cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10719596
title: A catalog of genes and species of the brown rat (Rattus norvegicus) gut microbiota

description: Dataset overviewWe built a catalog of 5.9M genes found in the brown rat gut microbiota. Co-abundant genes were binned in 1627 Metagenomic Species for which we provide taxonomic labels.This dataset can be used to analyze shotgun sequencing data of the brown rat gut microbiota.
Data sources Rat fecal (and milk) samples characterized by shotgun metagenomic sequencing during the Mamiprooffi project. Sequencing data will be submitted soon on the European Nucleotide Archive (Bioproject PRJEB57230)The gene catalog of the Sprague-Dawley rat gut metagenome published by Pan et al.
Metagenomic assemblyMetagenomic assembly was performed on the Mamiprooffi samples (Data Source 1) with SPAdes (parameters: --iontorrent --careful). Contigs of less than 1500 bp or successfully aligned on the rat genome (Rnor_6.0) were removed.Non-redundant gene catalogGenes were predicted on all contigs with Prodigal (parameters : -m -p meta ). Genes with missing start codon or shorter than 99 bp were discarded.Then, partial and complete genes were separately clustered with cd-hit-est (parameters -c 0.95 -aS 0.90 -G 0 -d 0 -M 0 -T 0 ). Finally, these two non-redundant gene sets were merged with the previously published catalog (Data Source 2) using cd-hit-est-2d by considering at first complete genes (contact us for futher details).Functionnal annotationKEGG Orthologs (KOs) were assigned to genes of the final catalog with KofamScan (version 1.3.0, KEGG 107 database)
Metagenomic SpeciesUsing the Meteor software suite, reads from samples in Bioprojects PRJEB57230 and PRJEB22973 were mapped against the final non redundant catalog to build a raw gene abundance table (5.9 million genes quantified in 370 samples). This table was submitted to MSPminer and Canopy. A total of 1627 clusters of co-abundant genes or MetaGenomic Species (MGS) were discovered.Quality control of each MGS was manually performed by visualizing heatmaps representative of the normalized gene abundance profiles.
Taxonomic annotation of Metagenomic SpeciesMGS taxonomic annotation was performed by aligning all core and accessory genes against the GTDB r214 representative genomes using blastn [4] (version 2.10.1, task = megablast, word_size = 16). The 20 best hits for each gene were kept. A species-level assignment was given if > 50% of the genes matched a GTDB representative genome with a mean identity ≥ 95% and mean gene length coverage ≥ 90%. The remaining MGS were assigned to a higher taxonomic levels (genus to superkingdom) if more than 50% of their genes had the same annotation.
DOI: 10.5281/zenodo.10784512
title: A catalog of genes and species of the brown rat (Rattus norvegicus) gut microbiota

description: Dataset overviewWe built a catalog of 5.9M genes found in the brown rat gut microbiota. Co-abundant genes were binned in 1627 Metagenomic Species for which we provide taxonomic labels.This dataset can be used to analyze shotgun sequencing data of the brown rat gut microbiota.
Data sources Rat fecal (and milk) samples characterized by shotgun metagenomic sequencing during the Mamiprooffi project. Sequencing data will be submitted soon on the European Nucleotide Archive (Bioproject PRJEB57230)The gene catalog of the Sprague-Dawley rat gut metagenome published by Pan et al.
Metagenomic assemblyMetagenomic assembly was performed on the Mamiprooffi samples (Data Source 1) with SPAdes (parameters: --iontorrent --careful). Contigs of less than 1500 bp or successfully aligned on the rat genome (Rnor_6.0) were removed.Non-redundant gene catalogGenes were predicted on all contigs with Prodigal (parameters : -m -p meta ). Genes with missing start codon or shorter than 99 bp were discarded.Then, partial and complete genes were separately clustered with cd-hit-est (parameters -c 0.95 -aS 0.90 -G 0 -d 0 -M 0 -T 0 ). Finally, these two non-redundant gene sets were merged with the previously published catalog (Data Source 2) using cd-hit-est-2d by considering at first complete genes (contact us for futher details).Functionnal annotationKEGG Orthologs (KOs) were assigned to genes of the final catalog with KofamScan (version 1.3.0, KEGG 107 database)
Metagenomic SpeciesUsing the Meteor software suite, reads from samples in Bioprojects PRJEB57230 and PRJEB22973 were mapped against the final non redundant catalog to build a raw gene abundance table (5.9 million genes quantified in 370 samples). This table was submitted to MSPminer and Canopy. A total of 1627 clusters of co-abundant genes or MetaGenomic Species (MGS) were discovered.Quality control of each MGS was manually performed by visualizing heatmaps representative of the normalized gene abundance profiles.
Taxonomic annotation of Metagenomic SpeciesMGS taxonomic annotation was performed by aligning all core and accessory genes against the GTDB r214 representative genomes using blastn [4] (version 2.10.1, task = megablast, word_size = 16). The 20 best hits for each gene were kept. A species-level assignment was given if > 50% of the genes matched a GTDB representative genome with a mean identity ≥ 95% and mean gene length coverage ≥ 90%. The remaining MGS were assigned to a higher taxonomic levels (genus to superkingdom) if more than 50% of their genes had the same annotation.
DOI: 10.5281/zenodo.11498725
title: A catalog of genes and species of the brown rat (Rattus norvegicus) gut microbiota

description: Dataset overviewWe built a catalog of 5.9M genes found in the brown rat gut microbiota. Co-abundant genes were binned in 1627 Metagenomic Species for which we provide taxonomic labels.This dataset can be used to analyze shotgun sequencing data of the brown rat gut microbiota.
Data sources Rat fecal (and milk) samples characterized by shotgun metagenomic sequencing during the Mamiprooffi project. Sequencing data will be submitted soon on the European Nucleotide Archive (Bioproject PRJEB57230)The gene catalog of the Sprague-Dawley rat gut metagenome published by Pan et al.
Metagenomic assemblyMetagenomic assembly was performed on the Mamiprooffi samples (Data Source 1) with SPAdes (parameters: --iontorrent --careful). Contigs of less than 1500 bp or successfully aligned on the rat genome (Rnor_6.0) were removed.Non-redundant gene catalogGenes were predicted on all contigs with Prodigal (parameters : -m -p meta ). Genes with missing start codon or shorter than 99 bp were discarded.Then, partial and complete genes were separately clustered with cd-hit-est (parameters -c 0.95 -aS 0.90 -G 0 -d 0 -M 0 -T 0 ). Finally, these two non-redundant gene sets were merged with the previously published catalog (Data Source 2) using cd-hit-est-2d by considering at first complete genes (contact us for futher details).Functionnal annotationKEGG Orthologs (KOs) were assigned to genes of the final catalog with KofamScan (version 1.3.0, KEGG 107 database)
Metagenomic SpeciesUsing the Meteor software suite, reads from samples in Bioprojects PRJEB57230 and PRJEB22973 were mapped against the final non redundant catalog to build a raw gene abundance table (5.9 million genes quantified in 370 samples). This table was submitted to MSPminer and Canopy. A total of 1627 clusters of co-abundant genes or MetaGenomic Species (MGS) were discovered.Quality control of each MGS was manually performed by visualizing heatmaps representative of the normalized gene abundance profiles.
Taxonomic annotation of Metagenomic SpeciesMGS taxonomic annotation was performed by aligning all core and accessory genes against the GTDB r214 representative genomes using blastn [4] (version 2.10.1, task = megablast, word_size = 16). The 20 best hits for each gene were kept. A species-level assignment was given if > 50% of the genes matched a GTDB representative genome with a mean identity ≥ 95% and mean gene length coverage ≥ 90%. The remaining MGS were assigned to a higher taxonomic levels (genus to superkingdom) if more than 50% of their genes had the same annotation.
DOI: 10.5281/zenodo.13119584
title: A catalog of genes and species of the brown rat (Rattus norvegicus) gut microbiota

description: Dataset overviewWe built a catalog of 5.9M genes found in the brown rat gut microbiota. Co-abundant genes were binned in 1627 Metagenomic Species for which we provide taxonomic labels.This dataset can be used to analyze shotgun sequencing data of the brown rat gut microbiota.
Data sources Rat fecal (and milk) samples characterized by shotgun metagenomic sequencing during the Mamiprooffi project. Sequencing data will be submitted soon on the European Nucleotide Archive (Bioproject PRJEB57230)The gene catalog of the Sprague-Dawley rat gut metagenome published by Pan et al.
Metagenomic assemblyMetagenomic assembly was performed on the Mamiprooffi samples (Data Source 1) with SPAdes (parameters: --iontorrent --careful). Contigs of less than 1500 bp or successfully aligned on the rat genome (Rnor_6.0) were removed.Non-redundant gene catalogGenes were predicted on all contigs with Prodigal (parameters : -m -p meta ). Genes with missing start codon or shorter than 99 bp were discarded.Then, partial and complete genes were separately clustered with cd-hit-est (parameters -c 0.95 -aS 0.90 -G 0 -d 0 -M 0 -T 0 ). Finally, these two non-redundant gene sets were merged with the previously published catalog (Data Source 2) using cd-hit-est-2d by considering at first complete genes (contact us for futher details).Functionnal annotationKEGG Orthologs (KOs) were assigned to genes of the final catalog with KofamScan (version 1.3.0, KEGG 107 database)
Metagenomic SpeciesUsing the Meteor software suite, reads from samples in Bioprojects PRJEB57230 and PRJEB22973 were mapped against the final non redundant catalog to build a raw gene abundance table (5.9 million genes quantified in 370 samples). This table was submitted to MSPminer and Canopy. A total of 1627 clusters of co-abundant genes or MetaGenomic Species (MGS) were discovered.Quality control of each MGS was manually performed by visualizing heatmaps representative of the normalized gene abundance profiles.
Taxonomic annotation of Metagenomic SpeciesMGS taxonomic annotation was performed by aligning all core and accessory genes against the GTDB r214 representative genomes using blastn [4] (version 2.10.1, task = megablast, word_size = 16). The 20 best hits for each gene were kept. A species-level assignment was given if > 50% of the genes matched a GTDB representative genome with a mean identity ≥ 95% and mean gene length coverage ≥ 90%. The remaining MGS were assigned to a higher taxonomic levels (genus to superkingdom) if more than 50% of their genes had the same annotation.
DOI: 10.5281/zenodo.13786316
title: A catalog of genes and species of the brown rat (Rattus norvegicus) gut microbiota

description: Dataset overviewWe built a catalog of 5.9M genes found in the brown rat gut microbiota. Co-abundant genes were binned in 1627 Metagenomic Species for which we provide taxonomic labels.This dataset can be used to analyze shotgun sequencing data of the brown rat gut microbiota.
Data sources Rat fecal (and milk) samples characterized by shotgun metagenomic sequencing during the Mamiprooffi project. Sequencing data will be submitted soon on the European Nucleotide Archive (Bioproject PRJEB57230)The gene catalog of the Sprague-Dawley rat gut metagenome published by Pan et al.
Metagenomic assemblyMetagenomic assembly was performed on the Mamiprooffi samples (Data Source 1) with SPAdes (parameters: --iontorrent --careful). Contigs of less than 1500 bp or successfully aligned on the rat genome (Rnor_6.0) were removed.Non-redundant gene catalogGenes were predicted on all contigs with Prodigal (parameters : -m -p meta ). Genes with missing start codon or shorter than 99 bp were discarded.Then, partial and complete genes were separately clustered with cd-hit-est (parameters -c 0.95 -aS 0.90 -G 0 -d 0 -M 0 -T 0 ). Finally, these two non-redundant gene sets were merged with the previously published catalog (Data Source 2) using cd-hit-est-2d by considering at first complete genes (contact us for futher details).Functionnal annotationKEGG Orthologs (KOs) were assigned to genes of the final catalog with KofamScan (version 1.3.0, KEGG 107 database)
Metagenomic SpeciesUsing the Meteor software suite, reads from samples in Bioprojects PRJEB57230 and PRJEB22973 were mapped against the final non redundant catalog to build a raw gene abundance table (5.9 million genes quantified in 370 samples). This table was submitted to MSPminer and Canopy. A total of 1627 clusters of co-abundant genes or MetaGenomic Species (MGS) were discovered.Quality control of each MGS was manually performed by visualizing heatmaps representative of the normalized gene abundance profiles.
Taxonomic annotation of Metagenomic SpeciesMGS taxonomic annotation was performed by aligning all core and accessory genes against the GTDB r214 representative genomes using blastn [4] (version 2.10.1, task = megablast, word_size = 16). The 20 best hits for each gene were kept. A species-level assignment was given if > 50% of the genes matched a GTDB representative genome with a mean identity ≥ 95% and mean gene length coverage ≥ 90%. The remaining MGS were assigned to a higher taxonomic levels (genus to superkingdom) if more than 50% of their genes had the same annotation.
DOI: 10.5281/zenodo.14184150
title: A catalog of genes and species of the brown rat (Rattus norvegicus) gut microbiota

description: Dataset overviewWe built a catalog of 5.9M genes found in the brown rat gut microbiota. Co-abundant genes were binned in 1627 Metagenomic Species for which we provide taxonomic labels.This dataset can be used to analyze shotgun sequencing data of the brown rat gut microbiota.
Data sources Rat fecal (and milk) samples characterized by shotgun metagenomic sequencing during the Mamiprooffi project. Sequencing data will be submitted soon on the European Nucleotide Archive (Bioproject PRJEB57230)The gene catalog of the Sprague-Dawley rat gut metagenome published by Pan et al.
Metagenomic assemblyMetagenomic assembly was performed on the Mamiprooffi samples (Data Source 1) with SPAdes (parameters: --iontorrent --careful). Contigs of less than 1500 bp or successfully aligned on the rat genome (Rnor_6.0) were removed.Non-redundant gene catalogGenes were predicted on all contigs with Prodigal (parameters : -m -p meta ). Genes with missing start codon or shorter than 99 bp were discarded.Then, partial and complete genes were separately clustered with cd-hit-est (parameters -c 0.95 -aS 0.90 -G 0 -d 0 -M 0 -T 0 ). Finally, these two non-redundant gene sets were merged with the previously published catalog (Data Source 2) using cd-hit-est-2d by considering at first complete genes (contact us for futher details).Functionnal annotationKEGG Orthologs (KOs) were assigned to genes of the final catalog with KofamScan (version 1.3.0, KEGG 107 database)
Metagenomic SpeciesUsing the Meteor software suite, reads from samples in Bioprojects PRJEB57230 and PRJEB22973 were mapped against the final non redundant catalog to build a raw gene abundance table (5.9 million genes quantified in 370 samples). This table was submitted to MSPminer and Canopy. A total of 1627 clusters of co-abundant genes or MetaGenomic Species (MGS) were discovered.Quality control of each MGS was manually performed by visualizing heatmaps representative of the normalized gene abundance profiles.
Taxonomic annotation of Metagenomic SpeciesMGS taxonomic annotation was performed by aligning all core and accessory genes against the GTDB r214 representative genomes using blastn [4] (version 2.10.1, task = megablast, word_size = 16). The 20 best hits for each gene were kept. A species-level assignment was given if > 50% of the genes matched a GTDB representative genome with a mean identity ≥ 95% and mean gene length coverage ≥ 90%. The remaining MGS were assigned to a higher taxonomic levels (genus to superkingdom) if more than 50% of their genes had the same annotation.
DOI: 10.23728/b2share.398d3981e1824e949bf6eeac052f1d5b
title: Physical and chemical data for Lake Lugano (Switzerland and Italy), 2022-2024

description: The dataset contains data of water transparency and multiparameter probe measurements (temperature, dissolved oxygen, pH, conductivity) in the north and south basins of Lake Lugano during 2022-2023.
description: All data use must be acknowledged with the following acknowledgement statement: 
Long-term research on Lake Lugano has been funded by the International Commission for the Protection of Swiss-Italian Waters (CIPAIS) and by Dipartimento del Territorio, Repubblica e Cantone Ticino.
DOI: 10.5281/zenodo.11913042
title: msiFlow: Automated Workflows for Reproducible and Scalable Multimodal Mass Spectrometry Imaging and Immunofluorescence Microscopy Data Processing and Analysis

description: This record contains example and result data of msiFlow.

msiFlow is a collection of automated workflows for reproducible and scalable multimodal mass spectrometry imaging (MSI) and immunofluorescence microscopy (IFM) data processing and analysis. Using an experimental mouse model for urinary tract infection, induced by uropathogenic E.coli (UPEC), we generated data by



matrix-assisted laser desorption ionisation mass spectrometry imaging with laser-induced postionisation (MALDI-2 MSI) using the Bruker timsTOFfleX instrument

transmission-mode MALDI-2 MSI (t-MALDI-2)

immunofluorescence microscopy (IFM) using the MACSima system from Miltenyi 


msiFlow was tested on MALDI-2 MSI, t-MALDI-2 MSI and IFM data of control and UPEC-infected mouse bladder sections. In IFM we used Ly6G and actin for staining neutrophils and the muscle layer. We validated msiFlow on MALDI MSI data of bone marrow (BM)-derived neutrophils. All data used and results generated by msiFlow are included in this dataset (besides the intermediate results of the MALDI-2 preprocessing due to data size).

The dataset contains the following zip files:




zip file
description


ly6g_heterogeneity.zip
example and result data (Ly6G clusters) for molecular_heterogeneity_flow


if_segmentation.zip
example and result data (Ly6G segmentation) for if_segmentation_flow


ly6g_heterogeneity_signatures.zip
example and result data (lipids for Ly6G clusters) for molecular_signatures_flow


ly6g_molecular_signatures.zip
example and result data (lipids for Ly6G) for molecular_signatures_flow


msi_if_registration.zip
example and result data for msi_if_registration_flow


msi_segmentation.zip
example and result data (segmented MSI bladder data) for msi_segmentation_flow


region_group_analysis.zip
example and result data (regulated lipids in different bladder tissue regions) for region_group_analysis_flow


macsima.zip
raw IFM data of UPEC-infected bladders containing Ly6G, actin and autofluorescence images


maldi-bm-neutrophils.zip
raw and pre-processed MALDI MSI data of BM-derived neutrophils


t-maldi-2.zip
raw t-MALDI-2 MSI data of a UPEC-infected bladder section


maldi-2-group-sampleno.zip
raw MALDI-2 MSI data of a control/UPEC bladder section
DOI: 10.5281/zenodo.11913041
title: msiFlow: Automated Workflows for Reproducible and Scalable Multimodal Mass Spectrometry Imaging and Immunofluorescence Microscopy Data Processing and Analysis

description: This record contains example and result data of msiFlow.

msiFlow is a collection of automated workflows for reproducible and scalable multimodal mass spectrometry imaging (MSI) and immunofluorescence microscopy (IFM) data processing and analysis. Using an experimental mouse model for urinary tract infection, induced by uropathogenic E.coli (UPEC), we generated data by



matrix-assisted laser desorption ionisation mass spectrometry imaging with laser-induced postionisation (MALDI-2 MSI) using the Bruker timsTOFfleX instrument

transmission-mode MALDI-2 MSI (t-MALDI-2)

immunofluorescence microscopy (IFM) using the MACSima system from Miltenyi 


msiFlow was tested on MALDI-2 MSI, t-MALDI-2 MSI and IFM data of control and UPEC-infected mouse bladder sections. In IFM we used Ly6G and actin for staining neutrophils and the muscle layer. We validated msiFlow on MALDI MSI data of bone marrow (BM)-derived neutrophils. Tentative lipid annotations were validated by MALDI DDA MSI and MALDI MS/MS. All data used and results generated by msiFlow are included in this dataset (besides the intermediate results of the MALDI-2 preprocessing due to data size).

The dataset contains the following zip files:




zip file
description


ly6g_heterogeneity.zip
example and result data (Ly6G clusters) for molecular_heterogeneity_flow


if_segmentation.zip
example and result data (Ly6G segmentation) for if_segmentation_flow


ly6g_heterogeneity_signatures.zip
example and result data (lipids for Ly6G clusters) for molecular_signatures_flow


ly6g_molecular_signatures.zip
example and result data (lipids for Ly6G) for molecular_signatures_flow


msi_if_registration.zip
example and result data for msi_if_registration_flow


msi_segmentation.zip
example and result data (segmented MSI bladder data) for msi_segmentation_flow


region_group_analysis.zip
example and result data (regulated lipids in different bladder tissue regions) for region_group_analysis_flow


macsima.zip
raw IFM data of UPEC-infected bladders containing Ly6G, actin and autofluorescence images


maldi-bm-neutrophils.zip
raw and pre-processed MALDI MSI data of BM-derived neutrophils


t-maldi-2.zip
raw t-MALDI-2 MSI data of a UPEC-infected bladder section


maldi-2-group-sampleno.zip
raw MALDI-2 MSI data of a control/UPEC bladder section


MALDI_DDA_MSI.zip
raw MALDI MSI data acquired in DDA mode


TIMS_MS_MS.zip
raw MALDI TIMS MS/MS data