cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.14266624
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: 10.5281/zenodo.14760957
title: Optical Genome and Epigenome Mapping of Clear Cell Renal Cell Carcinoma

description: Cancer cells display complex genomic aberrations that include large-scale genetic rearrangements and epigenetic modulation that are not easily captured by short-read sequencing. This study presents a novel approach for simultaneous profiling of long-range genetic and epigenetic changes in matched cancer samples, focusing on clear cell renal cell carcinoma (ccRCC). ccRCC is a common kidney cancer subtype frequently characterized by a 3p deletion and the inactivation of  the von Hippel–Lindau (VHL) gene.  We performed integrated genetic, cytogenetic and epigenetic analyses on paired tumor and adjacent non-tumorous tissue samples. Optical genome mapping identified genomic aberrations as structural and copy number variations, complementing exome-sequencing findings. Single-molecule methylome and hydroxymethylome mapping revealed a significant global reduction in 5hmC level in both sample pairs, and a correlation between both epigenetic signals and gene expression was observed. The single-molecule epigenetic analysis identified numerous differentially modified regions, some implicated in ccRCC pathogenesis, including the genes VHL, PRCC and PBRM1. Notably, pathways related to metabolism and cancer development were significantly enriched among these differential regions. This study demonstrates the feasibility of integrating optical genome and epigenome mapping for comprehensive characterization of matched tumor and adjacent tissue, uncovering both established and novel somatic aberrations.

 

Optical genome and epigenome mapping data of a ccRCC tumor and a normal adjacent tissue from two patients. 

Files include:



Optical Genome Mapping (OGM) files:


Bionano Genomics .bnx (molecules) files and assembly results:

Genetics_advanced_stage_ccRCC_tumor_molecules.bnx.gz

Genetics_early_stage_ccRCC_adjacent_molecules.bnx.gz

Genetics_early_stage_ccRCC_tumor_molecules.bnx.gz

Genetics_advanced_stage_ccRCC_adjacent_molecules.bnx.gz

Genetics_advanced_ccRCC_adjacent_DeNovoAssembly.zip

Genetics_early_ccRCC_adjacent_DeNovoAssembly.zip

Genetics_advanced_ccRCC_tumor_DeNovoAssembly.zip

Genetics_early_ccRCC_tumor_DeNovoAssembly.zip

2. Optical Epigenome Mapping (OEM):

 Bionano Genomics alignment files (.xmap, _q.cmap, _r.cmap) of 5hmC and unmethylation (reduced representation optical methylation mapping - ROM, with MtaqI) experiments, and processed epigenetic signal bedgraph files, of an early state ccRCC tumor and normal adjacent tissue:

OEM_early_stage.rar

Similar data, obtained from an advanced stage ccRCC sample, can be found in: 10.5281/zenodo.14266624
DOI: 10.5281/zenodo.14760958
title: Optical Genome and Epigenome Mapping of Clear Cell Renal Cell Carcinoma

description: Cancer cells display complex genomic aberrations that include large-scale genetic rearrangements and epigenetic modulation that are not easily captured by short-read sequencing. This study presents a novel approach for simultaneous profiling of long-range genetic and epigenetic changes in matched cancer samples, focusing on clear cell renal cell carcinoma (ccRCC). ccRCC is a common kidney cancer subtype frequently characterized by a 3p deletion and the inactivation of  the von Hippel–Lindau (VHL) gene.  We performed integrated genetic, cytogenetic and epigenetic analyses on paired tumor and adjacent non-tumorous tissue samples. Optical genome mapping identified genomic aberrations as structural and copy number variations, complementing exome-sequencing findings. Single-molecule methylome and hydroxymethylome mapping revealed a significant global reduction in 5hmC level in both sample pairs, and a correlation between both epigenetic signals and gene expression was observed. The single-molecule epigenetic analysis identified numerous differentially modified regions, some implicated in ccRCC pathogenesis, including the genes VHL, PRCC and PBRM1. Notably, pathways related to metabolism and cancer development were significantly enriched among these differential regions. This study demonstrates the feasibility of integrating optical genome and epigenome mapping for comprehensive characterization of matched tumor and adjacent tissue, uncovering both established and novel somatic aberrations.

 

Optical genome and epigenome mapping data of a ccRCC tumor and a normal adjacent tissue from two patients. 

Files include:



Optical Genome Mapping (OGM) files:


Bionano Genomics .bnx (molecules) files and assembly results:

Genetics_advanced_stage_ccRCC_tumor_molecules.bnx.gz

Genetics_early_stage_ccRCC_adjacent_molecules.bnx.gz

Genetics_early_stage_ccRCC_tumor_molecules.bnx.gz

Genetics_advanced_stage_ccRCC_adjacent_molecules.bnx.gz

Genetics_advanced_ccRCC_adjacent_DeNovoAssembly.zip

Genetics_early_ccRCC_adjacent_DeNovoAssembly.zip

Genetics_advanced_ccRCC_tumor_DeNovoAssembly.zip

Genetics_early_ccRCC_tumor_DeNovoAssembly.zip

2. Optical Epigenome Mapping (OEM):

 Bionano Genomics alignment files (.xmap, _q.cmap, _r.cmap) of 5hmC and unmethylation (reduced representation optical methylation mapping - ROM, with MtaqI) experiments, and processed epigenetic signal bedgraph files, of an early state ccRCC tumor and normal adjacent tissue:

OEM_early_stage.rar

Similar data, obtained from an advanced stage ccRCC sample, can be found in: 10.5281/zenodo.14266624
DOI: 10.5281/zenodo.14882488
title: Oracle Bone Inscriptions Dataset with Additional Contextual Reconstruction from Fragmented Pieces
DOI: 10.15468/dl.kx97bk
title: Occurrence Download

description: A dataset containing 3527 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Neogobius melanostomus (Pallas, 1814), Lepomis gibbosus (Linnaeus, 1758), Ameiurus melas (Rafinesque, 1820), Proterorhinus marmoratus (Pallas, 1814), Pseudorasbora parva (Temminck & Schlegel, 1846), Sander volgensis (Gmelin, 1789))",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "Year is less than or equal to 2020",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Material sample, Specimen)"
 ]
 }
 },
 "Country is Germany",
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 1000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 3527 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002836-250214102907787/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.28428731
title: Geoprocessing Data in QGIS (training)

description: This repo contains a series of datasets connected to training on geoprocessing.Within the zipped folder there are two subfolder, one containing raster data and the second one containing vector data.
DOI: 10.15468/dl.vkfasg
title: Occurrence Download

description: A dataset containing 67535 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Continent is Europe",
 "Country is Italy",
 "DatasetKey is Pl@ntNet observations",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year 2021-2025"
 ]
}

 The dataset includes 67535 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002837-250214102907787/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.48532/059000
title: GSA
title: Cardiff GSA Cohort
DOI: 10.15468/dl.ubzuwc
title: Occurrence Download

description: A dataset containing 21361 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Material sample, Material citation, Specimen)",
 "TaxonKey is Pachycephala Vigors, 1825"
 ]
}

 The dataset includes 21361 records from 87 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002838-250214102907787/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34740/kaggle/dsv/10772829
title: Bangladesh Historical MaxMin Temperature Data-9512
DOI: 10.15468/dl.6nkca4
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Penicillium pulvis Houbraken, Visagie, Samson & Seifert"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002839-250214102907787/datasets/export for details.
DOI: 10.6084/m9.figshare.28429283
title: LCTopo

description: A dataset (LCTopo) that integrate the topographic characteristics of lakes are proposed here.
DOI: 10.6084/m9.figshare.28429283.v1
title: <b>Integrating topographic characteristics to construct lake and catchment topology on the Tibetan Plateau</b>

description: A dataset (LCTopo) that integrate the topographic characteristics of lakes are proposed here.
DOI: 10.15468/dl.feh986
title: Occurrence Download

description: A dataset containing 20 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Colletotrichum chrysophilum W.A.S.Vieira, W.G.Lima, M.P.S.Câmara & V.P.Doyle"
 ]
}

 The dataset includes 20 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002840-250214102907787/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.2908/tag00044
title: Erzeugung von Rindfleisch in Schlachthöfen
title: Production of bovine meat in slaughterhouses
title: Production de viande bovine en abattoirs

description: Total carcass weight (in 1000 t) of bovine animals (calves, bullocks, bulls, heifers and cows) slaughtered in slaughterhouses.
description: Poids carcasse total (en 1000 t) des bovins (veaux, boeufs, taureaux, génisses et vaches) abattus en abattoir.
description: Gesamtschlachtgewicht (in 1000 T) von Rindern (Kälber, Ochsen, Bullen, Färsen und Kühe), die in Schlachthäusern geschlachtet wurden.
DOI: 10.2908/tag00045
title: Production of sheepmeat and goat meat in slaughterhouses
title: Production de viande ovine et caprine en abattoirs
title: Erzeugung von Schaf- und Ziegenfleisch in Schlachthöfen

description: Gesamtschlachtgewicht (in 1000 T) von Schafen, einschließlich Lämmern und Ziegen, die in Schlachthäusern geschlachtet wurden.
description: Poids carcasse total (en 1000 t) des ovins, dont les agneaux, et des caprins abattus en abattoir.
description: Total carcass weight (in 1000 t) of sheep, including lambs, and goats slaughtered in slaughterhouses.
DOI: 10.15468/dl.etntfy
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Colletotrichum abscissum Pinho & O.L.Pereira"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002841-250214102907787/datasets/export for details.
DOI: 10.5281/zenodo.14587455
title: EEG2Code_240 data
DOI: 10.5525/gla.researchdata.1870
title: The two costs of neglect: evaluating the health and economic impacts of anthrax in an endemic area of rural Africa
DOI: 10.5281/zenodo.12665435
title: Supporting FDSC data for Bissbort et al. ACS

description: This dataset contains FDSC heat flow curves that were used for Fig 1a in Bissbort et al. submitted to The Journal of Physical Chemistry Letters ACS.
DOI: 10.5281/zenodo.12665436
title: Supporting FDSC data for Bissbort et al. ACS

description: This dataset contains FDSC heat flow curves that were used for Fig 1a in Bissbort et al. submitted to The Journal of Physical Chemistry Letters ACS.
DOI: 10.48532/060000
title: Imperial APC
title: Imperial Amyloid PET Cohort
DOI: 10.15468/dl.n6x4uv
title: Occurrence Download

description: A dataset containing 99 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Habenaria kyimbilae Schltr."
 ]
}

 The dataset includes 99 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002843-250214102907787/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.anwrm3
title: Occurrence Download

description: A dataset containing 11004 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Cryptomeria japonica (Thunb. ex L.f.) D.Don"
 ]
}

 The dataset includes 11004 records from 356 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002842-250214102907787/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.28429295
title: 的类风湿关节炎滑膜差异基因研究 多种机器学习算法

description: <b>目的：</b>本研究的目的是将各种机器学习算法与生物信息学技术相结合，深入分析类风湿关节炎 （RA） 患者滑膜细胞中的差异表达基因，揭示这些基因与 RA 滑膜细胞相关的潜在分子机制，为临床治疗策略的创新提供新思路。<b>方法：</b>我们从公共数据库 GEO 中下载了 GSE1919、GSE12021、GSE55457 和 GSE77298 数据集作为训练集，GSE89408 数据集被用作独立的验证集。我们对训练集进行了标准化，并应用了 ComBat 算法来消除批量效应，从而获得了一个合并的基因表达数据集。随后，我们进行差异表达分析，筛选出在疾病条件下发生显著变化的基因，并进行富集分析。为了更准确地识别与疾病特征密切相关的基因，我们使用了三种机器学习算法：Lasso 回归、随机森林和 SVM 来独立分析合并的基因表达数据集，并采用三种方法的结果的交集来构建与疾病特征相关的更稳健的基因列表。此外，我们在训练集上验证了这些重要的疾病特征相关基因，并使用 GSE89408 数据集进行了独立的外部验证。同时，我们还进行了免疫浸润分析，深入探讨了这些基因在类风湿关节炎发生发展中的作用机制。<b>结果和结论：</b>本研究显示，RA 患者滑膜细胞中的基因表达模式与对照组相比存在显著差异，尤其是 HCP5 和 WISP3 等疾病特征相关基因的表达显著上调。这些发现为理解 RA 的基因表达调控机制提供了新的视角，为探索未来的治疗策略提供了重要的科学证据。
DOI: 10.14278/rodare.3197
title: Data publication: Simulation results on Aminophenyl Viologen

description: Structural and electronic properties simulated using DFT/PBE level of theory with TS dispersion correction as implemented in FHI-Aims code.
DOI: 10.14278/rodare.3198
title: Data publication: Simulation results on Aminophenyl Viologen

description: Structural and electronic properties simulated using DFT/PBE level of theory with TS dispersion correction as implemented in FHI-Aims code.
DOI: 10.14278/rodare.3349
title: Data to "Assessment of post-SCF Methods with Localized Basis Sets for Periodic Systems using FCI-QMC"

description: The data contains two archives: One containing all files to calculate the FCIDUMP files in CP2K, and the remaining input and output files of the FCIQMC calculations using NECI, and a second one with all files for DFT and correlated calculations using CP2K.
DOI: 10.14278/rodare.3350
title: Data to "Assessment of post-SCF Methods with Localized Basis Sets for Periodic Systems using FCI-QMC"

description: The data contains two archives: One containing all files to calculate the FCIDUMP files in CP2K, and the remaining input and output files of the FCIQMC calculations using NECI, and a second one with all files for DFT and correlated calculations using CP2K.
DOI: 10.15468/dl.tmwxe9
title: Occurrence Download

description: A dataset containing 953928 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Eudynamys scolopaceus (Linnaeus, 1758)"
 ]
}

 The dataset includes 953928 records from 163 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002828-250214102907787/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sf75es
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Italy",
 "StateProvince is Campania",
 "TaxonKey is one of (Cervus elaphus Linnaeus, 1758, Capreolus capreolus (Linnaeus, 1758))",
 "Year 2020-2025"
 ]
}

 The dataset includes 6 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002845-250214102907787/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.14278/rodare.1422
title: Data publication: Data-Driven Quest for Two-Dimensional Non-van der Waals Materials

description: This dataset includes the primary research data for the publication "Data-Driven Quest for Two-Dimensional Non-van der Waals Materials", https://doi.org/10.1021/acs.nanolett.1c03841.
DOI: 10.14278/rodare.1853
title: Data publication: A New Group of Two-Dimensional Non-van der Waals Materials with Ultra Low Exfoliation Energies

description: This dataset includes the primary research data for the publication "A New Group of Two-Dimensional Non-van der Waals Materials with Ultra Low Exfoliation Energies".
DOI: 10.14278/rodare.1951
title: Data publication: A New Group of Two-Dimensional Non-van der Waals Materials with Ultra Low Exfoliation Energies

description: This dataset includes the primary research data for the publication "A New Group of Two-Dimensional Non-van der Waals Materials with Ultra Low Exfoliation Energies".
DOI: 10.14278/rodare.2034
title: Data publication: A New Group of Two-Dimensional Non-van der Waals Materials with Ultra Low Exfoliation Energies

description: This dataset includes the primary research data for the publication "A New Group of Two-Dimensional Non-van der Waals Materials with Ultra Low Exfoliation Energies".
DOI: 10.15468/dl.5j3634
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Aspergillus neoniger Varga, Frisvad & Samson"
 ]
}

 The dataset includes 5 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002846-250214102907787/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.14278/rodare.2497
title: Data publication: Magnetic State Control of Non-van der Waals 2D Materials by Hydrogenation

description: This dataset includes the primary research data for the publication "Magnetic State Control of Non-van der Waals 2D Materials by Hydrogenation".
DOI: 10.14278/rodare.2678
title: Data publication: Magnetic State Control of Non-van der Waals 2D Materials by Hydrogenation

description: This dataset includes the primary research data for the publication "Magnetic State Control of Non-van der Waals 2D Materials by Hydrogenation".
DOI: 10.48532/061000
title: MRC_LOAD
title: MRC Genetic Resource for LOAD
DOI: 10.15468/dl.es6bqs
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Kalmanozyma brasiliensis (J.V.C.Oliveira, T.A.Borges, R.A.C.Santos, L.F.D.Freitas, C.A.Rosa, G.H.Goldman & D.M.Riano-Pachon) Q.M.Wang, F.Y.Bai, Begerow & Boekhout, 2015"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002847-250214102907787/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.2908/tag00014
title: Number of dairy cows
title: Nombre de vaches laitières
title: Anzahl der Milchkühe

description: Anzahl der Tiere in 1000, wie in der jährlichen Viehbestandserhebung in November/Dezember angegeben.
description: Expressed in 1000 heads, as reported in the annual livestock survey that is carried out in November/December.
description: Exprimé en milliers, tel que rapporté dans l'enquête annuelle sur le cheptel de novembre/décembre.
DOI: 10.2908/tag00016
title: Number of bovine animals
title: Nombre de têtes de bétail
title: Anzahl der Rinder

description: Anzahl der Tiere in 1000, wie in der jährlichen Viehbestandserhebung in November/Dezember angegeben.
description: Expressed in 1000 heads, as reported in the annual livestock survey that is carried out in November/December.
description: Exprimé en milliers, tel que rapporté dans l'enquête annuelle sur le cheptel de novembre/décembre.
DOI: 10.6084/m9.figshare.27646659
title: Local discontinuous Galerkin methods with implicit–explicit BDF time marching for Newell–Whitehead–Segel equations

description: The Newell–Whitehead–Segel type equations with time-dependent Dirichlet boundary conditions are solved by the local discontinuous Galerkin (LDG) method coupled with the implicit–explicit backward difference formulas (IMEX-BDF). With a suitable setting of numerical fluxes and by the aid of the multiplier technique and the a priori error assumption technique, the optimal error estimate for the corresponding fully discrete LDG-IMEX-BDF schemes is obtained by energy analysis, under the condition τ≤Ch1/s, where <i>h</i> and <i>τ</i> are mesh size and time step, respectively, the positive constant <i>C</i> is independent of <i>h</i>, and s=1,…,5 is the order of the IMEX-BDF method. Numerical experiments are also presented to verify the accuracy of the considered schemes.