cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.30621274.v2
title: Systematic mapping of small nucleolar RNA interactions in human cells

description: Altered expression of box C/D small nucleolar RNAs (snoRNAs) is implicated in human diseases, including cancer. Box C/D snoRNAs canonically direct site-specific, 2’-<i>O</i>-methylation but the extent to which they participate in other functions remains unclear. To identify RNA interactions of box C/D snoRNAs in human cells, we applied two techniques based on UV crosslinking, proximity ligation and sequencing of RNA hybrids (CLASH and FLASH). These identified hundreds of novel snoRNA interactions with rRNA, snoRNAs and mRNAs. We developed an informatic pipeline to rigorously call interactions predicted to direct methylation. Multiple snoRNA-rRNA interactions identified were not predicted to direct RNA methylation. These potentially modulate methylation efficiency and/or contribute to folding dynamics during ribosomal subunit biogenesis. snoRNA-mRNA hybrids included 1,300 interactions between 117 snoRNA families and 940 mRNAs. Human U3 is substantially more abundant than other snoRNAs and represented about 50% of snoRNA-mRNA hybrids. The distribution of U3 interactions across mRNAs also differed from other snoRNAs. Following U3 depletion, mRNAs showing altered abundance were strongly enriched for U3 CLASH interactions. Most human snoRNAs are excised from pre-mRNA introns. Enrichment for snoRNA association with branch point regions of introns that contain snoRNA genes was common, suggesting widespread regulation of snoRNA maturation. Dataset for human snoRNA interactionsPipeline for calling methylation guidesrRNA modification sites are targeted by competing, non-guide snoRNAsSplicing signals in introns that encode snoRNAs are preferentially targeted for snoRNA binding Dataset for human snoRNA interactions Pipeline for calling methylation guides rRNA modification sites are targeted by competing, non-guide snoRNAs Splicing signals in introns that encode snoRNAs are preferentially targeted for snoRNA binding
DOI: 10.1594/pangaea.927128
title: Multibeam bathymetry raw data (Kongsberg EM 122 entire dataset) of RV MARIA S. MERIAN during cruise MSM30

description: Multibeam bathymetry raw data using the ship's own Kongsberg EM 122 multibeam echosounder was almost continuously recorded during RV MARIA S. MERIAN cruise MSM30. Data was recorded on 25 days between 2013-07-17 and 2013-08-14. This dataset contains a survey in the North Atlantic Ocean south of Svalbard. The approximate average depth of the entire dataset is around 1200m.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. Ancillary sound velocity profiles (SVP) files from the cruise are archived at the BSH, thus SVP files are added to this dataset. Also data analysis of the multibeam raw data revealed that 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 since the gridded hillshade data showed relatively few obstacles. However, a few files are of bad data quality. The reason is unknown.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.962923
title: Continuous thermosalinograph oceanography along RV MARIA S. MERIAN cruise track MSM114/2

description: Underway temperature and salinity data was collected along the cruise track with two autonomous measurement systems. Usually, the systems are changed after 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. Neither temperature nor salinity calibration was performed. For details to all processing steps see Data Processing Report.
DOI: 10.6084/m9.figshare.30621274.v1
title: Systematic mapping of small nucleolar rna interactions in human cells

description: Altered expression of box C/D small nucleolar RNAs (snoRNAs) is implicated in human diseases, including cancer. Box C/D snoRNAs canonically direct site-specific, 2’-<i>O</i>-methylation but the extent to which they participate in other functions remains unclear. To identify RNA interactions of box C/D snoRNAs in human cells, we applied two techniques based on UV crosslinking, proximity ligation and sequencing of RNA hybrids (CLASH and FLASH). These identified hundreds of novel snoRNA interactions with rRNA, snoRNAs and mRNAs. We developed an informatic pipeline to rigorously call interactions predicted to direct methylation. Multiple snoRNA-rRNA interactions identified were not predicted to direct RNA methylation. These potentially modulate methylation efficiency and/or contribute to folding dynamics during ribosomal subunit biogenesis. snoRNA-mRNA hybrids included 1,300 interactions between 117 snoRNA families and 940 mRNAs. Human U3 is substantially more abundant than other snoRNAs and represented about 50% of snoRNA-mRNA hybrids. The distribution of U3 interactions across mRNAs also differed from other snoRNAs. Following U3 depletion, mRNAs showing altered abundance were strongly enriched for U3 CLASH interactions. Most human snoRNAs are excised from pre-mRNA introns. Enrichment for snoRNA association with branch point regions of introns that contain snoRNA genes was common, suggesting widespread regulation of snoRNA maturation. Dataset for human snoRNA interactionsPipeline for calling methylation guidesrRNA modification sites are targeted by competing, non-guide snoRNAsSplicing signals in introns that encode snoRNAs are preferentially targeted for snoRNA binding Dataset for human snoRNA interactions Pipeline for calling methylation guides rRNA modification sites are targeted by competing, non-guide snoRNAs Splicing signals in introns that encode snoRNAs are preferentially targeted for snoRNA binding
DOI: 10.1594/pangaea.944651
title: Multibeam bathymetry raw data (Atlas Hydrosweep DS echo sounder entire dataset) of RV SONNE during cruise SO97/2

description: Raw multibeam bathymetry data were collected aboard RV Sonne during cruise SO97/2 using an Atlas Hydrosweep DS multibeam echosounder. The expedition took place during 1994-08-24 and 1994-09-05 from Dutch Harbour, USA to Tokyo, Japan in the Pacific Ocean. Data were recorded outside EEZs at an average depth of approximately 3000m. The data are unedited and come in .0/ dux format which is equivalent to the mbsystem .mb21 format. There is no information about sound velocity correction made. There are no extra SVP files provided in this publication. Data are unprocessed and can therefore contain incorrect depth measurements (artifacts) if not further processed. Note that refraction errors can be expected due to the lack of proper SVP. The data are stored at the Federal Maritime and Hydrographic Agency of Germany (Bundesamt für Seeschifffahrt und Hydrographie, BSH) and have been submitted to PANGAEA database for data curation and publication.
DOI: 10.1594/pangaea.959836
title: Water column raw data (Kongsberg EM 122 entire dataset) of RV MARIA S. MERIAN during cruise MSM30

description: Water column raw data using the ship's own Kongsberg EM 122 multibeam echosounder was recorded on 25 days between 2013-07-17 and 2013-08-14 RV MARIA S: MERIAN cruise MSM30 in the North Atlantic Ocean south of Svalbard. The data were continuously recorded along the .all file storage of the corresponding multibeam raw dataset https://doi.org/10.1594/PANGAEA.945591.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. Ancillary sound velocity profiles (SVP) files from the cruise are archived at the BSH and added to raw dataset https://doi.org/10.1594/PANGAEA.945591. 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).
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.30295449
title: DeepRNA-Reg: a deep-learning based approach for comparative analysis of CLIP experiments

description: DeepRNA-Reg employs advances in deep learning to enable high-fidelity comparative analysis of paired datasets of high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (HITS-CLIP). In a HITS-CLIP experimental paradigm where Ago2 targeting is selectively perturbed via gene knock-out of a microRNA cluster, DeepRNA-Reg offers a superior prediction set when compared with the current best prescription for differential HITS-CLIP analysis. Furthermore, DeepRNA-Reg predictions adhered better to the ground-truth of RNA primary and secondary structural motifs that enable miRNA-mediated targeting of RNA. In the tested data sets, DeepRNA-Reg uncovered novel mediators in the mechanism of microRNA-mediated restraint of type-2 immunity in T-Helper 2 cells. In a comparative analysis, DeepRNA-Reg predictions show greater translatability across distinct biological milieux, offering prediction sets with wide applicability for investigators.
DOI: 10.6084/m9.figshare.30295449.v1
title: DeepRNA-Reg: a deep-learning based approach for comparative analysis of CLIP experiments

description: DeepRNA-Reg employs advances in deep learning to enable high-fidelity comparative analysis of paired datasets of high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (HITS-CLIP). In a HITS-CLIP experimental paradigm where Ago2 targeting is selectively perturbed via gene knock-out of a microRNA cluster, DeepRNA-Reg offers a superior prediction set when compared with the current best prescription for differential HITS-CLIP analysis. Furthermore, DeepRNA-Reg predictions adhered better to the ground-truth of RNA primary and secondary structural motifs that enable miRNA-mediated targeting of RNA. In the tested data sets, DeepRNA-Reg uncovered novel mediators in the mechanism of microRNA-mediated restraint of type-2 immunity in T-Helper 2 cells. In a comparative analysis, DeepRNA-Reg predictions show greater translatability across distinct biological milieux, offering prediction sets with wide applicability for investigators.
DOI: 10.1594/pangaea.954994
title: Water column raw data (Kongsberg EM 122 entire dataset) of RV SONNE during cruise SO270

description: Water column raw data using the ship's own Kongsberg EM 122 multibeam echosounder was not continuously recorded during RV SONNE cruise SO270. Data was only recorded on 4 days between 2019-10-04 and 2019-10-22 in the Indian Ocean at the Saya de Malha Bank / Sommerville Bank.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. Ancillary sound velocity profiles (SVP) files from the cruise are archived at the BSH and added to the corresponding multibeam raw dataset doi:10.1594/PANGAEA.954993This 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).
DOI: 10.1594/pangaea.964269
title: Continuous thermosalinograph oceanography along RV POLARSTERN cruise track PS131

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.28631862
title: Wide-spectrum profiling of plasma cell-free RNA and the potential for health-monitoring

description: Circulating cell-free RNA (cfRNA) has emerged as a promising analyte for disease detection. However, the comprehensive profiling of diverse cfRNA types remains under-characterized. Here, we applied a new wide-spectrum cfRNA sequencing method and simultaneously captured rRNA, tRNA, mRNA, miRNA, lncRNA and all mitochondrial RNA. The cfRNA compositions, size distributions and highly abundant cfRNA genes were analysed for each type of cfRNA. We depicted the cfRNA cell types of origin profiles of 66 generally healthy individuals and found that BMI showed a significant impact on the kidney-derived cfRNA proportion. Three individuals with some liver problems were identified because of relatively high levels of hepatocyte-specific cfRNA. The abundance levels of different genes and RNA types, including mRNA, miRNA and lncRNA, were significantly correlated with the liver function test results. The genes of individual cfRNA variances were enriched in pathways associated with common diseases such as liver diseases, virus infections, cancers and metabolic diseases. This study provided a profiling of cfRNA and displayed the potential of cfRNA as a biomarker in health monitoring.
DOI: 10.6084/m9.figshare.28631862.v1
title: Wide-spectrum profiling of plasma cell-free RNA and the potential for health-monitoring

description: Circulating cell-free RNA (cfRNA) has emerged as a promising analyte for disease detection. However, the comprehensive profiling of diverse cfRNA types remains under-characterized. Here, we applied a new wide-spectrum cfRNA sequencing method and simultaneously captured rRNA, tRNA, mRNA, miRNA, lncRNA and all mitochondrial RNA. The cfRNA compositions, size distributions and highly abundant cfRNA genes were analysed for each type of cfRNA. We depicted the cfRNA cell types of origin profiles of 66 generally healthy individuals and found that BMI showed a significant impact on the kidney-derived cfRNA proportion. Three individuals with some liver problems were identified because of relatively high levels of hepatocyte-specific cfRNA. The abundance levels of different genes and RNA types, including mRNA, miRNA and lncRNA, were significantly correlated with the liver function test results. The genes of individual cfRNA variances were enriched in pathways associated with common diseases such as liver diseases, virus infections, cancers and metabolic diseases. This study provided a profiling of cfRNA and displayed the potential of cfRNA as a biomarker in health monitoring.
DOI: 10.6084/m9.figshare.29517702
title: Fusion transcripts landscape in hepatocellular carcinoma and potential impact on the expression of fusion partners

description: Fusion transcripts (FTs) are RNA molecules, also known as chimeric transcripts, formed through chromosomal rearrangements or transcriptional processes, contributing to tumorigenesis. This study systematically examined tumour-specific FTs in hepatocellular carcinoma (HCC) using high-throughput RNA sequencing data from independent datasets and The Cancer Genome Atlas (TCGA). Our <i>meta cohort</i> analysis included 328 HCC samples. Using STAR-Fusion, we identified 15 novel tumour-specific FTs, with SERPINA1-H19 as the most recurrent fusion event. Comparative expression analysis of fusion partner genes revealed significant downregulation in HCC tumours relative to normal adjacent liver tissues (NAT). We validated the expression levels of the key partner genes with 436 TCGA samples serving as an <i>in silico validation cohort</i> and in <i>wet lab validation cohorts</i> with 42 samples. ALB, APOA2, IGF2, MT2A, SERPINA1, and H19, which are key liver-associated genes, were frequently involved in tumour-specific fusion events suggesting either a loss of tumour suppressor property or gaining a novel function playing a role in hepatocarcinogenesis. Detailed characterization of SERPINA1-H19 identified 16 transcript variants with distinct structural modifications that may impact its functional output. Furthermore, low expression of SERPINA1 and H19 was associated with more aggressive HCC phenotypes. Overall, this study established a comprehensive repository of FTs for the first time, offering valuable insights into their role in HCC and their potential to serve as diagnostic and prognostic biomarkers for HCC.
DOI: 10.1594/pangaea.954993
title: Multibeam bathymetry raw data (Kongsberg EM 122 entire dataset) of RV SONNE during cruise SO270

description: Multibeam bathymetry raw data using the ship's own Kongsberg EM 122 multibeam echosounder was almost continuously recorded during RV SONNE cruise SO270. Data was recorded on 40 days between 2019-09-13 and 2019-10-22. This dataset contains an elongated transit survey in the Indian Ocean over the Mid-Idian Ocean Basin also crossing the Fuji Seamount (mainly deep sea area's). In addition, this dataset contains survey data from the Saya de Malha Bank and Sommerville Bank with shallow water depth. The approximate average depth of the entire dataset is around 4100m.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. Ancillary sound velocity profiles (SVP) files from the cruise are archived at the BSH, thus SVP files are added to this dataset. Also data analysis of the multibeam raw data revealed that 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 since the gridded hillshade data showed relatively few obstacles.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.28652454
title: Nucleolar ribosomal RNA synthesis continues in differentiating lens fiber cells until abrupt nuclear degradation required for ocular lens transparency

description: Cellular differentiation requires highly coordinated action of all three transcriptional systems to produce rRNAs, mRNAs and various ‘short’ and ‘long’ non-coding RNAs by RNA Polymerase I, II and III systems, respectively. RNA Polymerase I catalyzes transcription of about 400 copies of mammalian rDNA genes, generating 18S, 5.8S and 28S rRNA molecules. Lens fiber cell differentiation is a unique process to study transcriptional mechanisms of individual crystallin genes as their very high transcriptional outputs are directly comparable only to globin genes in erythrocytes. Importantly, both terminally differentiated lens fiber cells and mammalian erythrocytes degrade their nuclei through different mechanisms. In lens, the generation of the organelle-free zone (OFZ) includes the degradation of mitochondria, endoplasmic reticulum, Golgi apparatus and nuclei. Here, using RNA fluorescence <i>in situ</i> hybridization (FISH), we evaluated nascent rRNA transcription, located in the nucleoli, during the process of mouse lens fiber cell differentiation. Lens fiber cell nuclei undergo morphological changes including chromatin condensation prior to their denucleation. Remarkably, nascent rRNA transcription persists in all nuclei that are in direct proximity of the OFZ. Additionally, changes in both nuclei and nucleoli shape were evaluated via immunofluorescence detection of fibrillarin, nucleolin, UBF and other proteins. These studies demonstrate for the first time that highly condensed lens fiber cell nuclei have the capacity to support nascent rRNA transcription. Thus, we propose that ‘late’ production of rRNA molecules and consequently of ribosomes increases crystallin protein synthesis machinery within the mature lens fibers.
DOI: 10.6084/m9.figshare.28652454.v1
title: Nucleolar ribosomal RNA synthesis continues in differentiating lens fiber cells until abrupt nuclear degradation required for ocular lens transparency

description: Cellular differentiation requires highly coordinated action of all three transcriptional systems to produce rRNAs, mRNAs and various ‘short’ and ‘long’ non-coding RNAs by RNA Polymerase I, II and III systems, respectively. RNA Polymerase I catalyzes transcription of about 400 copies of mammalian rDNA genes, generating 18S, 5.8S and 28S rRNA molecules. Lens fiber cell differentiation is a unique process to study transcriptional mechanisms of individual crystallin genes as their very high transcriptional outputs are directly comparable only to globin genes in erythrocytes. Importantly, both terminally differentiated lens fiber cells and mammalian erythrocytes degrade their nuclei through different mechanisms. In lens, the generation of the organelle-free zone (OFZ) includes the degradation of mitochondria, endoplasmic reticulum, Golgi apparatus and nuclei. Here, using RNA fluorescence <i>in situ</i> hybridization (FISH), we evaluated nascent rRNA transcription, located in the nucleoli, during the process of mouse lens fiber cell differentiation. Lens fiber cell nuclei undergo morphological changes including chromatin condensation prior to their denucleation. Remarkably, nascent rRNA transcription persists in all nuclei that are in direct proximity of the OFZ. Additionally, changes in both nuclei and nucleoli shape were evaluated via immunofluorescence detection of fibrillarin, nucleolin, UBF and other proteins. These studies demonstrate for the first time that highly condensed lens fiber cell nuclei have the capacity to support nascent rRNA transcription. Thus, we propose that ‘late’ production of rRNA molecules and consequently of ribosomes increases crystallin protein synthesis machinery within the mature lens fibers.