cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.1594/pangaea.962742
title: Master tracks in different resolutions of SONNE cruise SO297, Talcahuano - Guayaquil, 2023-02-24 - 2023-04-11

description: Raw data acquired by position sensors on board RV SONNE during expedition SO297 were processed to receive a validated master track which can be used as reference of further expedition data. During SO297 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 "Other version" references.
DOI: 10.6084/m9.figshare.29364084
title: Early posttranscriptional response to tetracycline exposure in a gram-negative soil bacterium reveals unexpected attenuation mechanism of a DUF1127 gene

description: The gram-negative, soil-dwelling plant symbiont <i>Sinorhizobium meliloti</i> shares its free-living habitat with antibiotic producers. To learn about early steps of its adaptation to antibiotics, we analysed transcriptome changes after 10 min exposure to subinhibitory amount of tetracycline (Tc). RNA-seq revealed 297 differentially expressed genes. Besides ten upregulated ribosomal genes, there was no recognizable functional pattern in the observed changes. However, polar differential expression pattern was observed: Mostly, upregulated genes were first and downregulated genes downstream in operons. Furthermore, we detected mRNA stabilization upon Tc exposure for several up- and down-regulated genes. Thus, mRNA stabilization contributed to increased mRNA levels, but for downstream genes its effect was probably counteracted by premature transcriptional termination caused by disrupted coupling between transcription and translation. Using reporter constructs, we found that a DUF1127 gene, showing highest mRNA increase, is controlled by transcription attenuation depending on the translation of an upstream ORF (uORF). Our data suggest the following model: The attenuation strongly depends on the accessibility of C-rich codons at the beginning of the uORF. The accessibility is guaranteed by translation of the uORF, and is possible in a time window after a ribosome moves downstream and before a next ribosome occupies the ribosomal binding site (RBS). The accessibility is blocked either by impaired translation initiation or, in the absence of ribosome binding, by base-pairing between the RBS and the C-rich codons. We propose that this is used by bacteria to monitor ribosome availability and translation efficiency, and to ensure reciprocal expression of the DUF1127 gene.
DOI: 10.6084/m9.figshare.29364084.v1
title: Early posttranscriptional response to tetracycline exposure in a gram-negative soil bacterium reveals unexpected attenuation mechanism of a DUF1127 gene

description: The Gram-negative, soil-dwelling plant symbiont <i>Sinorhizobium meliloti</i> shares its free-living habitat with antibiotic producers. To learn about early steps of its adaptation to antibiotics, we analysed transcriptome changes after 10 min exposure to subinhibitory amount of tetracycline (Tc). RNA-seq revealed 297 differentially expressed genes. Besides ten upregulated ribosomal genes, there was no recognizable functional pattern in the observed changes. However, polar differential expression pattern was observed: Mostly, upregulated genes were first and downregulated genes downstream in operons. Furthermore, we detected mRNA stabilization upon Tc exposure for several up- and down-regulated genes. Thus, mRNA stabilization contributed to increased mRNA levels, but for downstream genes its effect was probably counteracted by premature transcriptional termination caused by disrupted coupling between transcription and translation. Using reporter constructs, we found that a DUF1127 gene, showing highest mRNA increase, is controlled by transcription attenuation depending on the translation of an upstream ORF (uORF). Our data suggest the following model: The attenuation strongly depends on the accessibility of C-rich codons at the begin of the uORF. The accessibility is guaranteed by translation of the uORF, and is possible in a time window after a ribosome moves downstream and before a next ribosome occupies the ribosomal binding site (RBS). The accessibility is blocked either by impaired translation initiation or, in the absence of ribosome binding, by base-pairing between the RBS and the C-rich codons. We propose that this is used by bacteria to monitor ribosome availability and translation efficiency, and to ensure reciprocal expression of the DUF1127 gene.
DOI: 10.6084/m9.figshare.29364084.v2
title: Early posttranscriptional response to tetracycline exposure in a gram-negative soil bacterium reveals unexpected attenuation mechanism of a DUF1127 gene

description: The gram-negative, soil-dwelling plant symbiont <i>Sinorhizobium meliloti</i> shares its free-living habitat with antibiotic producers. To learn about early steps of its adaptation to antibiotics, we analysed transcriptome changes after 10 min exposure to subinhibitory amount of tetracycline (Tc). RNA-seq revealed 297 differentially expressed genes. Besides ten upregulated ribosomal genes, there was no recognizable functional pattern in the observed changes. However, polar differential expression pattern was observed: Mostly, upregulated genes were first and downregulated genes downstream in operons. Furthermore, we detected mRNA stabilization upon Tc exposure for several up- and down-regulated genes. Thus, mRNA stabilization contributed to increased mRNA levels, but for downstream genes its effect was probably counteracted by premature transcriptional termination caused by disrupted coupling between transcription and translation. Using reporter constructs, we found that a DUF1127 gene, showing highest mRNA increase, is controlled by transcription attenuation depending on the translation of an upstream ORF (uORF). Our data suggest the following model: The attenuation strongly depends on the accessibility of C-rich codons at the beginning of the uORF. The accessibility is guaranteed by translation of the uORF, and is possible in a time window after a ribosome moves downstream and before a next ribosome occupies the ribosomal binding site (RBS). The accessibility is blocked either by impaired translation initiation or, in the absence of ribosome binding, by base-pairing between the RBS and the C-rich codons. We propose that this is used by bacteria to monitor ribosome availability and translation efficiency, and to ensure reciprocal expression of the DUF1127 gene.
DOI: 10.6084/m9.figshare.29929420
title: Developing the risk prediction model (ProlncSig) from lipoxygenase pathway-related lncRNAs for prognosis prediction in breast cancer

description: Alterations in cellular metabolism are known to play a crucial role in the development and progression of cancer. The lipoxygenase pathway, which controls unsaturated fatty acid metabolism, has been shown to regulate tumour progression and is commonly altered in breast cancer. In this study, we first obtained 11 lipoxygenase pathway genes from the Molecular Signatures Database (MSigDB). We then explored the lipoxygenase pathway-related long non-coding RNAs (lncRNAs) in breast cancer tissues from The Cancer Genome Atlas (TCGA) database. Information from our analysis was used to construct a risk prediction model (ProlncSig) to predict breast cancer prognosis. We found that ProlncSig could accurately identify breast cancer patients that had significantly shorter overall survival from those that had longer overall survival. Moreover, ProlncSig performs better in predicting prognosis than the clinicopathological features. Furthermore, GO and KEGG enrichment analysis showed that ProlncSig risk score had a high correlation with immune signature. We developed and validated an accurate prognostic risk prediction model (ProlncSig) based on lipoxygenase pathway-related lncRNAs, which has strong potential to provide prognostic information and may provide novel guidance for immunotherapeutic strategies for breast cancer patients.
DOI: 10.6084/m9.figshare.29929420.v1
title: Developing the risk prediction model (ProlncSig) from lipoxygenase pathway-related lncRNAs for prognosis prediction in breast cancer

description: Alterations in cellular metabolism are known to play a crucial role in the development and progression of cancer. The lipoxygenase pathway, which controls unsaturated fatty acid metabolism, has been shown to regulate tumour progression and is commonly altered in breast cancer. In this study, we first obtained 11 lipoxygenase pathway genes from the Molecular Signatures Database (MSigDB). We then explored the lipoxygenase pathway-related long non-coding RNAs (lncRNAs) in breast cancer tissues from The Cancer Genome Atlas (TCGA) database. Information from our analysis was used to construct a risk prediction model (ProlncSig) to predict breast cancer prognosis. We found that ProlncSig could accurately identify breast cancer patients that had significantly shorter overall survival from those that had longer overall survival. Moreover, ProlncSig performs better in predicting prognosis than the clinicopathological features. Furthermore, GO and KEGG enrichment analysis showed that ProlncSig risk score had a high correlation with immune signature. We developed and validated an accurate prognostic risk prediction model (ProlncSig) based on lipoxygenase pathway-related lncRNAs, which has strong potential to provide prognostic information and may provide novel guidance for immunotherapeutic strategies for breast cancer patients.
DOI: 10.1594/pangaea.962171
title: Master tracks in different resolutions of Maria S. Merian cruise MSM114/2, Mindelo - Punta Arenas, 2023-01-23 - 2023-02-22

description: Raw data acquired by position sensors on board RV MERIAN during expedition MSM114/2 were processed to receive a validated master track which can be used as reference of further expedition data. During MSM114/2 the motion reference unit Kongsberg SeaTex AS MRU-5 combined with Kongsberg SeaTex AS Seapath 320 and the GPS receivers Trimble SPS855 and SAAB R4 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.962557
title: Continuous thermosalinograph oceanography along RV METEOR cruise track M156

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. Temperature and salinity were calibrated against CTD data from 5 m depth. For details to all processing steps see Data Processing Report.
description: Temperature was calibrated independently for both TSGs against CTD data from 5 m depth. Value added to temperature data TSG1 = -0.012168. Value added to temperature data TSG2 = -0.005092.Salinity was calibrated independently for both TSGs against CTD data from 5 m depth (tim is the time in days since Expocode of this cruise (06M320190703), i.e. since 2019-07-03T00:00:00): Value added to salinity data TSG1 = 0.0003976*tim+0.02588. A regime shift was observed for TSG2 during the cruise. Therefore, the calibration was split. Value added to TSG2 salinity data before 2019-07-19T17:58:00: 0.0009344*tim+0.01213. Valued added to TSG2 salinity data from timestep 2019-07-19T17:58:00 and ongoing: 0.0019887*tim-0.03591.
DOI: 10.1594/pangaea.962731
title: Shipboard ADCP current measurements (75 kHz) during RV MARIA S. MERIAN cruise MSM116

description: Current velocities of the upper water column along the cruise track of R/V Maria S. Merian cruise MSM116 were collected by a vessel-mounted 75 kHz RDI Ocean Surveyor ADCP. The ADCP transducer was located at 6.0 m below the water line. The instrument was operated in narrowband mode (WM10) with a bin size of 8.00 m, a blanking distance of 8.00 m, and a total of 100 bins, covering the depth range between 22.0 m and 814.0 m. Beam velocities as recorded by the data acquistion software VmDAS were transformed to ship coordinates and after merging with the navigation data from the ship's Motion Reference Unit and Global Positioning systems into earth coordinates. Single-ping data / ping ensembles were screened for bottom signals and, where appropriate, a bottom mask was manually processed. The ship's velocity was calculated from position fixes obtained by the Global Positioning System (GPS). Accuracy of the ADCP velocities mainly depends on the quality of the position fixes and the ship's heading data. Further errors stem from a misalignment of the transducer with the ship's centerline. Data post-processing included water track calibration of the misalignment angle (-47.4945° +/- 0.5545°) and scale factor (1.0045 +/- 0.0101) of the Ocean Surveyor signal. The velocity data were averaged in time using an average interval of 60 s. Velocity quality flagging is based on following threshold criteria: abs(UC) or abs(VC) &gt; 1.5 m/s, rms(UC_z) or rms(VC_z) &gt; 0.3.
DOI: 10.6084/m9.figshare.30272688
title: Altering rRNA 2’O-methylation pattern during neuronal differentiation is regulated by FMRP

description: The Fragile X Messenger Ribonucleoprotein (FMRP) is a selective RNA-binding protein that localizes to the cytoplasm and the nucleus. The loss of FMRP results in Fragile X Syndrome (FXS), an autism spectrum disorder. FMRP interacts with ribosomes and regulates the translation of mRNAs essential for neuronal development and synaptic plasticity. However, the biochemical nature of this translation regulation is unknown. Here, we report that a potential feature of FMRP-mediated translation regulation during neuronal differentiation is the modulation of 2’-O-methylation of ribosomal RNA. 2’O-methylation, facilitated by C/D box snoRNAs in the nucleus, is a major epitranscriptome mark on rRNA, essential for ribosome assembly and function. We found that FMRP influences a distinct rRNA 2’O-Methylation pattern across neuronal differentiation. We show that in H9 ESCs, FMRP interacts with a selected set of C/D box snoRNA in the nucleus, resulting in the generation of ribosomes with a distinct pattern of rRNA 2’O-Methylation. This epitranscriptome pattern on rRNA undergoes a significant change during the differentiation of ESCs to neuronal precursors and cortical neurons. ESCs exhibit substantial levels of hypomethylated residues on rRNA, which progressively decrease in neuronal precursors and post-mitotic cortical neurons. This reduction correlates with changes in global protein synthesis across different stages of differentiation. Importantly, this stepwise change in the 2’O-methylation pattern during neuronal differentiation is altered in the absence of FMRP, which could impact neuronal development and contribute to dysregulated protein synthesis observed in Fragile X Syndrome.
DOI: 10.6084/m9.figshare.30272688.v1
title: Altering rRNA 2’O-methylation pattern during neuronal differentiation is regulated by FMRP

description: The Fragile X Messenger Ribonucleoprotein (FMRP) is a selective RNA-binding protein that localizes to the cytoplasm and the nucleus. The loss of FMRP results in Fragile X Syndrome (FXS), an autism spectrum disorder. FMRP interacts with ribosomes and regulates the translation of mRNAs essential for neuronal development and synaptic plasticity. However, the biochemical nature of this translation regulation is unknown. Here, we report that a potential feature of FMRP-mediated translation regulation during neuronal differentiation is the modulation of 2’-O-methylation of ribosomal RNA. 2’O-methylation, facilitated by C/D box snoRNAs in the nucleus, is a major epitranscriptome mark on rRNA, essential for ribosome assembly and function. We found that FMRP influences a distinct rRNA 2’O-Methylation pattern across neuronal differentiation. We show that in H9 ESCs, FMRP interacts with a selected set of C/D box snoRNA in the nucleus, resulting in the generation of ribosomes with a distinct pattern of rRNA 2’O-Methylation. This epitranscriptome pattern on rRNA undergoes a significant change during the differentiation of ESCs to neuronal precursors and cortical neurons. ESCs exhibit substantial levels of hypomethylated residues on rRNA, which progressively decrease in neuronal precursors and post-mitotic cortical neurons. This reduction correlates with changes in global protein synthesis across different stages of differentiation. Importantly, this stepwise change in the 2’O-methylation pattern during neuronal differentiation is altered in the absence of FMRP, which could impact neuronal development and contribute to dysregulated protein synthesis observed in Fragile X Syndrome.
DOI: 10.1594/pangaea.962560
title: Continuous thermosalinograph oceanography along RV METEOR cruise track M158

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. Temperature and salinity were calibrated against CTD data from 5 m depth. For details to all processing steps see Data Processing Report.
description: Temperature was calibrated independently for both TSGs against CTD data from 5 m depth. Value added to temperature data TSG1 = -0.003846. Value added to temperature data TSG2 = -0.001303.Salinity was calibrated independently for both TSGs against CTD data from 5 m depth (tim is the time in days since Expocode of this cruise (06M320190919), i.e. since 2019-09-19T00:00:00): Value added to salinity data TSG1 = 0.0001321*tim+0.02864. Value added to salinity data TSG2 = -0.0006277*tim+0.11930.TSG1 was chosen for publication.
DOI: 10.1594/pangaea.962562
title: Shipboard ADCP current measurements (38 kHz) during RV MARIA S. MERIAN cruise MSM116

description: Current velocities of the upper water column along the cruise track of R/V Maria S. Merian cruise MSM116 were collected by a vessel-mounted 38 kHz RDI Ocean Surveyor ADCP. The ADCP transducer was located at 6.0 m below the water line. The instrument was operated in narrowband mode (WM10) with a bin size of 32.00 m, a blanking distance of 16.00 m, and a total of 50 bins, covering the depth range between 54.0 m and 1622.0 m. Beam velocities as recorded by the data acquistion software VmDAS were transformed to ship coordinates and after merging with the navigation data from the ship's Motion Reference Unit and Global Positioning systems into earth coordinates. Single-ping data / ping ensembles were screened for bottom signals and, where appropriate, a bottom mask was manually processed. The ship's velocity was calculated from position fixes obtained by the Global Positioning System (GPS). Accuracy of the ADCP velocities mainly depends on the quality of the position fixes and the ship's heading data. Further errors stem from a misalignment of the transducer with the ship's centerline. Data post-processing included water track calibration of the misalignment angle (0.3986° +/- 0.5027°) and scale factor (1.0020 +/- 0.0095) of the Ocean Surveyor signal. The velocity data were averaged in time using an average interval of 60 s. Velocity quality flagging is based on following threshold criteria: abs(UC) or abs(VC) &gt; 1.5 m/s, rms(UC_z) or rms(VC_z) &gt; 0.3.
DOI: 10.1594/pangaea.962922
title: Continuous thermosalinograph oceanography along RV METEOR cruise track M159

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. Temperature and salinity were calibrated against CTD data from 5 m depth. For details to all processing steps see Data Processing Report.
description: Temperature was calibrated independently for both TSGs against CTD data from 5 m depth. Value added to temperature data TSG1 = -0.003614. Value added to temperature data TSG2 = -0.002931.Salinity was calibrated independently for both TSGs against CTD data from 5 m depth (tim is the time in days since Expocode of this cruise (06M320191029), i.e. since 2019-10-29T00:00:00): Value added to salinity data TSG1 = 0.0008654*tim-0.01436. Value added to salinity data TSG2 = 0.0005527*tim-0.00249.TSG1 was chosen for publication.
DOI: 10.6084/m9.figshare.30621274
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