cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.1594/pangaea.963999
title: Multibeam bathymetry raw data (Atlas Hydrosweep DS 2 echo sounder entire dataset) of RV METEOR during cruise M37/1

description: Multibeam bathymetry raw data using the ship's own Atlas Hydrographic Hydrosweep DS 2 multibeam echo sounder was not continuously recorded during RV METEOR cruise M37/1. Data was recorded on 15 days between 1996-12-05 and 1996-12-19. This dataset contains a survey North Atlantic Ocean mostly in the area around the Canary Islands. The approximate average depth is around 3800 m and ranges between 90m (min depth) and 13000m (unplausible max depth).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.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 bad to good since the gridded hillshade data showed relatively few obstacles in shallow waters and bad data in deeper areas.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.28902015
title: The implication of non-AUG-initiated N-terminally extended proteoforms in cancer

description: Dysregulated translation is a hallmark of cancer, and recent genome-wide studies in tumour cells have uncovered widespread translation of non-canonical reading frames that often initiate at non-AUG codons. If an upstream non-canonical start site is located within a frame with an annotated coding sequence (CDS), such translation events can lead to the production of proteoforms with altered N-termini (PANTs). Certain examples of PANTs from oncogenes (e.g. c-MYC) and tumour suppressors (e.g. PTEN) have been previously linked to cancer. We have performed a systematic computational analysis on recently identified non-AUG initiation-derived N-terminal extensions of cancer-associated proteins, and we discuss how these extended proteoforms may acquire new oncogenic properties. We identified a loss of stability for the N-terminally extended proteoforms of oncogenes TCF-4 and SOX2. Furthermore, we discovered likely functional short linear motifs within the N-terminal extensions of oncogenes and tumour suppressors (SOX2, SUFU, SFPQ, TOP1 and SPEN/SHARP) that could provide an explanation for previously described functionalities or interactions of the proteins. In all, we identify novel cases where PANTs likely show different localization, functions, partner binding or turnover rates compared to the annotated proteoforms. Therefore, we propose that alterations in the stringency of translation initiation, often seen under conditions of cellular stress, may result in reprogramming of translation to generate novel PANTs that influence cancer progression.
DOI: 10.6084/m9.figshare.28902015.v1
title: The implication of non-AUG-initiated N-terminally extended proteoforms in cancer

description: Dysregulated translation is a hallmark of cancer, and recent genome-wide studies in tumour cells have uncovered widespread translation of non-canonical reading frames that often initiate at non-AUG codons. If an upstream non-canonical start site is located within a frame with an annotated coding sequence (CDS), such translation events can lead to the production of proteoforms with altered N-termini (PANTs). Certain examples of PANTs from oncogenes (e.g. c-MYC) and tumour suppressors (e.g. PTEN) have been previously linked to cancer. We have performed a systematic computational analysis on recently identified non-AUG initiation-derived N-terminal extensions of cancer-associated proteins, and we discuss how these extended proteoforms may acquire new oncogenic properties. We identified a loss of stability for the N-terminally extended proteoforms of oncogenes TCF-4 and SOX2. Furthermore, we discovered likely functional short linear motifs within the N-terminal extensions of oncogenes and tumour suppressors (SOX2, SUFU, SFPQ, TOP1 and SPEN/SHARP) that could provide an explanation for previously described functionalities or interactions of the proteins. In all, we identify novel cases where PANTs likely show different localization, functions, partner binding or turnover rates compared to the annotated proteoforms. Therefore, we propose that alterations in the stringency of translation initiation, often seen under conditions of cellular stress, may result in reprogramming of translation to generate novel PANTs that influence cancer progression.
DOI: 10.6084/m9.figshare.29423972
title: Comprehensive analysis of tRNA-derived fragment expression in endometriosis using PANDORA-seq technology

description: Endometriosis is a common gynaecological disease and there is no reliable non-invasive biomarker for its unknown pathogenesis. TRF is differentially expressed in a variety of cancers and is a new non-invasive biomarker. The aim of this study was to reveal the full landscape of tRF expression profile in endometriosis using PANDORA-seq, which will provide strong target support for early diagnosis and treatment. PANDORA-seq was used to detect the eutopic and ectopic endometrial tissues of 4 patients with ovarian endometriosis and 4 normal endometrial tissues in the control group, and qRT-PCR was performed to verify. The target genes of DEtRF were predicted by TargetScan and miRanda, and the potential functions of differential tRFs were studied by bioinformatics such as Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), so as to further elucidate the pathogenesis of endometriosis. Under the screening conditions of |Fold Change| ≥ 2 and Padj &lt; 0.05, a total of 13 common differentially expressed tRFs were identified when comparing the disease groups, defined as endometriosis-affected eutopic endometrial tissue (EU) and ectopic endometrial tissue (EC), with the control group consisting of eutopic endometrial tissue from normal uteri (EN). Eleven DEtRFs target genes were highly enriched in endometriosis-related signalling pathways, such as MAPK, Ras, p53 and mitophagy-related pathways. Differentially expressed tRF may be involved in the development of endometriosis by regulating target genes in MAPK and autophagy signalling pathways. DEtRF is expected to be a new non-invasive biomarker for endometriosis.
DOI: 10.6084/m9.figshare.29423972.v1
title: Comprehensive analysis of tRNA-derived fragment expression in endometriosis using PANDORA-seq technology

description: Endometriosis is a common gynaecological disease and there is no reliable non-invasive biomarker for its unknown pathogenesis. TRF is differentially expressed in a variety of cancers and is a new non-invasive biomarker. The aim of this study was to reveal the full landscape of tRF expression profile in endometriosis using PANDORA-seq, which will provide strong target support for early diagnosis and treatment. PANDORA-seq was used to detect the eutopic and ectopic endometrial tissues of 4 patients with ovarian endometriosis and 4 normal endometrial tissues in the control group, and qRT-PCR was performed to verify. The target genes of DEtRF were predicted by TargetScan and miRanda, and the potential functions of differential tRFs were studied by bioinformatics such as Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), so as to further elucidate the pathogenesis of endometriosis. Under the screening conditions of |Fold Change| ≥ 2 and Padj &lt; 0.05, a total of 13 common differentially expressed tRFs were identified when comparing the disease groups, defined as endometriosis-affected eutopic endometrial tissue (EU) and ectopic endometrial tissue (EC), with the control group consisting of eutopic endometrial tissue from normal uteri (EN). Eleven DEtRFs target genes were highly enriched in endometriosis-related signalling pathways, such as MAPK, Ras, p53 and mitophagy-related pathways. Differentially expressed tRF may be involved in the development of endometriosis by regulating target genes in MAPK and autophagy signalling pathways. DEtRF is expected to be a new non-invasive biomarker for endometriosis.
DOI: 10.1594/pangaea.964300
title: Master tracks in different resolutions of METEOR cruise M194, Jeddah - Piraeus, 2023-10-10 - 2023-11-07

description: Raw data acquired by position sensors on board RV METEOR during expedition M194 were processed to receive a validated master track which can be used as reference of further expedition data. During M194 the motion reference unit Kongsberg SeaTex AS MRU-5 combined with Kongsberg SeaTex AS Seapath 320 and two C and C Technologies GPS receivers C-NAV3050 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 "Other version" references.
DOI: 10.6084/m9.figshare.29756939
title: Dynamic shifts in isomiR profiles during parasite maturation of <i>Fasciola hepatica</i>

description: We investigated the isomiR profiles of the parasitic worm <i>Fasciola hepatica</i> across three developmental stages: newly excysted juveniles (NEJ), juveniles (JUV), and adults. Our analysis revealed a distinct shift in isomiR distribution during maturation, with NEJs exhibiting a higher abundance and diversity of isomiRs compared to later stages. Notably, isomiRs were often the dominant miRNA form in NEJs, whereas a transition to canonical miRNAs occurred as the parasite matured. This temporal variation suggests that isomiR expression may be linked to the parasite’s life cycle. We observed that truncated isomiRs were more prevalent, with uracil additions at the 3’end and adenosine at the 5’ end being most common. At least 10% of the miRNA population consisted of 5’ end isomiRs, which have the potential to redirect target interactions towards metabolic and developmental pathways. Furthermore, we show that the cleavage sites in <i>F. hepatica</i> primary miRNAs are similar to those found in mammalian cells, and Dicer-mediated cleavage appears to play a significant role in isomiR generation. We believe that the diversification of miRNA sequences through isomiR production is an evolutionary adaptation that enhances the parasite’s ability to tune gene expression during infection and development. This regulatory plasticity may facilitate successful infection and long-term persistence within diverse mammalian hosts. Understanding the roles of isomiRs in parasitic worms could provide new insights into parasite biology and identify potential targets for controlling parasitic infections.
DOI: 10.6084/m9.figshare.29756939.v1
title: Dynamic shifts in isomiR profiles during parasite maturation of <i>Fasciola hepatica</i>

description: We investigated the isomiR profiles of the parasitic worm <i>Fasciola hepatica</i> across three developmental stages: newly excysted juveniles (NEJ), juveniles (JUV), and adults. Our analysis revealed a distinct shift in isomiR distribution during maturation, with NEJs exhibiting a higher abundance and diversity of isomiRs compared to later stages. Notably, isomiRs were often the dominant miRNA form in NEJs, whereas a transition to canonical miRNAs occurred as the parasite matured. This temporal variation suggests that isomiR expression may be linked to the parasite’s life cycle. We observed that truncated isomiRs were more prevalent, with uracil additions at the 3’end and adenosine at the 5’ end being most common. At least 10% of the miRNA population consisted of 5’ end isomiRs, which have the potential to redirect target interactions towards metabolic and developmental pathways. Furthermore, we show that the cleavage sites in <i>F. hepatica</i> primary miRNAs are similar to those found in mammalian cells, and Dicer-mediated cleavage appears to play a significant role in isomiR generation. We believe that the diversification of miRNA sequences through isomiR production is an evolutionary adaptation that enhances the parasite’s ability to tune gene expression during infection and development. This regulatory plasticity may facilitate successful infection and long-term persistence within diverse mammalian hosts. Understanding the roles of isomiRs in parasitic worms could provide new insights into parasite biology and identify potential targets for controlling parasitic infections.
DOI: 10.1594/pangaea.964294
title: Continuous thermosalinograph oceanography along RV POLARSTERN cruise track PS135/1

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.30508558
title: RNA binding of GAPDH controls transcript stability and protein translation in acute myeloid leukemia

description: Dysregulation of RNA binding proteins (RBPs) is a hallmark in cancerous cells. In acute myeloid leukaemia (AML) RBPs are key regulators of tumour proliferation. While classical RBPs have defined RNA binding domains, RNA recognition and function in AML by non-canonical RBPs (ncRBPs) remain unclear. Given the inherent complexity of targeting AML broadly, our goal was to uncover potential ncRBP candidates critical for AML survival using a CRISPR/Cas-based screening. We identified the glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH) as a pro-proliferative factor in AML cells. Based on cross-linking and immunoprecipitation (CLIP), we are defining the global targetome, detecting novel RNA targets mainly located within 5’UTRs, including GAPDH, RPL13a, and PKM. The knockdown of GAPDH unveiled genetic pathways related to ribosome biogenesis, translation initiation, and regulation. Moreover, we demonstrated a stabilizing effect through GAPDH binding to target transcripts including its own mRNA. The present findings provide new insights on the RNA functions and characteristics of GAPDH in AML.
DOI: 10.6084/m9.figshare.30508558.v1
title: RNA binding of GAPDH controls transcript stability and protein translation in acute myeloid leukemia

description: Dysregulation of RNA binding proteins (RBPs) is a hallmark in cancerous cells. In acute myeloid leukaemia (AML) RBPs are key regulators of tumour proliferation. While classical RBPs have defined RNA binding domains, RNA recognition and function in AML by non-canonical RBPs (ncRBPs) remain unclear. Given the inherent complexity of targeting AML broadly, our goal was to uncover potential ncRBP candidates critical for AML survival using a CRISPR/Cas-based screening. We identified the glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH) as a pro-proliferative factor in AML cells. Based on cross-linking and immunoprecipitation (CLIP), we are defining the global targetome, detecting novel RNA targets mainly located within 5’UTRs, including GAPDH, RPL13a, and PKM. The knockdown of GAPDH unveiled genetic pathways related to ribosome biogenesis, translation initiation, and regulation. Moreover, we demonstrated a stabilizing effect through GAPDH binding to target transcripts including its own mRNA. The present findings provide new insights on the RNA functions and characteristics of GAPDH in AML.
DOI: 10.1594/pangaea.963223
title: Multibeam bathymetry raw data (Kongsberg EM 122 entire dataset) of RV MARIA S. MERIAN during cruise MSM103

description: Multibeam bathymetry raw data was recorded in the North Atlantic during cruise MSM103 that took place between and 2021-09-12 and 2021-11-15. The data was collected using the ship's own Kongsberg EM 122. Sound velocity profiles (SVP) were applied on the data for calibration. Please see environmental data (zip file) and the cruise report for details.
description: These data should not be used for navigational purposes.
DOI: 10.1594/pangaea.964262
title: Master tracks in different resolutions of METEOR cruise M193, Limassol - Jeddah, 2023-09-08 - 2023-10-06

description: Raw data acquired by position sensors on board RV METEOR during expedition M193 were processed to receive a validated master track which can be used as reference of further expedition data. During M193 the motion reference unit Kongsberg SeaTex AS MRU-5 combined with Kongsberg SeaTex AS Seapath 320 and two C and C Technologies GPS receivers C-NAV3050 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 "Other version" references.
DOI: 10.1594/pangaea.963579
title: Multibeam bathymetry raw data (Kongsberg EM 122 entire dataset) of RV METEOR during cruise M189/2

description: During M189/2 that took place in the Atlantic between 2023-05-16 and 2023-06-04, multibeam bathymetry raw data were recorded using the vessel's built-in Kongsberg EM122 echosounder. Sound velocity profiles (SVP) were applied on the data for calibration. Please see environmental data (zip file) and the cruise report for details.
description: These data should not be used for navigational purposes.
DOI: 10.6084/m9.figshare.28142778
title: Expanding the immune-related targetome of miR-155-5p by integrating time-resolved RNA patterns into miRNA target prediction

description: The lack of a sufficient number of validated miRNA targets severely hampers the understanding of their biological function. Even for the well-studied miR-155-5p, there are only 239 experimentally validated targets out of 42,554 predicted targets. For a more complete assessment of the immune-related miR-155 targetome, we used an inverse correlation of time-resolved mRNA profiles and miR-155-5p expression of early CD4+ T cell activation to predict immune-related target genes. Using a high-throughput miRNA interaction reporter (HiTmIR) assay we examined 90 target genes and confirmed 80 genes as direct targets of miR-155-5p. Our study increases the current number of verified miR-155-5p targets approximately threefold and exemplifies a method for verifying miRNA targetomes as a prerequisite for the analysis of miRNA-regulated cellular networks.
DOI: 10.6084/m9.figshare.28142778.v1
title: Expanding the immune-related targetome of miR-155-5p by integrating time-resolved RNA patterns into miRNA target prediction

description: The lack of a sufficient number of validated miRNA targets severely hampers the understanding of their biological function. Even for the well-studied miR-155-5p, there are only 239 experimentally validated targets out of 42,554 predicted targets. For a more complete assessment of the immune-related miR-155 targetome, we used an inverse correlation of time-resolved mRNA profiles and miR-155-5p expression of early CD4+ T cell activation to predict immune-related target genes. Using a high-throughput miRNA interaction reporter (HiTmIR) assay we examined 90 target genes and confirmed 80 genes as direct targets of miR-155-5p. Our study increases the current number of verified miR-155-5p targets approximately threefold and exemplifies a method for verifying miRNA targetomes as a prerequisite for the analysis of miRNA-regulated cellular networks.
DOI: 10.1594/pangaea.954995
title: Multibeam bathymetry raw data (Kongsberg EM710 entire dataset) of RV SONNE during cruise SO270

description: Multibeam bathymetry raw data using the ship's own Kongsberg EM 710 multibeam echosounder was not continuously recorded during RV SONNE cruise SO270. Data was recorded on 26 days between 2019-09-23 and 2019-10-19. This dataset a survey data covering the Saya de Malha Bank and Sommerville Bank with shallow water depth. The approximate average depth of the entire dataset is around 300m.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).