cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.14266623
title: Long-Read Structural and Epigenetic Profiling of a Kidney Tumor-Matched Sample with Nanopore Sequencing and Optical Genome Mapping

description: Carcinogenesis often involves significant alterations in the cancer genome, marked by large structural and copy number variations (SVs and CNVs) that are difficult to capture with short-read sequencing. Traditionally, cytogenetic techniques are applied to detect such aberrations, but they are limited in resolution and do not cover features smaller than several hundred kilobases. Optical genome mapping (OGM) and nanopore sequencing (ONT) bridge this resolution gap and offer enhanced performance for cytogenetic applications. Additionally, both methods can capture epigenetic information as they profile native, individual DNA molecules. We compared the effectiveness of the two methods in characterizing the structural, copy number and epigenetic landscape of a clear cell renal cell carcinoma tumor. Both methods provided comparable results for basic karyotyping and CNVs, but differed in their ability to detect SVs of different sizes and types. ONT outperformed OGM in detecting small SVs, while OGM excelled in detecting larger SVs, including translocations. Differences were also observed among various ONT SV callers. Additionally, both methods provided insights into the tumor's methylome and hydroxymethylome. While ONT was superior in methylation calling, hydroxymethylation reports can be further optimized. Our findings underscore the importance of carefully selecting the most appropriate platform based on specific research questions.

 

OGM and ONT data of a ccRCC tumor and a normal adjacent tissue. 

Files include:



Optical Genome Mapping (OGM) files:


a. 5hmC:

5hmC_normal_alignemnt.rar  (.xmap, _q.cmap, _r.cmap)

5hmC_tumor_alignment.rar (.xmap, _q.cmap, _r.cmap)

5hmC_normal_min.cov20_normalized.bedgraph

5hmC_tumor_min.cov20_normalized.bedgraph

b. reduced representation optical methylation mapping (ROM with MtaqI):

normal_Mtaq_alignment.rar (.xmap, _q.cmap, _r.cmap)

tumor_Mtaq_alignment.rar (.xmap, _q.cmap, _r.cmap)

normal_Mtaq_min.cov20_normalized.bedgraph

tumor_Mtaq_min.cov20_normalized.bedgraph

c. SVs:

normal_variants_combine_filters_inMoleRefine1.smap

tumor_variants_combine_filters_inMoleRefine1.smap

 

2. Oxford nanopore sequencing (ONT) files:

a. ONT bedmethyl (modkit outputs):

ONT_modkit_5hmC_normal.bed

ONT_modkit_5hmC_tumor.bed

ONT_modkit_5mC_normal.bed

ONT_modkit_5mC_tumor.bed

b. SVs:

normal_ONT_EPI2ME_SV.vcf

tumor_ONT_EPI2ME_SV.vcf
DOI: 10.15468/dl.qfyj8q
title: Occurrence Download

description: A dataset containing 11378 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is North America",
 "Country is United States of America",
 "OccurrenceStatus is Present",
 "TaxonKey is Quercus stellata Wangenh."
 ]
}

 The dataset includes 11378 records from 136 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020356-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7483/opendata.totem.dz6r.41rb
title: 2011 Proton scattering data from Roman Pots at energy sqrt(s) = 7 TeV
DOI: 10.15468/dl.g82bba
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is one of (BRA.13.44_2, BRA.13.661_2)",
 "OccurrenceStatus is Present",
 "TaxonKey is Mammalia",
 "Year 2010-2024"
 ]
}

 The dataset includes 7 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020358-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.a8wef3
title: Occurrence Download

description: A dataset containing 517 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bathyraja trachura (Gilbert, 1892)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 517 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020359-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mafgsb
title: Occurrence Download

description: A dataset containing 468 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Galium ephedroides Willk."
 ]
}

 The dataset includes 468 records from 52 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020361-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.g7jwtr
title: Occurrence Download

description: A dataset containing 89 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Prunus salicina Lindl.",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is Living Specimen"
 ]
}

 The dataset includes 89 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020360-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.12943018
title: Global climatology of sea-surface methanethiol (MeSH) concentration fields

description: This dataset contains a global climatology of sea-surface MeSH concentration and sea-to-air flux, as described in this article (see README file):

Wohl, C., Villamayor, J., Galí, M., Mahajan, A. S., Fernández, R. P., Cuevas, C. A., Bossolasco, A., Li, Q., Kettle, A. J., Williams, T., Sarda-Esteve, R., Gros, V., Simó, R., and Alfonso Saiz-Lopez, A. (2024). Marine emissions of methanethiol increase aerosol cooling in the Southern Ocean. Science Advances, 10(48), eadq2465. DOI: 10.1126/sciadv.adq2465

Given the several choices and uncertainties associated with sea-air gas flux calculations, we refrain from providing flux estimates, and encourage data users to calculate their own emission fields in a way that maximizes consistency with their chosen geophysical fields or model setup.
DOI: 10.5281/zenodo.12943019
title: Global climatology of sea-surface methanethiol (MeSH) concentration fields and sea-air fluxes

description: This dataset contains a global climatology of sea-surface MeSH concentration and sea-to-air flux. All fields are on a 1ºx1º monthly grid. Concentrations are in nmol/L, sea-to-air fluxes in µmol/m2/d. A detailed description of the calculations will be made available here as soon as the related article is accepted for publication and has been assigned a doi.
DOI: 10.5281/zenodo.14283311
title: Global climatology of sea-surface methanethiol (MeSH) concentration fields

description: This dataset contains a global climatology of sea-surface MeSH concentration and sea-to-air flux, as described in this article (see README file):

Wohl, C., Villamayor, J., Galí, M., Mahajan, A. S., Fernández, R. P., Cuevas, C. A., Bossolasco, A., Li, Q., Kettle, A. J., Williams, T., Sarda-Esteve, R., Gros, V., Simó, R., and Alfonso Saiz-Lopez, A. (2024). Marine emissions of methanethiol increase aerosol cooling in the Southern Ocean. Science Advances, 10(48), eadq2465. DOI: 10.1126/sciadv.adq2465

Given the several choices and uncertainties associated with sea-air gas flux calculations, we refrain from providing flux estimates, and encourage data users to calculate their own emission fields in a way that maximizes consistency with their chosen geophysical fields or model setup.
DOI: 10.5281/zenodo.14231870
title: Data: Core-periphery detection in multilayer networks
DOI: 10.5281/zenodo.14231869
title: Data: Core-periphery detection in multilayer networks
DOI: 10.5281/zenodo.14283419
title: Structural insight into the inactive/active states of 5-HT1AR and molecular mechanism of electric fields in modulating 5-HT1AR

description: The input files and parameter files of the MD simulations in the APO, SRO, EF0.01, and EF0.03 systems are included in the upload data.
DOI: 10.5281/zenodo.14283420
title: Structural insight into the inactive/active states of 5-HT1AR and molecular mechanism of electric fields in modulating 5-HT1AR

description: The input files and parameter files of the MD simulations in the APO, SRO, EF0.01, and EF0.03 systems are included in the upload data.
DOI: 10.15468/dl.gspdxq
title: Occurrence Download

description: A dataset containing 11987804 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Dutch Vegetation Database"
 ]
}

 The dataset includes 11987804 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020307-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qhc56a
title: Occurrence Download

description: A dataset containing 1893 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Pyrola aphylla Sm."
 ]
}

 The dataset includes 1893 records from 66 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020990-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ek5z7c
title: Occurrence Download

description: A dataset containing 10646 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-10.63165 41.33549,15.18890 41.33549,15.18890 51.66371,-10.63165 51.66371,-10.63165 41.33549))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Morchellaceae"
 ]
}

 The dataset includes 10646 records from 175 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020989-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kdrkvv
title: Occurrence Download

description: A dataset containing 12 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Minervarya muangkanensis (Suwannapoom, Yuan, Jiang, Yan, Gao & Che, 2017))",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 12 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0059448-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-4185
title: Baptist, vol. [11], no. 4 (1927)

description: [description english/roman)] Monthly
DOI: 10.15468/dl.nh6e9a
title: Occurrence Download

description: A dataset containing 861 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Wahlenbergia lobelioides (L.f.) Link",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 861 records from 50 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0255800-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hrumhn
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Astragalus lachnolobus Kovalevsk. & Vved."
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0076467-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-4318
title: Baptist, vol. [11], no. 9 (1927)

description: [description english/roman)] Monthly
DOI: 10.15468/dl.tegj6e
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Vietnamophryne inexpectata Poyarkov, Suwannapoom, Pawangkhanant, Aksornneam, Duong, Korost & Che, 2018)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0059471-230224095556074/datasets/export for details.
DOI: 10.25549/pcra-c14-5707
title: Baptist Ukrainy = [Ukrainian Baptist], no. 11 ([November] 1927)

description: [description english/roman)] 12 issues per year
DOI: 10.15468/dl.qfuvuw
title: Occurrence Download

description: A dataset containing 489 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pseudophoxinus callensis (Guichenot, 1850)"
 ]
}

 The dataset includes 489 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0343610-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mufny2
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Toxabramis hoffmanni Linnaeus, 1934"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0343608-210914110416597/datasets/export for details.
DOI: 10.25549/pcra-c14-5530
title: Baptist Ukrainy = [Ukrainian Baptist], no. 8 ([August] 1927)

description: [description english/roman)] 12 issues per year
DOI: 10.15468/dl.c5tcpj
title: Occurrence Download

description: A dataset containing 68 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Rubus humifusus Bab."
 ]
}

 The dataset includes 68 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0106148-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-5082
title: Baptist Ukrainy = [Ukrainian Baptist], no. 1 ([January] 1927)

description: [description english/roman)] 12 issues per year
DOI: 10.15468/dl.82ncq5
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Eigenmannia matintapereira Peixoto, Dutra & Wosiacki, 2015"
 ]
}

 The dataset includes 3 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0343627-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yznp96
title: Occurrence Download

description: A dataset containing 594 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Asclepias mexicana Cav."
 ]
}

 The dataset includes 594 records from 67 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031036-230810091245214/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-5744
title: Baptist Ukrainy = [Ukrainian Baptist], no. 12 ([December] 1927)

description: [description english/roman)] 12 issues per year
DOI: 10.15468/dl.dvre3v
title: Occurrence Download

description: A dataset containing 17 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Mylochromis mola (Trewavas, 1935)"
 ]
}

 The dataset includes 17 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0339128-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ta6me7
title: Occurrence Download

description: A dataset containing 139 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is one of (USA.6_1, USA.32_1)",
 "TaxonKey is Cicuta maculata L."
 ]
}

 The dataset includes 139 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031043-230810091245214/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-ouc11200647
title: Baptist Ukrainy = [Ukrainian Baptist], no. 11 ([November] 1927)

description: [description english/roman)] 12 issues per year
DOI: 10.15468/dl.t47gta
title: Occurrence Download

description: A dataset containing 13 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Caragana gobica Sanchir"
 ]
}

 The dataset includes 13 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009736-230918134249559/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vchxs4
title: Occurrence Download

description: A dataset containing 3043 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "Continent is Europe",
 "Year is greater than 1978",
 "Year is less than 2014",
 "HasGeospatialIssue is false",
 "TaxonKey is Hypericum foliosum Dryand. ex Aiton"
 ]
}

 The dataset includes 3043 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0059477-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yt4g36
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Sarcohyla miahuatlanensis (Meik, Smith, Canseco-Márquez & Campbell, 2006))",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0059447-230224095556074/datasets/export for details.
DOI: 10.25549/pcra-c14-5195
title: Baptist Ukrainy = [Ukrainian Baptist], no. 2 ([February] 1927)

description: [description english/roman)] 12 issues per year
DOI: 10.15468/dl.zphpzz
title: Occurrence Download

description: A dataset containing 55 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "HasCoordinate is false",
 "TaxonKey is Arenaria capillipes (Boiss.) Boiss."
 ]
}

 The dataset includes 55 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0108471-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f3bvft
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Rhinella iserni (Jiménez de la Espada, 1875))",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0059538-230224095556074/datasets/export for details.
DOI: 10.25549/pcra-c14-5128
title: Baptist Ukrainy = [Ukrainian Baptist], no. 1 ([January] 1927)

description: [description english/roman)] 12 issues per year
DOI: 10.15468/dl.t2jm4s
title: Occurrence Download

description: A dataset containing 1402 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-23.87077 31.44365,53.87077 31.44365,53.87077 62.55635,-23.87077 62.55635,-23.87077 31.44365))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Gobius cruentatus Gmelin, 1789"
 ]
}

 The dataset includes 1402 records from 36 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015689-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f2upcc
title: Occurrence Download

description: A dataset containing 1411 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Incilius coniferus (Cope, 1862), Incilius coccifer (Cope, 1866))",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 1411 records from 38 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0059564-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-195070
title: An interview with Pentecostal Andreyev, s.d.

description: [description english/roman)] Interview of Aleksei Leonidovich Andreyev, senior elder brother of the AUECB (All-Union Council of Evangelical Christian-Baptists) in Ukraine, by Nikolay Nikolayevich Mel'nikov with fellow employees of the former Union of CFE (Christians of Faith Evangelical) (Pentecostals), 1946-1950?
DOI: 10.15468/dl.q2v5rk
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Quasipaa acanthophora Dubois & Ohler, 2009)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0059485-230224095556074/datasets/export for details.
DOI: 10.15468/dl.hkr59a
title: Occurrence Download

description: A dataset containing 86 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Calomyscus mystax Kashkarov, 1925"
 ]
}

 The dataset includes 86 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0349855-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-194776
title: 1948 - position on the statute of Union
DOI: 10.15468/dl.cp742h
title: Occurrence Download

description: A dataset listing the 1371 species recorded in GBIF matching the query:
{
 "DatasetKey" : [
 "is Natural History Museum Rotterdam - Observations"
 ]
}

 The dataset's 1371 records were derived from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0059571-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.