cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17044/scilifelab.22670290.v2
title: Population allele frequencies, environmental data, and individual genotypes of Atlantic horse mackerel (<em>Trachurus trachurus</em>) collected across the east Atlantic ocean

description: Pool-wise allele frequencies, environmental data, and individual genotypes used in the manuscript entitled "The genomic basis and environmental correlates of local adaptation in the Atlantic horse mackerel (<em>Trachurus trachurus</em>)" (EVA-2023-003-OA). 
In the pool-wise allele frequencies file (tab-separated text gzipped file), pool sample names are indicated in the columns header and SNP markers are in rows (the first two columns indicate the chromosome, CHROM, and base pair position, POS). 
In the individual genotype data file (VCF format), rows 1-17 correspond to the general header of the file, row 18 shows the header indicating markers and sample information, genotype data starts in row 19 onwards. The header in row 18 indicates:
Col 1: chromosome (CHROM)
Col 2: position (POS)
Col 3: SNP ID (ID)
Col 4: reference allele (REF)
Col 5: alternative allele (ALT)
Col 6: marker quality (QUAL)
Col 7: filter (FILTER)
Col 8: information (INFO)
Col 9: genotype format (FORMAT)
Col 10-onwards: samples, one per column
In the environmental data file (tab-separated text file), each row corresponds to a pool sample and each column to environmental data such as depth, Longitude (Lon), Latitude (Lat), and eight environmental variables:
Mean depth mean current velocity (m/s) (BO21_curvelmean_bdmean)
Mean depth mean dissolved oxygen (umol/m3) (BO21_dissoxmean_bdmean)
Mean depth mean iron content (umol/m3) (BO21_ironmean_bdmean)
Mean depth mean nitrate (umol/m3) (BO21_nitratemean_bdmean)
Mean depth mean primary productivity (g/m3/day) (BO21_ppmean_bdmean)
Mean depth mean salinity (PSS) (BO21_salinitymean_bdmean)
Mean depth mean temperature (°C) (BO21_tempmean_bdmean)
Mean depth mean temperature range (°C) (BO21_temprange_bdmean)
DOI: 10.17044/scilifelab.22270225.v2
title: Metagenomic dataset from Swedish urban lakes

description: We release metagenomic data of seven urban, eutrophic Swedish lakes that have been extensively studied and characterized in terms of biogeochemistry. Here we provide the supplementary tables and the full set of metagenome-assembled genomes of 17 metagenomic samples.- We have 10 metagenomic samples from Lake Mälaren which is the third largest lake in Sweden and serves as the main drinking water supply to ~1.5 million residents in Stockholm and neighboring cities. This dataset is the first insight into the bacterial dynamics of Lake Mälaren during the summer seasonal gradient (early July – late August 2021).- We sampled two additional lakes (Trehoringen and Langsjön) in Uppsala to compare summer microbial communities in lakes in Central Sweden.- Additionally, we sequenced, assembled and binned microbial communities in five Swedish lakes in the urban Stockholm-Uppsala region from 2002 that were previously characterized using older techniques (Eiler and Bertilsson, 2004). These five highly eutrophic lakes have a long history of seasonal cyanobacterial blooms in the summer (Eiler and Bertilsson, 2004).Our goal was to collect and sequence data that could be used to generate hypothesis and preliminary view of micrbial community or urban lakes around Stockholm with special emphasis on Lake Mälaren which proved drinking water to millions of people. In these data we release 17 shot-gun metagenomes in the European Nucleotide Archive (ENA) and are accessible under project number PRJEB54817. Moreover, in this repository we provide the 2378 MAGs that include the 514 species representative genomes (SRG, calculated &lt;95% average nucleotide identity - ANI).Finally, here you also can find the 4 supplementary tables that include the following information.· Table S1. Sample metadata· Table S2. Metagenomic assembly statistics (QUAST)· Table S3. List of metagenome assembled genomes (MAGs), checkM statistics and GTDB taxonomic classification. Dereplicated species representative genomes are marked with x· Table S4. Species representative genomes (SRGs) abundance in copies per million reads
DOI: 10.7483/opendata.cms.f20l.wbp8
title: /TprimeBToTH_TLep_Hbb_LH_MT600_MH100_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16MiniAODv2-106X_mcRun2_asymptotic_v17-v2/MINIAODSIM
DOI: 10.17044/scilifelab.22730684
title: Long-read whole genome sequencing of human T cells

description: This dataset represent long read sequencing of single human T cells isolated from a human donor.
The data set include Illumina whole genome sequencing of 16 single T cells and PacBio HiFi whole genome sequenicng of 5 single T cells   
<br>
DOI: 10.17044/scilifelab.22730684.v1
title: Long-read whole genome sequencing of human T cells

description: This dataset represent long read sequencing of single human T cells isolated from a human donor.
The data set include Illumina whole genome sequencing of 16 single T cells and PacBio HiFi whole genome sequenicng of 5 single T cells   
<br>
DOI: 10.7483/opendata.cms.e1ak.frn9
title: /TprimeBToTH_TLep_Hbb_LH_MT600_MH100_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16NanoAODv9-106X_mcRun2_asymptotic_v17-v1/NANOAODSIM
DOI: 10.17044/scilifelab.22769996
title: NBIS-AF2-standard and NBIS-AF2-multimer: CASP15 baseline predictions, Multiple Sequence Alignments and ancillary outputs

description: This dataset contains all AlphaFold (v2.2) monomeric and multimeric predictions used as baseline during CASP15, as well as the input Multiple Sequence Alignments (MSAs) and binary outputs such as distograms etc.
<br>
Computations for the CASP15 baseline predictions and MSAs were performed at NSC BerzeLiUs and Tetralith provided by the  Swedish National Infrastructure for Computing (SNIC), partially funded  by the Swedish Research Council through grant agreement no. 2018-05973.
<br>
The Snakemake workflow used to generate the models is open source and available at: https://github.com/clami66/AF_server/
<br>
Documentation for better reproducibility: http://bioinfo.ifm.liu.se/casp15/reproduce/
DOI: 10.7483/opendata.cms.a91h.6lss
title: /TprimeBToTH_TLep_Hbb_LH_MT600_MH125_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16MiniAODv2-106X_mcRun2_asymptotic_v17-v2/MINIAODSIM
DOI: 10.17044/scilifelab.22770161
title: Spatial Multimodal analysis (SMA) - Mass Spectrometry Imaging (MSI)

description: The files above are MALDI-MSI (Matrix Assisted Laser Desorption Ionization - Mass Spectrometry Imaging) experiments. The dataset contains both imzML, which is the common MSI open file type, and csv, containing x, y positions in tissue as well as m/z and intensity, which is a more user friendly format. A major difference between the two types is that the imzML contains raw data, whereas the csv data is peak-picked, explaining the discrepancy in file sizes. The data contained in this dataset should be enough to recreate the MSI parts of the manuscript.
<br>
The purpose of the experiments was to demonstrate that MALDI-MSI and ST (Spatial Transcriptomics) could be done on the same tissue. MALDI-MSI was done first, and ST second, so there is no expected difference in the tissue compared to a regular MALDI-MSI run, however, the experiments where ST was run subsequent to MALDI-MSI required non-conductive glass which is not the standard in the MSI- field. To compare, experiments done on the commonly used conductive (ITO) glass slides are also contained in this dataset
<br>
For any questions about the dataset or to request access to any files not uploaded here, please contact per.andren@farmbio.uu.se
DOI: 10.7483/opendata.cms.1dlx.7y51
title: /TprimeBToTH_TLep_Hbb_LH_MT600_MH125_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16NanoAODv9-106X_mcRun2_asymptotic_v17-v1/NANOAODSIM
DOI: 10.7483/opendata.cms.sumb.bz4b
title: /TprimeBToTH_TLep_Hbb_LH_MT600_MH150_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16MiniAODv2-106X_mcRun2_asymptotic_v17-v2/MINIAODSIM
DOI: 10.17044/scilifelab.22284709
title: Atlas of 5'P mRNA decay in bacteria

description: Regulation of mRNA stability is a central process in gene expression. Here, report an atlas of 5´ monophosphorylated mRNA decay intermediates (5´P) in 96 species. We use those data to demonstrate that in species with 5´-3´exonuclease activity, the exoribonuclease RNase J follows the trailing ribosome, producing an <em>in vivo</em> single-nucleotide toeprint of its 5´ position. While in other species, ribosome position alters endonucleolytic cleavage sites. Our work demonstrates the universal connection between RNA decay and translation and paves the way for use of metadegradome sequencing to investigate post-transcriptional regulation of unculturable species present and complex microbial communities.
<br>
Data was analyzed using our fivepseq software.  Improved computational analysis of ribosome dynamics from 5′P degradome data using fivepseq. Lilit Nersisyan, Maria Ropat & Vicent Pelechano. <em>NAR Genomics and Bioinformatics</em>, Volume 2, Issue 4, December 2020, lqaa099, https://doi.org/10.1093/nargab/lqaa099
DOI: 10.7483/opendata.cms.dac3.kavj
title: /TprimeBToTH_TLep_Hbb_LH_MT600_MH150_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16NanoAODv9-106X_mcRun2_asymptotic_v17-v1/NANOAODSIM
DOI: 10.17044/scilifelab.22303531.v2
title: Multimodal classification of molecular subtypes in pediatric acute lymphoblastic leukemia

description: This dataset contains genome-wide DNA methylation data generated from 384 pediatric acute lymphoblastic leukemia (ALL) samples originating from bone marrow or peripheral blood samples taken at ALL diagnosis (n = 384). Further details regarding the samples are available in Supplementary Table S2 from Krali et al., 2023 (DOI to publication when available). 
Genome-wide DNA methylation was analyzed at the SNP&SEQ Technology Platform, SciLifeLab, National Genomics Infrastructure Uppsala, Sweden. 250 ng of bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using the standard protocol from Illumina (iScan SQ instrument). 
This metadata record contains information about the raw idat files generated from the Infinium DNA methylation arrays. The raw idat files were processed with Methylation Module (1.8.5) software in Genome Studio (V2010.3). Peak-based correction was used to normalize the beta-value matrix.
The raw idat files along with a samplesheet, processed beta-value matrix, annotation file for CpG annotation will be made available upon request. Limited phenotype information is available in the Supplemental Table S2 of the manuscript. All scripts that give a walk-through to our project, including the modelling process with Machine Learning can be found in our GitHub repository.
Terms for access
The DNA methylation dataset is only to be used for research that is seeking to advance the understanding of the influence of epigenetic factors on leukemia etiology and biology.
The data should not be used for other purposes, i.e. investigating the epigenetic signatures that may lead to identification of a person.
<br>
For retrieving the data used for the scope of this publication, please contact datacentre@scilifelab.se.
DOI: 10.17044/scilifelab.22770161.v1
title: Spatial Multimodal analysis (SMA) - Mass Spectrometry Imaging (MSI)

description: The files above are MALDI-MSI (Matrix Assisted Laser Desorption Ionization - Mass Spectrometry Imaging) experiments. The dataset contains both imzML, which is the common MSI open file type, and csv, containing x, y positions in tissue as well as m/z and intensity, which is a more user friendly format. A major difference between the two types is that the imzML contains raw data, whereas the csv data is peak-picked, explaining the discrepancy in file sizes. The data contained in this dataset should be enough to recreate the MSI parts of the manuscript.
<br>
The purpose of the experiments was to demonstrate that MALDI-MSI and ST (Spatial Transcriptomics) could be done on the same tissue. MALDI-MSI was done first, and ST second, so there is no expected difference in the tissue compared to a regular MALDI-MSI run, however, the experiments where ST was run subsequent to MALDI-MSI required non-conductive glass which is not the standard in the MSI- field. To compare, experiments done on the commonly used conductive (ITO) glass slides are also contained in this dataset
<br>
For any questions about the dataset or to request access to any files not uploaded here, please contact per.andren@farmbio.uu.se
DOI: 10.17044/scilifelab.22769996.v1
title: NBIS-AF2-standard and NBIS-AF2-multimer: CASP15 baseline predictions, Multiple Sequence Alignments and ancillary outputs

description: This dataset contains all AlphaFold (v2.2) monomeric and multimeric predictions used as baseline during CASP15, as well as the input Multiple Sequence Alignments (MSAs) and binary outputs such as distograms etc.
<br>
Computations for the CASP15 baseline predictions and MSAs were performed at NSC BerzeLiUs and Tetralith provided by the  Swedish National Infrastructure for Computing (SNIC), partially funded  by the Swedish Research Council through grant agreement no. 2018-05973.
<br>
The Snakemake workflow used to generate the models is open source and available at: https://github.com/clami66/AF_server/
<br>
Documentation for better reproducibility: http://bioinfo.ifm.liu.se/casp15/reproduce/
DOI: 10.7483/opendata.cms.8m7t.jqek
title: /TprimeBToTH_TLep_Hbb_LH_MT600_MH175_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16MiniAODv2-106X_mcRun2_asymptotic_v17-v2/MINIAODSIM
DOI: 10.17044/scilifelab.22770161.v2
title: Spatial Multimodal analysis (SMA) - Mass Spectrometry Imaging (MSI)

description: The files above are MALDI-MSI (Matrix Assisted Laser Desorption Ionization - Mass Spectrometry Imaging) experiments. The dataset contains both imzML, which is the common MSI open file type, and csv, containing x, y positions in tissue as well as m/z and intensity, which is a more user friendly format. A major difference between the two types is that the imzML contains raw data, whereas the csv data is peak-picked, explaining the discrepancy in file sizes. The data contained in this dataset should be enough to recreate the MSI parts of the manuscript.
<br>
The purpose of the experiments was to demonstrate that MALDI-MSI and ST (Spatial Transcriptomics) could be done on the same tissue. MALDI-MSI was done first, and ST second, so there is no expected difference in the tissue compared to a regular MALDI-MSI run, however, the experiments where ST was run subsequent to MALDI-MSI required non-conductive glass which is not the standard in the MSI- field. To compare, experiments done on the commonly used conductive (ITO) glass slides are also contained in this dataset
<br>
For any questions about the dataset or to request access to any files not uploaded here, please contact per.andren@farmbio.uu.se
DOI: 10.7483/opendata.cms.qoav.772s
title: /TprimeBToTH_TLep_Hbb_LH_MT600_MH175_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16NanoAODv9-106X_mcRun2_asymptotic_v17-v1/NANOAODSIM
DOI: 10.15468/dl.fwfsmv
title: Occurrence Download

description: A dataset containing 659 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is Spain",
 "TaxonKey is Quercus canariensis Willd."
 ]
}

 The dataset includes 659 records from 36 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071212-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7483/opendata.cms.8v63.9jnr
title: /TprimeBToTH_TLep_Hbb_LH_MT600_MH200_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16MiniAODv2-106X_mcRun2_asymptotic_v17-v2/MINIAODSIM
DOI: 10.7483/opendata.cms.rxcz.hoqo
title: /TprimeBToTH_TLep_Hbb_LH_MT600_MH200_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16NanoAODv9-106X_mcRun2_asymptotic_v17-v1/NANOAODSIM
DOI: 10.7483/opendata.cms.thuz.vn3y
title: /TprimeBToTH_TLep_Hbb_LH_MT600_MH250_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16MiniAODv2-106X_mcRun2_asymptotic_v17-v2/MINIAODSIM
DOI: 10.7483/opendata.cms.hpcy.fdo4
title: /TprimeBToTH_TLep_Hbb_LH_MT600_MH250_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16NanoAODv9-106X_mcRun2_asymptotic_v17-v1/NANOAODSIM
DOI: 10.17037/data.00004498
title: IMPLEMENT-CVD Phase 1: Health system factors affecting implementation of fixed-dose combination therapy for hypertension in Kenya
DOI: 10.7483/opendata.cms.lpaj.swow
title: /TprimeBToTH_TLep_Hbb_LH_MT600_MH25_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16MiniAODv2-106X_mcRun2_asymptotic_v17-v2/MINIAODSIM
DOI: 10.7483/opendata.cms.rp8k.y8m9
title: /TprimeBToTH_TLep_Hbb_LH_MT600_MH25_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16NanoAODv9-106X_mcRun2_asymptotic_v17-v1/NANOAODSIM
DOI: 10.17044/scilifelab.23180981
title: Twist Solid GMS560 v0.6.1 panel of normals

description: The data included here are part of a collection of different types of reference data used in the bioinformatic analysis pipeline called Twist Solid GMS560. The pipeline is based on the Hydra-genetics framework and analyses NGS short read data from the GMS560 Twist panel which is used on solid cancer samples.
The data in this specific item include panel of normals and artifact filer files generated for the Twist GMS560 panel. Panel of normals and artifacts are specific to panel used and sequencing machine. Programs using these files include MSIsensor-Pro, GATK CNV, CNVkit, SVDB, PureCN, and small variant filtering.
DOI: 10.17044/scilifelab.23217512
title: Twist Solid GMS560 v0.6.1 references arriba

description: The data included here are part of a collection of different types of reference data used in the bioinformatic analysis pipeline called Twist Solid GMS560. The pipeline is based on the Hydra-genetics framework and analyses NGS short read data from the GMS560 Twist panel which is used on solid cancer samples.
The data in this specific item include general publicly available reference files used in the pipeline by the RNA fusion calling program Arriba (https://github.com/suhrig/arriba). Downloading data from here will ensure compatible and correct versions.
DOI: 10.7483/opendata.cms.1dzz.1hul
title: /TprimeBToTH_TLep_Hbb_LH_MT600_MH350_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16MiniAODv2-106X_mcRun2_asymptotic_v17-v2/MINIAODSIM
DOI: 10.17044/scilifelab.23217512.v1
title: Twist Solid GMS560 v0.6.1 references arriba

description: The data included here are part of a collection of different types of reference data used in the bioinformatic analysis pipeline called Twist Solid GMS560. The pipeline is based on the Hydra-genetics framework and analyses NGS short read data from the GMS560 Twist panel which is used on solid cancer samples.
The data in this specific item include general publicly available reference files used in the pipeline by the RNA fusion calling program Arriba (https://github.com/suhrig/arriba). Downloading data from here will ensure compatible and correct versions.
DOI: 10.17044/scilifelab.23220164
title: Twist Solid GMS560 v0.6.1 references fuseq_wes

description: The data included here are part of a collection of different types of reference data used in the bioinformatic analysis pipeline called Twist Solid GMS560. The pipeline is based on the Hydra-genetics framework and analyses NGS short read data from the GMS560 Twist panel which is used on solid cancer samples.
The data in this specific item include general publicly available reference files used in the pipeline by the fusion calling program FuSeq_WES (https://github.com/nghiavtr/FuSeq_WES). Downloading data from here will ensure compatible and correct versions.
DOI: 10.17044/scilifelab.23220164.v1
title: Twist Solid GMS560 v0.6.1 references fuseq_wes

description: The data included here are part of a collection of different types of reference data used in the bioinformatic analysis pipeline called Twist Solid GMS560. The pipeline is based on the Hydra-genetics framework and analyses NGS short read data from the GMS560 Twist panel which is used on solid cancer samples.
The data in this specific item include general publicly available reference files used in the pipeline by the fusion calling program FuSeq_WES (https://github.com/nghiavtr/FuSeq_WES). Downloading data from here will ensure compatible and correct versions.
DOI: 10.7483/opendata.cms.ww3e.yrjh
title: /TprimeBToTH_TLep_Hbb_LH_MT600_MH350_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16NanoAODv9-106X_mcRun2_asymptotic_v17-v1/NANOAODSIM
DOI: 10.17044/scilifelab.23220416
title: Twist Solid GMS560 v0.6.1 references

description: The data included here are part of a collection of different types of reference data used in the bioinformatic analysis pipeline called Twist Solid GMS560. The pipeline is based on the Hydra-genetics framework and analyses NGS short read data from the GMS560 Twist panel which is used on solid cancer samples.
The data in this specific item include general publicly available reference files used in the pipeline by many different programs. Downloading data from here will ensure compatible and correct versions.
DOI: 10.17044/scilifelab.23220416.v1
title: Twist Solid GMS560 v0.6.1 references

description: The data included here are part of a collection of different types of reference data used in the bioinformatic analysis pipeline called Twist Solid GMS560. The pipeline is based on the Hydra-genetics framework and analyses NGS short read data from the GMS560 Twist panel which is used on solid cancer samples.
The data in this specific item include general publicly available reference files used in the pipeline by many different programs. Downloading data from here will ensure compatible and correct versions.
DOI: 10.7483/opendata.cms.tjrl.bqb3
title: /TprimeBToTH_TLep_Hbb_LH_MT600_MH450_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16MiniAODv2-106X_mcRun2_asymptotic_v17-v2/MINIAODSIM
DOI: 10.7483/opendata.cms.iawn.9j36
title: /TprimeBToTH_TLep_Hbb_LH_MT600_MH450_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16NanoAODv9-106X_mcRun2_asymptotic_v17-v1/NANOAODSIM
DOI: 10.15468/dl.fjkb7h
title: Occurrence Download

description: A dataset containing 619 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Isomira hypocrita Mulsant, 1856",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 619 records from 65 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071213-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.