cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9637508
title: Additional file 2: of The transcriptome of peripheral blood mononuclear cells in patients with clinical subtypes of late age-related macular degeneration

description: Complete data of gene expression comparison across the three subtypes of late AMD. (XLSX 2968 kb)
DOI: 10.6084/m9.figshare.9637499.v1
title: Additional file 1: of The transcriptome of peripheral blood mononuclear cells in patients with clinical subtypes of late age-related macular degeneration

description: Gene annotation list. (XLSX 1932 kb)
DOI: 10.6084/m9.figshare.9637502.v1
title: MOESM3 of Wavelet-based verification of a relative paleointensity record from the North Pacific

description: Additional file 3: Table S2. The relative paleointensity data of NPGP1401-2A.
DOI: 10.6084/m9.figshare.9637505.v1
title: Additional file 10: of Evaluation of novel rapid detection kits for dengue virus NS1 antigen in Dhaka, Bangladesh, in 2017

description: Sequences of NS1 region obtained in this study. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.9637496
title: MOESM2 of Wavelet-based verification of a relative paleointensity record from the North Pacific

description: Additional file 2: Table S1. The paleomagnetic data of NPGP1401-2A.
DOI: 10.6084/m9.figshare.9637508.v1
title: Additional file 2: of The transcriptome of peripheral blood mononuclear cells in patients with clinical subtypes of late age-related macular degeneration

description: Complete data of gene expression comparison across the three subtypes of late AMD. (XLSX 2968 kb)
DOI: 10.6084/m9.figshare.9637496.v1
title: MOESM2 of Wavelet-based verification of a relative paleointensity record from the North Pacific

description: Additional file 2: Table S1. The paleomagnetic data of NPGP1401-2A.
DOI: 10.6084/m9.figshare.9637445
title: Additional file 4: of AlleleAnalyzer: a tool for personalized and allele-specific sgRNA design

description: Table S4. PAM site annotation example set for the first 100 variants from the 1KGP on chromosome 1. Full dataset is available as denoted in the data availability section. (XLSX 21 kb)
DOI: 10.6084/m9.figshare.9637445.v1
title: Additional file 4: of AlleleAnalyzer: a tool for personalized and allele-specific sgRNA design

description: Table S4. PAM site annotation example set for the first 100 variants from the 1KGP on chromosome 1. Full dataset is available as denoted in the data availability section. (XLSX 21 kb)
DOI: 10.6084/m9.figshare.9637433
title: Additional file 3: of AlleleAnalyzer: a tool for personalized and allele-specific sgRNA design

description: Table S3. Comparison of AlleleAnalyzer features with other commonly used CRISPR sgRNA design tools. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.9637433.v1
title: Additional file 3: of AlleleAnalyzer: a tool for personalized and allele-specific sgRNA design

description: Table S3. Comparison of AlleleAnalyzer features with other commonly used CRISPR sgRNA design tools. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.9637424
title: Additional file 2: of AlleleAnalyzer: a tool for personalized and allele-specific sgRNA design

description: Table S2. AlleleAnalyzer guides for SpCas9 and SaCas9 in BEST1 for optimal coverage of the 1000 genomes cohort, as shown in Fig.Â 3b-e. Guides with â ---â as sequence indicate loss of PAM site due to a variant, and therefore non-targetability of that allele. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.9637424.v1
title: Additional file 2: of AlleleAnalyzer: a tool for personalized and allele-specific sgRNA design

description: Table S2. AlleleAnalyzer guides for SpCas9 and SaCas9 in BEST1 for optimal coverage of the 1000 genomes cohort, as shown in Fig.Â 3b-e. Guides with â ---â as sequence indicate loss of PAM site due to a variant, and therefore non-targetability of that allele. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.9637388
title: Additional file 8: of RNASeq analysis of giant cane reveals the leaf transcriptome dynamics under long-term salt stress

description: Figure S5. Kog functional classification. Clusters of orthologous groups (KOG) classification. All unigenes were aligned to KOG database to predict and classify possible functions. Out of 255,809 unigenes, 49,848 sequences were assigned to 25 KOG classifications. (A) RNA processing and modification; (B) chromatin structure and dynamics; (C) energy production and conversion; (D) cell cycle control, cell division, chromosome partitioning; (E) amino acid transport and metabolism; (F) nucleotide transport and metabolism; (G) carbohydrate transport and metabolism; (H) coenzyme transport and metabolism; (I) lipid transport and metabolism; (J) transition, ribosomal structure and biogenesis; (K) transcription; (L) replication, recombination and repair; (M) cell wall/membrane/envelope biogenesis; (N) cell motility; (O) posttranslational modification, protein turnover, chaperones; (P) inorganic ion transport and metabolism; (Q) secondary metabolites biosynthesis, transport and catabolism; (R) general function prediction only; (S) function unknown; (T) signal transduction mechanisms; (U) intracellular trafficking, secretion, and vesicular transport; (V) defense mechanisms; (W) extracellular structures; (X) unnamed protein; (Y) nuclear structure; (Z) cytoskeleton. (RTF 5034 kb)
DOI: 10.6084/m9.figshare.9637382
title: Additional file 6: of RNASeq analysis of giant cane reveals the leaf transcriptome dynamics under long-term salt stress

description: Table S4. Clusters specific regulated by salinity (XLSX 23 kb)
DOI: 10.6084/m9.figshare.9637385
title: Additional file 7: of RNASeq analysis of giant cane reveals the leaf transcriptome dynamics under long-term salt stress

description: Table S5. Protein family and domain description. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.9637388.v1
title: Additional file 8: of RNASeq analysis of giant cane reveals the leaf transcriptome dynamics under long-term salt stress

description: Figure S5. Kog functional classification. Clusters of orthologous groups (KOG) classification. All unigenes were aligned to KOG database to predict and classify possible functions. Out of 255,809 unigenes, 49,848 sequences were assigned to 25 KOG classifications. (A) RNA processing and modification; (B) chromatin structure and dynamics; (C) energy production and conversion; (D) cell cycle control, cell division, chromosome partitioning; (E) amino acid transport and metabolism; (F) nucleotide transport and metabolism; (G) carbohydrate transport and metabolism; (H) coenzyme transport and metabolism; (I) lipid transport and metabolism; (J) transition, ribosomal structure and biogenesis; (K) transcription; (L) replication, recombination and repair; (M) cell wall/membrane/envelope biogenesis; (N) cell motility; (O) posttranslational modification, protein turnover, chaperones; (P) inorganic ion transport and metabolism; (Q) secondary metabolites biosynthesis, transport and catabolism; (R) general function prediction only; (S) function unknown; (T) signal transduction mechanisms; (U) intracellular trafficking, secretion, and vesicular transport; (V) defense mechanisms; (W) extracellular structures; (X) unnamed protein; (Y) nuclear structure; (Z) cytoskeleton. (RTF 5034 kb)
DOI: 10.6084/m9.figshare.9637376
title: Additional file 5: of RNASeq analysis of giant cane reveals the leaf transcriptome dynamics under long-term salt stress

description: Table S3. Transcription factors responsive to salt, to drought or both to salt and drought stresses in A. donax (XLSX 44 kb)
DOI: 10.6084/m9.figshare.9637382.v1
title: Additional file 6: of RNASeq analysis of giant cane reveals the leaf transcriptome dynamics under long-term salt stress

description: Table S4. Clusters specific regulated by salinity (XLSX 23 kb)
DOI: 10.6084/m9.figshare.9637385.v1
title: Additional file 7: of RNASeq analysis of giant cane reveals the leaf transcriptome dynamics under long-term salt stress

description: Table S5. Protein family and domain description. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.9637376.v1
title: Additional file 5: of RNASeq analysis of giant cane reveals the leaf transcriptome dynamics under long-term salt stress

description: Table S3. Transcription factors responsive to salt, to drought or both to salt and drought stresses in A. donax (XLSX 44 kb)
DOI: 10.6084/m9.figshare.9637367
title: Additional file 3: of RNASeq analysis of giant cane reveals the leaf transcriptome dynamics under long-term salt stress

description: Table S1. and Figure S4.. Validation of A. donax DEGs by Real Time qRT-PCR (XLSX 14 kb)
DOI: 10.6084/m9.figshare.9637367.v1
title: Additional file 3: of RNASeq analysis of giant cane reveals the leaf transcriptome dynamics under long-term salt stress

description: Table S1. and Figure S4.. Validation of A. donax DEGs by Real Time qRT-PCR (XLSX 14 kb)
DOI: 10.6084/m9.figshare.9637361
title: Additional file 2: of RNASeq analysis of giant cane reveals the leaf transcriptome dynamics under long-term salt stress

description: Figure S2. Picture of giant reed phenotype under salt stress. Figure S3. Length distribution of transcripts and Unigenes (ZIP 1076 kb)
DOI: 10.6084/m9.figshare.9637361.v1
title: Additional file 2: of RNASeq analysis of giant cane reveals the leaf transcriptome dynamics under long-term salt stress

description: Figure S2. Picture of giant reed phenotype under salt stress. Figure S3. Length distribution of transcripts and Unigenes (ZIP 1076 kb)
DOI: 10.6084/m9.figshare.9637331
title: Additional file 4: of Differences in gene expression in whitefly associated with CYSDV-infected and virus-free melon, and comparison with expression in whiteflies fed on ToCV- and TYLCV-infected tomato

description: A list of 69 differentially regulated orphan genes found in CYSDV whiteflies compared to VF whiteflies following feeding for 72â h and 7â days. (XLSX 21 kb)
DOI: 10.6084/m9.figshare.9637331.v1
title: Additional file 4: of Differences in gene expression in whitefly associated with CYSDV-infected and virus-free melon, and comparison with expression in whiteflies fed on ToCV- and TYLCV-infected tomato

description: A list of 69 differentially regulated orphan genes found in CYSDV whiteflies compared to VF whiteflies following feeding for 72â h and 7â days. (XLSX 21 kb)
DOI: 10.6084/m9.figshare.9637319
title: Additional file 3: of Differences in gene expression in whitefly associated with CYSDV-infected and virus-free melon, and comparison with expression in whiteflies fed on ToCV- and TYLCV-infected tomato

description: A list of 59 common differentially expressed genes between ToCV whiteflies and CYSDV whiteflies compared to virus free whiteflies at all three different feeding time points. (XLSX 33144 kb)
DOI: 10.6084/m9.figshare.9637319.v1
title: Additional file 3: of Differences in gene expression in whitefly associated with CYSDV-infected and virus-free melon, and comparison with expression in whiteflies fed on ToCV- and TYLCV-infected tomato

description: A list of 59 common differentially expressed genes between ToCV whiteflies and CYSDV whiteflies compared to virus free whiteflies at all three different feeding time points. (XLSX 33144 kb)
DOI: 10.6084/m9.figshare.9637322
title: Additional file 2: of The cholinergic anti-inflammatory pathway in resistant hypertension treated with renal denervation

description: Table S2. HRV variables SDNN, SDMRR, HR, HF, LF/HF in RDN patients at baseline, day 1 and at 3 and 6 months. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.9637322.v2
title: Additional file 2: of The cholinergic anti-inflammatory pathway in resistant hypertension treated with renal denervation

description: Table S2. HRV variables SDNN, SDMRR, HR, HF, LF/HF in RDN patients at baseline, day 1 and at 3 and 6 months. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.9637313
title: Additional file 2: of Differences in gene expression in whitefly associated with CYSDV-infected and virus-free melon, and comparison with expression in whiteflies fed on ToCV- and TYLCV-infected tomato

description: a. KEGG annotation, KO, and score values of the 28 genes out of a total of 82 up-regulated in CYSDV whiteflies versus virus-free whiteflies at 72 h. b. Pathway reconstruction results from the 28 genes out of a total of 82 up-regulated in CYSDV whiteflies versus virus-free whiteflies at 72 h. c. KEGG annotation, KO, and score values of the 40 genes out of a total of 139 down-regulated in CYSDV whiteflies versus virus-free whiteflies at 72 h. d. Pathway reconstruction results from the 40 genes out of a total of 139 down-regulated in CYSDV whiteflies versus virus-free whiteflies at 72 h. e. KEGG annotation, KO, and score values of the 12 genes out of a total of 49 up-regulated in CYSDV whiteflies versus virus-free whiteflies at 7 d. f. Pathway reconstruction results from the 12 genes out of a total of 49 up-regulated in CYSDV whiteflies versus virus-free whiteflies at 7 d. (XLSX 49 kb)
DOI: 10.6084/m9.figshare.9637310
title: Additional file 1: of Differences in gene expression in whitefly associated with CYSDV-infected and virus-free melon, and comparison with expression in whiteflies fed on ToCV- and TYLCV-infected tomato

description: a. The number of Illumina raw and processed reads produced per RNA-Seq library from virus free (“VF”) whiteflies, Bemisia tabaci MEAM1, and whiteflies fed on cucurbit yellow stunting disorder virus (CYSDV) infected melon plants (“CYSDV”) for 24 h, 72 h, and 7 d. b. Correlation matrix analysis for multiple biological replicates obtained from RNA-Seq libraries prepared from virus free (VF) whiteflies fed on uninfected melon plants and whiteflies fed on cucurbit yellow stunting disorder virus (CYSDV) infected melon plants for periods of for 24 h, 72 h, and 7 d. c. Differentially expressed genes between virus free (VF) whiteflies fed on uninfected melon and whiteflies fed on cucurbit yellow stunting disorder virus (CYSDV) infected melon plants for 24 h, 72 h, and 7 d. (XLSX 33 kb)
DOI: 10.6084/m9.figshare.9637313.v1
title: Additional file 2: of Differences in gene expression in whitefly associated with CYSDV-infected and virus-free melon, and comparison with expression in whiteflies fed on ToCV- and TYLCV-infected tomato

description: a. KEGG annotation, KO, and score values of the 28 genes out of a total of 82 up-regulated in CYSDV whiteflies versus virus-free whiteflies at 72 h. b. Pathway reconstruction results from the 28 genes out of a total of 82 up-regulated in CYSDV whiteflies versus virus-free whiteflies at 72 h. c. KEGG annotation, KO, and score values of the 40 genes out of a total of 139 down-regulated in CYSDV whiteflies versus virus-free whiteflies at 72 h. d. Pathway reconstruction results from the 40 genes out of a total of 139 down-regulated in CYSDV whiteflies versus virus-free whiteflies at 72 h. e. KEGG annotation, KO, and score values of the 12 genes out of a total of 49 up-regulated in CYSDV whiteflies versus virus-free whiteflies at 7 d. f. Pathway reconstruction results from the 12 genes out of a total of 49 up-regulated in CYSDV whiteflies versus virus-free whiteflies at 7 d. (XLSX 49 kb)
DOI: 10.6084/m9.figshare.9637322.v1
title: Additional file 2: of The cholinergic anti-inflammatory pathway in resistant hypertension treated with renal denervation

description: Table S2. HRV variables SDNN, SDMRR, HR, HF, LF/HF in RDN patients at baseline, day 1 and at 3 and 6 months. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.9637310.v1
title: Additional file 1: of Differences in gene expression in whitefly associated with CYSDV-infected and virus-free melon, and comparison with expression in whiteflies fed on ToCV- and TYLCV-infected tomato

description: a. The number of Illumina raw and processed reads produced per RNA-Seq library from virus free (“VF”) whiteflies, Bemisia tabaci MEAM1, and whiteflies fed on cucurbit yellow stunting disorder virus (CYSDV) infected melon plants (“CYSDV”) for 24 h, 72 h, and 7 d. b. Correlation matrix analysis for multiple biological replicates obtained from RNA-Seq libraries prepared from virus free (VF) whiteflies fed on uninfected melon plants and whiteflies fed on cucurbit yellow stunting disorder virus (CYSDV) infected melon plants for periods of for 24 h, 72 h, and 7 d. c. Differentially expressed genes between virus free (VF) whiteflies fed on uninfected melon and whiteflies fed on cucurbit yellow stunting disorder virus (CYSDV) infected melon plants for 24 h, 72 h, and 7 d. (XLSX 33 kb)
DOI: 10.6084/m9.figshare.9637316
title: Additional file 1. of The cholinergic anti-inflammatory pathway in resistant hypertension treated with renal denervation

description: Table S1. Blood pressure in RDN patients at baseline, day 1 and at 3 and 6 months. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.9637316.v2
title: Additional file 1. of The cholinergic anti-inflammatory pathway in resistant hypertension treated with renal denervation

description: Table S1. Blood pressure in RDN patients at baseline, day 1 and at 3 and 6 months. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.9637316.v1
title: Additional file 1. of The cholinergic anti-inflammatory pathway in resistant hypertension treated with renal denervation

description: Table S1. Blood pressure in RDN patients at baseline, day 1 and at 3 and 6 months. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.9637262
title: Additional file 8: of Stoichiometric gene-to-reaction associations enhance model-driven analysis performance: Metabolic response to chronic exposure to Aldrin in prostate cancer

description: Results of the analyses comparing predictive capabilities of GPR-based and S-GPR-based approaches using iMat, Gimme, GonĂ§alves et al. 2012 and MADE algorithms. (XLSX 309 kb)
DOI: 10.6084/m9.figshare.9637262.v1
title: Additional file 8: of Stoichiometric gene-to-reaction associations enhance model-driven analysis performance: Metabolic response to chronic exposure to Aldrin in prostate cancer

description: Results of the analyses comparing predictive capabilities of GPR-based and S-GPR-based approaches using iMat, Gimme, GonĂ§alves et al. 2012 and MADE algorithms. (XLSX 309 kb)
DOI: 10.6084/m9.figshare.9637259
title: Additional file 2: of Evaluating the quality of the 1000 genomes project data

description: Statistics for the experimental sequencing. (XLSX 21 kb)
DOI: 10.6084/m9.figshare.9637256
title: Additional file 7: of Stoichiometric gene-to-reaction associations enhance model-driven analysis performance: Metabolic response to chronic exposure to Aldrin in prostate cancer

description: Comparison of the reliability of model predictions between HMR2 + algorithm-based GPRs and Recon2. (XLSX 501 kb)
DOI: 10.6084/m9.figshare.9637247
title: Additional file 6: of Stoichiometric gene-to-reaction associations enhance model-driven analysis performance: Metabolic response to chronic exposure to Aldrin in prostate cancer

description: GSMMs: Genome-scale metabolic models used in the analysis. (ZIP 2743 kb)
DOI: 10.6084/m9.figshare.9637256.v1
title: Additional file 7: of Stoichiometric gene-to-reaction associations enhance model-driven analysis performance: Metabolic response to chronic exposure to Aldrin in prostate cancer

description: Comparison of the reliability of model predictions between HMR2 + algorithm-based GPRs and Recon2. (XLSX 501 kb)
DOI: 10.6084/m9.figshare.9637241
title: Additional file 5: of Stoichiometric gene-to-reaction associations enhance model-driven analysis performance: Metabolic response to chronic exposure to Aldrin in prostate cancer

description: Gene-to-reaction building algorithm: Algorithm to build GPR and S-GPR (written in Python). (ZIP 2623 kb)
DOI: 10.6084/m9.figshare.9637247.v1
title: Additional file 6: of Stoichiometric gene-to-reaction associations enhance model-driven analysis performance: Metabolic response to chronic exposure to Aldrin in prostate cancer

description: GSMMs: Genome-scale metabolic models used in the analysis. (ZIP 2743 kb)
DOI: 10.6084/m9.figshare.9637238
title: Additional file 4: of Stoichiometric gene-to-reaction associations enhance model-driven analysis performance: Metabolic response to chronic exposure to Aldrin in prostate cancer

description: GSMM readjustments/refinement process. This file includes; i) Definition of Metabolites included in the biomass reaction, ii) Required Metabolic Functionalities (RMF) necessary to apply GIMME algorithm, iii) Experimentally measured metabolites annotated in HMR2 and iv) automatically generated GPR and S-GPR of each catalytic reaction in HMR2 (algorithm in Additional file 5) (XLSX 190 kb)
DOI: 10.6084/m9.figshare.9637235
title: Additional file 3: of Stoichiometric gene-to-reaction associations enhance model-driven analysis performance: Metabolic response to chronic exposure to Aldrin in prostate cancer

description: Transcriptomic data. Transcriptomic data of Aldrin-exposed and non-exposed DU149 PC cells and gene expression analysis. (XLSX 4835 kb)
DOI: 10.6084/m9.figshare.9637241.v1
title: Additional file 5: of Stoichiometric gene-to-reaction associations enhance model-driven analysis performance: Metabolic response to chronic exposure to Aldrin in prostate cancer

description: Gene-to-reaction building algorithm: Algorithm to build GPR and S-GPR (written in Python). (ZIP 2623 kb)
DOI: 10.6084/m9.figshare.9637238.v1
title: Additional file 4: of Stoichiometric gene-to-reaction associations enhance model-driven analysis performance: Metabolic response to chronic exposure to Aldrin in prostate cancer

description: GSMM readjustments/refinement process. This file includes; i) Definition of Metabolites included in the biomass reaction, ii) Required Metabolic Functionalities (RMF) necessary to apply GIMME algorithm, iii) Experimentally measured metabolites annotated in HMR2 and iv) automatically generated GPR and S-GPR of each catalytic reaction in HMR2 (algorithm in Additional file 5) (XLSX 190 kb)
DOI: 10.6084/m9.figshare.9637226
title: Additional file 2: of Stoichiometric gene-to-reaction associations enhance model-driven analysis performance: Metabolic response to chronic exposure to Aldrin in prostate cancer

description: Mapping metabolomic and lipidomics on GSMMs: Metabolomic and Lipidomic data mapped on HMR2 and Recon2 models. (XLSX 296 kb)
DOI: 10.6084/m9.figshare.9637235.v1
title: Additional file 3: of Stoichiometric gene-to-reaction associations enhance model-driven analysis performance: Metabolic response to chronic exposure to Aldrin in prostate cancer

description: Transcriptomic data. Transcriptomic data of Aldrin-exposed and non-exposed DU149 PC cells and gene expression analysis. (XLSX 4835 kb)
DOI: 10.6084/m9.figshare.9637226.v1
title: Additional file 2: of Stoichiometric gene-to-reaction associations enhance model-driven analysis performance: Metabolic response to chronic exposure to Aldrin in prostate cancer

description: Mapping metabolomic and lipidomics on GSMMs: Metabolomic and Lipidomic data mapped on HMR2 and Recon2 models. (XLSX 296 kb)
DOI: 10.6084/m9.figshare.9637217
title: Additional file 1: of Stoichiometric gene-to-reaction associations enhance model-driven analysis performance: Metabolic response to chronic exposure to Aldrin in prostate cancer

description: Metabolomic and Fluxomic experimental data. Metabolomic data and ROI analysis result from Aldrin-exposed and non-exposed DU145 cells at time 0 and after 5â h. (XLSX 1253 kb)
DOI: 10.6084/m9.figshare.9637217.v1
title: Additional file 1: of Stoichiometric gene-to-reaction associations enhance model-driven analysis performance: Metabolic response to chronic exposure to Aldrin in prostate cancer

description: Metabolomic and Fluxomic experimental data. Metabolomic data and ROI analysis result from Aldrin-exposed and non-exposed DU145 cells at time 0 and after 5â h. (XLSX 1253 kb)