cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12680275
title: Additional file 5 of Characterization of the bacterial communities of psyllids associated with Rutaceae in Bhutan by high throughput sequencing

description: Additional file 5: Supplementary Table 3. OTU name and abundance based on the 16S rRNA amplicon dataset rarefied to 5612 sequences, for each of the 48 psyllid samples.
DOI: 10.6084/m9.figshare.12680278
title: Additional file 6 of Characterization of the bacterial communities of psyllids associated with Rutaceae in Bhutan by high throughput sequencing

description: Additional file 6: Supplementary Table 4. Representative set of 16S rRNA gene sequences of OTUs from five psyllid species from Bhutan.
DOI: 10.6084/m9.figshare.12680280
title: Additional file 1 of Total RNA and genomic DNA of Lactobacillus gasseri OLL2809 induce interleukin-12 production in the mouse macrophage cell line J774.1 via toll-like receptors 7 and 9

description: Additional file 1: Figure A1. Effects of cytochalasin D treatment on viability of J774.1 cells (a) and IL-12 production stimulated with Pam3CSK4. Figure A2. Viability of J774.1 cells during MYD88 inhibition assay. Figure A3. Viability of J774.1 cells during TLRs 7 and 9 antagonist assay. (XLS 294 kb)
DOI: 10.6084/m9.figshare.12680272.v1
title: Additional file 4 of Characterization of the bacterial communities of psyllids associated with Rutaceae in Bhutan by high throughput sequencing

description: Additional file 4: Supplementary Table 2. Sample metadata and alpha diversity metrics.
DOI: 10.6084/m9.figshare.12680278.v1
title: Additional file 6 of Characterization of the bacterial communities of psyllids associated with Rutaceae in Bhutan by high throughput sequencing

description: Additional file 6: Supplementary Table 4. Representative set of 16S rRNA gene sequences of OTUs from five psyllid species from Bhutan.
DOI: 10.6084/m9.figshare.12680280.v1
title: Additional file 1 of Total RNA and genomic DNA of Lactobacillus gasseri OLL2809 induce interleukin-12 production in the mouse macrophage cell line J774.1 via toll-like receptors 7 and 9

description: Additional file 1: Figure A1. Effects of cytochalasin D treatment on viability of J774.1 cells (a) and IL-12 production stimulated with Pam3CSK4. Figure A2. Viability of J774.1 cells during MYD88 inhibition assay. Figure A3. Viability of J774.1 cells during TLRs 7 and 9 antagonist assay. (XLS 294 kb)
DOI: 10.6084/m9.figshare.12680269
title: Additional file 3 of Characterization of the bacterial communities of psyllids associated with Rutaceae in Bhutan by high throughput sequencing

description: Additional file 3: Supplementary Table 1. Primer sequences and PCR conditions.
DOI: 10.6084/m9.figshare.12680275.v1
title: Additional file 5 of Characterization of the bacterial communities of psyllids associated with Rutaceae in Bhutan by high throughput sequencing

description: Additional file 5: Supplementary Table 3. OTU name and abundance based on the 16S rRNA amplicon dataset rarefied to 5612 sequences, for each of the 48 psyllid samples.
DOI: 10.6084/m9.figshare.12680260
title: Additional file 7 of A comprehensive survey of integron-associated genes present in metagenomes

description: Additional file 7Table S5. Over-representation test using Fisher?s exact test for GO-terms found in the metagenomics GO slim [78]. Significant p-values are shown in bold.
DOI: 10.6084/m9.figshare.12680269.v1
title: Additional file 3 of Characterization of the bacterial communities of psyllids associated with Rutaceae in Bhutan by high throughput sequencing

description: Additional file 3: Supplementary Table 1. Primer sequences and PCR conditions.
DOI: 10.6084/m9.figshare.12680257
title: Additional file 6 of A comprehensive survey of integron-associated genes present in metagenomes

description: Additional file 6Table S4. Over-representation test using Fisher’s exact test for COG functional categories [28]. Significant p-values are shown in bold.
DOI: 10.6084/m9.figshare.12680251
title: Additional file 4 of A comprehensive survey of integron-associated genes present in metagenomes

description: Additional file 4Table S3. Overrepresentation analysis of each COGs category between integron-associated and non-integron-associated genes found in the metagenomes. For each category, overrepresentation is given as odds ratio and the p-value of Fisher exact test.
DOI: 10.6084/m9.figshare.12680260.v1
title: Additional file 7 of A comprehensive survey of integron-associated genes present in metagenomes

description: Additional file 7Table S5. Over-representation test using Fisher?s exact test for GO-terms found in the metagenomics GO slim [78]. Significant p-values are shown in bold.
DOI: 10.6084/m9.figshare.12680248
title: Additional file 3 of A comprehensive survey of integron-associated genes present in metagenomes

description: Additional file 3Table S2. Gene ontology analysis of the integron-associated genes using PFAM families [30]. Out of the 13,397 non-redundant integron-associated genes in our catalog, 3488 matched a PFAM family with a known function, which were in turn mapped to the metagenomics GO slim [78]. Note that the GO terms are organized in decreasing order inside each category, molecular function, biological process and cellular component.
DOI: 10.6084/m9.figshare.12680257.v1
title: Additional file 6 of A comprehensive survey of integron-associated genes present in metagenomes

description: Additional file 6Table S4. Over-representation test using Fisher’s exact test for COG functional categories [28]. Significant p-values are shown in bold.
DOI: 10.6084/m9.figshare.12680242
title: Additional file 1 of A comprehensive survey of integron-associated genes present in metagenomes

description: Additional file 1Table S1. The full catalog of integron-associated genes identified in this study. Details for all attC sites and integron-associated genes presented in cassette structure, including sequence and functional annotation. Note that in order to preserve the cassette structure, genes and attC sites redundancy has not been removed.
DOI: 10.6084/m9.figshare.12680248.v1
title: Additional file 3 of A comprehensive survey of integron-associated genes present in metagenomes

description: Additional file 3Table S2. Gene ontology analysis of the integron-associated genes using PFAM families [30]. Out of the 13,397 non-redundant integron-associated genes in our catalog, 3488 matched a PFAM family with a known function, which were in turn mapped to the metagenomics GO slim [78]. Note that the GO terms are organized in decreasing order inside each category, molecular function, biological process and cellular component.
DOI: 10.6084/m9.figshare.12680251.v1
title: Additional file 4 of A comprehensive survey of integron-associated genes present in metagenomes

description: Additional file 4Table S3. Overrepresentation analysis of each COGs category between integron-associated and non-integron-associated genes found in the metagenomes. For each category, overrepresentation is given as odds ratio and the p-value of Fisher exact test.
DOI: 10.6084/m9.figshare.12680242.v1
title: Additional file 1 of A comprehensive survey of integron-associated genes present in metagenomes

description: Additional file 1Table S1. The full catalog of integron-associated genes identified in this study. Details for all attC sites and integron-associated genes presented in cassette structure, including sequence and functional annotation. Note that in order to preserve the cassette structure, genes and attC sites redundancy has not been removed.
DOI: 10.6084/m9.figshare.12680190
title: Additional file 8 of Cytokine-induced molecular responses in airway smooth muscle cells inform genome-wide association studies of asthma

description: Additional file 8. Genes that are DE in one group (cases or controls) that are not DE in the other group. Differentially expressed genes following cytokine exposure compared to baseline (vehicle) in cases or controls (FDR&lt;5%) that are not DE (FDR&gt;20%) in the opposite group.
DOI: 10.6084/m9.figshare.12680196
title: Additional file 1 of The commercially available STAT3 inhibitor 5,15-diphenylporphyrin (5,15-DPP) does not directly interact with STAT3 core residues 127–722

description: Additional file 1. Representative exported dataset of controls S3I-201 and 5,15-DPP from surface plasmon resonance spectroscopy screening experiment used to generate Fig. 2. Data for single concentration (80 μM) included are values collected at 30, 60 and 100 μL/min. Data for single concentration (100 μM) of 5, 15-DPP included at same flow rates.
DOI: 10.6084/m9.figshare.12680196.v1
title: Additional file 1 of The commercially available STAT3 inhibitor 5,15-diphenylporphyrin (5,15-DPP) does not directly interact with STAT3 core residues 127–722

description: Additional file 1. Representative exported dataset of controls S3I-201 and 5,15-DPP from surface plasmon resonance spectroscopy screening experiment used to generate Fig. 2. Data for single concentration (80 μM) included are values collected at 30, 60 and 100 μL/min. Data for single concentration (100 μM) of 5, 15-DPP included at same flow rates.
DOI: 10.6084/m9.figshare.12680178
title: Additional file 4 of Cytokine-induced molecular responses in airway smooth muscle cells inform genome-wide association studies of asthma

description: Additional file 4. List of differentially expressed genes in response to cytokine exposure (FDR&lt;1%). Transcripts differentially expressed in response to IL-13 and/or IL-17 compared to vehicle (FDR&lt;1%).
DOI: 10.6084/m9.figshare.12680184
title: Additional file 6 of Cytokine-induced molecular responses in airway smooth muscle cells inform genome-wide association studies of asthma

description: Additional file 6. Differentially expressed genes that are also associated with asthma (GWAS catalog). Genes previously identified as being associated with asthma were compared to the list of genes differentially expressed in response to IL-13 and/or IL-17 compared to vehicle.
DOI: 10.6084/m9.figshare.12680190.v1
title: Additional file 8 of Cytokine-induced molecular responses in airway smooth muscle cells inform genome-wide association studies of asthma

description: Additional file 8. Genes that are DE in one group (cases or controls) that are not DE in the other group. Differentially expressed genes following cytokine exposure compared to baseline (vehicle) in cases or controls (FDR&lt;5%) that are not DE (FDR&gt;20%) in the opposite group.
DOI: 10.6084/m9.figshare.12680178.v1
title: Additional file 4 of Cytokine-induced molecular responses in airway smooth muscle cells inform genome-wide association studies of asthma

description: Additional file 4. List of differentially expressed genes in response to cytokine exposure (FDR&lt;1%). Transcripts differentially expressed in response to IL-13 and/or IL-17 compared to vehicle (FDR&lt;1%).
DOI: 10.6084/m9.figshare.12680184.v1
title: Additional file 6 of Cytokine-induced molecular responses in airway smooth muscle cells inform genome-wide association studies of asthma

description: Additional file 6. Differentially expressed genes that are also associated with asthma (GWAS catalog). Genes previously identified as being associated with asthma were compared to the list of genes differentially expressed in response to IL-13 and/or IL-17 compared to vehicle.
DOI: 10.6084/m9.figshare.12680166
title: Additional file 19 of Cytokine-induced molecular responses in airway smooth muscle cells inform genome-wide association studies of asthma

description: Additional file 19. Loci enriched in the UK Biobank childhood-onset asthma GWAS. Summary of the 99 loci enriched in UK Biobank childhood-onset asthma GWAS.
DOI: 10.6084/m9.figshare.12680157
title: Additional file 16 of Cytokine-induced molecular responses in airway smooth muscle cells inform genome-wide association studies of asthma

description: Additional file 16. List of coQTLs identified through GWAS in ASMCs. coQTLs (P
DOI: 10.6084/m9.figshare.12680154
title: Additional file 15 of Cytokine-induced molecular responses in airway smooth muscle cells inform genome-wide association studies of asthma

description: Additional file 15. List of meQTL results (FDR=5%). meQTLs identified in IL-13 and/or IL-17A-exposed ASMCs at an FDR of 5%.
DOI: 10.6084/m9.figshare.12680157.v1
title: Additional file 16 of Cytokine-induced molecular responses in airway smooth muscle cells inform genome-wide association studies of asthma

description: Additional file 16. List of coQTLs identified through GWAS in ASMCs. coQTLs (P
DOI: 10.6084/m9.figshare.12680166.v1
title: Additional file 19 of Cytokine-induced molecular responses in airway smooth muscle cells inform genome-wide association studies of asthma

description: Additional file 19. Loci enriched in the UK Biobank childhood-onset asthma GWAS. Summary of the 99 loci enriched in UK Biobank childhood-onset asthma GWAS.
DOI: 10.6084/m9.figshare.12680148
title: Additional file 13 of Cytokine-induced molecular responses in airway smooth muscle cells inform genome-wide association studies of asthma

description: Additional file 13. Summary of BRI GWAS results. BRI GWAS SNPs (P&lt;10-5) identified through GWAS of bronchial responsiveness index (BRI) in the Hutterites.
DOI: 10.6084/m9.figshare.12680151
title: Additional file 14 of Cytokine-induced molecular responses in airway smooth muscle cells inform genome-wide association studies of asthma

description: Additional file 14. List of eQTL results (FDR=5%). eQTLs identified in IL-13 and/or IL-17A-exposed ASMCs at an FDR of 5%.
DOI: 10.6084/m9.figshare.12680151.v1
title: Additional file 14 of Cytokine-induced molecular responses in airway smooth muscle cells inform genome-wide association studies of asthma

description: Additional file 14. List of eQTL results (FDR=5%). eQTLs identified in IL-13 and/or IL-17A-exposed ASMCs at an FDR of 5%.
DOI: 10.6084/m9.figshare.12680154.v1
title: Additional file 15 of Cytokine-induced molecular responses in airway smooth muscle cells inform genome-wide association studies of asthma

description: Additional file 15. List of meQTL results (FDR=5%). meQTLs identified in IL-13 and/or IL-17A-exposed ASMCs at an FDR of 5%.
DOI: 10.6084/m9.figshare.12680148.v1
title: Additional file 13 of Cytokine-induced molecular responses in airway smooth muscle cells inform genome-wide association studies of asthma

description: Additional file 13. Summary of BRI GWAS results. BRI GWAS SNPs (P&lt;10-5) identified through GWAS of bronchial responsiveness index (BRI) in the Hutterites.
DOI: 10.6084/m9.figshare.12680128
title: Additional file 1 of GenAPI: a tool for gene absence-presence identification in fragmented bacterial genome sequences

description: Additional file 1: Table S1. Best non-self hit of all PAO1 reference genome BLAST experiment where 25% of the gene was blasted against the whole PAO1 genome. Only genes longer than 150 bp are reported, only the alignments with 98% identity and minimum 25% gene length were reported. rRNA genes were excluded from report as their sequences are identical. Paralog sequences were defined with BLASTP. Table S2. Assembly statistics of the simulated P. aeruginosa dataset reads. Table S3. Assembly statistics of the E. coli dataset reads. Table S4. Performance test of GenAPI, Roary, PBGA, PanDelos, panX, EDGAR and SaturnV using (a) a simulated S. typhi dataset with complete genome sequences used in Roary publication [4], (b) a simulated P. aeruginosa dataset with partly assembled gene instances (fragmented genome sequences) and (c) a dataset from the long-term experiment with E. coli [19]. TP – true positive gene deletion calls (true positive absent genes); FP – false positive gene deletion calls (false positive absent genes); FN – false negative gene deletion calls (false negative absent genes). TP, FN, and TN were counted only for genes that showed variation between genome sequences to avoid inflation of numbers from large amount of non-variable gene sequences. (d) As one of the absent genes was shorter than 150 bp, it was excluded from GenAPI analysis; when the requirement for the minimum gene length was reduced to 100 bp, all 181 absent genes were successfully identified. Table S5. List of known absent genes in simulated P. aeruginosa dataset [23]. 0 - gene is absent, 1 - gene is present. Table S6. List of known deleted genes and their prokka annotations in E. coli dataset [23]. Figure S1. Detailed scheme of the GenAPI workflow.
DOI: 10.6084/m9.figshare.12680128.v1
title: Additional file 1 of GenAPI: a tool for gene absence-presence identification in fragmented bacterial genome sequences

description: Additional file 1: Table S1. Best non-self hit of all PAO1 reference genome BLAST experiment where 25% of the gene was blasted against the whole PAO1 genome. Only genes longer than 150 bp are reported, only the alignments with 98% identity and minimum 25% gene length were reported. rRNA genes were excluded from report as their sequences are identical. Paralog sequences were defined with BLASTP. Table S2. Assembly statistics of the simulated P. aeruginosa dataset reads. Table S3. Assembly statistics of the E. coli dataset reads. Table S4. Performance test of GenAPI, Roary, PBGA, PanDelos, panX, EDGAR and SaturnV using (a) a simulated S. typhi dataset with complete genome sequences used in Roary publication [4], (b) a simulated P. aeruginosa dataset with partly assembled gene instances (fragmented genome sequences) and (c) a dataset from the long-term experiment with E. coli [19]. TP – true positive gene deletion calls (true positive absent genes); FP – false positive gene deletion calls (false positive absent genes); FN – false negative gene deletion calls (false negative absent genes). TP, FN, and TN were counted only for genes that showed variation between genome sequences to avoid inflation of numbers from large amount of non-variable gene sequences. (d) As one of the absent genes was shorter than 150 bp, it was excluded from GenAPI analysis; when the requirement for the minimum gene length was reduced to 100 bp, all 181 absent genes were successfully identified. Table S5. List of known absent genes in simulated P. aeruginosa dataset [23]. 0 - gene is absent, 1 - gene is present. Table S6. List of known deleted genes and their prokka annotations in E. coli dataset [23]. Figure S1. Detailed scheme of the GenAPI workflow.
DOI: 10.6084/m9.figshare.12680110
title: Additional file 9 of Differential contribution of p300 and CBP to regulatory element acetylation in mESCs

description: Additional file 9.
DOI: 10.6084/m9.figshare.12680101
title: Additional file 6 of Differential contribution of p300 and CBP to regulatory element acetylation in mESCs

description: Additional file 6.
DOI: 10.6084/m9.figshare.12680104
title: Additional file 7 of Differential contribution of p300 and CBP to regulatory element acetylation in mESCs

description: Additional file 7.
DOI: 10.6084/m9.figshare.12680107
title: Additional file 8 of Differential contribution of p300 and CBP to regulatory element acetylation in mESCs

description: Additional file 8.
DOI: 10.6084/m9.figshare.12680110.v1
title: Additional file 9 of Differential contribution of p300 and CBP to regulatory element acetylation in mESCs

description: Additional file 9.
DOI: 10.6084/m9.figshare.12680107.v1
title: Additional file 8 of Differential contribution of p300 and CBP to regulatory element acetylation in mESCs

description: Additional file 8.
DOI: 10.6084/m9.figshare.12680101.v1
title: Additional file 6 of Differential contribution of p300 and CBP to regulatory element acetylation in mESCs

description: Additional file 6.
DOI: 10.6084/m9.figshare.12680104.v1
title: Additional file 7 of Differential contribution of p300 and CBP to regulatory element acetylation in mESCs

description: Additional file 7.
DOI: 10.6084/m9.figshare.12680083
title: Additional file 10 of Differential contribution of p300 and CBP to regulatory element acetylation in mESCs

description: Additional file 10.
DOI: 10.6084/m9.figshare.12680083.v1
title: Additional file 10 of Differential contribution of p300 and CBP to regulatory element acetylation in mESCs

description: Additional file 10.
DOI: 10.6084/m9.figshare.12680016
title: Additional file 8 of SpectralTAD: an R package for defining a hierarchy of topologically associated domains using spectral clustering

description: Additional file 8: Table S3 Enrichment by Method. Enrichment/Depletion results are provided for all genomic annotations tested. Permutation p-values summarized using Fisher’s method are shown. Data is sorted alphabetically by category and then by genomic annotation.
DOI: 10.6084/m9.figshare.12680016.v1
title: Additional file 8 of SpectralTAD: an R package for defining a hierarchy of topologically associated domains using spectral clustering

description: Additional file 8: Table S3 Enrichment by Method. Enrichment/Depletion results are provided for all genomic annotations tested. Permutation p-values summarized using Fisher’s method are shown. Data is sorted alphabetically by category and then by genomic annotation.
DOI: 10.6084/m9.figshare.12680007
title: Additional file 5 of SpectralTAD: an R package for defining a hierarchy of topologically associated domains using spectral clustering

description: Additional file 5: Table S2. Experimental Data sources. Genome annotation (hg19/GRCh37) [50] data for GM12878 cell line used in the analysis, sorted by category, then by data type.
DOI: 10.6084/m9.figshare.12679998
title: Additional file 2 of SpectralTAD: an R package for defining a hierarchy of topologically associated domains using spectral clustering

description: Additional file 2: Table S1. Summary of gaps. The percentage of gaps is summarized for all chromosomes at 10 kb, 25 kb, and 50 kb resolution using raw GM12878 data [3]. Gaps are separated based on whether they are centromeric or other (unsequenced, or poorly organized chromatin).
DOI: 10.6084/m9.figshare.12680007.v1
title: Additional file 5 of SpectralTAD: an R package for defining a hierarchy of topologically associated domains using spectral clustering

description: Additional file 5: Table S2. Experimental Data sources. Genome annotation (hg19/GRCh37) [50] data for GM12878 cell line used in the analysis, sorted by category, then by data type.
DOI: 10.6084/m9.figshare.12679998.v1
title: Additional file 2 of SpectralTAD: an R package for defining a hierarchy of topologically associated domains using spectral clustering

description: Additional file 2: Table S1. Summary of gaps. The percentage of gaps is summarized for all chromosomes at 10 kb, 25 kb, and 50 kb resolution using raw GM12878 data [3]. Gaps are separated based on whether they are centromeric or other (unsequenced, or poorly organized chromatin).
DOI: 10.6084/m9.figshare.12679977
title: Additional file 11 of SpectralTAD: an R package for defining a hierarchy of topologically associated domains using spectral clustering

description: Additional file 11: Table S4. Hi-C Data sources. Information about experimental [3, 39] and simulated [42] Hi-C data.
DOI: 10.6084/m9.figshare.12679977.v1
title: Additional file 11 of SpectralTAD: an R package for defining a hierarchy of topologically associated domains using spectral clustering

description: Additional file 11: Table S4. Hi-C Data sources. Information about experimental [3, 39] and simulated [42] Hi-C data.
DOI: 10.6084/m9.figshare.12679951
title: Additional file 2 of A graphical approach to assess the goodness-of-fit of random-effects linear models when the goal is to measure individual benefits of medical treatments in severely ill patients

description: Additional file 2. SAS/IML code. Computer code implementing the graphical approach and calculating Cramer-von Mises discrepancies.
DOI: 10.6084/m9.figshare.12679956
title: Additional file 2 of High prevalence of t895 and t9364 spa types of methicillin-resistant Staphylococcus aureus in a tertiary-care hospital in Mexico: different lineages of clonal complex 5

description: Additional file 2: Table S2. Minimum Inhibitory Concentration (μg/mL) data for the MRSA strains. Table S2 shows the MIC for each antibiotic for the MRSA strains.