cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3597146_d2
title: Additional file 8: of Transcriptome sequencing of Mycosphaerella fijiensis during association with Musa acuminata reveals candidate pathogenicity genes

description: Table S5. Analysis of CAZyme families. Table shows (A) a summary of all the CAZyme families with differentially expressed genes, and (B) annotations for each gene. A) Summary of all the CAZyme families with differentially expressed genes, and numbers of CAZymes in each family with higher expression in the medium versus in infected leaf tissue. B) For each of the differentially expressed CAZymes, the table indicates the CAZy annotation, the conserved domains identified using NCBIâ  s Conserved Domain Database, a summary of blastp results using the NCBI nr protein sequence database, JGI gene and protein IDs, the NCBI accession, the location of the gene on the scaffold, the baseMean value (mean of normalized read counts), the log2 fold change (log2FC), the standard error of the log2 fold change estimate (lfcSE), the Wald statistic (stat), the p-value, and the p-value adjusted for multiple testing (adjusted p-value). Genes with higher expression in medium are colored in blue, and genes with higher expression in infected leaf tissue are colored in green. (XLS 80Â kb)
DOI: 10.6084/m9.figshare.c.3597146_d3
title: Additional file 18: of Transcriptome sequencing of Mycosphaerella fijiensis during association with Musa acuminata reveals candidate pathogenicity genes

description: Table S10. RT-qPCR primers used for validation of RNA-Seq results. For each gene of interest, the first tab of the Excel spreadsheet shows the name of the gene, the name and sequence of the forward and reverse primers, and the expected size of the product. The second tab of the spreadsheet shows the reference gene used in Fig.Â 1 for each gene of interest. (XLS 9Â kb)
DOI: 10.6084/m9.figshare.c.3597146_d4
title: Additional file 5: of Transcriptome sequencing of Mycosphaerella fijiensis during association with Musa acuminata reveals candidate pathogenicity genes

description: Table S3. Identification of M. fijiensis salicylate hydroxylase homolog. The Epichloë festucae salicylate hydroxylase sequence (accession number = AIY25489.1) [45] was used to do a blastp search against the M. fijiensis protein sequences using the NCBI non-redundant protein sequence database. For each of the top 10 hits, the table includes a link to the NCBI accession, JGI gene and protein IDs, bitscore, E-value, and percent identity and similarity. Protein sequences corresponding to genes with higher expression in infected leaf tissue are colored green. (XLS 37 kb)
DOI: 10.6084/m9.figshare.c.3597158_d2
title: Additional file 3: Table S3. of Classification of polyhedral shapes from individual anisotropically resolved cryo-electron tomography reconstructions

description: (in separate Excel spreadsheet due to size): List of 123 polyhedra in the library P $$ \mathcal{P} $$ , together with class and topological profiles (TP). Polyhedral pairs with identical TP are noted. (XLSX 99Â kb)
DOI: 10.6084/m9.figshare.c.3597179_d1
title: Additional file 1: of Explaining the geographic spread of emerging epidemics: a framework for comparing viral phylogenies and environmental landscape data

description: Example files and tutorial related to the present study. (ZIP 36167 kb)
DOI: 10.6084/m9.figshare.c.3597146_d13
title: Additional file 10: of Transcriptome sequencing of Mycosphaerella fijiensis during association with Musa acuminata reveals candidate pathogenicity genes

description: Table S7. Blastp results for genes in differentially expressed gene clusters in infected leaf tissue. For each gene in differentially expressed gene clusters, tables indicate its description in Figs.Â 7 and 9, and Additional file 13: Figures S7 and Additional file 14: Figure S8, the JGI gene and protein IDs, the log2 fold change, the adjusted p-value for differential expression, the NCBI accession number, the location of the gene on the M. fijiensis genome scaffold, GO, KOG, and Interpro descriptions from JGI, domains identified using the Conserved Domain Database, and the top 10 blastp hits. Blastp hit information includes a description of the hit, the species where the hit was found, bitscore, E-value, percent identity and similarity, and the NCBI accession. Each tab within the Excel file describes a different cluster, with tabs A-M showing clusters with higher expression in infected leaf tissue (colored in green), and tabs N-R showing clusters with higher expression in culture medium (colored in blue). (XLS 1644Â kb)
DOI: 10.6084/m9.figshare.c.3597146_d14
title: Additional file 3: of Transcriptome sequencing of Mycosphaerella fijiensis during association with Musa acuminata reveals candidate pathogenicity genes

description: Table S1. DESeq2 statistics for each gene in the M. fijiensis genome. For each gene, the table indicates the JGI protein and gene IDs, the location of each gene on the scaffold, the baseMean value (mean of normalized read counts), the log2 fold change (log2FC), the standard error of the log2 fold change estimate (lfcSE), the Wald statistic (stat), the p-value, and the p-value adjusted for multiple testing (adjusted p-value). (XLS 3065Â kb)
DOI: 10.6084/m9.figshare.c.3597146_d16
title: Additional file 6: of Transcriptome sequencing of Mycosphaerella fijiensis during association with Musa acuminata reveals candidate pathogenicity genes

description: Table S4. Differentially expressed transcription factors in infected leaf tissue versus mycelium grown in liquid medium. For each differentially expressed transcription factor gene, the table indicates the conserved domains identified using NCBIâ  s Conserved Domain Database, a summary of blastp results using the NCBI nr protein sequence database, and whether the transcription factor is present in one of the gene clusters that were identified in Additional file 10: Table S7 and [17]. The Table also indicates the JGI gene and protein IDs, the location of the gene on the scaffold, the baseMean value (mean of normalized read counts), the log2 fold change (log2FC), the standard error of the log2 fold change estimate (lfcSE), the Wald statistic (stat), the p-value, and the p-value adjusted for multiple testing (adjusted p-value). Genes with higher expression in medium are colored in blue, and genes with higher expression in infected leaf tissue are colored in green. (XLS 41Â kb)
DOI: 10.6084/m9.figshare.c.3597146_d17
title: Additional file 19: of Transcriptome sequencing of Mycosphaerella fijiensis during association with Musa acuminata reveals candidate pathogenicity genes

description: Table S11. PCR amplification conditions for scaffold 13 and 20 genes. For each gene amplified from scaffolds 13 and 20, the table indicates the gene’s description in Fig. 11, its NCBI accession number, the JGI Gene ID, the scaffold from which it is amplified, the description of the protein product, the sequences of the forward and reverse primers used for amplification, the annealing temperature, the extension time, and the expected product size. (XLS 12 kb)
DOI: 10.15468/dl.pdexqf
title: Occurrence Download

description: A dataset containing 14 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pleuronectes herzensteini (Jordan & Snyder, 1901)",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 14 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032359-241126133413365/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.c.3597146_d18
title: Additional file 15: of Transcriptome sequencing of Mycosphaerella fijiensis during association with Musa acuminata reveals candidate pathogenicity genes

description: Table S9. Homologs of genes on scaffolds 15 and 21 of the M. fijiensis genome. For each gene on scaffolds 15 and 21, a blastp search was done using the NCBI non-redundant protein sequence database to identify conserved domains and the best 10 homologs by bitscore for each sequence. For each M. fijiensis sequence of interest, the table includes the JGI protein and gene IDs, a link to the NCBI accession, the location of the gene on each scaffold and a link to the genome browser, the log2 fold change (log2FC), the p-value for differential expression adjusted for multiple testing (adjusted p-value), GO, Interpro, and KOG annotations from JGI, conserved domains identified using NCBIâ  s Conserved Domain Database, and a summary of blastp results using the NCBI nr protein sequence database: species where the homolog was found, a description of the homolog, the bitscore, the E-value, the percent identity and similarity, and a link to the NCBI accession. Genes with higher expression in infected leaf tissue are colored in green. (XLS 235Â kb)
DOI: 10.6084/m9.figshare.c.3597146_d19
title: Additional file 4: of Transcriptome sequencing of Mycosphaerella fijiensis during association with Musa acuminata reveals candidate pathogenicity genes

description: Table S2. Differentially expressed genes in infected leaf tissue versus mycelium grown in liquid medium. For each gene, the table includes the JGI protein and gene IDs, the location of each gene on the scaffold, the baseMean value (mean of normalized read counts), the log2 fold change (log2FC), the standard error of the log2 fold change estimate (lfcSE), the Wald statistic (stat), the p-value, the p-value adjusted for multiple testing (adjusted p-value), a summary of blastp results using the NCBI nr protein sequence database, and the conserved domains identified using NCBIâ  s Conserved Domain Database. (XLS 618Â kb)
DOI: 10.6084/m9.figshare.c.3597209_d9
title: Additional file 3: Table S3. of Analysis of wheat microspore embryogenesis induction by transcriptome and small RNA sequencing using the highly responsive cultivar “Svilena”

description: GO annotation for transcript reconstruction. GO annotation for restructured de novo assembled transcripts based on functional homology using Blast2GO [16] and Trinotate [17]. (XLS 1212 kb)
DOI: 10.6084/m9.figshare.c.3597209_d10
title: Additional file 1: Table S1. of Analysis of wheat microspore embryogenesis induction by transcriptome and small RNA sequencing using the highly responsive cultivar “Svilena”

description: Transcript reconstruction. Reconstruction of de novo assembled contigs to wheat transcripts based on known wheat cDNAs. (XLS 1968 kb)
DOI: 10.6084/m9.figshare.c.3597221_d5
title: Additional file 2: of Co-linearity and divergence of the A subgenome of Brassica juncea compared with other Brassica species carrying different A subgenomes

description: Information of the linkage map of the B. juncea constructed with SY-PM population. (XLSX 1052Â kb)
DOI: 10.6084/m9.figshare.c.3597209_d11
title: Additional file 5: Table S5. of Analysis of wheat microspore embryogenesis induction by transcriptome and small RNA sequencing using the highly responsive cultivar “Svilena”

description: Stage specific transcripts. Listing of restructured de novo assembled transcripts with stage-specific expression (at least 0.5 qnrpm in all replicates) including BLASTx top hits. (XLS 88 kb)
DOI: 10.6084/m9.figshare.c.3597209_d12
title: Additional file 13: Table S12. of Analysis of wheat microspore embryogenesis induction by transcriptome and small RNA sequencing using the highly responsive cultivar “Svilena”

description: miRNA prediction results. Results from miRNA precursor predictions using miRDeep-P [59] performed from sRNA sequencing data individually for all stage replicates. (XLS 790 kb)
DOI: 10.6084/m9.figshare.c.3597209_d13
title: Additional file 6: Table S6. of Analysis of wheat microspore embryogenesis induction by transcriptome and small RNA sequencing using the highly responsive cultivar “Svilena”

description: DE transcripts in T1 and T2. Listing of transcript identifiers for DE, restructured de novo transcripts up- and downregulated in the stage transitions. (XLS 275 kb)
DOI: 10.6084/m9.figshare.c.3597221_d7
title: Additional file 4: of Co-linearity and divergence of the A subgenome of Brassica juncea compared with other Brassica species carrying different A subgenomes

description: Comparison between the three A subgenomes. Ten sheets present the comparison from A1 to A10 among the three A subgenomes. The lines with blue color in one segment show an inversion event. (XLSX 2894Â kb)
DOI: 10.6084/m9.figshare.c.3597251_d1
title: Additional file 10: of HIV-1 and HIV-2 exhibit similar mutation frequencies and spectra in the absence of G-to-A hypermutation

description: Table S5. Identification and masking of plasmid error hotspots. Plasmid error hotspots (i.e. common sites for background errors due to PCR or sequencing) were identified by examining the distribution of mutation frequencies at every individual position for the HIV-1 and HIV-2 plasmid controls. Plasmid error hotspots were defined as upper outliers within the distribution using the 1.5Â Ă Â IQR rule. Hotspots identified in both HIV-1 and HIV-2 plasmids were masked from all samples prior to mutational analyses, as they would most likely represent background errors in the biological samples.
DOI: 10.15468/dl.kwa5a8
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Limanda herzensteini Jordan & Snyder, 1901",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032361-241126133413365/datasets/export for details.
DOI: 10.6084/m9.figshare.c.3597251_d8
title: Additional file 9: of HIV-1 and HIV-2 exhibit similar mutation frequencies and spectra in the absence of G-to-A hypermutation

description: Table S4. Identification of G-to-A hypermutation hotspots in HIV-1 and HIV-2. G-to-A hypermutation hotspots were identified as statistical upper outliers according to the 1.5Â Ă Â IQR rule. For each hotspot, the relative ranking, position, dinucleotide context, mutation frequency, and coding effects are indicated.
DOI: 10.6084/m9.figshare.c.3597251_d9
title: Additional file 6: of HIV-1 and HIV-2 exhibit similar mutation frequencies and spectra in the absence of G-to-A hypermutation

description: Dataset S2. HIV-1 and HIV-2 hypermutant frequencies determined by Illumina sequencing. For each sample, this dataset lists the numbers of total read pairs, hypermutant read pairs, and hypermutation frequencies for all four possible types of transition hypermutants (G-to-A, A-to-G, C-to-T, T-to-C). Hypermutants were defined as read pairs (~Â 120Â bp in length) containing two or more of the same type of mutation. The data is shown both grouped across all amplicons and separated by amplicon (as different tabs within the spreadsheet).
DOI: 10.6084/m9.figshare.c.3597278_d1
title: Additional file 1: of Factors associated with late recurrence after completion of 5-year adjuvant tamoxifen in estrogen receptor positive breast cancer

description: This file includes raw-data of 583 patientsâ   characteristics and survival. (XLSX 40Â kb)
DOI: 10.25378/janelia.24944601.v1
title: Near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of Interphase COS-7 cell (jrc_cos7-1b)

description: <b>This acquisition is part of the CellMap 2024 Segmentation Challenge</b><b>Challenge DOI:</b> https://doi.org/10.25378/janelia.c.7456966<b>Challenge Website:</b> https://cellmapchallenge.janelia.org/<b>Sample</b>: Wild-type, interphase COS-7 cell (ATCC CRL-1651)<b>Sample Description</b>: A dataset featuring isotropic 3D electron microscopy data of a cultured, wild-type, interphase COS-7 cell (ATCC CRL-1651). The sample preparation involved high-pressure freezing, freeze-substitution resin embedding with 2% OsO₄, 0.1% UA, and 3% H₂O in acetone, followed by resin embedding in Eponate 12. Melanie Freeman (Infinimmune) and David Hoffman (10x Genomics) provided the sample, which was prepared for imaging by H. Amalia Pasolli (Rockefeller). The imaging process was conducted by C. Shan Xu (Yale), and post-processing was carried out by Eric T. Trautman and Stephan Preibisch (HHMI/Janelia).<b>Protocol</b>: High pressure freezing, freeze-substitution resin embedding with 2% OsO₄ 0.1% UA 3% H₂O in acetone; resin embedding in Eponate 12.<b>Contributions</b>: Sample provided by Melanie Freeman (Infinimmune) and David Hoffman (10x Genomics), prepared for imaging by H. Amalia Pasolli (Rockefeller), imaging by C. Shan Xu (Yale), with post-processing by Eric T. Trautman and Stephan Preibisch (HHMI/Janelia).<b>Acquisition ID</b>: jrc_cos7-1b<b>Voxel size (nm)</b>: 2 x 2 x 2 (x, y, z)<b>Data dimensions (µm)</b>:<b> </b>40.69 x 9.05 x 2.23 (x, y, z)<b>Imaging start date</b>: 2016-10-4<b>Imaging duration (days)</b>: 5<b>Landing energy (eV)</b>: 400<b>Imaging current (nA)</b>: 0.25<b>Scanning speed (MHz)</b>: 0.400<b>Dataset URL</b>: s3://janelia-cosem-datasets/jrc_cos7-1b/jrc_cos7-1b.zarr/recon-1/em/<b>EM DOI</b>: https://doi.org/10.25378/janelia.24944601<b>Visualization Website</b>: https://openorganelle.janelia.org/datasets/jrc_cos7-1b<b>Publication</b>: Xu et al, 2017, Xu et al., 2021
DOI: 10.6084/m9.figshare.c.3597251_d10
title: Additional file 1: of HIV-1 and HIV-2 exhibit similar mutation frequencies and spectra in the absence of G-to-A hypermutation

description: Table S1. Quantification of plasmid carryover from virus production. The levels of HIV-1 or HIV-2 plasmids from transfections remaining in genomic DNA samples were determined using quantitative PCR-based approaches.
DOI: 10.25378/janelia.24943716.v1
title: Near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of interphase COS-7 cell (jrc_cos7-1a)

description: <b>This acquisition is part of the CellMap 2024 Segmentation Challenge</b><b>Challenge DOI:</b> https://doi.org/10.25378/janelia.c.7456966<b>Challenge Website:</b> https://cellmapchallenge.janelia.org/<b>Sample</b>: Wild-type, interphase COS-7 cell (ATCC CRL-1651)<b>Sample Description</b>: A dataset featuring isotropic 3D electron microscopy data of a cultured, wild-type, interphase COS-7 cell (ATCC CRL-1651). The sample preparation involved high-pressure freezing, freeze-substitution resin embedding with 2% OsO₄, 0.1% UA, and 3% H₂O in acetone, followed by resin embedding in Eponate 12. Melanie Freeman (Infinimmune) and David Hoffman (10x Genomics) provided the sample, which was prepared for imaging by H. Amalia Pasolli (Rockefeller). The imaging process was conducted by C. Shan Xu (Yale), and post-processing was carried out by Eric Trautman and Stephan Preibisch (HHMI/Janelia).<b>Protocol</b>: High pressure freezing, freeze-substitution resin embedding with 2% OsO₄ 0.1% UA 3% H₂O in acetone; resin embedding in Eponate 12.<b>Contributions</b>: Sample provided by Melanie Freeman (Infinimmune) and David Hoffman (10x Genomics), prepared for imaging by H. Amalia Pasolli (Rockefeller), imaging by C. Shan Xu (Yale), with post-processing by Eric Trautman and Stephan Preibisch (HHMI/Janelia).<b>Acquisition ID</b>: jrc_cos7-1a<b>Voxel size (nm)</b>: 2 x 2 x 2 (x, y, z)<b>Data dimensions (µm)</b>:<b> </b>41.22 x 8.74 x 3.63 (x, y, z)<b>Imaging start date</b>: 2016-10-4<b>Imaging duration (days)</b>: 7<b>Primary energy (eV)</b>: 400<b>Imaging current (nA)</b>: 0.25<b>Scanning speed (MHz)</b>: 0.400<b>Dataset URL</b>: s3://janelia-cosem-datasets/jrc_cos7-1a/jrc_cos7-1a.zarr/recon-1/em/<b>EM DOI</b>: https://doi.org/10.25378/janelia.24943716<b>Visualization Website</b>: https://openorganelle.janelia.org/datasets/jrc_cos7-1a<b>Publication</b>: Xu et al., 2017<br><br>
DOI: 10.6084/m9.figshare.c.3597281_d1
title: Additional file 1: of Sustained release of rhBMP-2 from microporous tricalciumphosphate using hydrogels as a carrier

description: Dataset supporting Fig. 3. (TXT 3 kb)
DOI: 10.6084/m9.figshare.c.3597284_d1
title: Additional file 2: of Prevalence of gastrointestinal symptoms in patients with influenza, clinical significance, and pathophysiology of human influenza viruses in faecal samples: what do we know?

description: Studies describing detection and/or isolation of influenza virus in stools of laboratory confirmed influenza patients. (XLSX 12Â kb)
DOI: 10.6084/m9.figshare.c.3597290_d1
title: Additional file 5: of Combined clinical and genomic signatures for the prognosis of early stage non-small cell lung cancer based on gene copy number alterations

description: GO biological processes highly significantly enriched in the 150 preselected gene set for SCC. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.c.3597281_d2
title: Additional file 3: of Sustained release of rhBMP-2 from microporous tricalciumphosphate using hydrogels as a carrier

description: Dataset supporting Fig. 5. (TXT 1 kb)
DOI: 10.6084/m9.figshare.c.3597284_d2
title: Additional file 1: of Prevalence of gastrointestinal symptoms in patients with influenza, clinical significance, and pathophysiology of human influenza viruses in faecal samples: what do we know?

description: Studies describing compared prevalence of gastrointestinal symptoms in function of influenza viruses. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.c.3597281_d3
title: Additional file 2: of Sustained release of rhBMP-2 from microporous tricalciumphosphate using hydrogels as a carrier

description: Dataset supporting Fig. 4. (TXT 1 kb)
DOI: 10.25378/janelia.24944601
title: Near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of Interphase COS-7 cell (jrc_cos7-1b)

description: <b>This acquisition is part of the CellMap 2024 Segmentation Challenge</b><b>Challenge DOI:</b> https://doi.org/10.25378/janelia.c.7456966<b>Challenge Website:</b> https://cellmapchallenge.janelia.org/<b>Sample</b>: Wild-type, interphase COS-7 cell (ATCC CRL-1651)<b>Sample Description</b>: A dataset featuring isotropic 3D electron microscopy data of a cultured, wild-type, interphase COS-7 cell (ATCC CRL-1651). The sample preparation involved high-pressure freezing, freeze-substitution resin embedding with 2% OsO₄, 0.1% UA, and 3% H₂O in acetone, followed by resin embedding in Eponate 12. Melanie Freeman (Infinimmune) and David Hoffman (10x Genomics) provided the sample, which was prepared for imaging by H. Amalia Pasolli (Rockefeller). The imaging process was conducted by C. Shan Xu (Yale), and post-processing was carried out by Eric T. Trautman and Stephan Preibisch (HHMI/Janelia).<b>Protocol</b>: High pressure freezing, freeze-substitution resin embedding with 2% OsO₄ 0.1% UA 3% H₂O in acetone; resin embedding in Eponate 12.<b>Contributions</b>: Sample provided by Melanie Freeman (Infinimmune) and David Hoffman (10x Genomics), prepared for imaging by H. Amalia Pasolli (Rockefeller), imaging by C. Shan Xu (Yale), with post-processing by Eric T. Trautman and Stephan Preibisch (HHMI/Janelia).<b>Acquisition ID</b>: jrc_cos7-1b<b>Voxel size (nm)</b>: 2 x 2 x 2 (x, y, z)<b>Data dimensions (µm)</b>:<b> </b>40.69 x 9.05 x 2.23 (x, y, z)<b>Imaging start date</b>: 2016-10-4<b>Imaging duration (days)</b>: 5<b>Landing energy (eV)</b>: 400<b>Imaging current (nA)</b>: 0.25<b>Scanning speed (MHz)</b>: 0.400<b>Dataset URL</b>: s3://janelia-cosem-datasets/jrc_cos7-1b/jrc_cos7-1b.zarr/recon-1/em/<b>EM DOI</b>: https://doi.org/10.25378/janelia.24944601<b>Visualization Website</b>: https://openorganelle.janelia.org/datasets/jrc_cos7-1b<b>Publication</b>: Xu et al, 2017, Xu et al., 2021