cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.1594/pangaea.964271
title: Continuous thermosalinograph oceanography along RV POLARSTERN cruise track PS132

description: Raw data acquired by two SBE21 thermosalinograph and two auxiliary SBE38 temperature sensor (Sea-Bird Scientific, USA) installed in an underway seawater flow-through system on board RV Polarstern were processed to yield a calibrated and validated data set of temperature and salinity along the cruise track. Data were downloaded from DAVIS SHIP data base (https://dship.awi.de) at a resolution of 1 sec, and converted to temperature and conductivity using the pre-deployment factory calibration coefficients. The converted data were averaged to 1 min values, outliers were removed, and sensor drift was corrected using coefficients obtained from a post-season calibration performed at Sea-Bird at the end of the measurement season. Salinity was calculated from internal temperature, conductivity and pressure according to the PSS-78 Practical Salinity Scale. Processed data are provided as 1 min means of seawater temperature, conductivity and salinity, aligned with position data taken from the master track. Quality flags are appended according to the SeaDataNet Data Quality Control Procedures (version from May 2010). More details are described in the attached processing report.
DOI: 10.6084/m9.figshare.29269122
title: Dual synthesis pathways of scaRNA28 via intronic processing of transformation/transcription domain-associated protein transcripts and a novel independent transcription unit

description: Small Cajal body-specific RNAs (scaRNAs) are noncoding RNAs involved in the maturation of U-rich small nuclear RNAs. Except for a few that have their own transcription units, most scaRNA genes are embedded in introns and are predicted to be transcribed with host genes. Herein, we report that scaRNA28 is the first scaRNA with a dual synthesis pathway, and that this RNA is transcribed in an independent transcription unit (ITU) by RNA polymerase II while located in intron 2 of the transformation/transcription domain-associated protein (TRRAP) gene. We evaluated the scaRNA28 synthesis pathway using minigenes containing exon 2, intron 2, and exon 3 of <i>TRRAP</i>. A minigene with a mutation preventing 5′ splicing recognition of the exon 2/intron 2 junction generated scaRNA28, suggesting a pathway processing unspliced transcripts into scaRNA28. Even promoterless minigenes and DNA fragments with regions from exons 2 to 3 of <i>TRRAP</i> showed RNA polymerase II-dependent synthesis of scaRNA28, indicating a novel synthesis pathway involving an ITU. Linker-scanning mutational analysis revealed that the promoter region required for scaRNA28 expression in the ITU is located within 60 bases including exon 2/intron 2 junction of <i>TRRAP</i>, and especially the first two bases of intron 2 region, a putative part of the MYC-binding (E-box) motif, are essential for scaRNA28 expression in the ITU. MYC promotes scaRNA28 expression by binding to the promoter region in the ITU. Our findings demonstrated a novel transcriptional pathway for the synthesis of scaRNA28, the first scaRNA with a dual synthesis pathway.
DOI: 10.6084/m9.figshare.29269122.v1
title: Dual synthesis pathways of scaRNA28 via intronic processing of transformation/transcription domain-associated protein transcripts and a novel independent transcription unit

description: Small Cajal body-specific RNAs (scaRNAs) are noncoding RNAs involved in the maturation of U-rich small nuclear RNAs. Except for a few that have their own transcription units, most scaRNA genes are embedded in introns and are predicted to be transcribed with host genes. Herein, we report that scaRNA28 is the first scaRNA with a dual synthesis pathway, and that this RNA is transcribed in an independent transcription unit (ITU) by RNA polymerase II while located in intron 2 of the transformation/transcription domain-associated protein (TRRAP) gene. We evaluated the scaRNA28 synthesis pathway using minigenes containing exon 2, intron 2, and exon 3 of <i>TRRAP</i>. A minigene with a mutation preventing 5′ splicing recognition of the exon 2/intron 2 junction generated scaRNA28, suggesting a pathway processing unspliced transcripts into scaRNA28. Even promoterless minigenes and DNA fragments with regions from exons 2 to 3 of <i>TRRAP</i> showed RNA polymerase II-dependent synthesis of scaRNA28, indicating a novel synthesis pathway involving an ITU. Linker-scanning mutational analysis revealed that the promoter region required for scaRNA28 expression in the ITU is located within 60 bases including exon 2/intron 2 junction of <i>TRRAP</i>, and especially the first two bases of intron 2 region, a putative part of the MYC-binding (E-box) motif, are essential for scaRNA28 expression in the ITU. MYC promotes scaRNA28 expression by binding to the promoter region in the ITU. Our findings demonstrated a novel transcriptional pathway for the synthesis of scaRNA28, the first scaRNA with a dual synthesis pathway.
DOI: 10.6084/m9.figshare.30266345.v1
title: <i>miR-4484</i> suppresses hepatocellular carcinoma progression via targeting <i>KIF2C</i>

description: Aberrantly expressed microRNA-4484 (<i>miR-4484</i>) has recently garnered attention for its involvement in human diseases, but its specific role in hepatocellular carcinoma (HCC) remains largely unexplored. This study investigates the function of <i>miR-4484</i> in HCC progression and its regulatory interaction with <i>KIF2C</i>. Analysis of the data from the TCGA-LIHC database revealed that <i>miR-4484</i> expression is significantly downregulated in HCC tissues, with lower levels correlating with worse prognosis. <i>In vitro</i> experiments confirmed that <i>miR-4484</i> expression is lower in HCC cell lines compared to a normal liver cell line. Functional assays demonstrated that <i>miR-4484</i> overexpression via a <i>miR-4484</i> mimic suppressed cell proliferation and induced G1 phase arrest, whereas <i>miR-4484</i> inhibition promoted proliferation and facilitated cell cycle progression from G1 to S and G2 phases. Additionally, <i>KIF2C</i> expression was significantly upregulated in HCC tissues and cell lines, exhibiting an inverse correlation with <i>miR-4484</i> levels. Dual-Luciferase Reporter Assays confirmed that <i>miR-4484</i> directly binds to <i>KIF2C</i>, thereby regulating its expression and influencing cell proliferation and cell cycle progression. <i>In vivo</i>, subcutaneous intratumoral injection of the <i>miR-4484</i> mimic in nude mice significantly inhibited HCC tumour growth. These findings highlight <i>miR-4484</i> as a potential tumour suppressor in HCC through its direct targeting of <i>KIF2C</i>, underscoring its promise as a therapeutic target for HCC treatment.
DOI: 10.6084/m9.figshare.30315551
title: Precursor RNA structural patterns at SF3B1 mutation sensitive cryptic 3’ splice sites

description: SF3B1 is a core component of the spliceosome involved in branch point recognition and 3’ splice site selection. The SF3B1 K700E mutation (lysine to glutamic acid) is common in myelodysplastic syndrome and other blood disorders. SF3B1 K700E mutants utilize novel cryptic 3’ splice sites; however, the properties distinguishing SF3B1-sensitive splice junctions from other alternatively spliced junctions are unknown. We identify a subset of 192 cryptic 3’ splice junctions with significantly altered use in SF3B1 K700E cells, termed SF3B1-sensitive cryptic 3’ splice sites, and 2800 cryptic 3’ splice sites used in SF3B1 wild-type, termed SF3B1-resistant. We find that SF3B1-sensitive cryptic 3’ splice sites are embedded in extended polypyrimidine tracts. Furthermore, canonical splice sites paired to SF3B1-sensitive cryptic 3’ splice sites are significantly weaker than canonical 3’ splice sites paired to SF3B1-resistant cryptic 3’ splice sites. We test whether SF3B1-sensitive splice sites are structurally different from SF3B1-resistant 3’ splice sites using chemical probing. We develop experimental RNA structure data for 83 SF3B1-sensitive junctions and 39 SF3B1-resistant junctions. We find that the pattern of structural accessibility at the NAG splicing motif in cryptic and canonical 3’ splice sites is similar. However, the magnitude of accessibility differences is less in paired SF3B1-sensitive splice sites than in paired SF3B1-mutant splice sites. Additionally, SF3B1-sensitive splice junctions are more flexible than SF3B1-resistant junctions. Our results suggest that SF3B1-sensitive splice junctions have unique structure and sequence properties, containing poorly differentiated, weak splice sites that lead to altered 3’ splice site recognition in the presence of SF3B1 mutation.
DOI: 10.6084/m9.figshare.30315551.v1
title: Precursor RNA structural patterns at SF3B1 mutation sensitive cryptic 3’ splice sites

description: SF3B1 is a core component of the spliceosome involved in branch point recognition and 3’ splice site selection. The SF3B1 K700E mutation (lysine to glutamic acid) is common in myelodysplastic syndrome and other blood disorders. SF3B1 K700E mutants utilize novel cryptic 3’ splice sites; however, the properties distinguishing SF3B1-sensitive splice junctions from other alternatively spliced junctions are unknown. We identify a subset of 192 cryptic 3’ splice junctions with significantly altered use in SF3B1 K700E cells, termed SF3B1-sensitive cryptic 3’ splice sites, and 2800 cryptic 3’ splice sites used in SF3B1 wild-type, termed SF3B1-resistant. We find that SF3B1-sensitive cryptic 3’ splice sites are embedded in extended polypyrimidine tracts. Furthermore, canonical splice sites paired to SF3B1-sensitive cryptic 3’ splice sites are significantly weaker than canonical 3’ splice sites paired to SF3B1-resistant cryptic 3’ splice sites. We test whether SF3B1-sensitive splice sites are structurally different from SF3B1-resistant 3’ splice sites using chemical probing. We develop experimental RNA structure data for 83 SF3B1-sensitive junctions and 39 SF3B1-resistant junctions. We find that the pattern of structural accessibility at the NAG splicing motif in cryptic and canonical 3’ splice sites is similar. However, the magnitude of accessibility differences is less in paired SF3B1-sensitive splice sites than in paired SF3B1-mutant splice sites. Additionally, SF3B1-sensitive splice junctions are more flexible than SF3B1-resistant junctions. Our results suggest that SF3B1-sensitive splice junctions have unique structure and sequence properties, containing poorly differentiated, weak splice sites that lead to altered 3’ splice site recognition in the presence of SF3B1 mutation.
DOI: 10.1594/pangaea.957211
title: Multibeam bathymetry raw data (Kongsberg EM 122 entire dataset) of RV METEOR during cruise M176

description: Raw multibeam bathymetry data were collected aboard R/V Meteor during cruise M176 using a Kongsberg EM122 multibeam echosounder. The expedition took place during 2021-07-31 - 2021-08-29 from Emden - Emden (Germany) in the Northern Atlantic Ocean. Sound velocity profiles (SVP) were applied on the data for calibration. Please see environmental data and the cruise report for details. Due to technical issues of the echosounder that were encountered during the cruise, the data are erroneous. The data are unprocessed and can therefore contain incorrect depth measurements (artifacts) if not further processed. Note that refraction errors may occur when no proper SVP is applied. Acquisition and provision of the data are part of the DAM Underway Project.
description: These data should not be used for navigational purposes.
DOI: 10.1594/pangaea.964528
title: Multibeam bathymetry raw data (Atlas Hydrosweep DS echo sounder entire dataset) of RV METEOR during cruise M12/1

description: Multibeam bathymetry raw data using the ship's own Atlas Hydrographic Hydrosweep DS multibeam echo sounder was not continuously recorded during RV METEOR cruise M12/1. Data was recorded on 24 days between 1990-03-14 and 1990-04-13. This dataset contains a survey in the North and South Atlantic Ocean, covering mostly deep-water areas. The approximate average depth of the entire dataset is around 4200m.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, thus no SVP files are added to this dataset. Data analysis of the multibeam raw data could not reveal whether the SVP has been changed during the survey.This publication is conducted within the efforts of the German Marine Research Alliance in the core area 'Data management and Digitalization' (Deutsche Allianz Meeresforschung, DAM).Data are unprocessed and therefore contains incorrect depth measurements (artifacts) without further processing. Note that refraction errors can be expected due to the lack of proper SVP. Overall, it appears that the data quality is rather good to moderate since the gridded hillshade data showed relatively few obstacles. All files have been renamed from the suffix *.0 (stored at BSH) to *.dux.Data can be processed e.g. with the open source software package MB-System (Caress, D. W., and D. N. Chayes, MB-System: Mapping the Seafloor, http://www.mbari.org/products/research-software/mb-system/, 2022).
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).
DOI: 10.6084/m9.figshare.28889818
title: miRNA–mRNA integrated analysis reveals candidate genes associated with salt stress response in Halophytic <i>Sonneratia apetala</i>

description: <i>Sonneratia apetala</i> is a pioneering species of mangrove plants, which has evolved various mechanisms to tolerate salt-stress due to their long-term exposure to a salinized environment as compared to the of terrestrial freshwater plants. However, limited attempt has been made to uncover the underlying molecular mechanism of their saline adaptation. Here, we integrated mRNA and microRNA (miRNA) sequencing to identify the genes and pathways that may be involved in salt stress-response in the roots of <i>S. apetala</i>. A comprehensive full‑length transcriptome containing 295,501 high‑quality unigenes was obtained by PacBio sequencing technology. Of these, 6,686 genes exhibited significantly differential accumulation after salt stress treatment (<i>p</i> &lt; 0.001, <i>Q</i> &lt; 0.01). They were mainly implicated in plant signal transduction and diverse metabolic pathways, such as those involving phenylpropanoid biosynthesis, plant-pathogen interaction and protein processing. Also, our results identified the regulatory interaction between miRNA-target counterparts during salt stress. Taken together, we present the first global overview of the transcriptome of <i>S. apetala</i> roots, and identify potentially important genes and pathways associated with salt tolerance for further investigation. This study is expected to deliver novel insights in understanding the regulatory mechanism in <i>S. apetala</i> response to salt stress.
DOI: 10.6084/m9.figshare.28889818.v1
title: miRNA–mRNA integrated analysis reveals candidate genes associated with salt stress response in Halophytic <i>Sonneratia apetala</i>

description: <i>Sonneratia apetala</i> is a pioneering species of mangrove plants, which has evolved various mechanisms to tolerate salt-stress due to their long-term exposure to a salinized environment as compared to the of terrestrial freshwater plants. However, limited attempt has been made to uncover the underlying molecular mechanism of their saline adaptation. Here, we integrated mRNA and microRNA (miRNA) sequencing to identify the genes and pathways that may be involved in salt stress-response in the roots of <i>S. apetala</i>. A comprehensive full‑length transcriptome containing 295,501 high‑quality unigenes was obtained by PacBio sequencing technology. Of these, 6,686 genes exhibited significantly differential accumulation after salt stress treatment (<i>p</i> &lt; 0.001, <i>Q</i> &lt; 0.01). They were mainly implicated in plant signal transduction and diverse metabolic pathways, such as those involving phenylpropanoid biosynthesis, plant-pathogen interaction and protein processing. Also, our results identified the regulatory interaction between miRNA-target counterparts during salt stress. Taken together, we present the first global overview of the transcriptome of <i>S. apetala</i> roots, and identify potentially important genes and pathways associated with salt tolerance for further investigation. This study is expected to deliver novel insights in understanding the regulatory mechanism in <i>S. apetala</i> response to salt stress.
DOI: 10.1594/pangaea.964129
title: Multibeam bathymetry raw data (Atlas Hydrosweep DS echo sounder entire dataset) of RV METEOR during cruise M16/1

description: Multibeam bathymetry raw data using the ship's own Atlas Hydrographic Hydrosweep DS multibeam echo sounder was not continuously recorded during RV METEOR cruise M16/1. Data was recorded on 25 days between 1991-03-30 and 1991-04-24. This dataset contains a survey in the South Atlantic Ocean, also covering data around St. Helena. The approximate average depth of the entire dataset is around 4500m.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, thus no SVP files are added to this dataset. Data analysis of the multibeam raw data could not reveal whether the SVP has been changed during the survey.This publication is conducted within the efforts of the German Marine Research Alliance in the core area 'Data management and Digitalization' (Deutsche Allianz Meeresforschung, DAM).Data are unprocessed and therefore contains incorrect depth measurements (artifacts) without further processing. Note that refraction errors can be expected due to the lack of proper SVP. Overall, it appears that the data quality is rather moderate since the gridded hillshade data showed areas where the data coverage is occasionally interrupted. Note that the end date is wrong for file a031.dux (also indicated in the parameter "comment"). All files have been renamed from the suffix *.0 (stored at BSH) to *.dux.Data can be processed e.g. with the open source software package MB-System (Caress, D. W., and D. N. Chayes, MB-System: Mapping the Seafloor, http://www.mbari.org/products/research-software/mb-system/, 2022).
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).
DOI: 10.1594/pangaea.952353
title: Continuous thermosalinograph oceanography along RV POLARSTERN cruise track PS127

description: This dataset contains processed ocean temperature and salinity data at a depth of 11m along the cruise track. Raw data acquired by two SBE21 thermosalinographs and two auxiliary SBE38 temperature sensors (Sea-Bird Scientific, USA) installed in an underway seawater flow-through system on board RV Polarstern were processed to yield a calibrated and validated data set of temperature and salinity along the cruise track. Data were downloaded from DAVIS SHIP data base (https://dship.awi.de) at a resolution of 1 sec, and converted to temperature and conductivity using the pre-deployment factory calibration coefficients. The converted data were averaged to 1 min values, outliers were removed, and sensor drift was corrected using coefficients obtained from a post-season calibration performed at Sea-Bird at the end of the measurement season. Salinity was calculated from internal temperature, conductivity and pressure according to the PSS-78 Practical Salinity Scale. Processed data are provided as 1 min means of seawater temperature, conductivity and salinity, aligned with position data taken from the master track. Quality flags are appended according to the SeaDataNet Data Quality Control Procedures (version from May 2010). More details are described in the attached processing report.
DOI: 10.1594/pangaea.959029
title: Continuous thermosalinograph oceanography along RV SONNE cruise track SO290

description: Underway temperature and salinity data was collected along the cruise track with two autonomous measurement systems, called self-cleaning monitoring boxes (SMBs). Usually, the SMBs are changed after ~12 hours. While temperature is taken at the water inlet in about 4 m depth, salinity is estimated within the SMB from conductivity and interior temperature. No temperature and salinity calibration were performed. For details to all processing steps see Data Processing Report.
description: Salinity Offset SMB_A = -0.027799Not enough reliable sample data were available for SMB_B.
DOI: 10.6084/m9.figshare.29236728
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: 10.6084/m9.figshare.29236728.v2
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.959030
title: Continuous thermosalinograph oceanography along RV MARIA S. MERIAN cruise track MSM112

description: Underway temperature and salinity data was collected along the cruise track with two autonomous measurement systems. Usually, the systems are changed after 6-12 hours (the intervals changed throughout the cruise from 6 hours to 12 hours). While temperature is taken at the water inlet in about 6.5 m depth, salinity is estimated within the interior measurement container from conductivity and interior temperature. Temperature and salinity were calibrated against CTD data from 7 m depth. For details to all processing steps see Data Processing Report.