cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.29079265.v1
title: Additional file 16 of Limited impact of the siRNA pathway on transposable element expression in Aedes aegypti

description: Additional file 17: Figure S15 – Size distributions of small RNA reads following different levels of filtering. The plots are structured in three main columns – thorax samples are on the left, midgut samples in the center, and ovary samples on the right. Within each partitioned region, control mosquito libraries are shown on the left and Dcr2 mutant libraries are shown on the right. The rows correspond to reads subset based on filtering: First row – adapter-trimmed only (‘unfiltered/raw’), second row – filtered for reads mapping to miRNA, tRNA, snRNA, and snoRNA genes, third row – further filtered for reads mapping to annotated piRNA clusters, fourth row – only reads that map to piRNA clusters but not to any miRNA, tRNA, snRNA, or snoRNA genes. The percentage of 21nt reads is added to each plot. The error bars denote one standard deviation. When filtered for small RNA genes, a ‘block’ of reads can be seen in thorax samples, attributable to RNA degradation, while a piRNA-sized ‘hump’ can be seen most clearly in ovary samples, but also in midgut samples. Unfiltered reads from somatic tissues display a clear domination of the library by miRNA-sized reads, which are filtered away following intersection with annotated small RNA genes.
DOI: 10.6084/m9.figshare.29079271
title: Additional file 18 of Limited impact of the siRNA pathway on transposable element expression in Aedes aegypti

description: Additional file 19: Table S3 – Gene sets of interest. Groupings of genes into gene sets, as well as the retrieved genes and their Ae. aegypti homologs. Retrieved KEGG pathways and their component genes are also included.
DOI: 10.6084/m9.figshare.29079274
title: Additional file 19 of Limited impact of the siRNA pathway on transposable element expression in Aedes aegypti

description: Additional file 19: Table S3 – Gene sets of interest. Groupings of genes into gene sets, as well as the retrieved genes and their Ae. aegypti homologs. Retrieved KEGG pathways and their component genes are also included.
DOI: 10.6084/m9.figshare.29079277
title: Additional file 20 of Limited impact of the siRNA pathway on transposable element expression in Aedes aegypti

description: Additional file 20: Table S4 – Accession numbers and rudimentary metadata for re-analyzed datasets. NCBI [31, 33, 37] and EBI [17] accession numbers, sample names, and sequencing strategies for the re-analyzed data from Ae. aegypti and D. melanogaster Dcr2 or D. melanogaster double Dcr2 + Piwi mutants.
DOI: 10.6084/m9.figshare.29079277.v2
title: Additional file 20 of Limited impact of the siRNA pathway on transposable element expression in Aedes aegypti

description: Additional file 20: Table S4 – Accession numbers and rudimentary metadata for re-analyzed datasets. NCBI [31, 33, 37] and EBI [17] accession numbers, sample names, and sequencing strategies for the re-analyzed data from Ae. aegypti and D. melanogaster Dcr2 or D. melanogaster double Dcr2 + Piwi mutants.
DOI: 10.6084/m9.figshare.29079280
title: Additional file 21 of Limited impact of the siRNA pathway on transposable element expression in Aedes aegypti

description: Additional file 22: Table S6 – BED file of small RNA genes. Coordinates used for filtering out small RNAs originating from small RNA genes. Reads mapping to coordinates labelled as ‘miRNA’ in the last column were used for scaling of RPM between samples
DOI: 10.6084/m9.figshare.29079283
title: Additional file 22 of Limited impact of the siRNA pathway on transposable element expression in Aedes aegypti

description: Additional file 22: Table S6 – BED file of small RNA genes. Coordinates used for filtering out small RNAs originating from small RNA genes. Reads mapping to coordinates labelled as ‘miRNA’ in the last column were used for scaling of RPM between samples
DOI: 10.6084/m9.figshare.30475163.v6
title: Additional file of Limited impact of the siRNA pathway on transposable element expression in Aedes aegypti

description: Additional file of Limited impact of the siRNA pathway on transposable element expression in Aedes aegypti
DOI: 10.15468/dl.c5ejms
title: Occurrence Download

description: A dataset containing 2005 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hyla sarda"
 ]
}

 The dataset includes 2005 records from 80 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005981-251025141854904/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.30475178
title: Additional file of Abundant and metabolically flexible bacterial lineages underlie a vast potential for rubisco-mediated carbon fixation in the dark ocean

description: Additional file of Abundant and metabolically flexible bacterial lineages underlie a vast potential for rubisco-mediated carbon fixation in the dark ocean
DOI: 10.6084/m9.figshare.30475178.v2
title: Additional file of Abundant and metabolically flexible bacterial lineages underlie a vast potential for rubisco-mediated carbon fixation in the dark ocean

description: Additional file of Abundant and metabolically flexible bacterial lineages underlie a vast potential for rubisco-mediated carbon fixation in the dark ocean
DOI: 10.6084/m9.figshare.29374858.v1
title: Additional file 6 of Loop Catalog: a comprehensive HiChIP database of human and mouse samples

description: Additional file 6: Table S5. Peak Call Statistics for HiChIP and ChIP-seq
DOI: 10.6084/m9.figshare.29374858.v2
title: Additional file 6 of Loop Catalog: a comprehensive HiChIP database of human and mouse samples

description: Additional file 6: Table S5. Peak Call Statistics for HiChIP and ChIP-seq.
DOI: 10.6084/m9.figshare.29374867
title: Additional file 9 of Loop Catalog: a comprehensive HiChIP database of human and mouse samples

description: Additional file 9: Table S8: Quality Control Flags for FitHiChIP Loop Calling
DOI: 10.6084/m9.figshare.29374867.v2
title: Additional file 9 of Loop Catalog: a comprehensive HiChIP database of human and mouse samples

description: Additional file 9: Table S8: Quality Control Flags for FitHiChIP Loop Calling.
DOI: 10.6084/m9.figshare.29374870.v2
title: Additional file 10 of Loop Catalog: a comprehensive HiChIP database of human and mouse samples

description: Additional file 10: Table S9. Quality Control Flag Definitions for FitHiChIP Loop Calling.
DOI: 10.6084/m9.figshare.29374876
title: Additional file 12 of Loop Catalog: a comprehensive HiChIP database of human and mouse samples

description: Additional file 12: Table S11. Hi-C Loop Call Statistics for Mustache Loop Calling.
DOI: 10.6084/m9.figshare.29374876.v1
title: Additional file 12 of Loop Catalog: a comprehensive HiChIP database of human and mouse samples

description: Additional file 12: Table S11. Hi-C Loop Call Statistics for Mustache Loop Calling
DOI: 10.6084/m9.figshare.29374879.v1
title: Additional file 13 of Loop Catalog: a comprehensive HiChIP database of human and mouse samples

description: Additional file 13: Table S12. GWAS SGL Statistics for RA, AD, T1D, and PS
DOI: 10.6084/m9.figshare.29374882
title: Additional file 14 of Loop Catalog: a comprehensive HiChIP database of human and mouse samples

description: Additional file 14: Table S13. eQTL SGL Statistics for 6 Immune Cell Types.
DOI: 10.6084/m9.figshare.29374891
title: Additional file 17 of Loop Catalog: a comprehensive HiChIP database of human and mouse samples

description: Additional file 17: Table S16. Map of Hi-C to ChIP-seq Signals
DOI: 10.6084/m9.figshare.29374897
title: Additional file 19 of Loop Catalog: a comprehensive HiChIP database of human and mouse samples

description: Additional file 19: Table S18. Software and Package Version.
DOI: 10.6084/m9.figshare.29374846
title: Additional file 2 of Loop Catalog: a comprehensive HiChIP database of human and mouse samples

description: Additional file 2: Table S1. Summary of HiChIP Sequence Files.
DOI: 10.6084/m9.figshare.29374849
title: Additional file 3 of Loop Catalog: a comprehensive HiChIP database of human and mouse samples

description: Additional file 3: Table S2. HiC-Pro Quality Control Statistics.
DOI: 10.6084/m9.figshare.29374852
title: Additional file 4 of Loop Catalog: a comprehensive HiChIP database of human and mouse samples

description: Additional file 4: Table S3. Restriction Enzyme Sequences Used in the HiC-Pro Pipeline
DOI: 10.6084/m9.figshare.29374852.v2
title: Additional file 4 of Loop Catalog: a comprehensive HiChIP database of human and mouse samples

description: Additional file 4: Table S3. Restriction Enzyme Sequences Used in the HiC-Pro Pipeline.
DOI: 10.6084/m9.figshare.29374855
title: Additional file 5 of Loop Catalog: a comprehensive HiChIP database of human and mouse samples

description: Additional file 5: Table S4. ChIPLine Quality Control Statistics.
DOI: 10.6084/m9.figshare.29374855.v2
title: Additional file 5 of Loop Catalog: a comprehensive HiChIP database of human and mouse samples

description: Additional file 5: Table S4. ChIPLine Quality Control Statistics.
DOI: 10.6084/m9.figshare.29374858
title: Additional file 6 of Loop Catalog: a comprehensive HiChIP database of human and mouse samples

description: Additional file 6: Table S5. Peak Call Statistics for HiChIP and ChIP-seq
DOI: 10.6084/m9.figshare.29374861
title: Additional file 7 of Loop Catalog: a comprehensive HiChIP database of human and mouse samples

description: Additional file 7: Table S6. Assessment of HiChIP Reproducibility by Stratum-Adjusted Correlation Coefficients.
DOI: 10.6084/m9.figshare.29374864.v2
title: Additional file 8 of Loop Catalog: a comprehensive HiChIP database of human and mouse samples

description: Additional file 8: Table S7. HiChIP Loop Call Statistics for FitHiChIP and HiCCUPS Loop Calling.
DOI: 10.6084/m9.figshare.29374864.v1
title: Additional file 8 of Loop Catalog: a comprehensive HiChIP database of human and mouse samples

description: Additional file 8: Table S7. HiChIP Loop Call Statistics for FitHiChIP and HiCCUPS Loop Calling
DOI: 10.6084/m9.figshare.29374870
title: Additional file 10 of Loop Catalog: a comprehensive HiChIP database of human and mouse samples

description: Additional file 10: Table S9. Quality Control Flag Definitions for FitHiChIP Loop Calling.
DOI: 10.6084/m9.figshare.29374873
title: Additional file 11 of Loop Catalog: a comprehensive HiChIP database of human and mouse samples

description: Additional file 11: Table S10. List of High Confidence HiChIP Sample Sets.
DOI: 10.6084/m9.figshare.29374876.v2
title: Additional file 12 of Loop Catalog: a comprehensive HiChIP database of human and mouse samples

description: Additional file 12: Table S11. Hi-C Loop Call Statistics for Mustache Loop Calling.
DOI: 10.6084/m9.figshare.29374879
title: Additional file 13 of Loop Catalog: a comprehensive HiChIP database of human and mouse samples

description: Additional file 13: Table S12. GWAS SGL Statistics for RA, AD, T1D, and PS.
DOI: 10.6084/m9.figshare.29374879.v2
title: Additional file 13 of Loop Catalog: a comprehensive HiChIP database of human and mouse samples

description: Additional file 13: Table S12. GWAS SGL Statistics for RA, AD, T1D, and PS.
DOI: 10.6084/m9.figshare.30474533.v1
title: Additional file 5 of Rapid and cost-effective molecular karyotyping in wheat, barley, and their cross-progeny by chromosome-specific multiplex PCR

description: Supplementary Material 5: Sequencing results of 28 chromosome-specific PCR products with specific forward and reverse primers
DOI: 10.6084/m9.figshare.30474536.v1
title: Additional file 6 of Rapid and cost-effective molecular karyotyping in wheat, barley, and their cross-progeny by chromosome-specific multiplex PCR

description: Supplementary Material 6: In silico prediction of chromosome-specific MPCR products in the genomes of Triticum, Aegilops, and Hordeum species
DOI: 10.6084/m9.figshare.30474539
title: Additional file of Longevity-associated BPIFB4 gene counteracts the inflammatory signaling

description: Additional file of Longevity-associated BPIFB4 gene counteracts the inflammatory signaling
DOI: 10.6084/m9.figshare.30474527
title: Additional file 3 of Rapid and cost-effective molecular karyotyping in wheat, barley, and their cross-progeny by chromosome-specific multiplex PCR

description: Supplementary Material 3: The final list of chromosome-specific MPCR primers in the A, B, D, and H (sub-)genomes
DOI: 10.6084/m9.figshare.29374885
title: Additional file 15 of Loop Catalog: a comprehensive HiChIP database of human and mouse samples

description: Additional file 15: Table S14. 1D Conserved Anchor Motif Enrichment Analysis Statistics.
DOI: 10.6084/m9.figshare.29374885.v2
title: Additional file 15 of Loop Catalog: a comprehensive HiChIP database of human and mouse samples

description: Additional file 15: Table S14. 1D Conserved Anchor Motif Enrichment Analysis Statistics.
DOI: 10.15468/dl.7z87k2
title: Occurrence Download

description: A dataset containing 2343 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hyla savignyi"
 ]
}

 The dataset includes 2343 records from 44 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005982-251025141854904/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.29374891.v2
title: Additional file 17 of Loop Catalog: a comprehensive HiChIP database of human and mouse samples

description: Additional file 17: Table S16. Map of Hi-C to ChIP-seq Signals.
DOI: 10.6084/m9.figshare.29374894
title: Additional file 18 of Loop Catalog: a comprehensive HiChIP database of human and mouse samples

description: Additional file 18: Table S17. Non-Convergence of KR, SCALE, VC, and VC_SQRT Contact Matrix Normalization Methods for 45 Samples
DOI: 10.6084/m9.figshare.29374891.v1
title: Additional file 17 of Loop Catalog: a comprehensive HiChIP database of human and mouse samples

description: Additional file 17: Table S16. Map of Hi-C to ChIP-seq Signals
DOI: 10.15468/dl.czp6hc
title: Occurrence Download

description: A dataset containing 23678 species occurrences available in GBIF matching the query:
{
 "and" : [
 "PublishingOrg is c803f6f5-2c6a-4b41-8c15-768d48ef1c8c",
 "TaxonKey is Animalia"
 ]
}

 The dataset includes 23678 records from 46 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005983-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wwrbau
title: Occurrence Download

description: A dataset listing the 92 species recorded in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((123.1 41.5,123.9 41.5,123.9 42.2,123.1 42.2,123.1 41.5))",
 "HasCoordinate is true",
 "TaxonKey is Lepidoptera"
 ]
}

 The dataset's 92 records were derived from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005975-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17470953
title: Machine learning in Perovskite Hydrides
DOI: 10.5281/zenodo.17470954
title: Machine learning in Perovskite Hydrides
DOI: 10.6084/m9.figshare.28681859.v1
title: Additional file 4 of A stress-dependent TDP-43 SUMOylation program preserves neuronal function

description: Supplementary Material 4.
DOI: 10.6084/m9.figshare.28681856.v1
title: Additional file 3 of A stress-dependent TDP-43 SUMOylation program preserves neuronal function

description: Supplementary Material 3.
DOI: 10.6084/m9.figshare.30475157
title: Additional file of The overlooked trio: sleep duration, sampling time and physical exercise alter levels of olink-assessed blood biomarkers of cardiovascular risk

description: Additional file of The overlooked trio: sleep duration, sampling time and physical exercise alter levels of olink-assessed blood biomarkers of cardiovascular risk
DOI: 10.15468/dl.3aczqh
title: Occurrence Download

description: A dataset containing 15393 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Squamata, Testudines, Crocodylia)",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is Fossil"
 ]
 }
 },
 "Year is greater than or equal to 1970",
 "CoordinateUncertaintyInMeters is less than 3000"
 ]
}

 The dataset includes 15393 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005984-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17470969
title: Appendix Table 3.5
DOI: 10.5281/zenodo.17470970
title: Appendix Table 3.5
DOI: 10.5281/zenodo.14884845
title: Processed single-cell RNA-seq datasets of PBMC (1k, 3k, 4k, 8k) re-aligned with Cell Ranger v9.0.1 and GENCODE v48 (GRCh38.p14)

description: This dataset contains processed single-cell RNA sequencing (scRNA-seq) data from peripheral blood mononuclear cells (PBMCs) with different cell counts (1k, 3k, 4k, 8k). The raw FASTQ files were downloaded from publicly available 10x Genomics datasets, and all samples were aligned using Cell Ranger v9.0.1 (February 6, 2025) with a custom-built reference genome based on GENCODE Release 48 (GRCh38.p14).

For each dataset, the following files are provided:





*_filtered_feature_bc_matrix.h5: filtered gene-barcode matrices




*_raw_feature_bc_matrix.h5: unfiltered matrices



To facilitate data interpretation, the table below summarizes key metadata for each dataset, including sample source and assay details.




Dataset
Number of cells
Species
Tissue
Disease
Assay




pbmc1k
~1,000
Human
Blood
Healthy
10x 3' v3


pbmc3k
~3,000
Human
Blood
Healthy
10x 3' v1


pbmc4k
~4,000
Human
Blood
Healthy
10x 3' v2


pbmc8k
~8,000
Human
Blood
Healthy
10x 3' v2
DOI: 10.15468/dl.3z3cne
title: Occurrence Download

description: A dataset containing 49 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hyla felixarabica"
 ]
}

 The dataset includes 49 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005986-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14868136
title: Processed single-cell RNA-seq datasets of PBMC (1k, 3k, 4k, 8k) re-aligned with Cell Ranger v9.0.1 and GENCODE v48 (GRCh38.p14)

description: This dataset contains processed single-cell RNA sequencing (scRNA-seq) data from peripheral blood mononuclear cells (PBMCs) with different cell counts (1k, 3k, 4k, 8k). The raw FASTQ files were downloaded from publicly available 10x Genomics datasets, and all samples were aligned using Cell Ranger v9.0.1 (February 6, 2025) with a custom-built reference genome based on GENCODE Release 48 (GRCh38.p14).

For each dataset, the following files are provided:





*_filtered_feature_bc_matrix.h5: filtered gene-barcode matrices




*_raw_feature_bc_matrix.h5: unfiltered matrices



To facilitate data interpretation, the table below summarizes key metadata for each dataset, including sample source and assay details.




Dataset
Number of cells
Species
Tissue
Disease
Assay




pbmc1k
~1,000
Human
Blood
Healthy
10x 3' v3


pbmc3k
~3,000
Human
Blood
Healthy
10x 3' v1


pbmc4k
~4,000
Human
Blood
Healthy
10x 3' v2


pbmc8k
~8,000
Human
Blood
Healthy
10x 3' v2
DOI: 10.5281/zenodo.14868137
title: 3k PBMCs from a healthy donor

description: This dataset contains single-cell RNA sequencing (scRNA-seq) data of 3,000 peripheral blood mononuclear cells (PBMCs) from a healthy donor, processed using the 10x Genomics Chromium platform. The raw data was obtained from 10x Genomics and subsequently aligned using Cell Ranger 8.0.1 with the GENCODE Release 47 (GRCh38.p14) reference genome.

The dataset includes the following output files from the Cell Ranger pipeline:



filtered_feature_bc_matrix.h5 – Filtered count matrix in HDF5 format

raw_feature_bc_matrix.h5 – Raw count matrix in HDF5 format


This dataset is valuable for researchers studying single-cell transcriptomics, immune cell profiling, and bioinformatics pipeline benchmarking.

File format: HDF5Reference Genome: GENCODE Release 47 (GRCh38.p14)Processing Pipeline: Cell Ranger 8.0.1

For any questions or collaborations, please feel free to contact the uploader.
DOI: 10.5281/zenodo.15716340
title: Factors Influencing Blockchain Resistance in the Financial Auditor Profession

description: Dataset excel from questionnaire and output from SMART PLS
DOI: 10.5281/zenodo.15716341
title: Factors Influencing Blockchain Resistance in the Financial Auditor Profession

description: Dataset excel from questionnaire and output from SMART PLS
DOI: 10.15468/dl.6xyb6n
title: Occurrence Download

description: A dataset containing 4216 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Anura, Caudata)",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is Fossil"
 ]
 }
 },
 "Year is greater than or equal to 1970",
 "CoordinateUncertaintyInMeters is less than 3000"
 ]
}

 The dataset includes 4216 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005990-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.t2axhh
title: Occurrence Download

description: A dataset containing 18 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hyla carthaginiensis"
 ]
}

 The dataset includes 18 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005988-251025141854904/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.30472571
title: Numerical source data for graphs

description: Depression involves dysregulation in distributed cortico-limbic networks, leading to behavioral deficits such as social avoidance. Ketamine is known for its rapid antidepressant effects. However, the complex multi-frequency interactions remain challenging, hindering systems-level understanding of depression and its treatment. Here, we present a frequency-varying multilayer brain functional network (FMBFN) analytical framework that characterizes brain-wide neural fluctuations and topological dimensions using in vivo local field potentials recording in eight regions and 16S RNA sequencing of gut microbiota. This approach quantifies multilayer topology to generate high-dimensional descriptors, enabling direct correlations with multimodal biological data and bridging neural activity with systemic domains. Applying the FMBFN framework, we show that chronic social defeat stress induces a pathological state of frequency-specific hyperconnectivity and disrupted global integration. Ketamine administration triggers a fundamental "network reset", characterized by global topological simplification and a dichotomous nodal reorganization—enhancing multilayer centrality in the lateral habenula while suppressing it in other regions. Finally, integration with gut microbiome data reveals bidirectional mediation between ketamine-altered bacteria and network reconfiguration, highlighting a functional gut-brain axis mechanism. In conclusion, the FMBFN framework provides a systems-level tool that bridges brain-wide functional architecture and gut microbiota, offering insights into psychiatric disorders and may inform future therapeutic strategies.