cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.28796129.v9
title: Supplementary Data S1 - DESeq2 result tables of all datasets analyzed along with flag columns for each of the 8 GO terms used throughout the manuscript. Metadata on the GO terms is included in the sheet "GO_metadata".

description: Supplementary Data S1 of the manuscript "<b>Hypoxia leads to reduced mito-nuclear gene expression and to increased mtDNA transcriptional pausing in human cells</b>" by Shtolz et al.<br>sheet name - <b>results: </b>DESeq2 "result" output. Main columns:<b>Name:</b> gene symbol<b>baseMean</b>: Mean normalized expression across all samples<b>log2FoldChange</b>: log<sub>2</sub> fold-change between treatment (hypoxia) and control (normoxia).<b>lfcSE</b>: Standard error of the log<sub>2 </sub>fold-change<b>stat</b>: Negative binomial test statistic.<b>p-value</b><b>padj:</b> Benjamin-Hodgkin-adjusted p-value<b>dataset</b>: Name of the dataset<b>cell line</b><b>Complex</b>: Complex association of gene (either complex I, II, III, IV and V of OXPHOS or the mito-ribosome)<b>Genome</b>: Genome of the gene (NUC for nucleus or MT for mitochondrial DNA, applied only to OXPHOS or mito-ribosome genes).<b>ensembl.gene</b>: Ensemble gene ID.<b>GO_000x: </b>8 columns, binary columns, one for each of the 8 GO terms used in the manuscript.sheet name - <b>GO_metadata</b>: contains information on each of the GO terms used in the manuscript and as columns in the "results" sheet.Data used to generate Figures 1, 2, 3a-c, 4a, 4b and 4e, and Supplementary Figures S1, S2, S5, S6 and S7.
DOI: 10.25574/05667
title: Chandra X-ray Observatory ObsId 05667

description: X-ray Properties of AGNs with Intermediate-mass Black Holes
DOI: 10.25574/05668
title: Chandra X-ray Observatory ObsId 05668

description: Gems in the Chandra Deep Fields: The Nature of Optically Passive X-ray Galaxies (aka XBONGs)
DOI: 10.5281/zenodo.17954344
title: Supplementary Appendices for "Quantitative Postnatal Maturation of the Feline Testis from 6 to 36 Months: A Stereological and DHH Immunomorphological Analysis"

description: These supplementary appendices provide the complete stereological and morphometric data supporting the manuscript “Quantitative Postnatal Maturation of the Feline Testis from 6 to 36 Months: A Stereological and DHH Immunomorphological Analysis”



Appendix A.1 includes graphical representations of age-dependent stereological dynamics of Leydig, Sertoli, and germ cells (Figure A1).

Appendix A.2 provides detailed numerical stereological estimators for all analyzed variables across age groups (Table A1). All data are presented as medians ± interquartile range (IQR) and analyzed using nonparametric tests (Kruskal–Wallis with Dunn’s post hoc). These materials ensure transparency and reproducibility of the stereological and morphometric analyses.

Appendix A.3, which provides the full numerical outputs of the Principal Component Analysis (PCA), including eigenvalues, percentage of explained variance, variable loadings for PC1 and PC2, and individual scores used to generate the PCA score and loading plots presented in Figure 3.
DOI: 10.5281/zenodo.17458073
title: Supplementary Appendices for "Quantitative Postnatal Maturation of the Feline Testis from 6 to 36 Months: A Stereological and DHH Immunomorphological Analysis"

description: These supplementary appendices provide the complete stereological and morphometric data supporting the manuscript “Quantitative Postnatal Maturation of the Feline Testis from 6 to 36 Months: A Stereological and DHH Immunomorphological Analysis”



Appendix A.1 includes graphical representations of age-dependent stereological dynamics of Leydig, Sertoli, and germ cells (Figure A1).

Appendix A.2 provides detailed numerical stereological estimators for all analyzed variables across age groups (Table A1). All data are presented as medians ± interquartile range (IQR) and analyzed using nonparametric tests (Kruskal–Wallis with Dunn’s post hoc). These materials ensure transparency and reproducibility of the stereological and morphometric analyses.

Appendix A.3, which provides the full numerical outputs of the Principal Component Analysis (PCA), including eigenvalues, percentage of explained variance, variable loadings for PC1 and PC2, and individual scores used to generate the PCA score and loading plots presented in Figure 3.
DOI: 10.6084/m9.figshare.30272572
title: Supplementary Data S11 - mtDNA copy number qPCR results

description: Supplementary Data S11 of the manuscript "<b>Hypoxia leads to reduced mito-nuclear gene expression and increased mtDNA transcriptional pausing in human cells</b>" by Shtolz et al.The data was used to generate Fig. 3d-g within the manuscriptDNA qPCR data used in the study to measure copy number. The data was generated as described in the Materials and Methods section:To quantify the relative mtDNA copy number, qPCR (Bio-Rad CFX96) was performed using SYBR Green (Applied Biosystems, Thermo Fisher Scientific) on genomic DNA samples with two primer pairs targeted to amplify two nDNA genes (<i>JUN</i> and either <i>ANKRD37 </i>or <i>ACTB</i>) and four primer pairs targeted to amplify four mtDNA fragments selected to represent four mtDNA regions (Table 1). Each sample and amplicon combination were analyzed in triplicate for four biological replicates of hypoxia experiments per cell line.<br>
DOI: 10.6084/m9.figshare.30272572.v2
title: Supplementary Data S3 - mtDNA copy number qPCR results

description: Supplementary Data S3 of the manuscript "<b>Hypoxia leads to reduced mito-nuclear gene expression and increased mtDNA transcriptional pausing in human cells</b>" by Shtolz et al.The data was used to generate Fig. 3d-g within the manuscriptDNA qPCR data used in the study to measure copy number. The data was generated as described in the Materials and Methods section:To quantify the relative mtDNA copy number, qPCR (Bio-Rad CFX96) was performed using SYBR Green (Applied Biosystems, Thermo Fisher Scientific) on genomic DNA samples with two primer pairs targeted to amplify two nDNA genes (<i>JUN</i> and either <i>ANKRD37 </i>or <i>ACTB</i>) and four primer pairs targeted to amplify four mtDNA fragments selected to represent four mtDNA regions (Table 1). Each sample and amplicon combination were analyzed in triplicate for four biological replicates of hypoxia experiments per cell line.<br>
DOI: 10.6084/m9.figshare.30272572.v3
title: Supplementary Data S11 - mtDNA copy number qPCR results

description: Supplementary Data S11 of the manuscript "<b>Hypoxia leads to reduced mito-nuclear gene expression and increased mtDNA transcriptional pausing in human cells</b>" by Shtolz et al.The data was used to generate Fig. 3d-g within the manuscriptDNA qPCR data used in the study to measure copy number. The data was generated as described in the Materials and Methods section:To quantify the relative mtDNA copy number, qPCR (Bio-Rad CFX96) was performed using SYBR Green (Applied Biosystems, Thermo Fisher Scientific) on genomic DNA samples with two primer pairs targeted to amplify two nDNA genes (<i>JUN</i> and either <i>ANKRD37 </i>or <i>ACTB</i>) and four primer pairs targeted to amplify four mtDNA fragments selected to represent four mtDNA regions (Table 1). Each sample and amplicon combination were analyzed in triplicate for four biological replicates of hypoxia experiments per cell line.<br>
DOI: 10.25574/05669
title: Chandra X-ray Observatory ObsId 05669

description: Gems in the Chandra Deep Fields: The Nature of Optically Passive X-ray Galaxies (aka XBONGs)
DOI: 10.6084/m9.figshare.30273856
title: Supplementary Data S13 - HIF1A K.O and hypoxia in HCT-116 cells

description: Supplementary Data S13 of the manuscript "<b>Hypoxia leads to reduced mito-nuclear gene expression and to increased mtDNA transcriptional pausing in human cells</b>" by Shtolz et al.DESeq2 "result" output on PRJNA607557. Main columns:<b>Name:</b> gene symbol<b>baseMean</b>: Mean normalized expression across all samples<b>log2FoldChange</b>: log<sub>2</sub> fold-change between treatment (hypoxia) and control (normoxia).<b>lfcSE</b>: Standard error of the log<sub>2</sub><sub> </sub>fold-change<b>stat</b>: Negative binomial test statistic.<b>p-value</b><b>padj:</b> Benjamin-Hodgkin-adjusted p-value<b>dataset</b>: Name of the dataset<b>cell line</b><b>Complex</b>: Complex association of gene (either complex I, II, III, IV and V of OXPHOS or the mito-ribosome)<b>Genome</b>: Genome of the gene (NUC for nucleus or MT for mitochondrial DNA).<b>ensembl.gene</b>: Ensemble gene ID.Data used to generate Fig. 4c,d and Supplementary Fig. S8a,b.
DOI: 10.6084/m9.figshare.30273856.v6
title: Supplementary Data S13 - HIF1A K.O and hypoxia in HCT-116 cells

description: Supplementary Data S13 of the manuscript "<b>Hypoxia leads to reduced mito-nuclear gene expression and to increased mtDNA transcriptional pausing in human cells</b>" by Shtolz et al.DESeq2 "result" output on PRJNA607557. Main columns:<b>Name:</b> gene symbol<b>baseMean</b>: Mean normalized expression across all samples<b>log2FoldChange</b>: log<sub>2</sub> fold-change between treatment (hypoxia) and control (normoxia).<b>lfcSE</b>: Standard error of the log<sub>2</sub><sub> </sub>fold-change<b>stat</b>: Negative binomial test statistic.<b>p-value</b><b>padj:</b> Benjamin-Hodgkin-adjusted p-value<b>dataset</b>: Name of the dataset<b>cell line</b><b>Complex</b>: Complex association of gene (either complex I, II, III, IV and V of OXPHOS or the mito-ribosome)<b>Genome</b>: Genome of the gene (NUC for nucleus or MT for mitochondrial DNA).<b>ensembl.gene</b>: Ensemble gene ID.Data used to generate Fig. 4c,d and Supplementary Fig. S8a,b.
DOI: 10.6084/m9.figshare.30273856.v7
title: Supplementary Data S13 - HIF1A K.O and hypoxia in HCT-116 cells

description: Supplementary Data S13 of the manuscript "<b>Hypoxia leads to reduced mito-nuclear gene expression and to increased mtDNA transcriptional pausing in human cells</b>" by Shtolz et al.DESeq2 "result" output on PRJNA607557. Main columns:<b>Name:</b> gene symbol<b>baseMean</b>: Mean normalized expression across all samples<b>log2FoldChange</b>: log<sub>2</sub> fold-change between treatment (hypoxia) and control (normoxia).<b>lfcSE</b>: Standard error of the log<sub>2</sub><sub> </sub>fold-change<b>stat</b>: Negative binomial test statistic.<b>p-value</b><b>padj:</b> Benjamin-Hodgkin-adjusted p-value<b>dataset</b>: Name of the dataset<b>cell line</b><b>Complex</b>: Complex association of gene (either complex I, II, III, IV and V of OXPHOS or the mito-ribosome)<b>Genome</b>: Genome of the gene (NUC for nucleus or MT for mitochondrial DNA).<b>ensembl.gene</b>: Ensemble gene ID.Data used to generate Fig. 4c,d and Supplementary Fig. S8a,b.
DOI: 10.25574/05670
title: Chandra X-ray Observatory ObsId 05670

description: Gems in the Chandra Deep Fields: The Nature of Optically Passive X-ray Galaxies (aka XBONGs)
DOI: 10.25574/05671
title: Chandra X-ray Observatory ObsId 05671

description: Gems in the Chandra Deep Fields: The Nature of Optically Passive X-ray Galaxies (aka XBONGs)
DOI: 10.25574/05672
title: Chandra X-ray Observatory ObsId 05672

description: Gems in the Chandra Deep Fields: The Nature of Optically Passive X-ray Galaxies (aka XBONGs)
DOI: 10.25574/05673
title: Chandra X-ray Observatory ObsId 05673

description: Gems in the Chandra Deep Fields: The Nature of Optically Passive X-ray Galaxies (aka XBONGs)
DOI: 10.6084/m9.figshare.30273919
title: Supplementary Data S12 - PRO-seq gene body analysis

description: Supplementary Data S12 of the manuscript "<b>Hypoxia leads to reduced mito-nuclear gene expression and to increased mtDNA transcriptional pausing in human cells</b>" by Shtolz et al.Result of DESeq2 analysis on PRO-seq data analyzed using PEPPR."result" output. Main columns:<b>Name:</b> gene symbol<b>baseMean</b>: Mean normalized expression across all samples<b>log2FoldChange</b>: log<sub>2</sub> fold-change between treatment (hypoxia) and control (normoxia).<b>lfcSE</b>: Standard error of the log<sub>2</sub><sub> </sub>fold-change<b>stat</b>: Negative binomial test statistic.<b>p-value</b><b>padj:</b> Benjamin-Hodgkin-adjusted p-value<b>dataset</b>: Name of the dataset<b>cell line</b><b>Complex</b>: Complex association of gene (either complex I, II, III, IV and V of OXPHOS or the mito-ribosome)<b>Genome</b>: Genome of the gene (NUC for nucleus or MT for mitochondrial DNA).<b>ensembl.gene</b>: Ensemble gene ID.Data used to generate Supplementary Fig. S11.
DOI: 10.6084/m9.figshare.30273919.v3
title: Supplementary Data S12 - PRO-seq gene body analysis

description: Supplementary Data S12 of the manuscript "<b>Hypoxia leads to reduced mito-nuclear gene expression and to increased mtDNA transcriptional pausing in human cells</b>" by Shtolz et al.Result of DESeq2 analysis on PRO-seq data analyzed using PEPPR."result" output. Main columns:<b>Name:</b> gene symbol<b>baseMean</b>: Mean normalized expression across all samples<b>log2FoldChange</b>: log<sub>2</sub> fold-change between treatment (hypoxia) and control (normoxia).<b>lfcSE</b>: Standard error of the log<sub>2</sub><sub> </sub>fold-change<b>stat</b>: Negative binomial test statistic.<b>p-value</b><b>padj:</b> Benjamin-Hodgkin-adjusted p-value<b>dataset</b>: Name of the dataset<b>cell line</b><b>Complex</b>: Complex association of gene (either complex I, II, III, IV and V of OXPHOS or the mito-ribosome)<b>Genome</b>: Genome of the gene (NUC for nucleus or MT for mitochondrial DNA).<b>ensembl.gene</b>: Ensemble gene ID.Data used to generate Supplementary Fig. S11.
DOI: 10.25574/05674
title: Chandra X-ray Observatory ObsId 05674

description: Gems in the Chandra Deep Fields: The Nature of Optically Passive X-ray Galaxies (aka XBONGs)
DOI: 10.6084/m9.figshare.30273919.v2
title: Supplementary Data S13 - PRO-seq gene body analysis

description: Supplementary Data S13 of the manuscript "<b>Hypoxia leads to reduced mito-nuclear gene expression and to increased mtDNA transcriptional pausing in human cells</b>" by Shtolz et al.Result of DESeq2 analysis on PRO-seq data analyzed using PEPPR."result" output. Main columns:<b>Name:</b> gene symbol<b>baseMean</b>: Mean normalized expression across all samples<b>log2FoldChange</b>: log<sub>2</sub> fold-change between treatment (hypoxia) and control (normoxia).<b>lfcSE</b>: Standard error of the log<sub>2</sub><sub> </sub>fold-change<b>stat</b>: Negative binomial test statistic.<b>p-value</b><b>padj:</b> Benjamin-Hodgkin-adjusted p-value<b>dataset</b>: Name of the dataset<b>cell line</b><b>Complex</b>: Complex association of gene (either complex I, II, III, IV and V of OXPHOS or the mito-ribosome)<b>Genome</b>: Genome of the gene (NUC for nucleus or MT for mitochondrial DNA).<b>ensembl.gene</b>: Ensemble gene ID.Data used to generate Supplementary Fig. S11.
DOI: 10.15468/dl.qs34t6
title: Occurrence Download

description: A dataset containing 204363 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is The reptiles and amphibians collection (RA) of the Muséum national d'Histoire Naturelle (MNHN - Paris)"
 ]
}

 The dataset includes 204363 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0055007-251120083545085/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.29631032
title: Supplementary Data S14 - BigWig tracks of all PRO-seq data used

description: Supplementary Data S14 - All BigWig files of PRO-seq data generated for the publication "<b>Hypoxia leads to reduced mito-nuclear gene expression and to increased mtDNA transcriptional pausing in human cells</b>" by Shtolz et al.The data was generated by running PEPRRO as described in the paper, and includes only the read-ends, mapped to hg38. The forward and reverse strand reads are separated into "plus" and "minus" files. Information on the samples is available in "metadata.xlsx".<br>
DOI: 10.6084/m9.figshare.29631032.v2
title: Supplementary Data S14 - BigWig tracks of all PRO-seq data used

description: Supplementary Data S14 - All BigWig files of PRO-seq data generated for the publication "<b>Hypoxia leads to reduced mito-nuclear gene expression and to increased mtDNA transcriptional pausing in human cells</b>" by Shtolz et al.The data was generated by running PEPRRO as described in the paper, and includes only the read-ends, mapped to hg38. The forward and reverse strand reads are separated into "plus" and "minus" files. Information on the samples is available in "metadata.xlsx".<br>
DOI: 10.25574/05675
title: Chandra X-ray Observatory ObsId 05675

description: Gems in the Chandra Deep Fields: The Nature of Optically Passive X-ray Galaxies (aka XBONGs)
DOI: 10.6084/m9.figshare.29631032.v1
title: Supplementary Data S6 - BigWig tracks of all PRO-seq data used

description: All BigWig files of PRO-seq data generated for the publication "<b>Hypoxia leads to reduced mito-nuclear gene expression and to increased mtDNA transcriptional pausing in human cells</b>" by Shtolz et al.The data was generated by running PEPRRO as described in the paper, and includes only the read-ends, mapped to hg38. The forward and reverse strand reads are separated into "plus" and "minus" files. Information on the samples is available in "metadata.xlsx".
DOI: 10.6084/m9.figshare.30814652
title: Supplementary Data S16 - Read end RPM for PRO-seq data around pausing sites

description: Supplementary Data S16 of the manuscript "<b>Hypoxia leads to reduced mito-nuclear gene expression and to increased mtDNA transcriptional pausing in human cells</b>" by Shtolz et al.This dataframe contains normalized read end RPM values at identified pause sites across different experimental conditions. It combines data from both mitochondrial DNA strands.<b>Columns:</b><b>cell</b>: Cell line name (e.g., 'hela', 'u87', 'd407')<b>treatment</b>: Experimental condition ('Control' or 'Hypoxia')<b>Position</b>: Mitochondrial DNA position (1-16569) where a pause site was identified<b>Read_End_RPM</b>: Normalized read end counts (Reads Per Million) at the pause site<b>Strand</b>: DNA strand where the pause site occurs ('Positive' for heavy strand or 'Negative' for light strand)<br>
DOI: 10.6084/m9.figshare.30814652.v1
title: Supplementary Data S8 - Read end RPM for PRO-seq data around pausing sites

description: Supplementary Data S8 of the manuscript "<b>Hypoxia leads to reduced mito-nuclear gene expression and to increased mtDNA transcriptional pausing in human cells</b>" by Shtolz et al.This dataframe contains normalized read end RPM values at identified pause sites across different experimental conditions. It combines data from both mitochondrial DNA strands.<b>Columns:</b><b>cell</b>: Cell line name (e.g., 'hela', 'u87', 'd407')<b>treatment</b>: Experimental condition ('Control' or 'Hypoxia')<b>Position</b>: Mitochondrial DNA position (1-16569) where a pause site was identified<b>Read_End_RPM</b>: Normalized read end counts (Reads Per Million) at the pause site<b>Strand</b>: DNA strand where the pause site occurs ('Positive' for heavy strand or 'Negative' for light strand)
DOI: 10.6084/m9.figshare.30814652.v2
title: Supplementary Data S16 - Read end RPM for PRO-seq data around pausing sites

description: Supplementary Data S16 of the manuscript "<b>Hypoxia leads to reduced mito-nuclear gene expression and to increased mtDNA transcriptional pausing in human cells</b>" by Shtolz et al.This dataframe contains normalized read end RPM values at identified pause sites across different experimental conditions. It combines data from both mitochondrial DNA strands.<b>Columns:</b><b>cell</b>: Cell line name (e.g., 'hela', 'u87', 'd407')<b>treatment</b>: Experimental condition ('Control' or 'Hypoxia')<b>Position</b>: Mitochondrial DNA position (1-16569) where a pause site was identified<b>Read_End_RPM</b>: Normalized read end counts (Reads Per Million) at the pause site<b>Strand</b>: DNA strand where the pause site occurs ('Positive' for heavy strand or 'Negative' for light strand)<br>
DOI: 10.25574/05676
title: Chandra X-ray Observatory ObsId 05676

description: Gems in the Chandra Deep Fields: The Nature of Optically Passive X-ray Galaxies (aka XBONGs)
DOI: 10.6084/m9.figshare.30814664
title: Supplementary Data S15 - pause sites identified using PRO-seq data

description: Supplementary Data S15 of the manuscript "<b>Hypoxia leads to reduced mito-nuclear gene expression and to increased mtDNA transcriptional pausing in human cells</b>" by Shtolz et al.Summary of the total number of pause sites identified for each combination of cell line, strand, and treatment condition.<b>Columns:</b><b>cell</b>: Cell line name (e.g., 'hela', 'u87', 'd407')<b>pause_sites</b>: Total count of pause sites identified for this combination<b>Strand</b>: DNA strand ('Positive' for heavy strand or 'Negative' for light strand)<b>Treatment</b>: Experimental condition ('Control' or 'Hypoxia')This dataframe provides a high-level summary for statistical comparisons and visualization of how many pause sites were detected under different experimental conditions, making it useful for comparative analyses between treatments and strands.
DOI: 10.6084/m9.figshare.30814664.v1
title: Supplementary Data S7 - pause sites identified using PRO-seq data

description: Supplementary Data S8 of the manuscript "<b>Hypoxia leads to reduced mito-nuclear gene expression and to increased mtDNA transcriptional pausing in human cells</b>" by Shtolz et al.Summary of the total number of pause sites identified for each combination of cell line, strand, and treatment condition.<b>Columns:</b><b>cell</b>: Cell line name (e.g., 'hela', 'u87', 'd407')<b>pause_sites</b>: Total count of pause sites identified for this combination<b>Strand</b>: DNA strand ('Positive' for heavy strand or 'Negative' for light strand)<b>Treatment</b>: Experimental condition ('Control' or 'Hypoxia')This dataframe provides a high-level summary for statistical comparisons and visualization of how many pause sites were detected under different experimental conditions, making it useful for comparative analyses between treatments and strands.
DOI: 10.6084/m9.figshare.30814664.v2
title: Supplementary Data S15 - pause sites identified using PRO-seq data

description: Supplementary Data S15 of the manuscript "<b>Hypoxia leads to reduced mito-nuclear gene expression and to increased mtDNA transcriptional pausing in human cells</b>" by Shtolz et al.Summary of the total number of pause sites identified for each combination of cell line, strand, and treatment condition.<b>Columns:</b><b>cell</b>: Cell line name (e.g., 'hela', 'u87', 'd407')<b>pause_sites</b>: Total count of pause sites identified for this combination<b>Strand</b>: DNA strand ('Positive' for heavy strand or 'Negative' for light strand)<b>Treatment</b>: Experimental condition ('Control' or 'Hypoxia')This dataframe provides a high-level summary for statistical comparisons and visualization of how many pause sites were detected under different experimental conditions, making it useful for comparative analyses between treatments and strands.
DOI: 10.15468/dl.dfmvcj
title: Occurrence Download

description: A dataset containing 253703 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Abies alba",
 "HasCoordinate is true",
 "Year is 1900,2025"
 ]
}

 The dataset includes 253703 records from 861 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0054975-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25574/05677
title: Chandra X-ray Observatory ObsId 05677

description: Gems in the Chandra Deep Fields: The Nature of Optically Passive X-ray Galaxies (aka XBONGs)