cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.35092/yhjc.12585431.v1
title: Supplemental Tables supporting "Inhibition of mitochondrial respiration impairs nutrient consumption and metabolite transport in human retinal pigment epithelium"

description: In the present study, we use targeted-metabolomics and metabolite tracing with <sup>13</sup>C glucose to investigate how inhibition of mitochondrial respiration influences the intracellular and extracellular metabolome in primary human RPE cells. Our findings demonstrate that · Inhibition of mitochondrial metabolism causes early and unique changes in medium metabolites;· RPE cells with dysfunctional mitochondria export less glucose, pyruvate, citrate, ketone bodies and other nutrients, but release massive amounts of lactate, hypoxanthine, and other nucleosides;· Changes of medium metabolites consistently reflect intracellular changes.<br><br>Here we provide supplement tables, including the method we used and details in mass spectrometry.<br><br>Supports preprint: Inhibition of mitochondrial respiration impairs nutrient consumption and metabolite transport in human retinal pigment epithelium. Rui Zhang, Abbi L Engel, Yekai Wang, Bo Li, Weiyong Shen, Mark C Gillies, Jennifer Chao, Jianhai Du. bioRxiv 2020.05.11.086827; doi: https://doi.org/10.1101/2020.05.11.086827<br><br>Preprint abstract: Mitochondrial respiration in mammalian cells not only generates ATP to meet their own energy needs but also couples with biosynthetic pathways to produce metabolites that can be exported to support neighboring cells. However, how defects in mitochondrial respiration influence these biosynthetic and exporting pathways remains poorly understood. Mitochondrial dysfunction in retinal pigment epithelium (RPE) cells is an emerging contributor to the death of their neighboring photoreceptors in degenerative retinal diseases including age-related macular degeneration. In this study, we used targeted-metabolomics and 13C tracing to investigate how inhibition of mitochondrial respiration influences the intracellular and extracellular metabolome. We found inhibition of mitochondrial respiration strikingly influenced both the intracellular and extracellular metabolome in primary RPE cells. Intriguingly, the extracellular metabolic changes sensitively reflected the intracellular changes. These changes included substantially enhanced glucose consumption and lactate production, reduced release of pyruvate, citrate and ketone bodies, and massive accumulation of multiple amino acids and nucleosides. In conclusion, these findings reveal a metabolic signature of nutrient consumption and release in mitochondrial dysfunction in RPE cells. Testing medium metabolites provides a sensitive and noninvasive method to assess mitochondrial function in nutrient utilization and transport.
DOI: 10.15156/bio/sh1229253.08fu
title: SH1229253.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1229254.08fu
title: SH1229254.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/th028949
title: TH028949
title: Diaphanocephalidae

description: Here we present the novel 'taxon hypothesis' (TH) concept to accommodate fungal 'species hypothesis' (SH) into existing classification frameworks for taxonomic communication. As supplied with Digital Object Identifiers (DOIs), THs are flexible in time and enable direct cross-communication of higher level taxa along with evolving classification schemes. Every TH includes given number of SHs and consequently fixed number of fungal rDNA ITS sequences. DNA sequences generated by High-throughput or Sanger sequencing studies and identified against UNITE SHs will be automatically assigned to THs as well.
DOI: 10.15156/bio/th028950
title: TH028950
title: Dromaeostrongylidae

description: Here we present the novel 'taxon hypothesis' (TH) concept to accommodate fungal 'species hypothesis' (SH) into existing classification frameworks for taxonomic communication. As supplied with Digital Object Identifiers (DOIs), THs are flexible in time and enable direct cross-communication of higher level taxa along with evolving classification schemes. Every TH includes given number of SHs and consequently fixed number of fungal rDNA ITS sequences. DNA sequences generated by High-throughput or Sanger sequencing studies and identified against UNITE SHs will be automatically assigned to THs as well.
DOI: 10.35092/yhjc.12098397.v2
title: Test Sample - DIPY Processed Parkinson's Progression Markers Initiative (PPMI) Data Derivatives

description: This is a small test sample data for Parkinson's Progression Markers Initiative (PPMI) data derivatives. It includes white matter tracts in common space (MNI space) and tracts in the subject's original space. It also includes anatomical measures extracted from diffusion data such as FA, RD, MD, AD for 5 patient subjects and 5 control subjects.<br>Data was processed using DIPY.<br>This data set was generated by Chandio, B.Q., <i>et al.</i> Bundle analytics, a computational framework for investigating the shapes and profiles of brain pathways across populations. <i>Sci Rep</i> <b>10, </b>17149 (2020) paper.<br>Read paper here: https://rdcu.be/b8rUr<br>
DOI: 10.35092/yhjc.12145626.v1
title: Dataset for Wang et al. 2020: Reconstituting Stratified Epithelial Branching Morphogenesis by Engineering Cell Adhesion

description: This dataset can be used to reproduce all plots in Wang et al., 2020 manuscript titled: "Reconstituting Stratified Epithelial Branching Morphogenesis by Engineering Cell Adhesion" in combination with the Jupyter notebook scripts available from this Github repository: https://github.com/snownontrace/public-scripts-Wang2020-branching-morphogenesis.git<br><br>1. Download and decompress the dataset zip file.<br>2. Place the "data" folder and the "scripts" folder (from GitHub) in the same folder.<br> Note: This folder organization is necessary because relative path is used to read in data in all scripts (e.g., '../data/specific_data_folder/data_table').<br>3. Run scripts to reproduce plots of interest. Refer to the table in the README file of the Github repository to find out which scripts were used to generate which figures.<br>Abstract:During embryogenesis, many organs undergo branching morphogenesis to form tree-like hierarchical structures. However, it remains unclear what drives branching in stratified epithelia, such as in embryonic salivary gland and pancreas. Here, we performed live-organ imaging of mouse embryonic salivary glands at single-cell resolution to reveal branching driven by expansion and folding of an epithelial surface cell sheet characterized by strong cell-matrix adhesion and weak cell-cell adhesion. We successfully reconstituted this early developmental process by experimentally suppressing E-cadherin expression and inducing basement membrane formation in 3D spheroid cultures of engineered cells. Reconstituted branching required integrin-mediated cell-matrix adhesions and was promoted by elevating cell-matrix adhesion strength. Thus, stratified epithelial branching is driven by the combination of strong cell-matrix adhesion and weak cell-cell adhesion of peripheral epithelial cells.<br>
DOI: 10.35092/yhjc.12148428.v1
title: Supplementary Table 2 RNAseq read count file for "RNA-seq reveals sub-zones in mouse adrenal zona fasciculata and the sexually dimorphic responses to thyroid hormone"

description: Supplementary Table 2 for the paper "RNA-seq reveals sub-zones in mouse adrenal zona fasciculata and the sexually dimorphic responses to thyroid hormone":<br>This is the RNAseq read count file which aims to study the effect of thyroid hormone treatment on the mouse adrenal gland. <br>Tab1: Sexual Dimorphic T3-responsive Genes (total 104 genes)Tab2: Male-biased genes (344 genes)<br>Tab3: Female-biased genes (555 genes)Tab4: T3-responsive genes in males (512 genes)Tab5: T3-responsive genes in females (1162 genes)
DOI: 10.35092/yhjc.12148428.v2
title: Supplementary Table 2 RNAseq read count file for "RNA-seq reveals sub-zones in mouse adrenal zona fasciculata and the sexually dimorphic responses to thyroid hormone"

description: Supplementary Table 2 for the paper "RNA-seq reveals sub-zones in mouse adrenal zona fasciculata and the sexually dimorphic responses to thyroid hormone":<br>This is the RNAseq read count file which aims to study the effect of thyroid hormone treatment on the mouse adrenal gland. <br>Tab1: Sexual Dimorphic T3-responsive Genes (total 104 genes)Tab2: Male-biased genes (344 genes)<br>Tab3: Female-biased genes (555 genes)Tab4: T3-responsive genes in males (512 genes)Tab5: T3-responsive genes in females (1162 genes)
DOI: 10.35092/yhjc.12148467.v1
title: Supplementary Table 1 RNAseq read count file for "RNA-seq reveals sub-zones in mouse adrenal zona fasciculata and the sexually dimorphic responses to thyroid hormone"

description: Original read count file for the paper "RNA-seq reveals sub-zones in mouse adrenal zona fasciculata and the sexually dimorphic responses to thyroid hormone".<br>This is the RNAseq read count file which aims to study the effect of thyroid hormone treatment on the mouse adrenal gland.
DOI: 10.35092/yhjc.12148467.v2
title: Supplementary Table 1 RNAseq read count file for "RNA-seq reveals sub-zones in mouse adrenal zona fasciculata and the sexually dimorphic responses to thyroid hormone"

description: Original read count file for the paper "RNA-seq reveals sub-zones in mouse adrenal zona fasciculata and the sexually dimorphic responses to thyroid hormone".<br>This is the RNAseq read count file which aims to study the effect of thyroid hormone treatment on the mouse adrenal gland.
DOI: 10.35092/yhjc.12401030.v2
title: Supplemental Table 1: Sample summary -- Chicken embryonic gonads exposed to ethynylestradiol or vehicle: Genetic Sex, Feminization Sore, CYP19A1 expression and rank, and RNAseq mapped read number

description: Supplemental Table 1 supporting: Keiko Shioda et al. “Transcriptomic and epigenetic preservation of genetic sex identity in estrogen-feminized male chicken embryonic gonads” Supplemental Table 1: Sample summary<br><br>Chicken embryos (29 total) were exposed to 20 microgram/egg ethynylestradiol or vehicle oil emulsion from incubation day 6, and their gonads were collected on day 19. This table summarizes sample ID, genetic sex, feminization sore, CYP19A1 expression and rank, and RNAseq mapped read number<br>
DOI: 10.35092/yhjc.12401141.v2
title: Supplemental Table 2: RNAseq data of chicken embryonic gonads exposed to ethynylestradiol or vehicle: Expression of protein-coding genes

description: Supplemental Table 2 supporting: Keiko Shioda et al. “Transcriptomic and epigenetic preservation of genetic sex identity in estrogen-feminized male chicken embryonic gonads” Supplemental Table 2: RNAseq normalized CPM.<br><br>Chicken embryos (29 total) were exposed to 20 microgram/egg ethynylestradiol or vehicle oil emulsion from incubation day 6, and their gonads were collected on day 19. This table shows TMM-normalized RNA-seq data (counts per million) of these chicken embryonic gonads for expression of protein-coding genes annotated in the chicken reference genome sequence galGal3.<br>
DOI: 10.35092/yhjc.12401147.v2
title: Supplemental Table 3: List of genes induced or suppressed in chicken embryonic gonads by in ovo exposure to ethynylestradiol

description: Supplemental Table 3 supporting: Keiko Shioda et al. “Transcriptomic and epigenetic preservation of genetic sex identity in estrogen-feminized male chicken embryonic gonads” Supplemental Table 3: Cluster Genes.<br><br>Chicken embryos (29 total) were exposed to 20 microgram/egg ethynylestradiol or vehicle oil emulsion from incubation day 6, and their gonads were collected on day 19. This table shows genes induced or suppressed by exposure to ethynylestradiol determined by RNA-seq.
DOI: 10.35092/yhjc.12401153.v2
title: Supplemental Table 4: List of genes differentially expressed in chicken embryonic gonads with various degrees of feminization after in ovo exposure to ethynylestradiol

description: Supplemental Table 4 supporting: Keiko Shioda et al. “Transcriptomic and epigenetic preservation of genetic sex identity in estrogen-feminized male chicken embryonic gonads” <br>Supplemental Table 4: Differentially expressed genes.<br><br>Chicken embryos (29 total) were exposed to 20 microgram/egg ethynylestradiol or vehicle oil emulsion from incubation day 6, and their gonads were collected on day 19. This table shows list of differentially expressed genes in chicken embryonic gonads showing various degrees of feminization after exposure to ethynylestradiol determined by RNA-seq. Induction or suppression comparing various degrees of feminization scores (FS= 0,1,2,3) are shown in the tag labels.<br>Each tag shows a list of DEGs with gene symbols, log2 fold changes (logFC), average log2 counts-per-million expression (logCPM), likelihood ratio statistics (LR) (1), p-values, and false discovery ratio (FDR) (2) calculated based on the generalized linear model (3). DEGs listed in each spreadsheet are selected using criteria indicated in the tags. For example, “FS0 vs FS1” indicates genes differentially expressed between FS=0 and FS=1 gonads. The spreadsheet “FS0 &lt; FS1 or FS2” lists genes whose expression in weaker in FS=0 compared to either FS=1 or FS=2. The spreadsheet “FS0 vs FS1 not FS3 UP” lists genes upregulated in FS=1 compared to FS=0, but genes upregulated in FS=3 compared to FS=0 were removed from this list.<br>[References]1. Xu M, Chen L. An empirical likelihood ratio test robust to individual heterogeneity for differential expression analysis of RNA-seq. Brief Bioinform. 2018;19(1):109-117.2. Reiner A, Yekutieli D, Benjamini Y. Identifying differentially expressed genes using false discovery rate controlling procedures. Bioinformatics. 2003;19(3):368-375.3. Nikolayeva O, Robinson MD. edgeR for differential RNA-seq and ChIP-seq analysis: an application to stem cell biology. Methods Mol Biol. 2014;1150:45-79.
DOI: 10.35092/yhjc.12401156.v2
title: Supplemental Table 5: List of genes following various profiles of feminization-dependent expression in chicken embryonic gonads after in ovo exposure to ethynylestradiol

description: Supplemental Table 5 supporting: Keiko Shioda et al. “Transcriptomic and epigenetic preservation of genetic sex identity in estrogen-feminized male chicken embryonic gonads” <br>Supplemental Table 5: Classified differentially expressed genes.<br><br>Chicken embryos (29 total) were exposed to 20 microgram/egg ethynylestradiol or vehicle oil emulsion from incubation day 6, and their gonads were collected on day 19. This table shows list of differentially expressed genes in chicken embryonic gonads following various profiles of feminization-dependent expression after in ovo exposure to ethynylestradiol determined by RNA-seq. Names of the representative feminization-dependent profiles are shown in the tag labels.
DOI: 10.35092/yhjc.12401162.v2
title: Supplemental Table 6: Gene ontology analysis of the CTNNB1 profile feminization-suppressible genes in chicken embryonic gonads after in ovo exposure to ethynylestradiol

description: Supplemental Table 6 supporting: Keiko Shioda et al. “Transcriptomic and epigenetic preservation of genetic sex identity in estrogen-feminized male chicken embryonic gonads” <br>Supplemental Table 6: Gene ontology analysis of CTNNB1 group differentially expressed genes.<br><br>Chicken embryos (29 total) were exposed to 20 microgram/egg ethynylestradiol or vehicle oil emulsion from incubation day 6, and their gonads were collected on day 19. Expression of several genes, represented by CTNNB1, in chicken embryonic gonads were strongly suppressed upon feminization after in ovo exposure to ethynylestradiol. This table shows outcome of a gene ontology analysis of the CTNNB1 group genes using the NIH LHRI DAVID service.
DOI: 10.35092/yhjc.12401171.v2
title: Supplemental Table 8: List of genes differentially expressed repetitive sequences in chicken embryonic gonads with various degrees of feminization after in ovo exposure to ethynylestradiol

description: Supplemental Table 8 supporting: Keiko Shioda et al. “Transcriptomic and epigenetic preservation of genetic sex identity in estrogen-feminized male chicken embryonic gonads” <br>Supplemental Table 8: Differentially expressed repetitive sequences.<br><br>Chicken embryos (29 total) were exposed to 20 microgram/egg ethynylestradiol or vehicle oil emulsion from incubation day 6, and their gonads were collected on day 19. This table shows list of differentially expressed repetitive sequences in chicken embryonic gonads showing various degrees of feminization after exposure to ethynylestradiol determined by RNA-seq. Induction or suppression comparing various degrees of feminization scores (FS= 0,1,2,3) are shown in the tag labels.
DOI: 10.35092/yhjc.12636119
title: Bioinformatics analysis of CEP350 tumor suppression in human TCGA cutaneous melanoma | Datasets Supporting: Tumor Suppressive Functions of CEP350 in Cutaneous Melanoma Cells

description: Bioinformatics analysis of CEP350 tumor suppression in human TCGA cutaneous melanoma. Publicly available datasets were downloaded from Genomic Data Commons Data Portal using data from the The Cancer Genome Atlas Program and the International Cancer Genome Consortium Data Portal for statistical analyses using R and Shiny.<br><br>Supplementary datasets and other information accompanying manuscript: Tumor Suppressive Functions of CEP350 in Cutaneous Melanoma Cells by Aziz Aiderus, Bin Fang, John M. Koomen and Michael B. Mann.<br>Abstract: We previously identified Cep350 as a novel melanoma haploinsufficient melanoma tumor suppressor gene using SB transposon-mediated mutagenesis to drive melanoma progression in Braf(V600E) mutant (SB|Braf) mice functionally demonstrated that the human CEP350 ortholog is a new melanoma tumor-suppressor gene in human cancer cell lines (Mann et al., Nature Genetics, 2015). Further dissection of the latent tumor suppressive functions of CEP350 in cutaneous melanoma cells is essential for understanding its role in melanoma imitation and progression. In this work, we investigated the role of the novel tumor suppressive functions of CEP350 in cutaneous melanoma cells using comparative informatics, molecular oncology, and proteomics approaches to demonstrate that CEP350 acts via altered cytoskeletal dynamics to contribute to BRAF-V600E driven melanoma.
DOI: 10.35092/yhjc.12636119.v1
title: Bioinformatics analysis of CEP350 tumor suppression in human TCGA cutaneous melanoma | Datasets Supporting: Tumor Suppressive Functions of CEP350 in Cutaneous Melanoma Cells

description: Bioinformatics analysis of CEP350 tumor suppression in human TCGA cutaneous melanoma. Publicly available datasets were downloaded from Genomic Data Commons Data Portal using data from the The Cancer Genome Atlas Program and the International Cancer Genome Consortium Data Portal for statistical analyses using R and Shiny.<br><br>Supplementary datasets and other information accompanying manuscript: Tumor Suppressive Functions of CEP350 in Cutaneous Melanoma Cells by Aziz Aiderus, Bin Fang, John M. Koomen and Michael B. Mann.<br>Abstract: We previously identified Cep350 as a novel melanoma haploinsufficient melanoma tumor suppressor gene using SB transposon-mediated mutagenesis to drive melanoma progression in Braf(V600E) mutant (SB|Braf) mice functionally demonstrated that the human CEP350 ortholog is a new melanoma tumor-suppressor gene in human cancer cell lines (Mann et al., Nature Genetics, 2015). Further dissection of the latent tumor suppressive functions of CEP350 in cutaneous melanoma cells is essential for understanding its role in melanoma imitation and progression. In this work, we investigated the role of the novel tumor suppressive functions of CEP350 in cutaneous melanoma cells using comparative informatics, molecular oncology, and proteomics approaches to demonstrate that CEP350 acts via altered cytoskeletal dynamics to contribute to BRAF-V600E driven melanoma.
DOI: 10.35092/yhjc.12636125
title: Phospho-proteomics tandem mass tag datasets from cells with CEP350 genetic alteration | Datasets Supporting: Tumor Suppressive Functions of CEP350 in Cutaneous Melanoma Cells

description: Signaling changes induced by haploinsufficient loss or over-expression of CEP350 by global phospho-serine/threonine profiling melanoma cells expressing oncogenic BRAF-V600E. Raw data produced by the Proteomics and Metabolomics Core Facility and data analysis performed by the Biostatistics and Bioinformatics Shared Resource at the H. Lee Moffitt Cancer Center & Research Institute.<br>Supplementary datasets and other information accompanying manuscript: Tumor Suppressive Functions of CEP350 in Cutaneous Melanoma Cells by Aziz Aiderus, Bin Fang, John M. Koomen and Michael B. Mann.<br>Abstract: We previously identified Cep350 as a novel melanoma haploinsufficient melanoma tumor suppressor gene using SB transposon-mediated mutagenesis to drive melanoma progression in Braf(V600E) mutant (SB|Braf) mice functionally demonstrated that the human CEP350 ortholog is a new melanoma tumor-suppressor gene in human cancer cell lines (Mann et al., Nature Genetics, 2015). Further dissection of the latent tumor suppressive functions of CEP350 in cutaneous melanoma cells is essential for understanding its role in melanoma imitation and progression. In this work, we investigated the role of the novel tumor suppressive functions of CEP350 in cutaneous melanoma cells using comparative informatics, molecular oncology, and proteomics approaches to demonstrate that CEP350 acts via altered cytoskeletal dynamics to contribute to BRAF-V600E driven melanoma.