cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.28059309.v1
title: Additional file 2 of EpiGePT: a pretrained transformer-based language model for context-specific human epigenomics

description: Additional file 2: Table S1: Comparison of the performance between fine-tuned EpiGePT and baseline methods in predicting HiChIP loops on the K562 cell line (positive-to-negative sample ratio of 1:1). Table S2: Comparison of the performance between fine-tuned EpiGePT and baseline methods in predicting HiChIP loops on the GM12878 cell line (positive-to-negative sample ratio of 1:1). Table S3: Comparison of the performance between fine-tuned EpiGePT and baseline methods in predicting HiChIP loops on the K562 cell line (positive-to-negative sample ratio of 1:2). Table S4: Comparison of the performance between fine-tuned EpiGePT and baseline methods in predicting HiChIP loops on the GM12878 cell line (positive-to-negative sample ratio of 1:2). Table S5: Description and comparison of EpiGePT with different settings. Table S6: The information of DNase-seq bam file across 129 biosamples from the ENCODE project. Table S7: The information of RNA-seq tab-separated values (tsv) file across 129 biosamples from the ENCODE project. Table S8: The preprocessed expression data of 711 human transcription factors from the ENCODE project across 129 biosamples. Table S9: The information of DNase-seq, CTCF and other six Histone markers bam file across 28 cell lines or tissues from the ENCODE project (hg19). Table S10: The information of RNA-seq tab-separated values (tsv) file across 28 cell lines or tissues from the ENCODE project (hg19). Table S11: The preprocessed expression data of 711 human transcription factors from the ENCODE project across 28 cell lines or tissues (hg19). Table S12: The information of RNA-seq tab-separated values (tsv) file across 104 cell lines or tissues from the ENCODE project (hg38). Table S13: The information of DNase-seq, CTCF and other six Histone markers bam file across 104 cell lines or tissues from the ENCODE project (hg38). Table S14: The preprocessed expression data of 711 human transcription factors from the ENCODE project across 104 cell lines or tissues (hg38). Table S15: The order and names of epigenomes of the expression matrices across 56 epigenomes from the ROADMAP project. Table S16: The preprocessed expression data of 642 human transcription factors across 56 epigenomes from the ROADMAP project. Table S17: The computational resource usage, including peak GPU memory and peak RAM consumption (NVIDIA GeForce RTX 3090). Table S18: The computational resource usage, including peak GPU memory and peak RAM consumption (NVIDIA GeForce RTX 4090). Table S19: The computational resource usage, including peak GPU memory and peak RAM consumption (NVIDIA RTX A6000).
DOI: 10.6084/m9.figshare.28059321.v1
title: Additional file 1 of Comprehensive analysis of housekeeping genes, tissue-specific genes, and dynamic regulation across developmental stages in pearl millet

description: Supplementary Material 1: Table S1 Summary of the quality of raw sequencing data for the 24 TDDSs; Table S2 Expression (TPM) matrix of the 35486 genes in the 24 TDDSs; Table S3 Gene ID and TAU scores of HKGs; Table S4 Gene ID of the 5 gene families for TIRGs annotated in genome of PI537069; Table S5 Primers sequence; Table S6 Gene ID and TAU scores of TSGs; Table S7 Tissue-specific transcription factors.
DOI: 10.6084/m9.figshare.28059321
title: Additional file 1 of Comprehensive analysis of housekeeping genes, tissue-specific genes, and dynamic regulation across developmental stages in pearl millet

description: Supplementary Material 1: Table S1 Summary of the quality of raw sequencing data for the 24 TDDSs; Table S2 Expression (TPM) matrix of the 35486 genes in the 24 TDDSs; Table S3 Gene ID and TAU scores of HKGs; Table S4 Gene ID of the 5 gene families for TIRGs annotated in genome of PI537069; Table S5 Primers sequence; Table S6 Gene ID and TAU scores of TSGs; Table S7 Tissue-specific transcription factors.
DOI: 10.6084/m9.figshare.28059334
title: Additional file 2 of Cannabinoids for treating psychiatric disorders in youth: a systematic review of randomized controlled trials

description: Supplementary Material 2.
DOI: 10.6084/m9.figshare.28059334.v1
title: Additional file 2 of Cannabinoids for treating psychiatric disorders in youth: a systematic review of randomized controlled trials

description: Supplementary Material 2.
DOI: 10.6084/m9.figshare.28059358
title: Additional file 1 of Genomic analyses revealed low genetic variation in the intron-exon boundary of the doublesex gene within the natural populations of An. gambiae s.l. in Burkina Faso

description: Supplementary Material 1.
DOI: 10.6084/m9.figshare.28059358.v1
title: Additional file 1 of Genomic analyses revealed low genetic variation in the intron-exon boundary of the doublesex gene within the natural populations of An. gambiae s.l. in Burkina Faso

description: Supplementary Material 1.
DOI: 10.6084/m9.figshare.28059361
title: Additional file 2 of Genomic analyses revealed low genetic variation in the intron-exon boundary of the doublesex gene within the natural populations of An. gambiae s.l. in Burkina Faso

description: Supplementary Material 2.
DOI: 10.6084/m9.figshare.28059361.v1
title: Additional file 2 of Genomic analyses revealed low genetic variation in the intron-exon boundary of the doublesex gene within the natural populations of An. gambiae s.l. in Burkina Faso

description: Supplementary Material 2.
DOI: 10.6084/m9.figshare.28059369
title: Additional file 7 of The F204S mutation in adrenodoxin oxidoreductase drives salinomycin resistance in Eimeria tenella

description: Additional file 7. Primers used in this study.
DOI: 10.6084/m9.figshare.28059369.v1
title: Additional file 7 of The F204S mutation in adrenodoxin oxidoreductase drives salinomycin resistance in Eimeria tenella

description: Additional file 7. Primers used in this study.
DOI: 10.15468/dl.z73gcd
title: Occurrence Download

description: A dataset containing 186 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "TaxonKey is one of (Plethodon vandykei Van Denburgh, 1906)"
 ]
}

 The dataset includes 186 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0040758-241126133413365/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.28059393
title: Additional file 3 of Evaluating causal associations of chronotype with pregnancy and perinatal outcomes and its interactions with insomnia and sleep duration: a mendelian randomization study

description: Additional file 3: Table S1. Definitions of outcomes. Table S2. Definition of chronotype in 23 and Me. Table S3. List of SNPs for chronotype and their female-specific estimates in UKB. Table S4. List of SNPs for insomnia and sleep duration. Table S5. Associations of chronotype SNPs with outcomes in MoBa, adjusting for fetal and paternal genotype Table S6. Results extracted from previous studies. Table S7. Associations of chronotype SNPs with outcomes in UKB, ALSPAC, BiB and MoBa. Table S8. Associations of insomnia SNPs with outcomes in UKB, ALSPAC, BiB and MoBa. Table S9. Associations of sleep duration SNPs with outcomes in UKB, ALSPAC, BiB and MoBa. Table S10. Female-specific estimates of IV-insomnia and IV-sleep duration associations in UKB.
DOI: 10.6084/m9.figshare.28059393.v1
title: Additional file 3 of Evaluating causal associations of chronotype with pregnancy and perinatal outcomes and its interactions with insomnia and sleep duration: a mendelian randomization study

description: Additional file 3: Table S1. Definitions of outcomes. Table S2. Definition of chronotype in 23 and Me. Table S3. List of SNPs for chronotype and their female-specific estimates in UKB. Table S4. List of SNPs for insomnia and sleep duration. Table S5. Associations of chronotype SNPs with outcomes in MoBa, adjusting for fetal and paternal genotype Table S6. Results extracted from previous studies. Table S7. Associations of chronotype SNPs with outcomes in UKB, ALSPAC, BiB and MoBa. Table S8. Associations of insomnia SNPs with outcomes in UKB, ALSPAC, BiB and MoBa. Table S9. Associations of sleep duration SNPs with outcomes in UKB, ALSPAC, BiB and MoBa. Table S10. Female-specific estimates of IV-insomnia and IV-sleep duration associations in UKB.
DOI: 10.6084/m9.figshare.28059397
title: Additional file 3 of Pulsatilla chinensis functions as a novel antihyperlipidemic agent by upregulating LDLR in an ERK-dependent manner

description: Additional file 3.
DOI: 10.6084/m9.figshare.28059394
title: Additional file 2 of Pulsatilla chinensis functions as a novel antihyperlipidemic agent by upregulating LDLR in an ERK-dependent manner

description: Additional file 2.
DOI: 10.6084/m9.figshare.28059397.v1
title: Additional file 3 of Pulsatilla chinensis functions as a novel antihyperlipidemic agent by upregulating LDLR in an ERK-dependent manner

description: Additional file 3.
DOI: 10.6084/m9.figshare.28059394.v1
title: Additional file 2 of Pulsatilla chinensis functions as a novel antihyperlipidemic agent by upregulating LDLR in an ERK-dependent manner

description: Additional file 2.
DOI: 10.6084/m9.figshare.28059409
title: Additional file 1 of Building a research agenda on preventing and addressing sexual assault and intimate partner violence against trans people: a two-stage priority-setting exercise

description: Supplementary Material 1. Data supporting the study’s conclusions (.xslx).
DOI: 10.6084/m9.figshare.28059409.v1
title: Additional file 1 of Building a research agenda on preventing and addressing sexual assault and intimate partner violence against trans people: a two-stage priority-setting exercise

description: Supplementary Material 1. Data supporting the study’s conclusions (.xslx).
DOI: 10.6084/m9.figshare.28059402.v1
title: Additional file 1 of Differential somatic coding variant landscapes between laser microdissected luminal epithelial cells from canine mammary invasive ductal solid carcinoma and comedocarcinoma

description: Additional file 1. Table S1. List of applied IHC antibodies.
DOI: 10.6084/m9.figshare.28059402
title: Additional file 1 of Differential somatic coding variant landscapes between laser microdissected luminal epithelial cells from canine mammary invasive ductal solid carcinoma and comedocarcinoma

description: Additional file 1. Table S1. List of applied IHC antibodies.
DOI: 10.6084/m9.figshare.28059414.v1
title: Additional file 5 of Differential somatic coding variant landscapes between laser microdissected luminal epithelial cells from canine mammary invasive ductal solid carcinoma and comedocarcinoma

description: Additional file 5. Table S2. Amplifications and deletions identified by VarScan 2 in canine invasive ductal solid carcinoma and comedocarcinoma compared with normal samples. Table S3A. Somatic variants and predicted pathogenicity in canine invasive ductal. solid carcinoma. Table S3B. Somatic variants and predicted pathogenicity in canine invasive ductal comedocarcinoma. Table S4A. Structural variants in canine invasive ductal solid carcinoma. Table S4B. Structural variants in canine invasive ductal. comedocarcinoma. Table S5. Mutual genes with variants in canine invasive ductal solid carcinoma and comedocarcinoma. Table S6A. KEGG pathways in canine invasive ductal solid carcinoma. Table S6B. KEGG pathways in canine invasive ductal. comedocarcinoma. Table S7. Driver genes identified by OncodriveCLUSTL from canine invasive ductal solid carcinoma and comedocarcinoma. Table S8. List of genes with non-silent variants in canine invasive ductal solid carcinoma and comedocarcinoma compared with COSMIC-CGC and KEGG databases.
DOI: 10.6084/m9.figshare.28059414
title: Additional file 5 of Differential somatic coding variant landscapes between laser microdissected luminal epithelial cells from canine mammary invasive ductal solid carcinoma and comedocarcinoma

description: Additional file 5. Table S2. Amplifications and deletions identified by VarScan 2 in canine invasive ductal solid carcinoma and comedocarcinoma compared with normal samples. Table S3A. Somatic variants and predicted pathogenicity in canine invasive ductal. solid carcinoma. Table S3B. Somatic variants and predicted pathogenicity in canine invasive ductal comedocarcinoma. Table S4A. Structural variants in canine invasive ductal solid carcinoma. Table S4B. Structural variants in canine invasive ductal. comedocarcinoma. Table S5. Mutual genes with variants in canine invasive ductal solid carcinoma and comedocarcinoma. Table S6A. KEGG pathways in canine invasive ductal solid carcinoma. Table S6B. KEGG pathways in canine invasive ductal. comedocarcinoma. Table S7. Driver genes identified by OncodriveCLUSTL from canine invasive ductal solid carcinoma and comedocarcinoma. Table S8. List of genes with non-silent variants in canine invasive ductal solid carcinoma and comedocarcinoma compared with COSMIC-CGC and KEGG databases.
DOI: 10.6084/m9.figshare.28059442.v1
title: Additional file 2 of Integrated network pharmacology and transcriptomics to explore the mechanism of compound Dihuang granule (CDG) protects dopaminergic neurons by regulating the Nrf2/HMOX1 pathway in the 6-OHDA/MPP+-induced model of Parkinson’s disease

description: Supplementary Material 2.
DOI: 10.6084/m9.figshare.28059445
title: Additional file 3 of Integrated network pharmacology and transcriptomics to explore the mechanism of compound Dihuang granule (CDG) protects dopaminergic neurons by regulating the Nrf2/HMOX1 pathway in the 6-OHDA/MPP+-induced model of Parkinson’s disease

description: Supplementary Material 3.
DOI: 10.6084/m9.figshare.28059442
title: Additional file 2 of Integrated network pharmacology and transcriptomics to explore the mechanism of compound Dihuang granule (CDG) protects dopaminergic neurons by regulating the Nrf2/HMOX1 pathway in the 6-OHDA/MPP+-induced model of Parkinson’s disease

description: Supplementary Material 2.
DOI: 10.6084/m9.figshare.28059445.v1
title: Additional file 3 of Integrated network pharmacology and transcriptomics to explore the mechanism of compound Dihuang granule (CDG) protects dopaminergic neurons by regulating the Nrf2/HMOX1 pathway in the 6-OHDA/MPP+-induced model of Parkinson’s disease

description: Supplementary Material 3.
DOI: 10.6084/m9.figshare.28059448
title: Additional file 4 of Integrated network pharmacology and transcriptomics to explore the mechanism of compound Dihuang granule (CDG) protects dopaminergic neurons by regulating the Nrf2/HMOX1 pathway in the 6-OHDA/MPP+-induced model of Parkinson’s disease

description: Supplementary Material 4.
DOI: 10.6084/m9.figshare.28059448.v1
title: Additional file 4 of Integrated network pharmacology and transcriptomics to explore the mechanism of compound Dihuang granule (CDG) protects dopaminergic neurons by regulating the Nrf2/HMOX1 pathway in the 6-OHDA/MPP+-induced model of Parkinson’s disease

description: Supplementary Material 4.
DOI: 10.6084/m9.figshare.28059451
title: Additional file 5 of Integrated network pharmacology and transcriptomics to explore the mechanism of compound Dihuang granule (CDG) protects dopaminergic neurons by regulating the Nrf2/HMOX1 pathway in the 6-OHDA/MPP+-induced model of Parkinson’s disease

description: Supplementary Material 5.
DOI: 10.6084/m9.figshare.28059451.v1
title: Additional file 5 of Integrated network pharmacology and transcriptomics to explore the mechanism of compound Dihuang granule (CDG) protects dopaminergic neurons by regulating the Nrf2/HMOX1 pathway in the 6-OHDA/MPP+-induced model of Parkinson’s disease

description: Supplementary Material 5.
DOI: 10.6084/m9.figshare.28059454.v1
title: Additional file 6 of Integrated network pharmacology and transcriptomics to explore the mechanism of compound Dihuang granule (CDG) protects dopaminergic neurons by regulating the Nrf2/HMOX1 pathway in the 6-OHDA/MPP+-induced model of Parkinson’s disease

description: Supplementary Material 6.
DOI: 10.6084/m9.figshare.28059457.v1
title: Additional file 7 of Integrated network pharmacology and transcriptomics to explore the mechanism of compound Dihuang granule (CDG) protects dopaminergic neurons by regulating the Nrf2/HMOX1 pathway in the 6-OHDA/MPP+-induced model of Parkinson’s disease

description: Supplementary Material 7.
DOI: 10.6084/m9.figshare.28059454
title: Additional file 6 of Integrated network pharmacology and transcriptomics to explore the mechanism of compound Dihuang granule (CDG) protects dopaminergic neurons by regulating the Nrf2/HMOX1 pathway in the 6-OHDA/MPP+-induced model of Parkinson’s disease

description: Supplementary Material 6.
DOI: 10.6084/m9.figshare.28059457
title: Additional file 7 of Integrated network pharmacology and transcriptomics to explore the mechanism of compound Dihuang granule (CDG) protects dopaminergic neurons by regulating the Nrf2/HMOX1 pathway in the 6-OHDA/MPP+-induced model of Parkinson’s disease

description: Supplementary Material 7.
DOI: 10.6084/m9.figshare.28059468
title: Additional file 1 of Dementia with lewy bodies patients with high tau levels display unique proteome profiles

description: Supplementary Material 1.
DOI: 10.6084/m9.figshare.28059468.v1
title: Additional file 1 of Dementia with lewy bodies patients with high tau levels display unique proteome profiles

description: Supplementary Material 1.
DOI: 10.6084/m9.figshare.28059471
title: Additional file 2 of Dementia with lewy bodies patients with high tau levels display unique proteome profiles

description: Supplementary Material 2.
DOI: 10.6084/m9.figshare.28059474
title: Additional file 3 of Dementia with lewy bodies patients with high tau levels display unique proteome profiles

description: Supplementary Material 3.
DOI: 10.6084/m9.figshare.28059471.v1
title: Additional file 2 of Dementia with lewy bodies patients with high tau levels display unique proteome profiles

description: Supplementary Material 2.
DOI: 10.6084/m9.figshare.28059474.v1
title: Additional file 3 of Dementia with lewy bodies patients with high tau levels display unique proteome profiles

description: Supplementary Material 3.
DOI: 10.15468/dl.dn5sez
title: Occurrence Download

description: A dataset containing 1161 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "TaxonKey is one of (Plethodon variolatus (Gilliams, 1818))"
 ]
}

 The dataset includes 1161 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0040759-241126133413365/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.28059493
title: Additional file 5 of Population genetics and molecular xenomonitoring of Biomphalaria freshwater snails along the southern shoreline of Lake Malawi, Malawi

description: Additional file 5: Dataset S1. Biomphalaria molecular xenomonitoring data.
DOI: 10.6084/m9.figshare.28059493.v1
title: Additional file 5 of Population genetics and molecular xenomonitoring of Biomphalaria freshwater snails along the southern shoreline of Lake Malawi, Malawi

description: Additional file 5: Dataset S1. Biomphalaria molecular xenomonitoring data.
DOI: 10.6084/m9.figshare.28059504
title: Additional file 1 of PtrA, Piz-t, and a novel minor-effect QTL (qBR12_3.3–4.4) collectively contribute to the durable blast-resistance of rice cultivar Tainung 84

description: Supplementary Material 1
DOI: 10.6084/m9.figshare.28059504.v1
title: Additional file 1 of PtrA, Piz-t, and a novel minor-effect QTL (qBR12_3.3–4.4) collectively contribute to the durable blast-resistance of rice cultivar Tainung 84

description: Supplementary Material 1
DOI: 10.6084/m9.figshare.28059507
title: Additional file 2 of PtrA, Piz-t, and a novel minor-effect QTL (qBR12_3.3–4.4) collectively contribute to the durable blast-resistance of rice cultivar Tainung 84

description: Supplementary Material 2
DOI: 10.6084/m9.figshare.28059507.v1
title: Additional file 2 of PtrA, Piz-t, and a novel minor-effect QTL (qBR12_3.3–4.4) collectively contribute to the durable blast-resistance of rice cultivar Tainung 84

description: Supplementary Material 2
DOI: 10.6084/m9.figshare.28059510
title: Additional file 3 of PtrA, Piz-t, and a novel minor-effect QTL (qBR12_3.3–4.4) collectively contribute to the durable blast-resistance of rice cultivar Tainung 84

description: Supplementary Material 3
DOI: 10.6084/m9.figshare.28059510.v1
title: Additional file 3 of PtrA, Piz-t, and a novel minor-effect QTL (qBR12_3.3–4.4) collectively contribute to the durable blast-resistance of rice cultivar Tainung 84

description: Supplementary Material 3
DOI: 10.6084/m9.figshare.28059517
title: Additional file 1 of Identification of Brucella RS15060 as a novel type IV secretion system effector associated with bacterial virulence

description: Additional file 1: Primers used in this study.
DOI: 10.5067/envisat/meris/l3b/rr/chl/2022.0
title: ENVISAT MERIS Level-3 Global Binned Chlorophyll (CHL) Data, version 2022.0
DOI: 10.6084/m9.figshare.28059517.v1
title: Additional file 1 of Identification of Brucella RS15060 as a novel type IV secretion system effector associated with bacterial virulence

description: Additional file 1: Primers used in this study.
DOI: 10.6084/m9.figshare.28059520
title: Additional file 2 of Identification of Brucella RS15060 as a novel type IV secretion system effector associated with bacterial virulence

description: Additional file 2: Strains and plasmids used in this study.
DOI: 10.6084/m9.figshare.28059520.v1
title: Additional file 2 of Identification of Brucella RS15060 as a novel type IV secretion system effector associated with bacterial virulence

description: Additional file 2: Strains and plasmids used in this study.
DOI: 10.6084/m9.figshare.28059523
title: Additional file 3 of Identification of Brucella RS15060 as a novel type IV secretion system effector associated with bacterial virulence

description: Additional file 3: Significantly different supernatant proteins of Brucella S2308 vs its SV123 mutant according to proteomics.
DOI: 10.6084/m9.figshare.28059523.v1
title: Additional file 3 of Identification of Brucella RS15060 as a novel type IV secretion system effector associated with bacterial virulence

description: Additional file 3: Significantly different supernatant proteins of Brucella S2308 vs its SV123 mutant according to proteomics.
DOI: 10.6084/m9.figshare.28059526
title: Additional file 4 of Identification of Brucella RS15060 as a novel type IV secretion system effector associated with bacterial virulence

description: Additional file 4: Presence or absence of supernatant proteins from Brucella S2308 and its SV123 mutant, as determined by proteomics analysis.
DOI: 10.6084/m9.figshare.28059526.v1
title: Additional file 4 of Identification of Brucella RS15060 as a novel type IV secretion system effector associated with bacterial virulence

description: Additional file 4: Presence or absence of supernatant proteins from Brucella S2308 and its SV123 mutant, as determined by proteomics analysis.
DOI: 10.5067/envisat/meris/l3b/rr/flh/2022.0
title: ENVISAT MERIS Level-3 Global Binned Fluorescence Line Height (FLH) Data, version 2022.0
DOI: 10.5067/envisat/meris/l3b/rr/iop/2022.0
title: ENVISAT MERIS Level-3 Global Binned Inherent Optical Properties (IOP) Data, version 2022.0
DOI: 10.5067/envisat/meris/l3b/rr/kd/2022.0
title: ENVISAT MERIS Level-3 Global Binned Diffuse Attenuation Coefficient for Downwelling Irradiance (KD) Data, version 2022.0
DOI: 10.6084/m9.figshare.28059537.v1
title: Additional file 2 of Sex differences in mitochondrial gene expression during viral myocarditis

description: Supplementary Material 2: Additional File 2: Mapped ChIPseq raw counts and statistics for Figure 13. iF = F-MYO; iM = M-MYO