cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17044/scilifelab.19248172.v2
title: Test dataset from: GenErode: a bioinformatics pipeline to investigate genome erosion in endangered and extinct species

description: This item contains a test dataset based on Sumatran rhinoceros (<em>Dicerorhinus sumatrensis</em>) whole-genome re-sequencing data that we publish along with the GenErode pipeline (https://github.com/NBISweden/GenErode; Kutschera et al. 2022) and that we reduced in size so that users have the possibility to get familiar with the pipeline before analyzing their own genome-wide datasets.
We extracted scaffold ‘Sc9M7eS_2_HRSCAF_41’ of size 40,842,778 bp from the Sumatran rhinoceros genome assembly (<em>Dicerorhinus sumatrensis harrissoni</em>; GenBank accession number GCA_014189135.1) to be used as reference genome in GenErode. Some GenErode steps require the reference genome of a closely related species, so we additionally provide three scaffolds from the White rhinoceros genome assembly (<em>Ceratotherium simum simum</em>; GenBank accession number GCF_000283155.1) with a combined length of 41,195,616 bp that are putatively orthologous to Sumatran rhinoceros scaffold ‘Sc9M7eS_2_HRSCAF_41’, along with gene predictions in GTF format. The repository also contains a Sumatran rhinoceros mitochondrial genome (GenBank accession number NC_012684.1) to be used as reference for the optional mitochondrial mapping step in GenErode.
The test dataset contains whole-genome re-sequencing data from three historical and three modern Sumatran rhinoceros samples from the now-extinct Malay Peninsula population from von Seth et al. (2021) that was subsampled to paired-end reads that mapped to Sumatran rhinoceros scaffold ‘Sc9M7eS_2_HRSCAF_41’, along with a small proportion of randomly selected reads that mapped to the Sumatran rhinoceros mitochondrial genome or elsewhere in the genome.
For GERP analyses, scaffolds from the genome assemblies of 30 mammalian outgroup species are provided that had reciprocal blast hits to gene predictions from Sumatran rhinoceros scaffold ‘Sc9M7eS_2_HRSCAF_41’. Further, a phylogeny of the White rhinoceros and the 30 outgroup species including divergence time estimates (in billions of years) from timetree.org is available.
Finally, the item contains configuration and metadata files that were used for three separate runs of GenErode to generate the results presented in Kutschera et al. (2022).
Bash scripts and a workflow description for the test dataset generation are available in the GenErode GitHub repository (https://github.com/NBISweden/GenErode/docs/extras/test_dataset_generation).
<br>
References:
Kutschera VE, Kierczak M, van der Valk T, von Seth J, Dussex N, Lord E, et al. GenErode: a bioinformatics pipeline to investigate genome erosion in endangered and extinct species. BMC Bioinformatics 2022;23:228. https://doi.org/10.1186/s12859-022-04757-0
von Seth J, Dussex N, Díez-Del-Molino D, van der Valk T, Kutschera VE, Kierczak M, et al. Genomic insights into the conservation status of the world’s last remaining Sumatran rhinoceros populations. Nature Communications 2021;12:2393.
DOI: 10.17044/scilifelab.19248172.v1
title: Test dataset from: GenErode: a bioinformatics pipeline to investigate genome erosion in endangered and extinct species

description: This item contains a test dataset based on Sumatran rhinoceros (<i>Dicerorhinus sumatrensis</i>) whole-genome re-sequencing data that we publish along with the GenErode pipeline (https://github.com/NBISweden/GenErode; Kutschera et al. 2022) and that we reduced in size so that users have the possibility to get familiar with the pipeline before analyzing their own genome-wide datasets. We extracted scaffold ‘Sc9M7eS_2_HRSCAF_41’ of size 40,842,778 bp from the Sumatran rhinoceros genome assembly (<i>Dicerorhinus sumatrensis harrissoni</i>; GenBank accession number GCA_014189135.1) to be used as reference genome in GenErode. Some GenErode steps require the reference genome of a closely related species, so we additionally provide three scaffolds from the White rhinoceros genome assembly (<i>Ceratotherium simum simum</i>; GenBank accession number GCF_000283155.1) with a combined length of 41,195,616 bp that are putatively orthologous to Sumatran rhinoceros scaffold ‘Sc9M7eS_2_HRSCAF_41’, along with gene predictions in GTF format. The repository also contains a Sumatran rhinoceros mitochondrial genome (GenBank accession number NC_012684.1) to be used as reference for the optional mitochondrial mapping step in GenErode. 


















The test dataset contains whole-genome re-sequencing data from three historical and
three modern Sumatran rhinoceros samples from the now-extinct Malay Peninsula
population from von Seth et al. (2021) that was subsampled to paired-end reads that mapped to Sumatran rhinoceros
scaffold ‘Sc9M7eS_2_HRSCAF_41’, along with a small proportion of randomly
selected reads that mapped to the Sumatran rhinoceros mitochondrial genome or
elsewhere in the genome.





 For GERP analyses, scaffolds from the genome assemblies of 30 mammalian outgroup species are provided that had reciprocal blast hits to gene predictions from Sumatran rhinoceros scaffold ‘Sc9M7eS_2_HRSCAF_41’. Further, a phylogeny of the White rhinoceros and the 30 outgroup species including divergence time estimates (in billions of years) from timetree.org is available. Finally, the item contains configuration and metadata files that were used for three separate runs of GenErode to generate the results presented in Kutschera et al. (2022). Bash scripts and a workflow description for the test dataset generation are available in the GenErode GitHub repository (https://github.com/NBISweden/GenErode/docs/extras/test_dataset_generation).<br>References: Kutschera VE, Kierczak M, van der Valk T, von Seth J, Dussex N, Lord E, et al. GenErode: a bioinformatics pipeline to investigate genome erosion in endangered and extinct species. bioRxiv. 2022;doi:10.1101/2022.03.04.482637. von Seth J, Dussex N, Díez-Del-Molino D, van der Valk T, Kutschera VE, Kierczak M, et al. Genomic insights into the conservation status of the world’s last remaining Sumatran rhinoceros populations. Nat Commun. 2021;12:2393.
DOI: 10.7483/opendata.cms.z43a.1rap
title: /TprimeBToTH_TLep_Hbb_LH_MT2700_MH100_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16MiniAODv2-106X_mcRun2_asymptotic_v17-v2/MINIAODSIM
DOI: 10.17044/scilifelab.19307021
title: Data: Gene expression profile in peripheral B-lymphocytes and sera of individuals with fibromyalgia

description: <strong>Overview</strong>
Fibromyalgia (FM) is an idiopathic chronic disease characterized by widespread musculoskeletal pain, hyperalgesia and allodynia, often accompanied by fatigue, cognitive dysfunction and other symptoms. We investigated the gene expression profile in peripheral B-cells in FM patients and healthy matched control individuals.
<br>
<strong>Summary</strong>
The uploaded data consist of count table and sample information and can be used for gene expression analysis of patients and controls.
<br>
<strong>Generation of Data</strong>
A total of 100 ng of RNA from purified B-cells of each participant (26 patients and 23 controls) was used for sequencing following rRNA depletion and library preparation (TruSeq stranded mRNA library preparation kit, cat# 20020595, Illumina Inc.). Unique dual indexes (cat# 20022371, Illumina Inc.) were used according to the manufacturers’ protocol (#1000000040498). The quality of libraries was evaluated using the Fragment Analyzer from Advanced Analytical (AATI) using the DNF-910 kit and adapter-ligated fragments were quantified by qPCR using the Library quantification kit for Illumina (KAPA Biosystems) on a CFX384Touch (Bio-Rad) prior to cluster generation and sequencing. Sequencing was carried out on an Illumina NovaSeq 6000 instrument (NovaSeq control software v 1.7.0/ RTA v3.4.4) according to the manufacturers’ instructions. Demultiplexing and conversion to FASTQ format was performed using the bcl2fastq2 (v2.20.0.422) software, provided by Illumina. 
<br>
<strong>Data</strong>
<em>Count Data: </em>Samples were analyzed with the nf-core RNA sequencing pipeline release 1.4.2 (github.com/nf-core/rnaseq). In brief, the pipeline processes raw data from FastQ inputs, aligns the reads, generates counts relative to genes or transcripts.
<br>
<em>Sample Data:</em> Information regarding SampleName, Sample and Condition
DOI: 10.17044/scilifelab.19307021.v1
title: Data: Gene expression profile in peripheral B-lymphocytes and sera of individuals with fibromyalgia

description: <strong>Overview</strong>
Fibromyalgia (FM) is an idiopathic chronic disease characterized by widespread musculoskeletal pain, hyperalgesia and allodynia, often accompanied by fatigue, cognitive dysfunction and other symptoms. We investigated the gene expression profile in peripheral B-cells in FM patients and healthy matched control individuals.
<br>
<strong>Summary</strong>
The uploaded data consist of count table and sample information and can be used for gene expression analysis of patients and controls.
<br>
<strong>Generation of Data</strong>
A total of 100 ng of RNA from purified B-cells of each participant (26 patients and 23 controls) was used for sequencing following rRNA depletion and library preparation (TruSeq stranded mRNA library preparation kit, cat# 20020595, Illumina Inc.). Unique dual indexes (cat# 20022371, Illumina Inc.) were used according to the manufacturers’ protocol (#1000000040498). The quality of libraries was evaluated using the Fragment Analyzer from Advanced Analytical (AATI) using the DNF-910 kit and adapter-ligated fragments were quantified by qPCR using the Library quantification kit for Illumina (KAPA Biosystems) on a CFX384Touch (Bio-Rad) prior to cluster generation and sequencing. Sequencing was carried out on an Illumina NovaSeq 6000 instrument (NovaSeq control software v 1.7.0/ RTA v3.4.4) according to the manufacturers’ instructions. Demultiplexing and conversion to FASTQ format was performed using the bcl2fastq2 (v2.20.0.422) software, provided by Illumina. 
<br>
<strong>Data</strong>
<em>Count Data: </em>Samples were analyzed with the nf-core RNA sequencing pipeline release 1.4.2 (github.com/nf-core/rnaseq). In brief, the pipeline processes raw data from FastQ inputs, aligns the reads, generates counts relative to genes or transcripts.
<br>
<em>Sample Data:</em> Information regarding SampleName, Sample and Condition
DOI: 10.7483/opendata.cms.o6s6.38e6
title: /TprimeBToTH_TLep_Hbb_LH_MT2700_MH100_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16NanoAODv9-106X_mcRun2_asymptotic_v17-v1/NANOAODSIM
DOI: 10.17044/scilifelab.19317512
title: Individualized IGHV Genotype Sequences of 14 SARS-CoV-2 Convalescent Donors

description: The dataset consists of bulk sequencing data from IgM libraries obtained by IgM specific cDNA synthesis and sequencing in forward and reverse directions using the Illumina MiSeq 2 x 300 bp kit. The samples from which the dataset is retrieved is a set of 14 peripheral blood mononuclear cells (PBMCs) samples collected seven months after the primary infection by SARS-CoV-2.<br>

Further details regarding the samples are available in Pushparaj et al., 2022 (https://doi.org/10.1016/j.immuni.2022.12.005)
<br>
To apply for conditional access to this dataset please contact datacentre@scilifelab.se.
DOI: 10.17044/scilifelab.19317512.v1
title: Individualized IGHV Genotype Sequences of 14 SARS-CoV-2 Convalescent Donors

description: The dataset consists of bulk sequencing data from IgM libraries obtained by IgM specific cDNA synthesis and sequencing in forward and reverse directions using the Illumina MiSeq 2 x 300 bp kit. The samples from which the dataset is retrieved is a set of 14 peripheral blood mononuclear cells (PBMCs) samples collected seven months after the primary infection by SARS-CoV-2.<br>

Further details regarding the samples are available in Pushparaj et al., 2022 (https://doi.org/10.1016/j.immuni.2022.12.005)
<br>
To apply for conditional access to this dataset please contact datacentre@scilifelab.se.
DOI: 10.15468/dl.yfj78c
title: Occurrence Download

description: A dataset containing 51043 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Patella Linnaeus, 1758",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 51043 records from 268 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071192-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.1594/pangaea.745999
title: (Table 3) Major- and trace-element composition of metalliferous sediments from the Messinian of ODP Hole 107-653A
DOI: 10.1594/pangaea.618839
title: Water temperature profile LD99-CR13
DOI: 10.1594/pangaea.741145
title: Lithology of sediment core BEANRIG, Beanrig Moss, United Kingdom

description: This dataset was archived on 2010-05-11 from the EPD database.
DOI: 10.1594/pangaea.547905
title: Nutrients measured on water bottle samples at station Bm_1997-09-16_5, Bajo Molle, Chile
DOI: 10.1594/pangaea.618842
title: Water temperature profile LD99-CR15a
DOI: 10.1594/pangaea.825543
title: P-Wave velocity (PWL) from IODP Hole 329-U1371C

description: Geocode = Depth CSF-A (m)
DOI: 10.1594/pangaea.806613
title: (Table 3) Losses in copper and zinc of diabases of ODP Hole 140-504B
DOI: 10.1594/pangaea.495654
title: Water temperature MBT profiles from cruise U74X003061M_1954
DOI: 10.1594/pangaea.678371
title: Ultra-violet measurements from station Payerne (2001-01)

description: UV-b values were originally given in mW/m² and then erroneously imported in W/m² using the same numbers. The numbers have been corrected (divided by 1000) on 2017-01-27. UV reflect values might still contain errors.
DOI: 10.1594/pangaea.805582
title: (Table 4) Major and trace element analyses of basalts and gabbro at DSDP Hole 82-556
DOI: 10.1594/pangaea.904957
title: (Tables S1-S3) Freeze-up sequence observations in Nunavik's Deception Bay from TerraSAR-X and time-lapse photography (2015-2017)
DOI: 10.1594/pangaea.830312
title: Headspace-gas measurements from IODP Hole 338-C0002K

description: Geocode = [m CSF-A] Top Core depth (below sea floor)
DOI: 10.1594/pangaea.674581
title: Radiosonde measurements from station Kwajalein (1997-11)
DOI: 10.1594/pangaea.674633
title: Radiosonde measurements from station Kwajalein (2004-02)
DOI: 10.1594/pangaea.747323
title: Meteorological observations during ALLIGATOR cruise from Halifax to Barbados started at 1793-07-04
DOI: 10.1594/pangaea.511028
title: Radiosonde at Georg-Forster station on 1986-11-09 12:00h

description: Height of tropopause 12772 m, total ozone 228.4 DU
DOI: 10.1594/pangaea.749755
title: Meteorological observations during IRENE cruise from Kaap de Goede Hoop to Texel started at 1821-12-18
DOI: 10.1594/pangaea.764053
title: Tab. 1: Results of ore-microscopic studies
DOI: 10.1594/pangaea.883270
title: Expanded measurements from station Lindenberg (2016-08)

description: 99999: No clouds detected
DOI: 10.1594/pangaea.820094
title: Geochemistry of IODP Site 321-U1338

description: DEPTH, sediment/rock [m] gives the DEPTH (CSF-A) [m].
DOI: 10.1594/pangaea.707102
title: Basic measurements of radiation at station Boulder (2008-09)
DOI: 10.1594/pangaea.472231
title: Physical oceanography measured at different bottle stations in 1996, Ancon, Peru
DOI: 10.1594/pangaea.510886
title: Radiosonde at Georg-Forster station on 1990-10-21 12:00h

description: Height of tropopause 11174 m, total ozone 177.4 DU
DOI: 10.1594/pangaea.694989
title: Concentrations of particulate organic carbon in water of the Aegean Sea at Station JUNE-1998-IR10
DOI: 10.1594/pangaea.814050
title: Gel particles in the sea-surface microlayer: bulk water
DOI: 10.1594/pangaea.817419
title: Ultra-violet measurements from station Tamanrasset (2011-11)
DOI: 10.1594/pangaea.883239
title: Meteorological synoptical observations from station Lindenberg (2016-04)
DOI: 10.1594/pangaea.814085
title: Availability of photographs from the Vernagtferner Basin for the year 1990
DOI: 10.1594/pangaea.831219
title: Temperature monitoring in the Thai Andaman Sea coral reefs from 2009-11 to 2010-04 - Surin West

description: CalMarO - Calcification by marine organisms, PEOPLE-2007-1-1-ITN Marie Curie Action: 215157BioAcid - German Ministry for Education and Research Project (Bmbf), Grant number 03F0608B, Bioacid 3.2.3, Coral Calcification in marginal reefsORCAS - Ocean Reef Coupling in the Andaman Sea - German Research Foundation (DFG), Grant number RI 1074/7-1
DOI: 10.1594/pangaea.858533
title: Genotypic data for nine microsatellite loci for the seagrass Zostera muelleri collections from Lake Macquarie, NSW, Australia

description: Seagrasses are ecosystem engineers that offer important habitat for a large number of species and provide a range of ecosystem services. Many seagrass ecosystems are dominated by a single species; with research showing that genotypic diversity at fine spatial scales plays an important role in maintaining a range of ecosystem functions. However, for most seagrass species, information on fine-scale patterns of genetic variation in natural populations is lacking. In this study we use a hierarchical sampling design to determine levels of genetic and genotypic diversity at different spatial scales (centimeters, meters, kilometers) in the Australian seagrass Zostera muelleri. Our analysis shows that at fine-spatial scales (&lt; 1 m) levels of genotypic diversity are relatively low (R (Plots) = 0.37 ± 0.06 SE), although there is some intermingling of genotypes. At the site (10's m) and meadow location (km) scale we found higher levels of genotypic diversity (R (sites) = 0.79 ± 0.04 SE; R (Locations) = 0.78 ± 0.04 SE). We found some sharing of genotypes between sites within meadows, but no sharing of genotypes between meadow locations. We also detected a high level of genetic structuring between meadow locations (FST = 0.278). Taken together, our results indicate that both sexual and asexual reproduction are important in maintaining meadows of Z. muelleri. The dominant mechanism of asexual reproduction appears to occur via localised rhizome extension, although the sharing of a limited number of genotypes over the scale of 10's of metres could also result from the localised dispersal and recruitment of fragments. The large number of unique genotypes at the meadow scale indicates that sexual reproduction is important in maintaining these populations, while the high level of genetic structuring suggests little gene flow and connectivity between our study sites. These results imply that recovery from disturbances will occur through both sexual and asexual regeneration, but the limited connectivity at the landscape-scale implies that recovery at meadow-scale losses is likely to be limited.
description: Supplement to: Sherman, Craig D H; York, Paul H; Smith, Timothy M; Macreadie, Peter I (2016): Fine-scale patterns of genetic variation in a widespread clonal seagrass species. Marine Biology, 163(4)
DOI: 10.1594/pangaea.720896
title: Documentation of sediment core GIK23508-1
DOI: 10.1594/pangaea.828376
title: Carbonate analysis from IODP Hole 323-U1341A

description: Geocode = Top depth CSF-A (m)
DOI: 10.1594/pangaea.707646
title: Meteorological synoptical observations from station Payerne (2004-03)
DOI: 10.1594/pangaea.733087
title: (Table 32) Data of X-ray radiographic analyses of clay minerals from DSDP Hole 49-410
DOI: 10.1594/pangaea.706275
title: Basic and other measurements of radiation at station Barrow (2007-09), Version 1

description: Ellsworth G. Dutton discovered a calibration glitch in the SWD "Short-wave downward (GLOBAL) radiation" data for Barrow, Alaska. SWD data was therefore removed from this dataset. Please refer to the updated Version 2 (see replaced by reference) with correct calibration.
DOI: 10.1594/pangaea.671362
title: Basic measurements of radiation at station Sede Boqer (2006-02)
DOI: 10.1594/pangaea.706330
title: Basic measurements of radiation at station Kwajalein (2007-07)
DOI: 10.1594/pangaea.667514
title: (Table 1) Occurence of sapropels and sapropelic sediments in the Tyrrhenian Sea, ODP Site 107-655

description: Ages computed from datum levels of Channell et al. (1990) and Mueller (1990). Base of NN20 (0.474 Ma) at 2.7 mbsf, base of NN19 (1.63 Ma) at 14.6 mbsf, base of NN17 (2.5 Ma) at 20.7 mbsf
DOI: 10.1594/pangaea.717848
title: Bacterial abundance of sediment core 54301-016
DOI: 10.1594/pangaea.808696
title: Basic measurements of radiation at station Nauru Island (2005-12)

description: Version 2, 2013-03-10
DOI: 10.1594/pangaea.718080
title: Other measurements at 10 m from station Sioux Falls (2005-09)
DOI: 10.1594/pangaea.905097
title: Continuous thermosalinograph oceanography along Heincke cruise track HE533
DOI: 10.1594/pangaea.498914
title: Physical oceanography from BT during cruise U90X008054B_1983
DOI: 10.1594/pangaea.719116
title: Ultra-violet measurements from station Bondville (2008-01)

description: UV-b values were originally given in mW/m² and then erroneously imported in W/m² using the same numbers. The numbers have been corrected (divided by 1000) on 2017-02-09.
DOI: 10.1594/pangaea.730143
title: (Table 13) Trace element contents in vein pyrites from basalts of the California Gulf, DSDP Hole 65-485A

description: Analyses have been carried out by V.I. Taskaev in the Far East Geological Institute, Far East Scientific Center of the USSR Academy of Sciences. Au and Ag have not been found.
DOI: 10.1594/pangaea.733118
title: (Table 33) Chemical composition of magmatic rocks from DSDP Hole 49-411
DOI: 10.1594/pangaea.748204
title: Hydrography on standard level calculated from water bottle samples of RV Northland from 1973 to 1977
DOI: 10.1594/pangaea.831272
title: Daily mean of meteorological measurements at oasis of Asrir test site in 2001

description: Dataset created by IMPETUS subproject B3. IMPETUS data set ID: 108
DOI: 10.1594/pangaea.762844
title: Color data of Hole 325-M0038A
DOI: 10.1594/pangaea.893282
title: Composite splice from Site MOT15-2
DOI: 10.1594/pangaea.720878
title: Documentation of sediment core GIK23449-7
DOI: 10.1594/pangaea.735200
title: Basic measurements of radiation at station Bermuda (2009-10)
DOI: 10.1594/pangaea.733363
title: Documentation of sediment core MSM12/651-2
DOI: 10.1594/pangaea.676671
title: (Table 1) Stable carbon and oxygen isotope composition of Lenticulina rotulata from Late Cretaceous sediments of ODP Hole 113-690C, South Atlantic
DOI: 10.1594/pangaea.733357
title: Documentation of sediment core MSM12/647-1
DOI: 10.1594/pangaea.748327
title: Hydrography on standard level calculated from water bottle samples of RV Hudson in 1970
DOI: 10.1594/pangaea.772937
title: (Table 4) Results from O-Sr-Nd-isotope analysis for igneous and metamorphic rocks from the Alborán Basin
DOI: 10.1594/pangaea.752682
title: Meteorological observations during VENUS cruise from Paramaribo to Curaçao started at 1843-06-28
DOI: 10.1594/pangaea.846291
title: Shearing experiments of IODP Hole 343-C0019E
DOI: 10.1594/pangaea.511121
title: Radiosonde at Georg-Forster station on 1988-05-04 00:00h

description: Height of tropopause 8555 m
DOI: 10.1594/pangaea.618951
title: Water temperature profile LD00-5-a
DOI: 10.1594/pangaea.693731
title: Mesozooplankton during KIEV cruise 02

description: Standard Judey net
DOI: 10.1594/pangaea.756389
title: (Table 2e) Migration forms of hydrocarbons in waters of the Gulf of Riga at Station Nem-94-635
DOI: 10.1594/pangaea.810627
title: (Table 3) Trace elements of basalts at DSDP Hole 74-525A (on a dried, 110 deg C basis)
DOI: 10.1594/pangaea.910419
title: Radiosonde measurements from station Eastern North Atlantic (2015-06)

description: Launches may be at irregular time intervals
DOI: 10.1594/pangaea.726784
title: (Table 1) Age determination of profile LAO22-95
DOI: 10.1594/pangaea.719595
title: Radiosonde measurements from station Bondville (2003-06)

description: Version 2, 2009-06-15; Start location: Lincoln, IL; Distance from radiation site: 82 km; If launch time is exactly 00Z or 12Z, the actual launch time is likely unknown