogramming in hepatocellular carcinoma cells

description: Sorafenib (Sfb) is a multikinase inhibitor regularly used for the management of patients with advanced hepatocellular carcinoma (HCC) that has been shown to increase very modestly life expectancy. We have shown that Sfb inhibits protein synthesis at the level of initiation in cancer cells. However, the global snapshot of mRNA translation following Sorafenib-treatment has not been explored so far. In this study, we performed a genome-wide polysome profiling analysis in Sfb-treated HCC cells and demonstrated that, despite global translation repression, a set of different genes remain efficiently translated or are even translationally induced. We reveal that, in response to Sfb inhibition, translation is tuned, which strongly correlates with the presence of established mRNA <i>cis</i>-acting elements and the corresponding protein factors that recognize them, including DAP5 and ARE-binding proteins. At the level of biological processes, Sfb leads to the translational down-regulation of key cellular activities, such as those related to the mitochondrial metabolism and the collagen synthesis, and the translational up-regulation of pathways associated with the adaptation and survival of cells in response to the Sfb-induced stress. Our findings indicate that Sfb induces an adaptive reprogramming of translation and provides valuable information that can facilitate the analysis of other drugs for the development of novel combined treatment strategies based on Sfb therapy.
DOI: 10.6084/m9.figshare.28638637.v1
title: Sorafenib-associated translation reprogramming in hepatocellular carcinoma cells

description: Sorafenib (Sfb) is a multikinase inhibitor regularly used for the management of patients with advanced hepatocellular carcinoma (HCC) that has been shown to increase very modestly life expectancy. We have shown that Sfb inhibits protein synthesis at the level of initiation in cancer cells. However, the global snapshot of mRNA translation following Sorafenib-treatment has not been explored so far. In this study, we performed a genome-wide polysome profiling analysis in Sfb-treated HCC cells and demonstrated that, despite global translation repression, a set of different genes remain efficiently translated or are even translationally induced. We reveal that, in response to Sfb inhibition, translation is tuned, which strongly correlates with the presence of established mRNA <i>cis</i>-acting elements and the corresponding protein factors that recognize them, including DAP5 and ARE-binding proteins. At the level of biological processes, Sfb leads to the translational down-regulation of key cellular activities, such as those related to the mitochondrial metabolism and the collagen synthesis, and the translational up-regulation of pathways associated with the adaptation and survival of cells in response to the Sfb-induced stress. Our findings indicate that Sfb induces an adaptive reprogramming of translation and provides valuable information that can facilitate the analysis of other drugs for the development of novel combined treatment strategies based on Sfb therapy.
DOI: 10.1594/pangaea.960382
title: Master track of Eugen Seibold cruise ES19C01, Playa Blanca - Caniçal, 2019-04-08 - 2019-04-10

description: This dataset contains the validated master track of the S/Y Eugen Seibold during expedition ES19C01, with a time resolution of about 10 seconds. This master track can be used as reference for further expedition data. For creating the master track, the 1-second resolution raw data acquired by the GPS position sensor on board S/Y Eugen Seibold were processed, averaging latitude and longitude within equidistant 10-second intervals. Quality control was performed visually and by checking the maximum speed calculated between neighbouring positions. In case of unrealistically high speeds, data points have been removed.
description: Details about the processing routine and the meaning of the quality flag are given in the Standard Operating Procedure (SOP). Cruise-specific remarks are given in the Data Processing Report (DPR).
DOI: 10.1594/pangaea.960971
title: Continuous thermosalinograph oceanography along RV METEOR cruise track M185

description: Underway temperature and salinity data was collected along the cruise track with two autonomous thermosalinograph (TSG) systems, each consisting of a SBE21 TSG together with a SBE38 Thermometer. Both systems worked independent from each other throughout the cruise. While temperature is taken at the water inlet in about 5 m depth, salinity is estimated within the interior TSG from conductivity and interior temperature. No correction against independent data was performed for temperature. Salinity was calibrated against independent water samples. Finally, TSG1 was chosen for publication. For details to all processing steps see Data Processing Report.
description: Salinity was calibrated independently against water samples from 5 m depth. Value added to TSG1 salinity data = 0.105134. Value added to TSG2 salinity data = 0.061345.
DOI: 10.6084/m9.figshare.29441597
title: Identification and characterization of new structured RNA classes in plants

description: Alternative splicing is a very important mechanism to diversify an organism’s transcriptome with minimal increases in genome size. It can modify the function of the finished protein or affect its regulation, e.g. induce nonsense-mediated decay (NMD) to degrade the transcript. Mechanisms that affect alternative splicing are therefore of great interest. It has been shown that splicing can be affected by RNA secondary structures within pre-mRNAs. These structured regions of RNA (strucRNA) would affect their transcript in <i>cis</i>, but only a few such cases are known in plants. In this study, we interrogate plant genomes for <i>cis</i>-regulatory strucRNAs. By applying a comparative-genomics-based approach to 130 plant genomes, we identified 16 strucRNA candidates. Five candidates likely regulate in <i>cis</i> using alternative splicing and NMD. Other predictions might not regulate alternative splicing, including four putative small nucleolar RNAs (snoRNAs). Of our five <i>cis</i>-regulatory strucRNAs that are implicated in alternative splicing control, two are now experimentally validated in follow-up studies. These results stand in contrast to the few previously validated examples. Although we were able to predict some strucRNAs, all motifs had generally modest levels of covariation, which is a pattern of mutations that indicates a conserved secondary structure. With few mutations, comparative-genomics-based approaches to find strucRNAs are less effective. Other approaches of finding regulatory RNAs in plants might thus be needed, and more available genomic or transcriptomic data might improve the quality and quantity of promising candidates.
DOI: 10.6084/m9.figshare.29441597.v1
title: Identification and characterization of new structured RNA classes in plants

description: Alternative splicing is a very important mechanism to diversify an organism’s transcriptome with minimal increases in genome size. It can modify the function of the finished protein or affect its regulation, e.g. induce nonsense-mediated decay (NMD) to degrade the transcript. Mechanisms that affect alternative splicing are therefore of great interest. It has been shown that splicing can be affected by RNA secondary structures within pre-mRNAs. These structured regions of RNA (strucRNA) would affect their transcript in <i>cis</i>, but only a few such cases are known in plants. In this study, we interrogate plant genomes for <i>cis</i>-regulatory strucRNAs. By applying a comparative-genomics-based approach to 130 plant genomes, we identified 16 strucRNA candidates. Five candidates likely regulate in <i>cis</i> using alternative splicing and NMD. Other predictions might not regulate alternative splicing, including four putative small nucleolar RNAs (snoRNAs). Of our five <i>cis</i>-regulatory strucRNAs that are implicated in alternative splicing control, two are now experimentally validated in follow-up studies. These results stand in contrast to the few previously validated examples. Although we were able to predict some strucRNAs, all motifs had generally modest levels of covariation, which is a pattern of mutations that indicates a conserved secondary structure. With few mutations, comparative-genomics-based approaches to find strucRNAs are less effective. Other approaches of finding regulatory RNAs in plants might thus be needed, and more available genomic or transcriptomic data might improve the quality and quantity of promising candidates.
DOI: 10.1594/pangaea.961033
title: Master track of Eugen Seibold cruise ES21C07, Mindelo - Mindelo, 2021-05-01 - 2021-05-02

description: This dataset contains the validated master track of the S/Y Eugen Seibold during expedition ES21C07, with a time resolution of about 10 seconds. This master track can be used as reference for further expedition data. For creating the master track, the 1-second resolution raw data acquired by the GPS position sensor on board S/Y Eugen Seibold were processed, averaging latitude and longitude within equidistant 10-second intervals. Quality control was performed visually and by checking the maximum speed calculated between neighbouring positions. In case of unrealistically high speeds, data points have been removed.
description: Details about the processing routine and the meaning of the quality flag are given in the Standard Operating Procedure (SOP). Cruise-specific remarks are given in the Data Processing Report (DPR).
DOI: 10.1594/pangaea.961049
title: Master track of Eugen Seibold cruise ES20C07, Ponta Delgada - Ponta Delgada, 2020-08-21 - 2020-08-24

description: This dataset contains the validated master track of the S/Y Eugen Seibold during expedition ES20C07, with a time resolution of about 10 seconds. This master track can be used as reference for further expedition data. For creating the master track, the 1-second resolution raw data acquired by the GPS position sensor on board S/Y Eugen Seibold were processed, averaging latitude and longitude within equidistant 10-second intervals. Quality control was performed visually and by checking the maximum speed calculated between neighbouring positions. In case of unrealistically high speeds, data points have been removed.
description: Details about the processing routine and the meaning of the quality flag are given in the Standard Operating Procedure (SOP). Cruise-specific remarks are given in the Data Processing Report (DPR).
DOI: 10.6084/m9.figshare.29446711
title: SARS-CoV-2 RNA-binding protein suppresses extracellular miRNA release

description: SARS-CoV-2 is the betacoronavirus causing the COVID-19 pandemic. Although the SARS-CoV-2 genome and transcriptome were reported previously, the function of individual viral proteins is largely unknown. Utilizing biochemical and molecular biology methods, we identified that four SARS-CoV-2 RNA-binding proteins (RBPs) regulate the host RNA metabolism by direct interaction with mature miRNA let-7b revealed by Nuclear Magnetic Resonance spectroscopy (NMR). SARS-CoV-2 RBP Nsp9 primarily binds mature miRNA let-7b, a direct ligand of the Toll-like Receptor 7 (TLR7), one of the potential SARS-CoV-2 therapeutics. Nsp9 suppresses host gene expression possibly by promoting let-7b-mediated silencing of a cellular RNA polymerase, POLR2D. In addition, Nsp9 inhibits extracellular release of let-7b and subsequent antiviral activity via TLR7. These results demonstrate that SARS-CoV-2 hijacks the host RNA metabolism to suppress antiviral responses and to shut down cellular transcription. Our findings of how a natural ligand of TLR7, miRNA let-7b, is suppressed by SARS-CoV-2 RBPs will advance our understanding of COVID-19 and SARS-CoV-2 therapeutics.
DOI: 10.6084/m9.figshare.29446711.v1
title: SARS-CoV-2 RNA-binding protein suppresses extracellular miRNA release

description: SARS-CoV-2 is the betacoronavirus causing the COVID-19 pandemic. Although the SARS-CoV-2 genome and transcriptome were reported previously, the function of individual viral proteins is largely unknown. Utilizing biochemical and molecular biology methods, we identified that four SARS-CoV-2 RNA-binding proteins (RBPs) regulate the host RNA metabolism by direct interaction with mature miRNA let-7b revealed by Nuclear Magnetic Resonance spectroscopy (NMR). SARS-CoV-2 RBP Nsp9 primarily binds mature miRNA let-7b, a direct ligand of the Toll-like Receptor 7 (TLR7), one of the potential SARS-CoV-2 therapeutics. Nsp9 suppresses host gene expression possibly by promoting let-7b-mediated silencing of a cellular RNA polymerase, POLR2D. In addition, Nsp9 inhibits extracellular release of let-7b and subsequent antiviral activity via TLR7. These results demonstrate that SARS-CoV-2 hijacks the host RNA metabolism to suppress antiviral responses and to shut down cellular transcription. Our findings of how a natural ligand of TLR7, miRNA let-7b, is suppressed by SARS-CoV-2 RBPs will advance our understanding of COVID-19 and SARS-CoV-2 therapeutics.
DOI: 10.1594/pangaea.958531
title: Water column raw data (Kongsberg EM710 entire dataset) of RV METEOR during cruise M104

description: Multibeam bathymetry raw data using the ship's own Kongsberg EM 710 multibeam echosounder was not continuously recorded during RV METEOR cruise M104. Data was recorded on 4 days between 2014-02-23 and 2014-02-27. This dataset contains a survey west of Namibia in the South Atlantic Ocean. The data are archived at the Federal Maritime and Hydrographic Agency of Germany (Bundesamt für Seeschifffahrt und Hydrographie, BSH) and provided to PANGAEA database for data curation and publication. No ancillary sound velocity profiles (SVP) files from the cruise are archived at the BSH and added to the corresponding multibeam raw dataset https://doi.org/10.1594/PANGAEA.958530This publication is conducted within the efforts of the German Marine Research Alliance in the core area 'Data management and Digitalization' (Deutsche Allianz Meeresforschung, DAM).
description: These data should not be used for navigational purposes.Data publishing was realized by Daniel Damaske, MARUM - Center for Marine Environmental Sciences (University Bremen).