cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.20001014.v1
title: Additional file 15 of Integrated proteogenomic characterization of urothelial carcinoma of the bladder

description: Additional file 15. Table S3: Differentially expressed mRNAs, proteins, and phosphoproteins between tumors and MNUs. Related to Figure 3, Additional file 3: Fig. S3. A. Lists of mRNAs, proteins, and phosphoproteins used for principal component analysis (PCA). B. Lists of differentially expressed mRNAs, proteins and phosphoproteins (Wilcoxon rank-sum test, FDR &lt; 0.01, Tumors/MNUs ratio &gt; 2 or &lt; 1/2) in tumors and MNUs. C. A list of genes with significant patient survival difference on both protein and mRNA level. D. A list of candidate target genes of UC.
DOI: 10.6084/m9.figshare.20001023
title: Additional file 18 of Integrated proteogenomic characterization of urothelial carcinoma of the bladder

description: Additional file 18. Table S6: Differentially expressed among immune clusters. Related to Figure 6, Additional file 6: Fig. S6. A. Data analysis by xCell. B. Information of Immune cluster. C. Data analysis by estimate. D. Peaks correlated with immune score. E. Expression of immune checkpoint. F. Pathways upregulated in each immune cluster. G. Targets of NFKB1. H. Information of patients received PD-1 immunotherapy. I. TRAF2 identified in patients.
DOI: 10.25403/upresearchdata.25122782
title: The analyses of various techniques to characterise HepG2 monolayer and spheroid cultured for 17 days and 21 days, respectively

description: The aim of this study was to characterise HepG2 cells differentially cultured as monolayer or three-dimensional spheroids, in the presence and absence of chronic enzyme-inducing drug cocktail exposure. Also, to evaluate the models’ feasibility over an extended culture time and compare their metabolic capabilities as candidates for hepatotoxicity screening platforms. This was done by generating HepG2 spheroids using the liquid overlay method for up to 21 days and culturing same origin HepG2 monolayers for 17 days. Cells were evaluated for morphology, viability, protein content, monolayer cell cycle profile, proteins mass profile differences, and the presence of hepatic markers in spheroids. The metabolic activity was assessed using liquid chromatography tandem mass spectrometry.
The monolayer and drug cocktail exposed monolayer cells were viable for up to 17 days while the spheroids and drug cocktail exposed spheroids were viable up to 21 days. CYP1A2 activity was detected in all cultures with slightly more acetaminophen (µmol/µg<sub>protein</sub>) detected in monolayer cultures. The activity confirms CYP1A2 expression detected in all spheroid cultures from Day 7 to Day 21. Furthermore, minimal hydroxybupropion, dextrorphan and hydroxymidazolam was detected in all cultures suggesting low CYP2B6, CYP2D6 and CYP3A4 activity, respectively. The metabolite levels were similar between induction and non-induction cultures suggesting that the induction drug cocktail had no significant effect on the metabolic capacity of the HepG2 cells under either of the culturing conditions used. Therefore, the metabolic activity may be due to accumulated innate metabolic capability and/or long-term culture.
Furthermore, the growth plateau observed in spheroid cultures’ protein levels after Day 4 and the hepatic markers (AFP, HNF-4α, CK18 and albumin) expression observed from Day 7, would be desirable for repeated hepatotoxicity testing. Other studies have shown HepG2 spheroid cell viability and increased hepatic marker expression for more than 21 days, with a relatively consistent metabolic profile after 21 days, suggesting a stable differentiated phenotype. This is beneficial for repeated, long-term drug exposure for acute and chronic hepatotoxicity screening.
DOI: 10.25403/upresearchdata.25122782.v1
title: The analyses of various techniques to characterise HepG2 monolayer and spheroid cultured for 17 days and 21 days, respectively

description: The aim of this study was to characterise HepG2 cells differentially cultured as monolayer or three-dimensional spheroids, in the presence and absence of chronic enzyme-inducing drug cocktail exposure. Also, to evaluate the models’ feasibility over an extended culture time and compare their metabolic capabilities as candidates for hepatotoxicity screening platforms. This was done by generating HepG2 spheroids using the liquid overlay method for up to 21 days and culturing same origin HepG2 monolayers for 17 days. Cells were evaluated for morphology, viability, protein content, monolayer cell cycle profile, proteins mass profile differences, and the presence of hepatic markers in spheroids. The metabolic activity was assessed using liquid chromatography tandem mass spectrometry.
The monolayer and drug cocktail exposed monolayer cells were viable for up to 17 days while the spheroids and drug cocktail exposed spheroids were viable up to 21 days. CYP1A2 activity was detected in all cultures with slightly more acetaminophen (µmol/µg<sub>protein</sub>) detected in monolayer cultures. The activity confirms CYP1A2 expression detected in all spheroid cultures from Day 7 to Day 21. Furthermore, minimal hydroxybupropion, dextrorphan and hydroxymidazolam was detected in all cultures suggesting low CYP2B6, CYP2D6 and CYP3A4 activity, respectively. The metabolite levels were similar between induction and non-induction cultures suggesting that the induction drug cocktail had no significant effect on the metabolic capacity of the HepG2 cells under either of the culturing conditions used. Therefore, the metabolic activity may be due to accumulated innate metabolic capability and/or long-term culture.
Furthermore, the growth plateau observed in spheroid cultures’ protein levels after Day 4 and the hepatic markers (AFP, HNF-4α, CK18 and albumin) expression observed from Day 7, would be desirable for repeated hepatotoxicity testing. Other studies have shown HepG2 spheroid cell viability and increased hepatic marker expression for more than 21 days, with a relatively consistent metabolic profile after 21 days, suggesting a stable differentiated phenotype. This is beneficial for repeated, long-term drug exposure for acute and chronic hepatotoxicity screening.
DOI: 10.6084/m9.figshare.20001008.v1
title: Additional file 13 of Integrated proteogenomic characterization of urothelial carcinoma of the bladder

description: Additional file 13. Table S1: Clinicopathologic information and multi-omics data in UC cohort. Related to Figure 1, Additional file 1: Fig. S1. A. Clinical data of UC samples. B. The sheet contains information of mutations identified by WES in the 116 UC. C. Average sequencing depth on target. D. Significantly mutated genes identified by MutSig. E. Genome signature analysis. F. RNA clean reads. G. Genes identified at protein level (unique peptide ≥2). H. RNA-protein pairs. I. Phosphosites identified in UC samples. J. HEK293T used for QC.
DOI: 10.6084/m9.figshare.22622533
title: Additional file 2 of A web tool for the global identification of pig breeds

description: Additional file 2: Table S1. Information on the breeds included in the chip reference dataset.
DOI: 10.6084/m9.figshare.20001008
title: Additional file 13 of Integrated proteogenomic characterization of urothelial carcinoma of the bladder

description: Additional file 13. Table S1: Clinicopathologic information and multi-omics data in UC cohort. Related to Figure 1, Additional file 1: Fig. S1. A. Clinical data of UC samples. B. The sheet contains information of mutations identified by WES in the 116 UC. C. Average sequencing depth on target. D. Significantly mutated genes identified by MutSig. E. Genome signature analysis. F. RNA clean reads. G. Genes identified at protein level (unique peptide ≥2). H. RNA-protein pairs. I. Phosphosites identified in UC samples. J. HEK293T used for QC.
DOI: 10.6084/m9.figshare.20001023.v1
title: Additional file 18 of Integrated proteogenomic characterization of urothelial carcinoma of the bladder

description: Additional file 18. Table S6: Differentially expressed among immune clusters. Related to Figure 6, Additional file 6: Fig. S6. A. Data analysis by xCell. B. Information of Immune cluster. C. Data analysis by estimate. D. Peaks correlated with immune score. E. Expression of immune checkpoint. F. Pathways upregulated in each immune cluster. G. Targets of NFKB1. H. Information of patients received PD-1 immunotherapy. I. TRAF2 identified in patients.
DOI: 10.6084/m9.figshare.20001026.v1
title: Additional file 19 of Integrated proteogenomic characterization of urothelial carcinoma of the bladder

description: Additional file 19. Table S7: Differentially expressed among immune clusters. Related to Figure 7, Additional file 7: Fig. S7. A. Gene analysis by WGCNA. B. Pathways upregulated in modules. C. Genes were screened from the MEblue module. D. Genes upregulated in each histologic group. E. Pathways upregulated in each histologic group.
DOI: 10.6084/m9.figshare.22622462
title: Additional file 5 of Identification of ZBTB4 as an immunological biomarker that can inhibit the proliferation and invasion of pancreatic cancer

description: Additional file 5: Table S3. Gene MANIA analysis of genes interacting with ZBTB4.
DOI: 10.6084/m9.figshare.22622536
title: Additional file 3 of A web tool for the global identification of pig breeds

description: Additional file 3: Table S2. Information on the individuals used as crossbreds, unknown breeds, and testing pure breeds.
DOI: 10.6084/m9.figshare.22622539
title: Additional file 4 of A web tool for the global identification of pig breeds

description: Additional file 4: Table S3. Information on the breeds used as independent testing dataset.
DOI: 10.6084/m9.figshare.22619378.v1
title: Additional file 4 of A variability in response of osteoclasts to zoledronic acid is mediated by smoking-associated modification in the DNA methylome

description: Additional file 4. Supplementary Table 2. Validation of top 59 significant smoking-dependent CpGs in an independent multi-omics BMD study [33]. Significant q-values are highlighted in bold, while highly significant q-values are also highlighted in red.
DOI: 10.6084/m9.figshare.22619387.v1
title: Additional file 7 of A variability in response of osteoclasts to zoledronic acid is mediated by smoking-associated modification in the DNA methylome

description: Additional file 7. Supplementary Table 5. This table shows the raw data for each CpG and each Phen#, success ratio was calculated as a proportion of #successful SNPs for that CpG to #all SNPs associated with that phenotype group, Phen#. “Success” means that the distance between location of a SNP and location of the CpG is less than the stated max distance. Series of incremental distances from 50,000 bp to 1,000 bp were tested, and then compared across the phenotype groups. The one-tailed Mann-Whitney U test was used to compare differences in success ratios between Phen1 and Phen 2 and “negative control” Phen4 as shown in Table 4.
DOI: 10.6084/m9.figshare.20001011
title: Additional file 14 of Integrated proteogenomic characterization of urothelial carcinoma of the bladder

description: Additional file 14. Table S2: CNV information in UC cohort. Related to Figure 2, Additional file 2: Fig. S2. A. This sheet contains somatic copy number gains and the relevant genes. B. This sheet contains somatic copy number losses and the relevant genes. C. List of cancer-associated genes (CAG), see Methods “Defining cancer-associated genes (CAG).” D. Lists of significant positive cis-effects in CNA-Protein and CAN-mRNA of chromosome 5p. E. Lists of significant positive cis-effects in CNA-Protein and CAN-mRNA of chromosome 7q.
DOI: 10.6084/m9.figshare.22622536.v1
title: Additional file 3 of A web tool for the global identification of pig breeds

description: Additional file 3: Table S2. Information on the individuals used as crossbreds, unknown breeds, and testing pure breeds.
DOI: 10.6084/m9.figshare.20001011.v1
title: Additional file 14 of Integrated proteogenomic characterization of urothelial carcinoma of the bladder

description: Additional file 14. Table S2: CNV information in UC cohort. Related to Figure 2, Additional file 2: Fig. S2. A. This sheet contains somatic copy number gains and the relevant genes. B. This sheet contains somatic copy number losses and the relevant genes. C. List of cancer-associated genes (CAG), see Methods “Defining cancer-associated genes (CAG).” D. Lists of significant positive cis-effects in CNA-Protein and CAN-mRNA of chromosome 5p. E. Lists of significant positive cis-effects in CNA-Protein and CAN-mRNA of chromosome 7q.
DOI: 10.6084/m9.figshare.20001017
title: Additional file 16 of Integrated proteogenomic characterization of urothelial carcinoma of the bladder

description: Additional file 16. Table S4: Differentially expressed proteins between MIBCs and NMIBCs. Related to Figure 4, Additional file 4: Fig. S4. A. Lists of differentially expressed proteins in MIBCs and NMIBCs. B. Lists of differentially expressed proteins in chromosome 5p gain compared with WT. C. The list of 9 significant positive cis-effects on chromosome 5p.
DOI: 10.6084/m9.figshare.20001032
title: Additional file 20 of Integrated proteogenomic characterization of urothelial carcinoma of the bladder

description: Additional file 20. Table S8: Modification identified in PGK1 and PKM2. Related to Figure 8. A. Modification identified in PGK1 and PKM2.
DOI: 10.6084/m9.figshare.20001020
title: Additional file 17 of Integrated proteogenomic characterization of urothelial carcinoma of the bladder

description: Additional file 17. Table S5: Multi-omics characteristics of proteomic subtypes in 116 UC samples. Related to Figure 5, Additional file 5: Fig. S5. A. Information of immune clusters. B. Genes upregulated in each proteomic subtype. C. Lists of upregulated proteins in one of the three proteomic subtypes. D. Contributions of 30 COSMIC signatures in 113 UC patients. E. Genes of each Signatures used in this figure. F. Survival analysis of selected factors.
DOI: 10.6084/m9.figshare.22619479
title: Additional file 2 of Comprehensive analysis of cuproptosis-related long noncoding RNA for predicting prognostic and diagnostic value and immune landscape in colorectal adenocarcinoma

description: Additional file 2: Table S2. The cuproptosis-related lncRNAs
DOI: 10.6084/m9.figshare.22622533.v1
title: Additional file 2 of A web tool for the global identification of pig breeds

description: Additional file 2: Table S1. Information on the breeds included in the chip reference dataset.
DOI: 10.6084/m9.figshare.22622539.v1
title: Additional file 4 of A web tool for the global identification of pig breeds

description: Additional file 4: Table S3. Information on the breeds used as independent testing dataset.
DOI: 10.15468/dl.mbhvys
title: Occurrence Download

description: A dataset containing 79 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Onobrychis subacaulis Boiss."
 ]
}

 The dataset includes 79 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0060837-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sauw4p
title: Occurrence Download

description: A dataset containing 669 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hemidactylus garnotii Duméril & Bibron, 1836",
 "Geometry POLYGON((-124.756451627043 24.5232175268442, -124.756451627043 49.3844869955705, -66.9490903544593 49.3844869955705, -66.9490903544593 24.5232175268442, -124.756451627043 24.5232175268442))"
 ]
}

 The dataset includes 669 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0060838-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vr2346
title: Occurrence Download

description: A dataset containing 173 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Oreocnide obovata (C.H.Wright) Merr."
 ]
}

 The dataset includes 173 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0060839-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rpr7ts
title: Occurrence Download

description: A dataset containing 50 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Oldenlandia pulvinata (Balf.f.) Vierh."
 ]
}

 The dataset includes 50 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0060840-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nft7p2
title: Occurrence Download

description: A dataset containing 12 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hemidactylus garnotti Scott et al., 1977",
 "Geometry POLYGON((-124.756451627043 24.5232175268442, -124.756451627043 49.3844869955705, -66.9490903544593 49.3844869955705, -66.9490903544593 24.5232175268442, -124.756451627043 24.5232175268442))"
 ]
}

 The dataset includes 12 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0060841-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hqyp2s
title: Occurrence Download

description: A dataset containing 10 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Onobrychis subnitens Bornm."
 ]
}

 The dataset includes 10 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0060842-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zxn5ju
title: Occurrence Download

description: A dataset containing 2760 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Oreocnide pedunculata (Shirai) Masam."
 ]
}

 The dataset includes 2760 records from 59 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0060843-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7jmntz
title: Occurrence Download

description: A dataset containing 72 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Oldenlandia pumila (L.f.) DC."
 ]
}

 The dataset includes 72 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0060844-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qaaf67
title: Occurrence Download

description: A dataset containing 42 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Onobrychis sulphurea Boiss. & Balansa"
 ]
}

 The dataset includes 42 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0060845-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mmv34g
title: Occurrence Download

description: A dataset containing 5106 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hemidactylus mabouia (Moreau De Jonnès, 1818)",
 "Geometry POLYGON((-124.756451627043 24.5232175268442, -124.756451627043 49.3844869955705, -66.9490903544593 49.3844869955705, -66.9490903544593 24.5232175268442, -124.756451627043 24.5232175268442))"
 ]
}

 The dataset includes 5106 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0060846-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rcymv8
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Oldenlandia rhabdina Bremek."
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0060847-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7467az
title: Occurrence Download

description: A dataset containing 1386 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Oreocnide rubescens (Blume) Miq."
 ]
}

 The dataset includes 1386 records from 43 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0060848-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sa95yb
title: Occurrence Download

description: A dataset containing 12242 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Onobrychis supina (Vill.) DC."
 ]
}

 The dataset includes 12242 records from 228 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0060849-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cqz8bj
title: Occurrence Download

description: A dataset containing 699 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hemidactylus parvimaculatus Deraniyagala, 1953",
 "Geometry POLYGON((-124.756451627043 24.5232175268442, -124.756451627043 49.3844869955705, -66.9490903544593 49.3844869955705, -66.9490903544593 24.5232175268442, -124.756451627043 24.5232175268442))"
 ]
}

 The dataset includes 699 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0060850-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fm2ytj
title: Occurrence Download

description: A dataset containing 35 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Oldenlandia richardsonioides (K.Schum.) Verdc."
 ]
}

 The dataset includes 35 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0060851-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ytnkrj
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Oreocnide semicrenata (Blume) Miq."
 ]
}

 The dataset includes 3 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0060852-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.q57ja5
title: Occurrence Download

description: A dataset containing 145 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hemidactylus platyurus (Schneider, 1797)",
 "Geometry POLYGON((-124.756451627043 24.5232175268442, -124.756451627043 49.3844869955705, -66.9490903544593 49.3844869955705, -66.9490903544593 24.5232175268442, -124.756451627043 24.5232175268442))"
 ]
}

 The dataset includes 145 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0060853-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.