cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25345/c5xg9fm9x
title: MassIVE MSV000092015 - Robust and scalable fluorosequencing technology
title: Title: Robust and scalable fluorosequencing technology Corresponding Author: Jagannath Swaminathan HLA peptides from mono-allelic B-cell line using tandem mass-spectrometry We purchased the monoallelic B-cell line (B721.221), with HLA allele A*2603, directly from the International Histocompatibility Working group (Seattle, Washington). We cultured the cells and isolated HLA peptides from approximately 300 million cells as previously described (Abelin et al. 2017). We identified the isolated HLA peptides using an LC-coupled tandem mass-spectrometer (ThermoFisher, Orbitrap Fusion Lumos) and a reference dataset of a human proteome (Swissprot), applying settings from the literature for analyzing HLA peptides (Bassani-Sternberg et al. 2015) and ProteomeDiscoverer 2.3 software (Thermofisher).
DOI: 10.6084/m9.figshare.23108180
title: Data and scripts from the paper "BIRD SPECIES RESPONSES TO DROUGHT IN TWO SOUTHERN CALIFORNIA COASTAL SAGE SCRUB COMMUNITIES" published in The Southwestern Naturalist.

description: The extended and extreme droughts that California has experienced in recent years, largely a product of climate change, have adversely affected a wide array of taxa. In the present study, we analyzed longterm data from 1983 to 2014 to assess the influence of drought on bird species in two protected coastal sage scrub habitats in southern California: the Voorhis Ecological Reserve, which lacks a supplemental water source, and the Bernard Field Station, which has a permanent source of supplemental water maintained by staff. We identified several species that exhibited significant increases or decreases in observations during drought. All species that increased in observations during drought were habitat generalists, and several species that decreased in observations during drought were habitat specialists. Most species that increased or decreased in observations during drought were also less likely to be observed at the Voorhis Ecological Reserve, while fewer were less likely to be observed at the Bernard Field Station. Several species that were observed significantly less often during drought were identified by previous studies to be likely to suffer from drought effects. Further, we identified species in our study that were observed less often during drought that are listed as California Bird Species of Special Concern: the cactus wren (Campylorhynchus brunneicapillus), loggerhead shrike (Lanius ludovicianus), northern harrier (Circus hudsonius), and coastal California gnatcatcher (Polioptila californica californica). Via the identification of drought effects across several bird species, our results add to a growing body of work that assists drought mitigation efforts.
DOI: 10.6084/m9.figshare.23108180.v1
title: Data and scripts from the paper "BIRD SPECIES RESPONSES TO DROUGHT IN TWO SOUTHERN CALIFORNIA COASTAL SAGE SCRUB COMMUNITIES" published in The Southwestern Naturalist.

description: The extended and extreme droughts that California has experienced in recent years, largely a product of climate change, have adversely affected a wide array of taxa. In the present study, we analyzed longterm data from 1983 to 2014 to assess the influence of drought on bird species in two protected coastal sage scrub habitats in southern California: the Voorhis Ecological Reserve, which lacks a supplemental water source, and the Bernard Field Station, which has a permanent source of supplemental water maintained by staff. We identified several species that exhibited significant increases or decreases in observations during drought. All species that increased in observations during drought were habitat generalists, and several species that decreased in observations during drought were habitat specialists. Most species that increased or decreased in observations during drought were also less likely to be observed at the Voorhis Ecological Reserve, while fewer were less likely to be observed at the Bernard Field Station. Several species that were observed significantly less often during drought were identified by previous studies to be likely to suffer from drought effects. Further, we identified species in our study that were observed less often during drought that are listed as California Bird Species of Special Concern: the cactus wren (Campylorhynchus brunneicapillus), loggerhead shrike (Lanius ludovicianus), northern harrier (Circus hudsonius), and coastal California gnatcatcher (Polioptila californica californica). Via the identification of drought effects across several bird species, our results add to a growing body of work that assists drought mitigation efforts.
DOI: 10.25378/janelia.22670176.v2
title: Near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of A431 epithelial cells (aic_desmosome-2)

description: <strong>Sample: </strong>Cultured A431 (ATCC CRL-1555) cells stably expressing Desmoplakin-eGFP (Addgene #32227) and mApple-VAPB, stained with MitoView650 <strong>Sample Description: </strong>The endoplasmic reticulum (ER) forms a dynamic network that contacts other cellular membranes to regulate stress responses, calcium signaling, and lipid transfer. Using high-resolution volume electron microscopy, we find that the ER forms a previously unknown association with keratin intermediate filaments and desmosomal cell-cell junctions. Peripheral ER assembles into mirror image-like arrangements at desmosomes and exhibits nanometer proximity to keratin filaments and the desmosome cytoplasmic plaque. ER tubules exhibit stable associations with desmosomes, and perturbation of desmosomes or keratin filaments alters ER organization and mobility. These findings indicate that desmosomes and the keratin cytoskeleton pattern the distribution of the ER network. Overall, this study reveals a previously unknown subcellular architecture defined by the structural integration of ER tubules with an epithelial intercellular junction. <strong>Protocol: </strong>High pressure freezing, freeze-substitution resin embedding with 2% OsO₄ 0.1% UA 3% H₂O in acetone; resin embedding in Eponate 12. <strong>Contributions: </strong>Sample prepared by Jesse Aaron and Satya Khuon (AIC Janelia), staining and resin embedding by Nirmala Iyer (HHMI/Janelia), trimming and imaging by Jesse Aaron and Satya Khoun (AIC Janelia), post-processing by Eric Trautman and Stephan Preibisch (HHMI/Janelia), manual segmentations by COSEM Project Team (HHMI/Janelia) and Kowalczyk Lab (Pennsylvania State College of Medicine), and automated segmentations by COSEM Project Team. <strong>Acquisition ID:</strong> aic_desmosome-2 <strong>Voxel size (nm):</strong> 8 x 8 x 8 (X, Y, Z) <strong>Data dimensions (µm): </strong>42.3 x 10.4 x 52.5 (X, Y, Z) <strong>Imaging start date:</strong> 2021-01-27 <strong>Dataset URL (Redirect): </strong>https://data.janelia.org/LnbXJ <strong>Visualization Website</strong>: https://openorganelle.janelia.org/datasets/aic_desmosome-2 <strong>Publications:</strong> "Architecture and dynamics of a novel desmosome-endoplasmic reticulum organelle" by Bharathan et al., 2022 <strong>DOI: </strong>https://doi.org/10.1101/2022.07.07.499185 <strong>Imaging duration (days): </strong>4 <strong>Landing energy (eV):</strong> 1200 <strong>Imaging current (nA):</strong> 2.0 <strong>Scanning speed (MHz):</strong> 0.500<br>
DOI: 10.25378/janelia.22670176
title: Near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of A431 epithelial cells (aic_desmosome-2)

description: <strong>Sample: </strong>Cultured A431 (ATCC CRL-1555) cells stably expressing Desmoplakin-eGFP (Addgene #32227) and mApple-VAPB, stained with MitoView650 <strong>Sample Description: </strong>The endoplasmic reticulum (ER) forms a dynamic network that contacts other cellular membranes to regulate stress responses, calcium signaling, and lipid transfer. Using high-resolution volume electron microscopy, we find that the ER forms a previously unknown association with keratin intermediate filaments and desmosomal cell-cell junctions. Peripheral ER assembles into mirror image-like arrangements at desmosomes and exhibits nanometer proximity to keratin filaments and the desmosome cytoplasmic plaque. ER tubules exhibit stable associations with desmosomes, and perturbation of desmosomes or keratin filaments alters ER organization and mobility. These findings indicate that desmosomes and the keratin cytoskeleton pattern the distribution of the ER network. Overall, this study reveals a previously unknown subcellular architecture defined by the structural integration of ER tubules with an epithelial intercellular junction. <strong>Protocol: </strong>High pressure freezing, freeze-substitution resin embedding with 2% OsO₄ 0.1% UA 3% H₂O in acetone; resin embedding in Eponate 12. <strong>Contributions: </strong>Sample prepared by Jesse Aaron and Satya Khuon (AIC Janelia), staining and resin embedding by Nirmala Iyer (HHMI/Janelia), trimming and imaging by Jesse Aaron and Satya Khoun (AIC Janelia), post-processing by Eric Trautman and Stephan Preibisch (HHMI/Janelia), manual segmentations by COSEM Project Team (HHMI/Janelia) and Kowalczyk Lab (Pennsylvania State College of Medicine), and automated segmentations by COSEM Project Team. <strong>Acquisition ID:</strong> aic_desmosome-2 <strong>Voxel size (nm):</strong> 8 x 8 x 8 (X, Y, Z) <strong>Data dimensions (µm): </strong>42.3 x 10.4 x 52.5 (X, Y, Z) <strong>Imaging start date:</strong> 2021-01-27 <strong>Dataset URL (Redirect): </strong>https://data.janelia.org/LnbXJ <strong>Visualization Website</strong>: https://openorganelle.janelia.org/datasets/aic_desmosome-2 <strong>Publications:</strong> "Architecture and dynamics of a novel desmosome-endoplasmic reticulum organelle" by Bharathan et al., 2022 <strong>DOI: </strong>https://doi.org/10.1101/2022.07.07.499185 <strong>Imaging duration (days): </strong>4 <strong>Landing energy (eV):</strong> 1200 <strong>Imaging current (nA):</strong> 2.0 <strong>Scanning speed (MHz):</strong> 0.500<br>
DOI: 10.25378/janelia.22670176.v1
title: Near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of A431 epithelial cells (aic_desmosome-2)

description: <strong>Sample: </strong>Cultured A431 (ATCC CRL-1555) cells stably expressing Desmoplakin-eGFP (Addgene #32227) and mApple-VAPB, stained with MitoView650 <strong>Sample Description: </strong>The endoplasmic reticulum (ER) forms a dynamic network that contacts other cellular membranes to regulate stress responses, calcium signaling, and lipid transfer. Using high-resolution volume electron microscopy, we find that the ER forms a previously unknown association with keratin intermediate filaments and desmosomal cell-cell junctions. Peripheral ER assembles into mirror image-like arrangements at desmosomes and exhibits nanometer proximity to keratin filaments and the desmosome cytoplasmic plaque. ER tubules exhibit stable associations with desmosomes, and perturbation of desmosomes or keratin filaments alters ER organization and mobility. These findings indicate that desmosomes and the keratin cytoskeleton pattern the distribution of the ER network. Overall, this study reveals a previously unknown subcellular architecture defined by the structural integration of ER tubules with an epithelial intercellular junction. <strong>Protocol: </strong>High pressure freezing, freeze-substitution resin embedding with 2% OsO₄ 0.1% UA 3% H₂O in acetone; resin embedding in Eponate 12. <strong>Contributions: </strong>Sample prepared by Jesse Aaron and Satya Khuon (AIC Janelia), staining and resin embedding by Nirmala Iyer (HHMI/Janelia), trimming and imaging by Jesse Aaron and Satya Khoun (AIC Janelia), post-processing by Eric Trautman and Stephan Preibisch (HHMI/Janelia), manual segmentations by COSEM Project Team (HHMI/Janelia) and Kowalczyk Lab (Pennsylvania State College of Medicine), and automated segmentations by COSEM Project Team. <strong>Acquisition ID:</strong> aic_desmosome-2 <strong>Voxel size (nm):</strong> 8 x 8 x 8 (X, Y, Z) <strong>Data dimensions (µm): </strong>42.3 x 10.4 x 52.5 (X, Y, Z) <strong>Imaging start date:</strong> 2021-01-27 <strong>Dataset URL (Redirect): </strong>https://data.janelia.org/LnbXJ <strong>Visualization Website</strong>: https://openorganelle.janelia.org/datasets/aic_desmosome-2 <strong>Publications:</strong> "Architecture and dynamics of a novel desmosome-endoplasmic reticulum organelle" by Bharathan et al., 2022 <strong>DOI: </strong>https://doi.org/10.1101/2022.07.07.499185 <strong>Imaging duration (days): </strong>4 <strong>Landing energy (eV):</strong> 1200 <strong>Imaging current (nA):</strong> 2.0 <strong>Scanning speed (MHz):</strong> 0.500<br>
DOI: 10.25378/janelia.22674466
title: Refined, automatic organelle segmentations in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of A431 epithelial cells (aic_desmosome-2)

description: <strong>Sample: </strong>Cultured A431 (ATCC CRL-1555) cells stably expressing Desmoplakin-eGFP (Addgene #32227) and mApple-VAPB, stained with MitoView650 <strong>Sample Description: </strong>The endoplasmic reticulum (ER) forms a dynamic network that contacts other cellular membranes to regulate stress responses, calcium signaling, and lipid transfer. Using high-resolution volume electron microscopy, we find that the ER forms a previously unknown association with keratin intermediate filaments and desmosomal cell-cell junctions. Peripheral ER assembles into mirror image-like arrangements at desmosomes and exhibits nanometer proximity to keratin filaments and the desmosome cytoplasmic plaque. ER tubules exhibit stable associations with desmosomes, and perturbation of desmosomes or keratin filaments alters ER organization and mobility. These findings indicate that desmosomes and the keratin cytoskeleton pattern the distribution of the ER network. Overall, this study reveals a previously unknown subcellular architecture defined by the structural integration of ER tubules with an epithelial intercellular junction. <strong>Protocol: </strong>High pressure freezing, freeze-substitution resin embedding with 2% OsO₄ 0.1% UA 3% H₂O in acetone; resin embedding in Eponate 12. <strong>Contributions: </strong>Sample prepared by Jesse Aaron and Satya Khuon (AIC Janelia), staining and resin embedding by Nirmala Iyer (HHMI/Janelia), trimming and imaging by Jesse Aaron and Satya Khoun (AIC Janelia), post-processing by Eric Trautman and Stephan Preibisch (HHMI/Janelia), manual segmentations by COSEM Project Team (HHMI/Janelia) and Kowalczyk Lab (Pennsylvania State College of Medicine), and automated segmentations by COSEM Project Team. <strong>Acquisition ID:</strong> aic_desmosome-2 <strong>Voxel size (nm):</strong> 8 x 8 x 8 (X, Y, Z) <strong>Data dimensions (µm): </strong>42.3 x 10.4 x 52.5 (X, Y, Z) <strong>Imaging start date:</strong> 2021-01-27 <strong>Dataset URL (Redirect):</strong> https://data.janelia.org/T8l9C <strong>EM DOI: </strong>https://doi.org/10.25378/janelia.22670176 <strong>Visualization Website</strong>: https://openorganelle.janelia.org/datasets/aic_desmosome-2 <strong>Publications:</strong> "Architecture and dynamics of a novel desmosome-endoplasmic reticulum organelle" by Bharathan et al., 2022 <strong>Imaging duration (days): </strong>4 <strong>Landing energy (eV):</strong> 1200 <strong>Imaging current (nA):</strong> 2.0 <strong>Scanning speed (MHz):</strong> 0.500
DOI: 10.25378/janelia.22674466.v2
title: Refined, automatic organelle segmentations in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of A431 epithelial cells (aic_desmosome-2)

description: <strong>Sample: </strong>Cultured A431 (ATCC CRL-1555) cells stably expressing Desmoplakin-eGFP (Addgene #32227) and mApple-VAPB, stained with MitoView650 <strong>Sample Description: </strong>The endoplasmic reticulum (ER) forms a dynamic network that contacts other cellular membranes to regulate stress responses, calcium signaling, and lipid transfer. Using high-resolution volume electron microscopy, we find that the ER forms a previously unknown association with keratin intermediate filaments and desmosomal cell-cell junctions. Peripheral ER assembles into mirror image-like arrangements at desmosomes and exhibits nanometer proximity to keratin filaments and the desmosome cytoplasmic plaque. ER tubules exhibit stable associations with desmosomes, and perturbation of desmosomes or keratin filaments alters ER organization and mobility. These findings indicate that desmosomes and the keratin cytoskeleton pattern the distribution of the ER network. Overall, this study reveals a previously unknown subcellular architecture defined by the structural integration of ER tubules with an epithelial intercellular junction. <strong>Protocol: </strong>High pressure freezing, freeze-substitution resin embedding with 2% OsO₄ 0.1% UA 3% H₂O in acetone; resin embedding in Eponate 12. <strong>Contributions: </strong>Sample prepared by Jesse Aaron and Satya Khuon (AIC Janelia), staining and resin embedding by Nirmala Iyer (HHMI/Janelia), trimming and imaging by Jesse Aaron and Satya Khoun (AIC Janelia), post-processing by Eric Trautman and Stephan Preibisch (HHMI/Janelia), manual segmentations by COSEM Project Team (HHMI/Janelia) and Kowalczyk Lab (Pennsylvania State College of Medicine), and automated segmentations by COSEM Project Team. <strong>Acquisition ID:</strong> aic_desmosome-2 <strong>Voxel size (nm):</strong> 8 x 8 x 8 (X, Y, Z) <strong>Data dimensions (µm): </strong>42.3 x 10.4 x 52.5 (X, Y, Z) <strong>Imaging start date:</strong> 2021-01-27 <strong>Dataset URL (Redirect):</strong> https://data.janelia.org/T8l9C <strong>EM DOI: </strong>https://doi.org/10.25378/janelia.22670176 <strong>Visualization Website</strong>: https://openorganelle.janelia.org/datasets/aic_desmosome-2 <strong>Publications:</strong> "Architecture and dynamics of a novel desmosome-endoplasmic reticulum organelle" by Bharathan et al., 2022 <strong>Imaging duration (days): </strong>4 <strong>Landing energy (eV):</strong> 1200 <strong>Imaging current (nA):</strong> 2.0 <strong>Scanning speed (MHz):</strong> 0.500
DOI: 10.25378/janelia.22674466.v1
title: Refined, automatic organelle segmentations in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of A431 epithelial cells (aic_desmosome-2)

description: <strong>Sample: </strong>Cultured A431 (ATCC CRL-1555) cells stably expressing Desmoplakin-eGFP (Addgene #32227) and mApple-VAPB, stained with MitoView650 <strong>Sample Description: </strong>The endoplasmic reticulum (ER) forms a dynamic network that contacts other cellular membranes to regulate stress responses, calcium signaling, and lipid transfer. Using high-resolution volume electron microscopy, we find that the ER forms a previously unknown association with keratin intermediate filaments and desmosomal cell-cell junctions. Peripheral ER assembles into mirror image-like arrangements at desmosomes and exhibits nanometer proximity to keratin filaments and the desmosome cytoplasmic plaque. ER tubules exhibit stable associations with desmosomes, and perturbation of desmosomes or keratin filaments alters ER organization and mobility. These findings indicate that desmosomes and the keratin cytoskeleton pattern the distribution of the ER network. Overall, this study reveals a previously unknown subcellular architecture defined by the structural integration of ER tubules with an epithelial intercellular junction. <strong>Protocol: </strong>High pressure freezing, freeze-substitution resin embedding with 2% OsO₄ 0.1% UA 3% H₂O in acetone; resin embedding in Eponate 12. <strong>Contributions: </strong>Sample prepared by Jesse Aaron and Satya Khuon (AIC Janelia), staining and resin embedding by Nirmala Iyer (HHMI/Janelia), trimming and imaging by Jesse Aaron and Satya Khoun (AIC Janelia), post-processing by Eric Trautman and Stephan Preibisch (HHMI/Janelia), manual segmentations by COSEM Project Team (HHMI/Janelia) and Kowalczyk Lab (Pennsylvania State College of Medicine), and automated segmentations by COSEM Project Team. <strong>Acquisition ID:</strong> aic_desmosome-2 <strong>Voxel size (nm):</strong> 8 x 8 x 8 (X, Y, Z) <strong>Data dimensions (µm): </strong>42.3 x 10.4 x 52.5 (X, Y, Z) <strong>Imaging start date:</strong> 2021-01-27 <strong>Dataset URL (Redirect):</strong> https://data.janelia.org/T8l9C <strong>EM DOI: </strong>https://doi.org/10.25378/janelia.22670176 <strong>Visualization Website</strong>: https://openorganelle.janelia.org/datasets/aic_desmosome-2 <strong>Publications:</strong> "Architecture and dynamics of a novel desmosome-endoplasmic reticulum organelle" by Bharathan et al., 2022 <strong>Imaging duration (days): </strong>4 <strong>Landing energy (eV):</strong> 1200 <strong>Imaging current (nA):</strong> 2.0 <strong>Scanning speed (MHz):</strong> 0.500
DOI: 10.25378/janelia.22675078
title: Near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of A431 epithelial cells (aic_desmosome-3)

description: <strong>Sample: </strong>Cultured A431 (ATCC CRL-1555) cells stably expressing Desmoplakin-eGFP (Addgene #32227) and mApple-VAPB, stained with MitoView650 <strong>Sample Description: </strong>The endoplasmic reticulum (ER) forms a dynamic network that contacts other cellular membranes to regulate stress responses, calcium signaling, and lipid transfer. Using high-resolution volume electron microscopy, we find that the ER forms a previously unknown association with keratin intermediate filaments and desmosomal cell-cell junctions. Peripheral ER assembles into mirror image-like arrangements at desmosomes and exhibits nanometer proximity to keratin filaments and the desmosome cytoplasmic plaque. ER tubules exhibit stable associations with desmosomes, and perturbation of desmosomes or keratin filaments alters ER organization and mobility. These findings indicate that desmosomes and the keratin cytoskeleton pattern the distribution of the ER network. Overall, this study reveals a previously unknown subcellular architecture defined by the structural integration of ER tubules with an epithelial intercellular junction. <strong>Protocol: </strong>High pressure freezing, freeze-substitution resin embedding with 2% OsO₄ 0.1% UA 3% H₂O in acetone; resin embedding in Eponate 12. <strong>Contributions: </strong>Sample prepared by Jesse Aaron and Satya Khuon (AIC Janelia), staining and resin embedding by Nirmala Iyer (HHMI/Janelia), trimming and imaging by Jesse Aaron and Satya Khoun (AIC Janelia), post-processing by Eric Trautman and Stephan Preibisch (HHMI/Janelia), manual segmentations by COSEM Project Team (HHMI/Janelia) and Kowalczyk Lab (Pennsylvania State College of Medicine), and automated segmentations by COSEM Project Team. <strong>Acquisition ID:</strong> aic_desmosome-3 <strong>Voxel size (nm):</strong> 4 x 4 x 4 (X, Y, Z) <strong>Data dimensions (µm): </strong> 14.9 x 12.9 x 48.4 (X, Y, Z) <strong>Imaging start date:</strong> 2021-03-18 <strong>Dataset URL (Redirect): </strong>https://data.janelia.org/ve6M8 <strong>Visualization Website</strong>: https://openorganelle.janelia.org/datasets/aic_desmosome-3 <strong>Publications:</strong> "Architecture and dynamics of a novel desmosome-endoplasmic reticulum organelle" by Bharathan et al., 2022 <strong>DOI: </strong>https://doi.org/10.1101/2022.07.07.499185 <strong>Imaging duration (days): 8</strong> <strong>Landing energy (eV):</strong> 700 <strong>Imaging current (nA):</strong> .25 <strong>Scanning speed (MHz):</strong> 0.200