cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.35092/yhjc.9696308
title: IFNg FCS files to support Figs 3 & 4 in "The ancestral environment shapes antiviral CD8+ T cell responses across generations"

description: Figure 3: F0 exposure to TCDD has developmental, but not transgenerational effects on the CD8+ T response to IAV in the lung of male TCDD lineage offspring<br>7-8 male mice from each treatment group were infected with IAV and the CD8+ T cell response in the lung was measured 8 days later.<br>(I) The flow plot depicts the mean percent of IFNg+CD8+ T cells in the lung of F1 offspring. (J) The mean number of IFNg+CD8+ T cells in the lung of F1 offspring. (K) The flow plots show the mean percent of IFNg+CD8+ T cells in the lung of F3 offspring. (L) The mean number of IFNg+CD8+ T cells in the lung of F3 offspring.<br>Figure 4: In the MLN, F0 AHR activation alters the CD8+ T cell response of female and male F1 but not F3 generation offspring. F1 and F3 generation offspring were generated as shown in Fig 1A. 7-9 adult F1 and F3 generation offspring from each treatment group were infected with IAV and MLN cells were harvested on day 8 (males) or 9 (females) post infection. The graphs depict the mean number of cells from vehicle and TCDD offspring found in the MLN on day 8 or 9 post IAV infection. <br>(C) The number of IFNg+CD8+ T cells in female F1 (left) and F3 (right) offspring. (G) The number of IFNg+CD8+ T cells in male F1 (left) and F3 (right) generation offspring. <br>
DOI: 10.35092/yhjc.9696308.v1
title: IFNg FCS files to support Figs 3 & 4 in "The ancestral environment shapes antiviral CD8+ T cell responses across generations"

description: Figure 3: F0 exposure to TCDD has developmental, but not transgenerational effects on the CD8+ T response to IAV in the lung of male TCDD lineage offspring<br>7-8 male mice from each treatment group were infected with IAV and the CD8+ T cell response in the lung was measured 8 days later.<br>(I) The flow plot depicts the mean percent of IFNg+CD8+ T cells in the lung of F1 offspring. (J) The mean number of IFNg+CD8+ T cells in the lung of F1 offspring. (K) The flow plots show the mean percent of IFNg+CD8+ T cells in the lung of F3 offspring. (L) The mean number of IFNg+CD8+ T cells in the lung of F3 offspring.<br>Figure 4: In the MLN, F0 AHR activation alters the CD8+ T cell response of female and male F1 but not F3 generation offspring. F1 and F3 generation offspring were generated as shown in Fig 1A. 7-9 adult F1 and F3 generation offspring from each treatment group were infected with IAV and MLN cells were harvested on day 8 (males) or 9 (females) post infection. The graphs depict the mean number of cells from vehicle and TCDD offspring found in the MLN on day 8 or 9 post IAV infection. <br>(C) The number of IFNg+CD8+ T cells in female F1 (left) and F3 (right) offspring. (G) The number of IFNg+CD8+ T cells in male F1 (left) and F3 (right) generation offspring. <br>
DOI: 10.35092/yhjc.9995672
title: Cell Health - Cell Painting Single Cell Profiles

description: Single Cell Databases of Cell Painting Profiles for the Cell Health Project. These data are used to aggregate profiles in a CRISPR knockout experiment. The data are used to predict cell health assays.DataWe collected Cell Painting measurements on a CRISPR experiment. The experiment targeted 59 genes, which included 119 unique guides (~2 per gene), across 3 cell lines. The cell lines included A549, ES2, and HCC44.About 40% of all CRISPR guides were reproducible. This is ok since we are not actually interested in the CRISPR treatment specifically, but instead, just its corresponding readout in each cell health assay.ApproachWe performed the following approach:Split data into 85% training and 15% test sets.Normalized data by plate (z-score).Selected optimal hyperparamters using 5-fold cross-validationTrained elastic net regression models to predict each of the 70 cell health assay readouts, independently.Trained using shuffled data as well.Report performance on training and test sets.We also trained logistic regression classifiers using the same approach above<br>See https://github.com/broadinstitute/cell-health for more details.<br>
DOI: 10.35092/yhjc.9995672.v1
title: Cell Health - Cell Painting Single Cell Profiles

description: Single Cell Databases of Cell Painting Profiles for the Cell Health Project. These data are used to aggregate profiles in a CRISPR knockout experiment. The data are used to predict cell health assays.<br>DataWe collected Cell Painting measurements on a CRISPR experiment. The experiment targeted 59 genes, which included 119 unique guides (~2 per gene), across 3 cell lines. The cell lines included A549, ES2, and HCC44.About 40% of all CRISPR guides were reproducible. This is ok since we are not actually interested in the CRISPR treatment specifically, but instead, just its corresponding readout in each cell health assay.ApproachWe performed the following approach:Split data into 85% training and 15% test sets.Normalized data by plate (z-score).Selected optimal hyperparamters using 5-fold cross-validationTrained elastic net regression models to predict each of the 70 cell health assay readouts, independently.Trained using shuffled data as well.Report performance on training and test sets.We also trained logistic regression classifiers using the same approach above<br>See https://github.com/broadinstitute/cell-health for more details.<br>
DOI: 10.15156/bio/sh1229236.08fu
title: SH1229236.08FU

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/sh1229237.08fu
title: SH1229237.08FU

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/th028931
title: TH028931
title: Rhabdiasidae

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/th028932
title: TH028932
title: Rhabditidae

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/th028933
title: TH028933
title: Rotylenchulidae

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.10250438.v1
title: H1N1 pdm PA::GFP intracellular movement in DMSO treated A549 cells during infection

description: TIFF series of diSPIM datasets, fused and deconvolved, from A549 cells infected with H1N1 pdm PA::GFP and treated with DMSO. Each TIFF file is a full cell volume of 50 planes, with isotropic resolution of 330nm, each .zip file is an independent replicate with at least 1 or 2 cells analyzed for 3D tracking of cytoplasmic foci with 500 time stamps. These data correspond to Supplementary Movie 6 and analysis of these movies provided data presented in Figure 4 and Supplementary Figure 8.<br>Supplementary Movie 6: A549 cells infected with H1N1 pandemic influenza expressing GFP-tagged PA protein (control treatment). <br>Figure 4: Effect of cytoskeleton depolymerization on motion dynamics of influenza vRNP in A549 cells. <br>Supplementary Figure 8: Impact of cytoskeletal depolymerizing drugs on the transport of PA::GFP.
DOI: 10.35092/yhjc.10250534
title: H1N1 pdm PA::GFP intracellular movement in Nocodazole (16 µm) treated A549 cells during infection

description: TIFF series of diSPIM datasets, fused and deconvolved, from A549 cells infected with H1N1 pdm PA::GFP and treated with nocodazole (16 µm). Each TIFF file is a full cell volume of 50 planes, with isotropic resolution of 330nm, each .zip file is an independent replicate with at least 1 or 2 cells analyzed for 3D tracking of cytoplasmic foci with 500 time stamps. These data correspond to Supplementary Movie 7 and analysis of these movies provided data presented in Figure 4 and Supplementary Figure 8.<br>Supplementary Movie 7: A549 cells infected with H1N1 pandemic influenza expressing GFP-tagged PA protein and treated with nocodazole (16 µm). <br>Figure 4: Effect of cytoskeleton depolymerization on motion dynamics of influenza vRNP in A549 cells. <br>Supplementary Figure 8: Impact of cytoskeletal depolymerizing drugs on the transport of PA::GFP.
DOI: 10.35092/yhjc.10250666
title: H1N1 pdm PA::GFP intracellular movement in Latrunculin A (1 µm) treated A549 cells during infection

description: TIFF series of diSPIM datasets, fused and deconvolved, from A549 cells infected with H1N1 pdm PA::GFP and treated with latrunculin A (1 µm). Each TIFF file is a full cell volume of 50 planes, with isotropic resolution of 330nm, each .zip file is an independent replicate with at least 1 or 2 cells analyzed for 3D tracking of cytoplasmic foci with 500 time stamps. These data correspond to Supplementary Movie 8 and analysis of these movies provided data presented in Figure 4 and Supplementary Figure 8.<br>Supplementary Movie 8: A549 cells infected with H1N1 pandemic influenza expressing GFP-tagged PA protein and treated with latrunculin A (1 µm). <br>Figure 4: Effect of cytoskeleton depolymerization on motion dynamics of influenza vRNP in A549 cells. <br>Supplementary Figure 8: Impact of cytoskeletal depolymerizing drugs on the transport of PA::GFP.
DOI: 10.35092/yhjc.10250702
title: GFP-Rab11A intracellular movement in IAV [A/WSN/33(H1N1)] infected A549 cells

description: TIFF series of diSPIM datasets, fused and deconvolved, from A549 GFP-Rab11A cells infected with influenza A virus [A/WSN/33(H1N1)]. Each TIFF file is a full cell volume of 50 planes, with isotropic resolution of 330nm, each .zip file is an independent replicate with at least 1 or 2 cells analyzed for 3D tracking of cytoplasmic foci with 500 time stamps. Analysis of these data correspond to data presented in Figure 5 and Supplementary Figure 10. <br>Figure 5: Effect of viral infection on Rab11A motion: comparing RSV infection with IAV (WSN) infection.<br><br>Supplementary Figure 10: Impact of viral infection on the transport of GFP-Rab11A.
DOI: 10.35092/yhjc.10250702.v1
title: GFP-Rab11A intracellular movement in IAV [A/WSN/33(H1N1)] infected A549 cells

description: TIFF series of diSPIM datasets, fused and deconvolved, from A549 GFP-Rab11A cells infected with influenza A virus [A/WSN/33(H1N1)]. Each TIFF file is a full cell volume of 50 planes, with isotropic resolution of 330nm, each .zip file is an independent replicate with at least 1 or 2 cells analyzed for 3D tracking of cytoplasmic foci with 500 time stamps. Analysis of these data correspond to data presented in Figure 5 and Supplementary Figure 10. <br>Figure 5: Effect of viral infection on Rab11A motion: comparing RSV infection with IAV (WSN) infection.<br><br>Supplementary Figure 10: Impact of viral infection on the transport of GFP-Rab11A.
DOI: 10.35092/yhjc.10255676
title: GFP-Rab11A intracellular movement in RSV infected A549 cells

description: TIFF series of diSPIM datasets, fused and deconvolved, from A549 GFP-Rab11A cells infected with Respiratory Syncytial Virus. Each TIFF file is a full cell volume of 50 planes, with isotropic resolution of 330nm, each .zip file is an independent replicate with at least 1 or 2 cells analyzed for 3D tracking of cytoplasmic foci with 500 time stamps. These data correspond to Supplementary Movie 9 and analysis of these movies provided data presented in Figure 5 and Supplementary Figure 10. <br>Supplementary Movie 9: A549 GFP-Rab11A cells infected with RFP-expressing RSV. <br>Figure 5: Effect of viral infection on Rab11A motion: comparing RSV infection with IAV (WSN) infection. <br>Supplementary Figure 10: Impact of viral infection on the transport of GFP-Rab11A.
DOI: 10.35092/yhjc.10255676.v1
title: GFP-Rab11A intracellular movement in RSV infected A549 cells

description: TIFF series of diSPIM datasets, fused and deconvolved, from A549 GFP-Rab11A cells infected with Respiratory Syncytial Virus. Each TIFF file is a full cell volume of 50 planes, with isotropic resolution of 330nm, each .zip file is an independent replicate with at least 1 or 2 cells analyzed for 3D tracking of cytoplasmic foci with 500 time stamps. These data correspond to Supplementary Movie 9 and analysis of these movies provided data presented in Figure 5 and Supplementary Figure 10. <br>Supplementary Movie 9: A549 GFP-Rab11A cells infected with RFP-expressing RSV. <br>Figure 5: Effect of viral infection on Rab11A motion: comparing RSV infection with IAV (WSN) infection. <br>Supplementary Figure 10: Impact of viral infection on the transport of GFP-Rab11A.
DOI: 10.35092/yhjc.10255862
title: Two-color imaging of GFP-Rab11A and WSN H1N1 PA::mRuby in IAV infected A549 cells

description: TIFF series of diSPIM datasets, fused and deconvolved, from A549 GFP-Rab11A cells infected with WSN H1N1 PA::mRuby influenza virus. Each TIFF file is a full cell volume of 50 planes, with isotropic resolution of 330nm, each .zip file is an independent replicate with at least 1 or 2 cells analyzed for 3D tracking of cytoplasmic foci with over 100 time stamps. These data correspond to Supplementary Movie 11 and analysis of these movies provided data presented in Figure 6 and Supplementary Figure 11.<br>Supplementary Movie 11: A549 GFP-Rab11A infected with PA::mRuby virus.<br>Figure 6: Two-color imaging of PA::mRuby infected GFP-Rab11A A549 cells.<br>Supplementary Figure 11: Additional motion parameters for two-color imaging datasets.
DOI: 10.35092/yhjc.10255862.v1
title: Two-color imaging of GFP-Rab11A and WSN H1N1 PA::mRuby in IAV infected A549 cells

description: TIFF series of diSPIM datasets, fused and deconvolved, from A549 GFP-Rab11A cells infected with WSN H1N1 PA::mRuby influenza virus. Each TIFF file is a full cell volume of 50 planes, with isotropic resolution of 330nm, each .zip file is an independent replicate with at least 1 or 2 cells analyzed for 3D tracking of cytoplasmic foci with over 100 time stamps. These data correspond to Supplementary Movie 11 and analysis of these movies provided data presented in Figure 6 and Supplementary Figure 11.<br>Supplementary Movie 11: A549 GFP-Rab11A infected with PA::mRuby virus.<br>Figure 6: Two-color imaging of PA::mRuby infected GFP-Rab11A A549 cells.<br>Supplementary Figure 11: Additional motion parameters for two-color imaging datasets.
DOI: 10.35092/yhjc.10255922
title: GFP-Rab11A intracellular movement in IBV [B/Texas/02/2013] infected A549 cells

description: TIFF series of diSPIM datasets, fused and deconvolved, from A549 GFP-Rab11A cells infected with influenza virus B/Texas/02/2013. Each TIFF file is a full cell volume of 50 planes, with isotropic resolution of 330nm, each .zip file is an independent replicate with at least 1 or 2 cells analyzed for 3D tracking of cytoplasmic foci with 500 time stamps. The data from these cells corresponds to Supplementary Movie 10 and analysis of these movies provided data presented in Supplementary Figure 10.<br>Supplementary Movie 10: A549 GFP-Rab11A cells infected with influenza virus B/Texas/02/2013 <br>Supplementary Figure 10: Impact of viral infection on the transport of GFP-Rab11A.
DOI: 10.35092/yhjc.10255922.v1
title: GFP-Rab11A intracellular movement in IBV [B/Texas/02/2013] infected A549 cells

description: TIFF series of diSPIM datasets, fused and deconvolved, from A549 GFP-Rab11A cells infected with influenza virus B/Texas/02/2013. Each TIFF file is a full cell volume of 50 planes, with isotropic resolution of 330nm, each .zip file is an independent replicate with at least 1 or 2 cells analyzed for 3D tracking of cytoplasmic foci with 500 time stamps. The data from these cells corresponds to Supplementary Movie 10 and analysis of these movies provided data presented in Supplementary Figure 10.<br>Supplementary Movie 10: A549 GFP-Rab11A cells infected with influenza virus B/Texas/02/2013 <br>Supplementary Figure 10: Impact of viral infection on the transport of GFP-Rab11A.
DOI: 10.35092/yhjc.10261136
title: Transport of transferrin in A549 cells

description: TIFF series of diSPIM datasets, fused and deconvolved, of Alexa 569-transferrin transport in A549 cells. Each TIFF file is a full cell volume of 50 planes, with isotropic resolution of 330nm, each .zip file is an independent replicate with at least 1 or 2 cells analyzed for 3D tracking of cytoplasmic foci with 500 time stamps. The data from these cells corresponds to data presented in Supplementary Figure 2.<br>Supplementary Figure 2: Comparison of motion parameters for transferrin between native A549 cells and GFP-Rab11A A549 cells.<br>
DOI: 10.35092/yhjc.10261136.v1
title: Transport of transferrin in A549 cells

description: TIFF series of diSPIM datasets, fused and deconvolved, of Alexa 569-transferrin transport in A549 cells. Each TIFF file is a full cell volume of 50 planes, with isotropic resolution of 330nm, each .zip file is an independent replicate with at least 1 or 2 cells analyzed for 3D tracking of cytoplasmic foci with 500 time stamps. The data from these cells corresponds to data presented in Supplementary Figure 2.<br>Supplementary Figure 2: Comparison of motion parameters for transferrin between native A549 cells and GFP-Rab11A A549 cells.<br>
DOI: 10.35092/yhjc.10261922
title: Transport of transferrin in A549 GFP-Rab11A cells

description: TIFF series of diSPIM datasets, fused and deconvolved, of Alexa 568- transferrin transport in A549 GFP-Rab11A cells. Each TIFF file is a full cell volume of 50 planes, with isotropic resolution of 330nm, each .zip file is an independent replicate with at least 1 or 2 cells analyzed for 3D tracking of cytoplasmic foci with 500 time stamps. The data from these cells corresponds to data presented in Supplementary Figure 2.<br>Supplementary Figure 2: Comparison of motion parameters for transferrin between native A549 cells and GFP-Rab11A A549 cells.
DOI: 10.35092/yhjc.10266557
title: Read-Me Details on the datasets provided in the collection.

description: Read-Me Details on the datasets provided in the collection.
DOI: 10.35092/yhjc.11319911
title: ImmClassifier training datasets for machine learning

description: 7 training datasets for machine learning module for ImmClassifier <br>Located at feature_data/ folder under ImmClassifier project folder<br>ImmClassifier classifies immune cells using single-cell RNA-Seq data using machine learning methods. <br>The Machine learning module is one part of the ImmClassifier architecture<br><br><br>
DOI: 10.35092/yhjc.11319911.v1
title: ImmClassifier training datasets for machine learning

description: 7 training datasets for machine learning module for ImmClassifier <br>Located at feature_data/ folder under ImmClassifier project folder<br>ImmClassifier classifies immune cells using single-cell RNA-Seq data using machine learning methods. <br>The Machine learning module is one part of the ImmClassifier architecture<br><br><br>
DOI: 10.35092/yhjc.11319998
title: ANOVA analysis comparing Fast SOL, Slow SOL and EDL fiber mechanics from the manuscript "Rats genetically selected for low and high aerobic capacity exhibit altered soleus muscle myofilament functions"

description: ANOVA analysis comparing Fast SOL, Slow SOL and EDL fiber mechanics from the manuscript Biesiadecki et al titled "Rats genetically selected for low and high aerobic capacity exhibit altered soleus muscle myofilament functions"
DOI: 10.35092/yhjc.11319998.v1
title: ANOVA analysis comparing Fast SOL, Slow SOL and EDL fiber mechanics from the manuscript "Rats genetically selected for low and high aerobic capacity exhibit altered soleus muscle myofilament functions"

description: ANOVA analysis comparing Fast SOL, Slow SOL and EDL fiber mechanics from the manuscript Biesiadecki et al titled "Rats genetically selected for low and high aerobic capacity exhibit altered soleus muscle myofilament functions"