cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6817841
title: Additional file 5: of Refining a steroidogenic model: an analysis of RNA-seq datasets from insect prothoracic glands

description: Table S5. Tabulation of the 231 differentially spliced loci identified by Cufflinks in Bombyx mori PGs between V-0 and V-6 of the 5th instar. In cases where a gene model was included between the test ID coordinates (Column C), this is indicated using the nomenclature of KAIKObase ( http://sgp.dna.affrc.go.jp/KAIKObase/ ) or it is left empty. Each test was annotated with its corresponding data from the Bowtie2 output [28] (columns U to AB) and the results of the Blastp analysis against the Bm protein reference sequences (NCBI annotation release 102) (columns AC and AD). (XLSX 132 kb)
DOI: 10.6084/m9.figshare.6817844.v1
title: Additional file 6: of Refining a steroidogenic model: an analysis of RNA-seq datasets from insect prothoracic glands

description: Table S6. Tabulation of 98 unique differentially spliced loci based on the TransDecoder and Cufflinks output. Data from Additional file 5: Table S5 was manually annotated to filter out duplicate entries based on locus and protein sequence. In cases where a gene model was included between the test ID coordinates (Column C), this is indicated using the nomenclature of KAIKObase ( http://sgp.dna.affrc.go.jp/KAIKObase/ ) or it is left empty. Each test was annotated with its corresponding data from the Bowtie2 output [28] (columns R to Y) and the results of the Blastp analysis against the Bombyx mori protein reference sequences (NCBI annotation release 102) (columns Z and AA). (XLSX 131 kb)
DOI: 10.6084/m9.figshare.6817838
title: Additional file 4: of Refining a steroidogenic model: an analysis of RNA-seq datasets from insect prothoracic glands

description: Table S4. Tabulation of 51,035 tests carried out by Cufflinks to identify splicing events that lead to differential gene expression in Bombyx mori PGs between V-0 and V-6 of the 5th instar. In cases where a gene model was included between the test ID coordinates (Column C), this is indicated using the nomenclature of KAIKObase ( http://sgp.dna.affrc.go.jp/KAIKObase/ ) or it is left empty. Using this criterion, we identified 12 unmapped loci among the 231 differentially spliced loci. (XLSX 2546 kb)
DOI: 10.6084/m9.figshare.6817838.v1
title: Additional file 4: of Refining a steroidogenic model: an analysis of RNA-seq datasets from insect prothoracic glands

description: Table S4. Tabulation of 51,035 tests carried out by Cufflinks to identify splicing events that lead to differential gene expression in Bombyx mori PGs between V-0 and V-6 of the 5th instar. In cases where a gene model was included between the test ID coordinates (Column C), this is indicated using the nomenclature of KAIKObase ( http://sgp.dna.affrc.go.jp/KAIKObase/ ) or it is left empty. Using this criterion, we identified 12 unmapped loci among the 231 differentially spliced loci. (XLSX 2546 kb)
DOI: 10.6084/m9.figshare.6817841.v1
title: Additional file 5: of Refining a steroidogenic model: an analysis of RNA-seq datasets from insect prothoracic glands

description: Table S5. Tabulation of the 231 differentially spliced loci identified by Cufflinks in Bombyx mori PGs between V-0 and V-6 of the 5th instar. In cases where a gene model was included between the test ID coordinates (Column C), this is indicated using the nomenclature of KAIKObase ( http://sgp.dna.affrc.go.jp/KAIKObase/ ) or it is left empty. Each test was annotated with its corresponding data from the Bowtie2 output [28] (columns U to AB) and the results of the Blastp analysis against the Bm protein reference sequences (NCBI annotation release 102) (columns AC and AD). (XLSX 132 kb)
DOI: 10.6084/m9.figshare.6817832
title: Additional file 3: of Refining a steroidogenic model: an analysis of RNA-seq datasets from insect prothoracic glands

description: Table S3. Tabulation of 16,550 unique loci based on the TransDecoder and Cufflinks output. Data from Additional file 2: Table S2 was manually annotated to filter out duplicate entries based on locus and protein sequence. Columns E to H are the TransDecoder output, columns I to P are the Cufflinks output, columns R to Y are the Bowtie2 output [28], columns Z and AA are the results of the Blastp analysis against the Bm protein reference sequences (NCBI annotation release 102) and columns AB to AE are the results of the g:Orth [40] and OrthoDB [107] output. In cases where a gene model was included between the test ID coordinates (Column D), this is indicated using the nomenclature of KAIKObase ( http://sgp.dna.affrc.go.jp/KAIKObase/ ) or it is left empty. Using this criterion, we identified 2265 unmapped loci. (XLSX 8960 kb)
DOI: 10.6084/m9.figshare.6817832.v1
title: Additional file 3: of Refining a steroidogenic model: an analysis of RNA-seq datasets from insect prothoracic glands

description: Table S3. Tabulation of 16,550 unique loci based on the TransDecoder and Cufflinks output. Data from Additional file 2: Table S2 was manually annotated to filter out duplicate entries based on locus and protein sequence. Columns E to H are the TransDecoder output, columns I to P are the Cufflinks output, columns R to Y are the Bowtie2 output [28], columns Z and AA are the results of the Blastp analysis against the Bm protein reference sequences (NCBI annotation release 102) and columns AB to AE are the results of the g:Orth [40] and OrthoDB [107] output. In cases where a gene model was included between the test ID coordinates (Column D), this is indicated using the nomenclature of KAIKObase ( http://sgp.dna.affrc.go.jp/KAIKObase/ ) or it is left empty. Using this criterion, we identified 2265 unmapped loci. (XLSX 8960 kb)
DOI: 10.6084/m9.figshare.6817826
title: Additional file 2: of Refining a steroidogenic model: an analysis of RNA-seq datasets from insect prothoracic glands

description: Table S2. Tabulation of 43,242 tests carried out by TransDecoder on the Cufflinks output. TransDecoder settings were adjusted to filter out ORFs encoding
DOI: 10.6084/m9.figshare.6817826.v1
title: Additional file 2: of Refining a steroidogenic model: an analysis of RNA-seq datasets from insect prothoracic glands

description: Table S2. Tabulation of 43,242 tests carried out by TransDecoder on the Cufflinks output. TransDecoder settings were adjusted to filter out ORFs encoding
DOI: 10.6084/m9.figshare.6817817
title: Additional file 26: of Refining a steroidogenic model: an analysis of RNA-seq datasets from insect prothoracic glands

description: Table S20. List of primers used to determine transcript abundance of the 650 genes shown in Additional file 7: Table S7. (XLSX 94 kb)
DOI: 10.6084/m9.figshare.6817817.v1
title: Additional file 26: of Refining a steroidogenic model: an analysis of RNA-seq datasets from insect prothoracic glands

description: Table S20. List of primers used to determine transcript abundance of the 650 genes shown in Additional file 7: Table S7. (XLSX 94 kb)
DOI: 10.6084/m9.figshare.6817805
title: Additional file 25: of Refining a steroidogenic model: an analysis of RNA-seq datasets from insect prothoracic glands

description: Table S19. Checklist of compliance with the MIQE guidelines [127]. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.6817805.v1
title: Additional file 25: of Refining a steroidogenic model: an analysis of RNA-seq datasets from insect prothoracic glands

description: Table S19. Checklist of compliance with the MIQE guidelines [127]. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.6817793
title: Additional file 24: of Refining a steroidogenic model: an analysis of RNA-seq datasets from insect prothoracic glands

description: Table S18. Integration of Bombyx mori plasma membrane receptor expression data in PG cells with RNA-seq data from Drosophila melanogaster orthologous genes. Our previous analysis results of plasma membrane receptors expressed in PG cells [27] was integrated with our Cufflinks data and with expression data from Dm [31]. Orthology annotation was based on one(Bombyx mori) to all (Drosophila melanogaster) using OrthoDB [107]. (XLSX 87 kb)
DOI: 10.6084/m9.figshare.12814634
title: Data: The role of connectivity in the interplay between climate change and the spread of alien fish in a large Mediterranean river

description: Environmental data of the Ebro River used for building species distribution models of the study:<br>Radinger J. & García-Berthou E. (2020) The role of connectivity in the interplay between climate change and the spread of alien fish in a large Mediterranean river. Global Change Biology. DOI: 10.1111/gcb.15320
DOI: 10.6084/m9.figshare.6817793.v1
title: Additional file 24: of Refining a steroidogenic model: an analysis of RNA-seq datasets from insect prothoracic glands

description: Table S18. Integration of Bombyx mori plasma membrane receptor expression data in PG cells with RNA-seq data from Drosophila melanogaster orthologous genes. Our previous analysis results of plasma membrane receptors expressed in PG cells [27] was integrated with our Cufflinks data and with expression data from Dm [31]. Orthology annotation was based on one(Bombyx mori) to all (Drosophila melanogaster) using OrthoDB [107]. (XLSX 87 kb)
DOI: 10.6084/m9.figshare.6817736
title: Additional file 9: of Arabidopsis thaliana ambient temperature responsive lncRNAs

description: Table S6. List of primers used for qPCR. (XLSX 9Â kb)
DOI: 10.6084/m9.figshare.6817736.v1
title: Additional file 9: of Arabidopsis thaliana ambient temperature responsive lncRNAs

description: Table S6. List of primers used for qPCR. (XLSX 9Â kb)
DOI: 10.6084/m9.figshare.6817730
title: Additional file 8: of Arabidopsis thaliana ambient temperature responsive lncRNAs

description: Table S5. Arabidopsis thaliana genomic region with sequence homology to FLINC. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.6817730.v1
title: Additional file 8: of Arabidopsis thaliana ambient temperature responsive lncRNAs

description: Table S5. Arabidopsis thaliana genomic region with sequence homology to FLINC. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.6817718
title: Additional file 4: of Liprin-Îą1 modulates cancer cell signaling by transmembrane protein CD82 in adhesive membrane domains linked to cytoskeleton

description: Table S3. Overview of the results from the Gene Set Enrichment Data analysis from HNSCC and breast cancer cells line comparing shPPFIA1 knockdown and shScr control cells. (XLSX 491 kb)
DOI: 10.6084/m9.figshare.6817718.v1
title: Additional file 4: of Liprin-Îą1 modulates cancer cell signaling by transmembrane protein CD82 in adhesive membrane domains linked to cytoskeleton

description: Table S3. Overview of the results from the Gene Set Enrichment Data analysis from HNSCC and breast cancer cells line comparing shPPFIA1 knockdown and shScr control cells. (XLSX 491 kb)
DOI: 10.6084/m9.figshare.6817712
title: Additional file 3: of Liprin-α1 modulates cancer cell signaling by transmembrane protein CD82 in adhesive membrane domains linked to cytoskeleton

description: Table S2. A lists of shared genes from RNA-seq data comparisons between shPPFIA1 knockdown and shScr control cells from HNSCC and breast cancer. A: Shared genes between UT-SCC-42A/42B and MDA-MB-231 cells grown in 3D collagen I. B: Shared genes between UT-SCC-42A/42B grown in 3D and UT-SCC-24B cells grown in 2D cell culture. C: Shared genes between MDA-MB-231 grown in 3D and UT-SCC-24B cells grown in 2D cell culture. D: Shared genes in MDA-MB-231 and UT-SCC-42A/42B cells grown in 3D and UT-SCC-24B cells grown in 2D cell culture. (XLSX 22 kb)
DOI: 10.6084/m9.figshare.6817712.v1
title: Additional file 3: of Liprin-α1 modulates cancer cell signaling by transmembrane protein CD82 in adhesive membrane domains linked to cytoskeleton

description: Table S2. A lists of shared genes from RNA-seq data comparisons between shPPFIA1 knockdown and shScr control cells from HNSCC and breast cancer. A: Shared genes between UT-SCC-42A/42B and MDA-MB-231 cells grown in 3D collagen I. B: Shared genes between UT-SCC-42A/42B grown in 3D and UT-SCC-24B cells grown in 2D cell culture. C: Shared genes between MDA-MB-231 grown in 3D and UT-SCC-24B cells grown in 2D cell culture. D: Shared genes in MDA-MB-231 and UT-SCC-42A/42B cells grown in 3D and UT-SCC-24B cells grown in 2D cell culture. (XLSX 22 kb)
DOI: 10.6084/m9.figshare.6817703
title: Additional file 2: of Liprin-α1 modulates cancer cell signaling by transmembrane protein CD82 in adhesive membrane domains linked to cytoskeleton

description: Table S1. Overview of gene expression changes in MDA-MB-231 breast cancer and UT-SCC-42A/B HNSCC cell lines after liprin-α1 knockdown using three different constructs targeting PPFIA1. (XLSX 692 kb)
DOI: 10.6084/m9.figshare.6817703.v1
title: Additional file 2: of Liprin-α1 modulates cancer cell signaling by transmembrane protein CD82 in adhesive membrane domains linked to cytoskeleton

description: Table S1. Overview of gene expression changes in MDA-MB-231 breast cancer and UT-SCC-42A/B HNSCC cell lines after liprin-α1 knockdown using three different constructs targeting PPFIA1. (XLSX 692 kb)
DOI: 10.6084/m9.figshare.6817694
title: Additional file 4: of Arabidopsis thaliana ambient temperature responsive lncRNAs

description: Table S4. Pearson correlation between lncRNAs and protein coding genes. For the NATs expression value of the corresponding sense transcript while for the lincRNAs the expression value of their two direct flanking protein coding genes in our data set was used. NA, indicates absence of detectable expression in our RNA-seq. (XLSX 15Â kb)
DOI: 10.6084/m9.figshare.6817694.v1
title: Additional file 4: of Arabidopsis thaliana ambient temperature responsive lncRNAs

description: Table S4. Pearson correlation between lncRNAs and protein coding genes. For the NATs expression value of the corresponding sense transcript while for the lincRNAs the expression value of their two direct flanking protein coding genes in our data set was used. NA, indicates absence of detectable expression in our RNA-seq. (XLSX 15Â kb)
DOI: 10.6084/m9.figshare.6817679
title: Additional file 3: of Arabidopsis thaliana ambient temperature responsive lncRNAs

description: Table S3. Differentially expressed lncRNAs (DElnc). List of lncRNAs differentially expressed between 16 °C and 25 °C day 1, 16 °C and 25 °C day 3, 16 °C and 25 °C day 5. DElnc are defined as transcripts with a change in expression of log2 Fold Change |1| and adjusted p-value according to the BH method for controlling false discovery
DOI: 10.6084/m9.figshare.6817679.v1
title: Additional file 3: of Arabidopsis thaliana ambient temperature responsive lncRNAs

description: Table S3. Differentially expressed lncRNAs (DElnc). List of lncRNAs differentially expressed between 16 °C and 25 °C day 1, 16 °C and 25 °C day 3, 16 °C and 25 °C day 5. DElnc are defined as transcripts with a change in expression of log2 Fold Change |1| and adjusted p-value according to the BH method for controlling false discovery
DOI: 10.6084/m9.figshare.6817670
title: Additional file 2 of An integrative network-based approach to identify novel disease genes and pathways: a case study in the context of inflammatory bowel disease

description: Significant clusters with selected pathways and enriched GO terms associated to them. (XLSX 31 kb)
DOI: 10.6084/m9.figshare.6817673
title: Additional file 20: of Refining a steroidogenic model: an analysis of RNA-seq datasets from insect prothoracic glands

description: Table S17. Cytochrome P450 genes of Bombyx mori. Annotation for each gene was enriched with data from [27, 28]. The sequence of each protein used to construct the posterior probability tree (Additional file 21: Figure S4.) is shown in column AA. (XLSX 136 kb)
DOI: 10.6084/m9.figshare.6817670.v1
title: Additional file 2 of An integrative network-based approach to identify novel disease genes and pathways: a case study in the context of inflammatory bowel disease

description: Significant clusters with selected pathways and enriched GO terms associated to them. (XLSX 31 kb)
DOI: 10.6084/m9.figshare.6817673.v1
title: Additional file 20: of Refining a steroidogenic model: an analysis of RNA-seq datasets from insect prothoracic glands

description: Table S17. Cytochrome P450 genes of Bombyx mori. Annotation for each gene was enriched with data from [27, 28]. The sequence of each protein used to construct the posterior probability tree (Additional file 21: Figure S4.) is shown in column AA. (XLSX 136 kb)
DOI: 10.6084/m9.figshare.6817667
title: Additional file 2: of Arabidopsis thaliana ambient temperature responsive lncRNAs

description: TableS2. List of lncRNAs located within a 5Â kb region of a gene involved in flowering time regulation. (XLSX 15Â kb)
DOI: 10.6084/m9.figshare.6817667.v1
title: Additional file 2: of Arabidopsis thaliana ambient temperature responsive lncRNAs

description: TableS2. List of lncRNAs located within a 5Â kb region of a gene involved in flowering time regulation. (XLSX 15Â kb)
DOI: 10.6084/m9.figshare.6817658
title: Additional file 1 of An integrative network-based approach to identify novel disease genes and pathways: a case study in the context of inflammatory bowel disease

description: List of predicted IBD genes. (XLSX 26 kb)
DOI: 10.6084/m9.figshare.6817658.v1
title: Additional file 1 of An integrative network-based approach to identify novel disease genes and pathways: a case study in the context of inflammatory bowel disease

description: List of predicted IBD genes. (XLSX 26 kb)
DOI: 10.6084/m9.figshare.6817652
title: Additional file 1: of Arabidopsis thaliana ambient temperature responsive lncRNAs

description: TableS1. LncRNAs annotation. List of lncRNAs retrieved in this study and corresponding identification in the Plant long non-coding RNA database (PlncDB) and Araport11. (XLSX 422Â kb)
DOI: 10.6084/m9.figshare.6817649
title: Additional file 1: of Refining a steroidogenic model: an analysis of RNA-seq datasets from insect prothoracic glands

description: Table S1. Tabulation of 61,260 tests carried out by Cufflinks on the raw transcriptomic data. In cases where a gene model was included between the examined locus, this is indicated using the nomenclature of KAIKObase ( http://sgp.dna.affrc.go.jp/KAIKObase/ ) or it is left empty. Using this criterion, we identified 10,775 unmapped loci. (XLSX 5956 kb)
DOI: 10.6084/m9.figshare.6817652.v1
title: Additional file 1: of Arabidopsis thaliana ambient temperature responsive lncRNAs

description: TableS1. LncRNAs annotation. List of lncRNAs retrieved in this study and corresponding identification in the Plant long non-coding RNA database (PlncDB) and Araport11. (XLSX 422Â kb)
DOI: 10.6084/m9.figshare.6817649.v1
title: Additional file 1: of Refining a steroidogenic model: an analysis of RNA-seq datasets from insect prothoracic glands

description: Table S1. Tabulation of 61,260 tests carried out by Cufflinks on the raw transcriptomic data. In cases where a gene model was included between the examined locus, this is indicated using the nomenclature of KAIKObase ( http://sgp.dna.affrc.go.jp/KAIKObase/ ) or it is left empty. Using this criterion, we identified 10,775 unmapped loci. (XLSX 5956 kb)
DOI: 10.6084/m9.figshare.6817643
title: Additional file 8: of Expression profile analysis reveals that Aspergillus fumigatus but not Aspergillus niger makes type II epithelial lung cells less immunological alert

description: Table S5. Conidia associated genes (CAGs) and germination associated genes (GeAGs) found in A. fumigatus and A. niger after 12Â h of co-cultivation with A549 cells. Electronic format. (XLS 83 kb)
DOI: 10.6084/m9.figshare.6817643.v1
title: Additional file 8: of Expression profile analysis reveals that Aspergillus fumigatus but not Aspergillus niger makes type II epithelial lung cells less immunological alert

description: Table S5. Conidia associated genes (CAGs) and germination associated genes (GeAGs) found in A. fumigatus and A. niger after 12Â h of co-cultivation with A549 cells. Electronic format. (XLS 83 kb)
DOI: 10.6084/m9.figshare.6817622
title: Additional file 6: of Expression profile analysis reveals that Aspergillus fumigatus but not Aspergillus niger makes type II epithelial lung cells less immunological alert

description: Table S4. Differentially gene expression and enriched GO terms of A549 cells after 12Â h of co-cultivation with A. niger. Electronic format. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.6817622.v1
title: Additional file 6: of Expression profile analysis reveals that Aspergillus fumigatus but not Aspergillus niger makes type II epithelial lung cells less immunological alert

description: Table S4. Differentially gene expression and enriched GO terms of A549 cells after 12Â h of co-cultivation with A. niger. Electronic format. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.6817610
title: Additional file 5: of Expression profile analysis reveals that Aspergillus fumigatus but not Aspergillus niger makes type II epithelial lung cells less immunological alert

description: Table S3. Differentially gene expression and enriched GO terms of A549 cells after 12Â h of co-cultivation with A. fumigatus. Electronic format. (XLSX 29 kb)
DOI: 10.6084/m9.figshare.6817610.v1
title: Additional file 5: of Expression profile analysis reveals that Aspergillus fumigatus but not Aspergillus niger makes type II epithelial lung cells less immunological alert

description: Table S3. Differentially gene expression and enriched GO terms of A549 cells after 12Â h of co-cultivation with A. fumigatus. Electronic format. (XLSX 29 kb)
DOI: 10.6084/m9.figshare.6817601
title: MOESM2 of A novel LCâ MS method using collagen marker peptides for species identification of glue applicable to samples with multiple animal origins

description: Additional file 2: Table S2. Detection patterns of marker peptides for glue samples with two different animal origins.
DOI: 10.6084/m9.figshare.6817601.v1
title: MOESM2 of A novel LCâ MS method using collagen marker peptides for species identification of glue applicable to samples with multiple animal origins

description: Additional file 2: Table S2. Detection patterns of marker peptides for glue samples with two different animal origins.
DOI: 10.6084/m9.figshare.6817595
title: Additional file 2: of Transcriptomic analyses of rice (Oryza sativa) genes and non-coding RNAs under nitrogen starvation using multiple omics technologies

description: Table S1. Read statistics of the four types of transcriptome data used in this study. Table S2. List of genes involved in nitrogen source uptake, assimilation and transport and their expression level in rice. Table S3. List of amino acid/peptide transporter genes and their expression level in rice. Table S4. Pipeline for identification of putative long non-coding RNAs in rice. Table S5. List of putative long non-coding RNAs identified in this study and their expression level in rice. Table S6. List of miRNAs analyzed in this study and their expression level in rice. Table S7. List of microRNA-targeted genes identified by Degradome-Seq. Table S8. Oligonucleotide sequences used in this study. (XLSX 1030Â kb)
DOI: 10.6084/m9.figshare.6817595.v1
title: Additional file 2: of Transcriptomic analyses of rice (Oryza sativa) genes and non-coding RNAs under nitrogen starvation using multiple omics technologies

description: Table S1. Read statistics of the four types of transcriptome data used in this study. Table S2. List of genes involved in nitrogen source uptake, assimilation and transport and their expression level in rice. Table S3. List of amino acid/peptide transporter genes and their expression level in rice. Table S4. Pipeline for identification of putative long non-coding RNAs in rice. Table S5. List of putative long non-coding RNAs identified in this study and their expression level in rice. Table S6. List of miRNAs analyzed in this study and their expression level in rice. Table S7. List of microRNA-targeted genes identified by Degradome-Seq. Table S8. Oligonucleotide sequences used in this study. (XLSX 1030Â kb)
DOI: 10.6084/m9.figshare.6817583
title: MOESM1 of A novel LCâ MS method using collagen marker peptides for species identification of glue applicable to samples with multiple animal origins

description: Additional file 1: Table S1. MRM transitions of marker peptides.