cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.26992933
title: Additional file 15 of The genome and transcriptome of the snail Biomphalaria sudanica s.l.: immune gene diversification and highly polymorphic genomic regions in an important African vector of Schistosoma mansoni

description: Additional file 15: Supplementary Table 14. Summary table of Biomphalaria sudanica C-type lectin-related proteins (CREP) and Fibrinogen-related proteins (FREP) annotated, providing protein ID, CREP/FREP subfamily, protein length, signal peptide, immunoglobulin domain (IgSF) and the c-lectin domain (CREP) or fibrinogen (FBD) domain (FREP)  positions, notes on each genes features and protein sequence. Coordinates given in the notes column specify the overlap of any remarkable features with domains C-lectin, FBD or IgSF.
DOI: 10.6084/m9.figshare.26992933.v1
title: Additional file 15 of The genome and transcriptome of the snail Biomphalaria sudanica s.l.: immune gene diversification and highly polymorphic genomic regions in an important African vector of Schistosoma mansoni

description: Additional file 15: Supplementary Table 14. Summary table of Biomphalaria sudanica C-type lectin-related proteins (CREP) and Fibrinogen-related proteins (FREP) annotated, providing protein ID, CREP/FREP subfamily, protein length, signal peptide, immunoglobulin domain (IgSF) and the c-lectin domain (CREP) or fibrinogen (FBD) domain (FREP)  positions, notes on each genes features and protein sequence. Coordinates given in the notes column specify the overlap of any remarkable features with domains C-lectin, FBD or IgSF.
DOI: 10.6084/m9.figshare.26992939.v1
title: Additional file 17 of The genome and transcriptome of the snail Biomphalaria sudanica s.l.: immune gene diversification and highly polymorphic genomic regions in an important African vector of Schistosoma mansoni

description: Additional file 17: Supplementary Table 16. Total number of genes included on each of the Fibrinogen-related protein (FREP) and C-type lectin-related protein (CREP) Phylogenetically Hierarchical Orthogroups (HOGs) across the analyzed Biomphalaria speciesgenomes and outgroups (B. glabrata strain BB02 (GCF_000457365.2 [5]), B. glabrata strain iBS90 (GCA_025434165.1 [6]), B. glabrata strain iM (GCA_025434175.1 [6]), and the species B. pfeifferi (GCA_030265305.1 [8]), B. straminea (GCA_021533235.1 [7]), Bulinus truncatus (GCA_021962125.1 [127]) and Elysia marginata (GCA_019649035.1 [128])). For B. sudanica, we specify both the raw counts (i.e. ‘Raw’, all the members of the HOG) and how many of these were selected for the phylogenetic analysis (i.e. ‘Selected’).
DOI: 10.6084/m9.figshare.26992936
title: Additional file 16 of The genome and transcriptome of the snail Biomphalaria sudanica s.l.: immune gene diversification and highly polymorphic genomic regions in an important African vector of Schistosoma mansoni

description: Additional file 16: Supplementary Table 15. Reference sequences of Fibrinogen-related protein (FREP) and C-type lectin-related protein (CREP) included in the phylogenetic analysis for both these protein families. Table details the sequence ID, source (reference), identifier provided within the family, length in amino acids and sequence. Sequences marked with an X at the end of their Sequence ID were used with the modifications detailed in Lu et al. (2020), rather than the original genome.
DOI: 10.6084/m9.figshare.26992936.v1
title: Additional file 16 of The genome and transcriptome of the snail Biomphalaria sudanica s.l.: immune gene diversification and highly polymorphic genomic regions in an important African vector of Schistosoma mansoni

description: Additional file 16: Supplementary Table 15. Reference sequences of Fibrinogen-related protein (FREP) and C-type lectin-related protein (CREP) included in the phylogenetic analysis for both these protein families. Table details the sequence ID, source (reference), identifier provided within the family, length in amino acids and sequence. Sequences marked with an X at the end of their Sequence ID were used with the modifications detailed in Lu et al. (2020), rather than the original genome.
DOI: 10.6084/m9.figshare.26992939
title: Additional file 17 of The genome and transcriptome of the snail Biomphalaria sudanica s.l.: immune gene diversification and highly polymorphic genomic regions in an important African vector of Schistosoma mansoni

description: Additional file 17: Supplementary Table 16. Total number of genes included on each of the Fibrinogen-related protein (FREP) and C-type lectin-related protein (CREP) Phylogenetically Hierarchical Orthogroups (HOGs) across the analyzed Biomphalaria speciesgenomes and outgroups (B. glabrata strain BB02 (GCF_000457365.2 [5]), B. glabrata strain iBS90 (GCA_025434165.1 [6]), B. glabrata strain iM (GCA_025434175.1 [6]), and the species B. pfeifferi (GCA_030265305.1 [8]), B. straminea (GCA_021533235.1 [7]), Bulinus truncatus (GCA_021962125.1 [127]) and Elysia marginata (GCA_019649035.1 [128])). For B. sudanica, we specify both the raw counts (i.e. ‘Raw’, all the members of the HOG) and how many of these were selected for the phylogenetic analysis (i.e. ‘Selected’).
DOI: 10.6084/m9.figshare.26992942
title: Additional file 18 of The genome and transcriptome of the snail Biomphalaria sudanica s.l.: immune gene diversification and highly polymorphic genomic regions in an important African vector of Schistosoma mansoni

description: Additional file 18: Supplementary Table 17. List of 1047 genes that were present in the most diverse regions of the Biomphalaria sudanica genome, providing information on genomic position, BLASTp hits, InterPro v5.56-89.0 [52] and Pfam v35 [114] domains and inferred protein function categorized into immune groups (as detailed in Methods).
DOI: 10.6084/m9.figshare.26992942.v1
title: Additional file 18 of The genome and transcriptome of the snail Biomphalaria sudanica s.l.: immune gene diversification and highly polymorphic genomic regions in an important African vector of Schistosoma mansoni

description: Additional file 18: Supplementary Table 17. List of 1047 genes that were present in the most diverse regions of the Biomphalaria sudanica genome, providing information on genomic position, BLASTp hits, InterPro v5.56-89.0 [52] and Pfam v35 [114] domains and inferred protein function categorized into immune groups (as detailed in Methods).
DOI: 10.6084/m9.figshare.26992945
title: Additional file 19 of The genome and transcriptome of the snail Biomphalaria sudanica s.l.: immune gene diversification and highly polymorphic genomic regions in an important African vector of Schistosoma mansoni

description: Additional file 19: Supplementary Table 18. Results of Biomphalaria sudanica gene family expansion and contraction analysis performed using topGO v2.48.0 [73] in R v4.3.1 [139] with the Weight01 algorithm, node size=10 and statistical test of Fisher (significant p-value ≤ 0.05). The test was performed by comparing the B. sudanica whole genome gene family composition to three separate lists (column=List) of the highly diverse genes identified; 1) ‘All’ 1047 highly diverse genes identified in the B. sudanica genome (as listed Supplementary Table 17), 2) ‘Group-2’ 245 genes classified as immune suspected genes from the highly diverse genes (group 2, Supplementary Table 17), and 3) ‘Group-2-3-4’ 247 genes shortlisted as the protein containing a transmembrane domain (TMD) and categorized in Immune Group 2, 3 (potential role in innate immunity) or 4 (an unknown function but contained TMD(s)) (Supplementary Table 17). Each group contains three tabs, showing gene family expansions and contractions in each set of genes in respects to their Molecular Function (MF), Cellular Component (CC) and Biological Process (BP).
DOI: 10.6084/m9.figshare.26992945.v1
title: Additional file 19 of The genome and transcriptome of the snail Biomphalaria sudanica s.l.: immune gene diversification and highly polymorphic genomic regions in an important African vector of Schistosoma mansoni

description: Additional file 19: Supplementary Table 18. Results of Biomphalaria sudanica gene family expansion and contraction analysis performed using topGO v2.48.0 [73] in R v4.3.1 [139] with the Weight01 algorithm, node size=10 and statistical test of Fisher (significant p-value ≤ 0.05). The test was performed by comparing the B. sudanica whole genome gene family composition to three separate lists (column=List) of the highly diverse genes identified; 1) ‘All’ 1047 highly diverse genes identified in the B. sudanica genome (as listed Supplementary Table 17), 2) ‘Group-2’ 245 genes classified as immune suspected genes from the highly diverse genes (group 2, Supplementary Table 17), and 3) ‘Group-2-3-4’ 247 genes shortlisted as the protein containing a transmembrane domain (TMD) and categorized in Immune Group 2, 3 (potential role in innate immunity) or 4 (an unknown function but contained TMD(s)) (Supplementary Table 17). Each group contains three tabs, showing gene family expansions and contractions in each set of genes in respects to their Molecular Function (MF), Cellular Component (CC) and Biological Process (BP).
DOI: 10.6084/m9.figshare.26992948
title: Additional file 20 of The genome and transcriptome of the snail Biomphalaria sudanica s.l.: immune gene diversification and highly polymorphic genomic regions in an important African vector of Schistosoma mansoni

description: Additional file 20: Supplementary Table 19. Pfam v35 [114] matches for function domains the 1047 most diverse genes identified in the Biomphalaria sudanica genome.
DOI: 10.6084/m9.figshare.26992948.v1
title: Additional file 20 of The genome and transcriptome of the snail Biomphalaria sudanica s.l.: immune gene diversification and highly polymorphic genomic regions in an important African vector of Schistosoma mansoni

description: Additional file 20: Supplementary Table 19. Pfam v35 [114] matches for function domains the 1047 most diverse genes identified in the Biomphalaria sudanica genome.
DOI: 10.6084/m9.figshare.26992951.v1
title: Additional file 21 of The genome and transcriptome of the snail Biomphalaria sudanica s.l.: immune gene diversification and highly polymorphic genomic regions in an important African vector of Schistosoma mansoni

description: Additional file 21: Supplementary Table 20. UniProt (uniport.org/ database as of May 25th 2022) matches for the 1047 most diverse genes identified in the Biomphalaria sudanica genome.
DOI: 10.6084/m9.figshare.26992957
title: Additional file 23 of The genome and transcriptome of the snail Biomphalaria sudanica s.l.: immune gene diversification and highly polymorphic genomic regions in an important African vector of Schistosoma mansoni

description: Additional file 23: Supplementary File 1. Complete functional annotation of Biomphalaria sudanica, including 23,598 genes assigned to have an open reading frame (ORF) and therefore predicted protein by TransDecoder.Predict v5.5.0 using the Trinity platform [51], the 2,248 raw RNA genes without predicted proteins predicted by StringTie2 v2.2.1 [50], 919 tRNA’s predicted in tRNAscan-SE 2.0 v2.0.9 [124], and 107 rRNA’s predicted in Barrnap v0.9 (github.com/tseemann/barrnap).
DOI: 10.6084/m9.figshare.26992957.v1
title: Additional file 23 of The genome and transcriptome of the snail Biomphalaria sudanica s.l.: immune gene diversification and highly polymorphic genomic regions in an important African vector of Schistosoma mansoni

description: Additional file 23: Supplementary File 1. Complete functional annotation of Biomphalaria sudanica, including 23,598 genes assigned to have an open reading frame (ORF) and therefore predicted protein by TransDecoder.Predict v5.5.0 using the Trinity platform [51], the 2,248 raw RNA genes without predicted proteins predicted by StringTie2 v2.2.1 [50], 919 tRNA’s predicted in tRNAscan-SE 2.0 v2.0.9 [124], and 107 rRNA’s predicted in Barrnap v0.9 (github.com/tseemann/barrnap).
DOI: 10.6084/m9.figshare.26992960
title: Additional file 24 of The genome and transcriptome of the snail Biomphalaria sudanica s.l.: immune gene diversification and highly polymorphic genomic regions in an important African vector of Schistosoma mansoni

description: Additional file 24: Supplementary File 2. Summary table of the 23,598 genes assigned to have an open reading frame (ORF) giving ORF type, length (amino acid) and prediction score from TransDecoder.Predict v5.5.0 using the Trinity platform [51].
DOI: 10.6084/m9.figshare.26992960.v1
title: Additional file 24 of The genome and transcriptome of the snail Biomphalaria sudanica s.l.: immune gene diversification and highly polymorphic genomic regions in an important African vector of Schistosoma mansoni

description: Additional file 24: Supplementary File 2. Summary table of the 23,598 genes assigned to have an open reading frame (ORF) giving ORF type, length (amino acid) and prediction score from TransDecoder.Predict v5.5.0 using the Trinity platform [51].
DOI: 10.6084/m9.figshare.26992963
title: Additional file 25 of The genome and transcriptome of the snail Biomphalaria sudanica s.l.: immune gene diversification and highly polymorphic genomic regions in an important African vector of Schistosoma mansoni

description: Additional file 25: Supplementary File 3. Summary InterProScan v5.56-89.0 [52] results for the predicted proteins. It includes the specific analysis, the signature accession and description identified, the start and stop location of the signature, its score, and associated InterPro Accession information.
DOI: 10.6084/m9.figshare.26992966
title: Additional file 26 of The genome and transcriptome of the snail Biomphalaria sudanica s.l.: immune gene diversification and highly polymorphic genomic regions in an important African vector of Schistosoma mansoni

description: Additional file 26: Supplementary File 4. Location of transmembrane domains identified on 4,922 genes (8,728 isoforms) determined through DeepTMHMM v1.0.13 [131].
DOI: 10.6084/m9.figshare.26992963.v1
title: Additional file 25 of The genome and transcriptome of the snail Biomphalaria sudanica s.l.: immune gene diversification and highly polymorphic genomic regions in an important African vector of Schistosoma mansoni

description: Additional file 25: Supplementary File 3. Summary InterProScan v5.56-89.0 [52] results for the predicted proteins. It includes the specific analysis, the signature accession and description identified, the start and stop location of the signature, its score, and associated InterPro Accession information.
DOI: 10.6084/m9.figshare.26992975
title: Additional file 29 of The genome and transcriptome of the snail Biomphalaria sudanica s.l.: immune gene diversification and highly polymorphic genomic regions in an important African vector of Schistosoma mansoni

description: Additional file 29: Supplementary File 7. Amino acid sequences of the 1047 shortlisted most diverse genes in the Biomphalaria sudanica genome, used for searches for novel pathogen recognition receptors.
DOI: 10.34740/kaggle/dsv/9367715
title: Full TMDB Movies Dataset 2024 (1M Movies)
DOI: 10.6084/m9.figshare.26992966.v1
title: Additional file 26 of The genome and transcriptome of the snail Biomphalaria sudanica s.l.: immune gene diversification and highly polymorphic genomic regions in an important African vector of Schistosoma mansoni

description: Additional file 26: Supplementary File 4. Location of transmembrane domains identified on 4,922 genes (8,728 isoforms) determined through DeepTMHMM v1.0.13 [131].
DOI: 10.6084/m9.figshare.26992828.v1
title: Additional file 1 of Exploring the role of ubiquitin regulatory X domain family proteins in cancers: bioinformatics insights, mechanisms, and implications for therapy

description: Additional file 1: Figure S1. Gene alteration in UBXDF in cancers. A UBXDF gene alterations in TCGA. B The OncoPrint with mutation spectrum and UBXDF gene alteration. Figure S2. A expression profile of cancer-noncancer tissues using TCGA individual cancer types data (noncancer tissue sample size &gt; =5). B Co-expression analysis between every two genes is presented. (Blue points indicate positive correlation, while red points indicate negative correlation.) C K-M curve of overall survival across cancer types and UBXDF members, p &lt;0.05. D Forest map shows the univariate cox regression results of UBXDF for OS. E UBXDF members protein expression in normal tissues. F UBXDF members protein expression in tumour tissues. Figure S3. Correlation analysis between UBXD–F expression and TME. A–D The association between UBXD–F expression and stromal score, tumour purity, ESTIMATE score and immune score in 33 TCGA cancer types. (Red points indicate positive correlation, while blue points indicate negative correlation). Table S1. Abbreviations and full names of nouns in the text. Table S2. A logFC & p value of the heatmap exhibiting the transcriptional level of the UBXDF in TCGA tumour types compared to adjacent normal tissues. B Co-expression network of UBXDF. C COX analysis between UBXDF and OS. D–G Correlation coefficient & p value of DNAss or RNAss matrix. H Correlation coefficient of CTRL and UBXDF. I Correlation coefficient of GDSC and UBXDF. Table S3. A Estimatescore for TCGA tumour samples.
DOI: 10.6084/m9.figshare.26992975.v1
title: Additional file 29 of The genome and transcriptome of the snail Biomphalaria sudanica s.l.: immune gene diversification and highly polymorphic genomic regions in an important African vector of Schistosoma mansoni

description: Additional file 29: Supplementary File 7. Amino acid sequences of the 1047 shortlisted most diverse genes in the Biomphalaria sudanica genome, used for searches for novel pathogen recognition receptors.
DOI: 10.6084/m9.figshare.26992996
title: Additional file 2 of The dynamic landscape of chromatin accessibility and active regulatory elements in the mediobasal hypothalamus influences the seasonal activation of the reproductive axis in the male quail under long light exposure

description: Additional file 2: Table S1. The library information of ATAC-seq. Table S2. The library information of transcriptome sequencing. Table S3. The library information of DAP-seq. Table S4. Transcription factor enrichment analysis results at the genome-wide level at SD28. Table S5. Transcription factor enrichment analysis results at the genome-wide level at LD3. Table S6. Transcription factor enrichment analysis results at the genome-wide level at LD7. Table S7. Transcription factor enrichment analysis results at the genome-wide level at LD28. Table S8. Differential analysis of chromatin regions and region annotations in all the comparison. Table S9. The unique DEGs in the SD28 vs LD7 comparison. Table S10. The unique DEGs in the SD28 vs LD28 comparison. Table S11. The Common DEGs between two comparison SD28 vs LD7 and SD28 vs LD28. Table S12. Detection of an overlapping gene in the atacUP_rnaUP region through combined analysis of ATAC-seq and RNA-seq at LD7. Table S13. Detection of an overlapping gene in the atacUP_rnaUP region through combined analysis of ATAC-seq and RNA-seq at LD28.
DOI: 10.5281/zenodo.12812074
title: Mycelium bioelectric native and light stimulated signal and robot control codes

description: The dataset and code include recordings of electrical signals from fungi, as well as those signals combined with light stimulation. Additionally, we have provided the code and dataset developed for signal analysis, along with the complete code that details how we controlled the robot using mycelium-directed signals in real-time.
DOI: 10.5281/zenodo.12810869
title: Mycelium bioelectric native and light stimulated signal and robot control codes

description: The dataset and code include recordings of electrical signals from fungi, as well as those signals combined with light stimulation. Additionally, we have provided the code and dataset developed for signal analysis, along with the complete code that details how we controlled the robot using mycelium-directed signals in real-time.
DOI: 10.5281/zenodo.12810870
title: Mycelium bioelectric native and light stimulated signal and robot control codes

description: The dataset and code include recordings of electrical signals from fungi, as well as those signals combined with light stimulation. Additionally, we have provided the code and dataset developed for signal analysis, along with the complete code that details how we controlled the robot using mycelium-directed signals in real-time.
DOI: 10.6084/m9.figshare.26992843.v1
title: Additional file 2 of Distinct regulatory networks control toxin gene expression in elapid and viperid snakes

description: Supplementary Material 2
DOI: 10.6084/m9.figshare.26992846.v1
title: Additional file 3 of Distinct regulatory networks control toxin gene expression in elapid and viperid snakes

description: Supplementary Material 3
DOI: 10.6084/m9.figshare.26992951
title: Additional file 21 of The genome and transcriptome of the snail Biomphalaria sudanica s.l.: immune gene diversification and highly polymorphic genomic regions in an important African vector of Schistosoma mansoni

description: Additional file 21: Supplementary Table 20. UniProt (uniport.org/ database as of May 25th 2022) matches for the 1047 most diverse genes identified in the Biomphalaria sudanica genome.
DOI: 10.6084/m9.figshare.26992996.v1
title: Additional file 2 of The dynamic landscape of chromatin accessibility and active regulatory elements in the mediobasal hypothalamus influences the seasonal activation of the reproductive axis in the male quail under long light exposure

description: Additional file 2: Table S1. The library information of ATAC-seq. Table S2. The library information of transcriptome sequencing. Table S3. The library information of DAP-seq. Table S4. Transcription factor enrichment analysis results at the genome-wide level at SD28. Table S5. Transcription factor enrichment analysis results at the genome-wide level at LD3. Table S6. Transcription factor enrichment analysis results at the genome-wide level at LD7. Table S7. Transcription factor enrichment analysis results at the genome-wide level at LD28. Table S8. Differential analysis of chromatin regions and region annotations in all the comparison. Table S9. The unique DEGs in the SD28 vs LD7 comparison. Table S10. The unique DEGs in the SD28 vs LD28 comparison. Table S11. The Common DEGs between two comparison SD28 vs LD7 and SD28 vs LD28. Table S12. Detection of an overlapping gene in the atacUP_rnaUP region through combined analysis of ATAC-seq and RNA-seq at LD7. Table S13. Detection of an overlapping gene in the atacUP_rnaUP region through combined analysis of ATAC-seq and RNA-seq at LD28.
DOI: 10.6084/m9.figshare.26992894
title: Additional file 2 of The genome and transcriptome of the snail Biomphalaria sudanica s.l.: immune gene diversification and highly polymorphic genomic regions in an important African vector of Schistosoma mansoni

description: Additional file 2: Supplementary Table 1. Summary metrics and NCBI identifiers for the generated genome (PacBio long-read) and transcriptome (PacBio long-read and Illumina short-read) sequences, and the complete annotation statistics. ^ tRNA pseudogenes are fragments of genes that were identified and not used for annotation. * Genes models that were predicted by but Stringtie no valid ORF was identified by Transdecoder and therefore not used in the annotation.