cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7659350.v1
title: Additional file 7: of Genome analysis of Salmonella enterica subsp. diarizonae isolates from invasive human infections reveals enrichment of virulence-related functions in lineage ST1256

description: Figure S2. Maximum likelihood core-genome phylogeny (species tree) for 76 Salmonella spp. strains. The core-genome was inferred from the 303 top-scoring markers selected of the 1650 consensus clusters computed by GET_HOMOLOGUES. The bar represents the expected number of substitutions per site under the best-fitting GTR + F + ASC + R3 model. Internal nodes are colored by the combined approximate Bayesian support / ultra-fast bootstrap support values, respectively, as indicated on the legend. The inset shows the distribution of Robinson-Foulds gene tree distances to the species-tree. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.7659341.v1
title: Additional file 6: of Genome analysis of Salmonella enterica subsp. diarizonae isolates from invasive human infections reveals enrichment of virulence-related functions in lineage ST1256

description: Table S5. S. enterica subsp. diarizonae genomes of strains isolated from diverse sources that were further analysed in this study. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.7659326
title: Additional file 4: of Genome analysis of Salmonella enterica subsp. diarizonae isolates from invasive human infections reveals enrichment of virulence-related functions in lineage ST1256

description: Table S3. S. enterica subsp. diarizonae genomes available in Enterobase in a accesible status (XLSX 162 kb)
DOI: 10.7284/102988
title: Anemometer data collected during research cruise CH0510 using a RM Young 05103 instrument system onboard the platform RV Cape Hatteras

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7659335.v2
title: Additional file 5: of Genome analysis of Salmonella enterica subsp. diarizonae isolates from invasive human infections reveals enrichment of virulence-related functions in lineage ST1256

description: Table S4. S. enterica subsp. diarizonae draft genomes used in the phylogenomic analyses (XLSX 30 kb)
DOI: 10.6084/m9.figshare.7659326.v2
title: Additional file 4: of Genome analysis of Salmonella enterica subsp. diarizonae isolates from invasive human infections reveals enrichment of virulence-related functions in lineage ST1256

description: Table S3. S. enterica subsp. diarizonae genomes available in Enterobase in a accesible status (XLSX 162 kb)
DOI: 10.6084/m9.figshare.7659335.v1
title: Additional file 5: of Genome analysis of Salmonella enterica subsp. diarizonae isolates from invasive human infections reveals enrichment of virulence-related functions in lineage ST1256

description: Table S4. S. enterica subsp. diarizonae draft genomes used in the phylogenomic analyses (XLSX 13 kb)
DOI: 10.7284/102459
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise CH0510 using a Sea-Bird SBE-911+ instrument system onboard the platform RV Cape Hatteras

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7659326.v1
title: Additional file 4: of Genome analysis of Salmonella enterica subsp. diarizonae isolates from invasive human infections reveals enrichment of virulence-related functions in lineage ST1256

description: Table S3. S. enterica subsp. diarizonae genomes available in Enterobase in a accesible status (XLSX 11 kb)
DOI: 10.7284/102505
title: Fluorometer data collected during research cruise CH0510 using a Turner 10-AU instrument system onboard the platform RV Cape Hatteras

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/102852
title: GNSS (Global Navigation Satellite System) data collected during research cruise CH0510 using a Northstar 952X instrument system onboard the platform RV Cape Hatteras

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7659296
title: Additional file 14: of Genome analysis of Salmonella enterica subsp. diarizonae isolates from invasive human infections reveals enrichment of virulence-related functions in lineage ST1256

description: Table S11. Virulence determinants distribution along S. enterica subsp. diarizonae ST associated and non-associated with human host (% vs total). (XLSX 10 kb)
DOI: 10.7284/102511
title: Gyrocompass data collected during research cruise CH0510 using a Sperry MK-37 instrument system onboard the platform RV Cape Hatteras

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7659296.v2
title: Additional file 14: of Genome analysis of Salmonella enterica subsp. diarizonae isolates from invasive human infections reveals enrichment of virulence-related functions in lineage ST1256

description: Table S11. Virulence determinants distribution along S. enterica subsp. diarizonae ST associated and non-associated with human host (% vs total). (XLSX 10 kb)
DOI: 10.7284/102794
title: Meteorological Station data collected during research cruise CH0510 using a RM Young 26700 instrument system onboard the platform RV Cape Hatteras

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7659284
title: Additional file 13: of Genome analysis of Salmonella enterica subsp. diarizonae isolates from invasive human infections reveals enrichment of virulence-related functions in lineage ST1256

description: Table S10. S. enterica subsp. diarizonae isolates statistically associated with human infections (% versus total). (XLSX 13 kb)
DOI: 10.6084/m9.figshare.7659296.v1
title: Additional file 14: of Genome analysis of Salmonella enterica subsp. diarizonae isolates from invasive human infections reveals enrichment of virulence-related functions in lineage ST1256

description: Table S11. Virulence determinants distribution along S. enterica subsp. diarizonae ST associated and non-associated with human host (% vs total). (XLSX 39 kb)
DOI: 10.7284/102510
title: Singlebeam Echosounder data collected during research cruise CH0510 using a Furuno FCV-292 instrument system onboard the platform RV Cape Hatteras

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7659272
title: Additional file 12: of Genome analysis of Salmonella enterica subsp. diarizonae isolates from invasive human infections reveals enrichment of virulence-related functions in lineage ST1256

description: Table S9. Presence/absence of slrP, sseK2, sseK3, GI6 and SPI-7 in S. enterica subsp. diarizonae draft genomes available at EnteroBase. (XLSX 39 kb)
DOI: 10.6084/m9.figshare.7659284.v2
title: Additional file 13: of Genome analysis of Salmonella enterica subsp. diarizonae isolates from invasive human infections reveals enrichment of virulence-related functions in lineage ST1256

description: Table S10. S. enterica subsp. diarizonae isolates statistically associated with human infections (% versus total). (XLSX 13 kb)
DOI: 10.7284/102509
title: Speedlog data collected during research cruise CH0510 using a Furuno DS-80 instrument system onboard the platform RV Cape Hatteras

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7659284.v1
title: Additional file 13: of Genome analysis of Salmonella enterica subsp. diarizonae isolates from invasive human infections reveals enrichment of virulence-related functions in lineage ST1256

description: Table S10. S. enterica subsp. diarizonae isolates statistically associated with human infections (% versus total). (XLSX 19 kb)
DOI: 10.6084/m9.figshare.7659266
title: Additional file 11: of Genome analysis of Salmonella enterica subsp. diarizonae isolates from invasive human infections reveals enrichment of virulence-related functions in lineage ST1256

description: Table S8. Virulence factors proteins encoded by S. enterica subsp. diarizonae genomes and representative genomes from other Salmonella species and subspecies (XLSX 19 kb)
DOI: 10.6084/m9.figshare.7659272.v2
title: Additional file 12: of Genome analysis of Salmonella enterica subsp. diarizonae isolates from invasive human infections reveals enrichment of virulence-related functions in lineage ST1256

description: Table S9. Presence/absence of slrP, sseK2, sseK3, GI6 and SPI-7 in S. enterica subsp. diarizonae draft genomes available at EnteroBase. (XLSX 39 kb)
DOI: 10.7284/102506
title: Winch data collected during research cruise CH0510 using a Markey DUSH-5 instrument system onboard the platform RV Cape Hatteras

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7659263
title: Additional file 10: of Genome analysis of Salmonella enterica subsp. diarizonae isolates from invasive human infections reveals enrichment of virulence-related functions in lineage ST1256

description: Table S7. Phophages carried by the S. enterica subsp. diarizonae SBO13 and SBO27 (XLSX 10 kb)
DOI: 10.6084/m9.figshare.7659266.v2
title: Additional file 11: of Genome analysis of Salmonella enterica subsp. diarizonae isolates from invasive human infections reveals enrichment of virulence-related functions in lineage ST1256

description: Table S8. Virulence factors proteins encoded by S. enterica subsp. diarizonae genomes and representative genomes from other Salmonella species and subspecies (XLSX 19 kb)
DOI: 10.6084/m9.figshare.7659272.v1
title: Additional file 12: of Genome analysis of Salmonella enterica subsp. diarizonae isolates from invasive human infections reveals enrichment of virulence-related functions in lineage ST1256

description: Table S9. Presence/absence of slrP, sseK2, sseK3, GI6 and SPI-7 in S. enterica subsp. diarizonae draft genomes available at EnteroBase. (XLSX 10 kb)
DOI: 10.7284/104789
title: Anemometer data collected during research cruise CH0511 using a RM Young 05103 instrument system onboard the platform RV Cape Hatteras

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7659266.v1
title: Additional file 11: of Genome analysis of Salmonella enterica subsp. diarizonae isolates from invasive human infections reveals enrichment of virulence-related functions in lineage ST1256

description: Table S8. Virulence factors proteins encoded by S. enterica subsp. diarizonae genomes and representative genomes from other Salmonella species and subspecies (XLSX 43 kb)
DOI: 10.6084/m9.figshare.7659263.v1
title: Additional file 10: of Genome analysis of Salmonella enterica subsp. diarizonae isolates from invasive human infections reveals enrichment of virulence-related functions in lineage ST1256

description: Table S7. Phophages carried by the S. enterica subsp. diarizonae SBO13 and SBO27 (XLSX 12 kb)
DOI: 10.6084/m9.figshare.7659263.v2
title: Additional file 10: of Genome analysis of Salmonella enterica subsp. diarizonae isolates from invasive human infections reveals enrichment of virulence-related functions in lineage ST1256

description: Table S7. Phophages carried by the S. enterica subsp. diarizonae SBO13 and SBO27 (XLSX 10 kb)
DOI: 10.7284/104790
title: Anemometer data collected during research cruise CH0511 using a RM Young 05103 instrument system onboard the platform RV Cape Hatteras

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/104784
title: Fluorometer data collected during research cruise CH0511 using a Turner 10-AU instrument system onboard the platform RV Cape Hatteras

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/104791
title: GNSS (Global Navigation Satellite System) data collected during research cruise CH0511 using a Northstar 952X instrument system onboard the platform RV Cape Hatteras

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/104788
title: Gyrocompass data collected during research cruise CH0511 using a Sperry MK-37 instrument system onboard the platform RV Cape Hatteras

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7659209
title: Additional file 8: of Glucocorticoid-driven transcriptomes in human airway epithelial cells: commonalities, differences and functional insight from cell lines and primary cells

description: GO terms associated with budesonide-induced genes in A549, BEAS-2B, and HBE cells using lower stringency cut-off. Budesonide-induced genes, as defined in Fig. 3b, in A549 (268 genes), BEAS-2B (300 genes), and HBE (196 genes) were used for DAVID GO analysis. Biological processes and molecular function terms that were significantly enriched (EASE score ≤ 0.1) with each list and represented by at least 5 genes were listed. The terms that are significantly enriched following family-wide false discovery rate correction (Benjamini ≤0.05) are colored red. (XLSX 38 kb)
DOI: 10.6084/m9.figshare.7659215
title: Additional file 9: of Glucocorticoid-driven transcriptomes in human airway epithelial cells: commonalities, differences and functional insight from cell lines and primary cells

description: Budesonide-repressed genes in A549, BEAS-2B or HBE cells. The 425 genes that were significantly repressed ≤0.5 fold (P ≤ 0.05) by budesonide at 6 h in A549 (A), BEAS-2B (B), or HBE (H) cells are listed. The last two columns (I and J), indicate the gene groups for each gene based on the induction thresholds, ≤0.5 fold (P ≤ 0.05) or ≤ 0.8, as shown in Fig. 5. Genes are sorted alphabetically according to their official gene symbol. (XLSX 49 kb)
DOI: 10.7284/104785
title: Meteorological Station data collected during research cruise CH0511 using a RM Young 26700 instrument system onboard the platform RV Cape Hatteras

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7659206
title: Additional file 4: of Conserved regulation of RNA processing in somatic cell reprogramming

description: Table of comparisons for differential analyses. The file contains an XLSX spreadsheet describing sample groups that were used for differential and gene set enrichment analyses. Comparisons are always between the end and start points of reprogramming (end point / start point or, in log-space, end point - start point). The table lists, from left to right, the Sequence Read Archive (SRA) study identifier, the organism from which the samples were derived, the sample groups of reprogramming start and end points, and a short name linking the comparisons to figures. (XLSX 5 kb)
DOI: 10.6084/m9.figshare.7659215.v1
title: Additional file 9: of Glucocorticoid-driven transcriptomes in human airway epithelial cells: commonalities, differences and functional insight from cell lines and primary cells

description: Budesonide-repressed genes in A549, BEAS-2B or HBE cells. The 425 genes that were significantly repressed ≤0.5 fold (P ≤ 0.05) by budesonide at 6 h in A549 (A), BEAS-2B (B), or HBE (H) cells are listed. The last two columns (I and J), indicate the gene groups for each gene based on the induction thresholds, ≤0.5 fold (P ≤ 0.05) or ≤ 0.8, as shown in Fig. 5. Genes are sorted alphabetically according to their official gene symbol. (XLSX 49 kb)
DOI: 10.6084/m9.figshare.7659203
title: Additional file 7: of Glucocorticoid-driven transcriptomes in human airway epithelial cells: commonalities, differences and functional insight from cell lines and primary cells

description: GO terms associated with budesonide-induced genes (≥2 fold, P ≤ 0.05) in A549, BEAS-2B, and HBE cells. Budesonide-induced genes ≥2 fold (P ≤ 0.05) in A549 (187 genes), BEAS-2B (240 genes), and HBE (86 genes) were subjected to GO analysis using DAVID. Biological processes (BP) and molecular function (MF) terms that were significantly enriched (EASE score ≤ 0.1) with each list and represented by at least 5 genes are listed. GO terms that are significantly enriched following family-wide false discovery rate correction (Benjamini ≤0.05) are colored red. (XLSX 26 kb)
DOI: 10.6084/m9.figshare.7659206.v1
title: Additional file 4: of Conserved regulation of RNA processing in somatic cell reprogramming

description: Table of comparisons for differential analyses. The file contains an XLSX spreadsheet describing sample groups that were used for differential and gene set enrichment analyses. Comparisons are always between the end and start points of reprogramming (end point / start point or, in log-space, end point - start point). The table lists, from left to right, the Sequence Read Archive (SRA) study identifier, the organism from which the samples were derived, the sample groups of reprogramming start and end points, and a short name linking the comparisons to figures. (XLSX 5 kb)
DOI: 10.6084/m9.figshare.7659209.v1
title: Additional file 8: of Glucocorticoid-driven transcriptomes in human airway epithelial cells: commonalities, differences and functional insight from cell lines and primary cells

description: GO terms associated with budesonide-induced genes in A549, BEAS-2B, and HBE cells using lower stringency cut-off. Budesonide-induced genes, as defined in Fig. 3b, in A549 (268 genes), BEAS-2B (300 genes), and HBE (196 genes) were used for DAVID GO analysis. Biological processes and molecular function terms that were significantly enriched (EASE score ≤ 0.1) with each list and represented by at least 5 genes were listed. The terms that are significantly enriched following family-wide false discovery rate correction (Benjamini ≤0.05) are colored red. (XLSX 38 kb)
DOI: 10.7284/104783
title: Singlebeam Echosounder data collected during research cruise CH0511 using a Knudsen 3260 instrument system onboard the platform RV Cape Hatteras

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7659203.v1
title: Additional file 7: of Glucocorticoid-driven transcriptomes in human airway epithelial cells: commonalities, differences and functional insight from cell lines and primary cells

description: GO terms associated with budesonide-induced genes (≥2 fold, P ≤ 0.05) in A549, BEAS-2B, and HBE cells. Budesonide-induced genes ≥2 fold (P ≤ 0.05) in A549 (187 genes), BEAS-2B (240 genes), and HBE (86 genes) were subjected to GO analysis using DAVID. Biological processes (BP) and molecular function (MF) terms that were significantly enriched (EASE score ≤ 0.1) with each list and represented by at least 5 genes are listed. GO terms that are significantly enriched following family-wide false discovery rate correction (Benjamini ≤0.05) are colored red. (XLSX 26 kb)
DOI: 10.6084/m9.figshare.7659191
title: Additional file 1: of Conserved regulation of RNA processing in somatic cell reprogramming

description: Gene set enrichment analysis of SRP016568. The file contains an XLSX spreadsheet summarizing the top 20 most enriched gene ontology (GO) terms among the 6278 genes that were significantly more highly expressed in iPSCs compared to foreskin fibroblasts in the study [21]. For comparison, the statistics for the same GO terms are also shown for the gene set enrichment analysis done using all 11705 differentially expressed genes. A total of 17249 genes were found to be expressed in the data sets and were used as background. The first four columns, from left to right, indicate the GO term identifier, name, ontology class/namespace, and the total number of (human) genes that are associated with the term. The next three columns indicate the number of genes associated with the term that were found more highly expressed in iPSCs, the false discovery rate (FDR; Benjamini-Hochberg) and the rank (by FDR) for the GO term enrichment. The remaining three columns indicate the same parameters for all differentially expressed genes. RNA-related GO terms have their names and identifiers in bold and italics. Asterisks next to GO term identifiers indicate that the term has the exact same set of genes associated with it as the preceding one and is thus redundant. (XLSX 6 kb)
DOI: 10.6084/m9.figshare.7659197
title: Additional file 2: of Conserved regulation of RNA processing in somatic cell reprogramming

description: RNA-Seq sample table. The file contains an XLSX spreadsheet of the RNA-Seq data sets used in this study. For each sample listed are, from left to right, the Sequence Read Archive (SRA) study and run identifier, the organism and the cell type from which the sample was derived, and a descriptive sample group name that was used to pool samples for further analysis. (XLSX 14 kb)
DOI: 10.7284/104787
title: Singlebeam Echosounder data collected during research cruise CH0511 using a Furuno FCV-292 instrument system onboard the platform RV Cape Hatteras

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7659191.v1
title: Additional file 1: of Conserved regulation of RNA processing in somatic cell reprogramming

description: Gene set enrichment analysis of SRP016568. The file contains an XLSX spreadsheet summarizing the top 20 most enriched gene ontology (GO) terms among the 6278 genes that were significantly more highly expressed in iPSCs compared to foreskin fibroblasts in the study [21]. For comparison, the statistics for the same GO terms are also shown for the gene set enrichment analysis done using all 11705 differentially expressed genes. A total of 17249 genes were found to be expressed in the data sets and were used as background. The first four columns, from left to right, indicate the GO term identifier, name, ontology class/namespace, and the total number of (human) genes that are associated with the term. The next three columns indicate the number of genes associated with the term that were found more highly expressed in iPSCs, the false discovery rate (FDR; Benjamini-Hochberg) and the rank (by FDR) for the GO term enrichment. The remaining three columns indicate the same parameters for all differentially expressed genes. RNA-related GO terms have their names and identifiers in bold and italics. Asterisks next to GO term identifiers indicate that the term has the exact same set of genes associated with it as the preceding one and is thus redundant. (XLSX 6 kb)
DOI: 10.6084/m9.figshare.7659197.v1
title: Additional file 2: of Conserved regulation of RNA processing in somatic cell reprogramming

description: RNA-Seq sample table. The file contains an XLSX spreadsheet of the RNA-Seq data sets used in this study. For each sample listed are, from left to right, the Sequence Read Archive (SRA) study and run identifier, the organism and the cell type from which the sample was derived, and a descriptive sample group name that was used to pool samples for further analysis. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.7659179
title: Additional file 15: of Conserved regulation of RNA processing in somatic cell reprogramming

description: Table of primers and PCR assays. The XLSX spreadsheet file contains a list of all primers used for the cloning of transgenes into retroviral vectors, qRT-PCR assays for pluripotency, differentiation, epithelial and mesenchymal markers, genomic PCR reactions for transgenes derived from iPSC clones, and Cd44 RT-PCR reactions. (XLSX 7 kb)
DOI: 10.6084/m9.figshare.7659182
title: Additional file 4: of Glucocorticoid-driven transcriptomes in human airway epithelial cells: commonalities, differences and functional insight from cell lines and primary cells

description: Genes significantly modulated by budesonide or dexamethasone in A549 cells. The 330 genes showing significant induction (fold ≥2, P ≤ 0.05), or repression (fold ≤0.5, P ≤ 0.05), by budesonide (300 nM) or dexamethasone (1 μM), compared to control at 6 h, are listed along with the fold change and P value for each glucocorticoid. Genes are sorted alphabetically according to their official gene symbol. (XLSX 30 kb)