cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12542105.v1
title: african_map_draw.xlsx

description: Mapping African FDI, growth, conflict
DOI: 10.6084/m9.figshare.12541754
title: DATEM Data share.xlsx

description: The influence of Diacetyl tartaric acid ester of monoglycerides (DATEM) on the properties of oil-in-water emulsions prepared by whey powder (WP) and maltodextrin (MD) was studied. Data contains droplets size, zeta potential, surface tension, viscosity, morphology and FT-IR analysis of emulsions.
DOI: 10.6084/m9.figshare.12542033.v1
title: Africa.xlsx

description: data set for the African FDI information
DOI: 10.6084/m9.figshare.12541754.v1
title: DATEM Data share.xlsx

description: The influence of Diacetyl tartaric acid ester of monoglycerides (DATEM) on the properties of oil-in-water emulsions prepared by whey powder (WP) and maltodextrin (MD) was studied. Data contains droplets size, zeta potential, surface tension, viscosity, morphology and FT-IR analysis of emulsions.
DOI: 10.6084/m9.figshare.12536627
title: Sample list

description: All samples list in LncAS2Cancer
DOI: 10.6084/m9.figshare.12536660
title: JVASP-28218 to JVASP-29112

description: JARVIS-DFT input/output files
DOI: 10.6084/m9.figshare.12536576
title: LncRNA annotation

description: LncRNA annotation
DOI: 10.6084/m9.figshare.12536627.v1
title: Sample list

description: All samples list in LncAS2Cancer
DOI: 10.6084/m9.figshare.12536573
title: POLLEN73S

description: The POLLEN73S is an annotated image dataset for the Brazilian Savannah pollen types, which consists of 2523 pollen grain images taken at different angles and distributed in 73 pollen types. The pollen grain examples were obtained from samples flowering species collected in the Brazilian Savannah, more precisely within a radius of 1.5 km from 20°23'16.8"S 54°36'36.3"W coordinates in Campo Grande City urban area, capital of Mato Grosso do Sul State in Brazil.
DOI: 10.6084/m9.figshare.12536444
title: Score file

description: The Reliable scores of splicing events in LncAS2Cancer
DOI: 10.6084/m9.figshare.12536444.v1
title: Score file

description: The Reliable scores of splicing events in LncAS2Cancer
DOI: 10.6084/m9.figshare.12535202
title: Syn-gtotree-example-tree-file

description: Syn-gtotree-example-tree-file
DOI: 10.6084/m9.figshare.12535250
title: Syn-gtotree-example-outputs

description: Syn-gtotree-example-outputs<br>Goes with page here: https://astrobiomike.github.io/genomics/phylogenomics
DOI: 10.6084/m9.figshare.12535202.v1
title: Syn-gtotree-example-tree-file

description: Syn-gtotree-example-tree-file
DOI: 10.6084/m9.figshare.12534842
title: gencode_fantom_intersect

description: The splicing event is recognized by both GENCODE and FANTOM
DOI: 10.6084/m9.figshare.12534458
title: miRNA-seq data Lean-EVs and MetS-EVs

description: miRNA-seq data Lean-EVs and MetS-EVs
DOI: 10.6084/m9.figshare.12534842.v1
title: gencode_fantom_intersect

description: The splicing event is recognized by both GENCODE and FANTOM
DOI: 10.6084/m9.figshare.12535250.v1
title: Syn-gtotree-example-iToL-cols-file

description: Syn-gtotree-example-iToL-cols-file
DOI: 10.6084/m9.figshare.12534065
title: Clean data of 3v3 circRNA seq (PBMCs of IgAN patients) part 2

description: The clean data of peripheral blood mononuclear cells' circRNA seq of 3 IgA nephropathy patients vs 3 healthy controls.Part 2 of 3 parts.
DOI: 10.6084/m9.figshare.12534065.v1
title: Clean data of 3v3 circRNA seq (PBMCs of IgAN patients) part 2

description: The clean data of peripheral blood mononuclear cells' circRNA seq of 3 IgA nephropathy patients vs 3 healthy controls.Part 2 of 3 parts.
DOI: 10.6084/m9.figshare.12535250.v3
title: Syn-gtotree-example-outputs

description: Syn-gtotree-example-outputs<br>Goes with page here: https://astrobiomike.github.io/genomics/phylogenomics
DOI: 10.6084/m9.figshare.12533999
title: LMIC Model

description: Aggregated LMIC Model<br>
DOI: 10.6084/m9.figshare.12535250.v2
title: Syn-gtotree-example-iToL-cols-file

description: Syn-gtotree-example-iToL-cols-file
DOI: 10.6084/m9.figshare.12533915
title: WHO ESFT

description: WHO EFST Model<br>
DOI: 10.6084/m9.figshare.12533513
title: Supplementary Material for: Sequence Evolution, Abundance, and Chromosomal Distribution of Ty1-copia Retrotransposons in the Saccharum spontaneum Genome

description: <i>Saccharum spontaneum</i> is a wild germplasm resource of the genus <i>Saccharum</i> that has many valuable traits. Ty1-copia retrotransposons constitute a large proportion of plant genomes and affect genome sequence organization and evolution. This study aims to analyze the sequence heterogeneity, phylogenetic diversity, copy number, and chromosomal dispersion patterns of Ty1-copia retrotransposons in <i>S. spontaneum</i>. A total of 44 Ty1-copia reverse transcriptase subclones isolated from <i>S. spontaneum</i> showed a range of heterogeneity, and all sequences were A-T rich, averaging approximately 54.59%. Phylogenetic analysis divided the 44 reverse transcriptase sequences into 5 distinct lineages (Retrofit/Ale, Sire/Maximus, Bianca, Tork/TAR, and Ty1-copia like). Dot-blot hybridization revealed that Ty1-copia retrotransposons consisted of a significant component of approximately 38,900 copies and 16,300 copies per genome in the accessions YN82-114 (2n = 10x = 80) and AP85-441 (2n = 4x = 32), respectively. The results of a local blast analysis showed that there are 15,069 Ty1-copia retrotransposon copies in the genome of AP85-441, of which the Retrofit/Ale lineage had the highest copy number, followed by the Tork/TAR, Sire/Maximus, and Bianca lineages. Furthermore, both FISH and the local blast analysis with AP85-441 genomic data demonstrated that the Ty1-copia retrotransposons were unevenly distributed throughout the chromosomes. Taken together, this study provides insights into the role of Ty1-copia retrotransposons in the evolution and organization of the <i>S. spontaneum</i> genome.
DOI: 10.6084/m9.figshare.12533915.v1
title: WHO ESFT

description: WHO EFST Model<br>
DOI: 10.6084/m9.figshare.12533999.v1
title: LMIC Model

description: Aggregated LMIC Model<br>
DOI: 10.6084/m9.figshare.12533513.v1
title: Supplementary Material for: Sequence Evolution, Abundance, and Chromosomal Distribution of Ty1-copia Retrotransposons in the Saccharum spontaneum Genome

description: <i>Saccharum spontaneum</i> is a wild germplasm resource of the genus <i>Saccharum</i> that has many valuable traits. Ty1-copia retrotransposons constitute a large proportion of plant genomes and affect genome sequence organization and evolution. This study aims to analyze the sequence heterogeneity, phylogenetic diversity, copy number, and chromosomal dispersion patterns of Ty1-copia retrotransposons in <i>S. spontaneum</i>. A total of 44 Ty1-copia reverse transcriptase subclones isolated from <i>S. spontaneum</i> showed a range of heterogeneity, and all sequences were A-T rich, averaging approximately 54.59%. Phylogenetic analysis divided the 44 reverse transcriptase sequences into 5 distinct lineages (Retrofit/Ale, Sire/Maximus, Bianca, Tork/TAR, and Ty1-copia like). Dot-blot hybridization revealed that Ty1-copia retrotransposons consisted of a significant component of approximately 38,900 copies and 16,300 copies per genome in the accessions YN82-114 (2n = 10x = 80) and AP85-441 (2n = 4x = 32), respectively. The results of a local blast analysis showed that there are 15,069 Ty1-copia retrotransposon copies in the genome of AP85-441, of which the Retrofit/Ale lineage had the highest copy number, followed by the Tork/TAR, Sire/Maximus, and Bianca lineages. Furthermore, both FISH and the local blast analysis with AP85-441 genomic data demonstrated that the Ty1-copia retrotransposons were unevenly distributed throughout the chromosomes. Taken together, this study provides insights into the role of Ty1-copia retrotransposons in the evolution and organization of the <i>S. spontaneum</i> genome.
DOI: 10.6084/m9.figshare.12533309
title: Supplementary Material for: A Novel de novo Frameshift Mutation in the BCL11A Gene in a Patient with Intellectual Disability Syndrome and Epilepsy

description: Intellectual disability syndrome (IDS) associated with a hereditary persistence of fetal haemoglobin (HbF), also known as Dias-Logan syndrome, is commonly characterised by psychomotor developmental delay, intelectual disability, language delay, strabismus, thin upper lip, abnormalities of external ears, microcephaly, downslanting palpebral fissures. Sporadically, autism spectrum disorders and blue sclerae in infancy have been reported in IDS. Rarely, IDS-affected patients present with epilepsy and/or epileptic syndromes. It has been shown that a haploinsufficiency of the B cell leukaemia/lymphoma 11A gene (<i>BCL11A</i>) is responsible for IDS. Herein, we identified a novel de novo frameshift deletion (c.271delG; p.E91Afs*2) in the <i>BCL11A</i> gene in a boy affected with IDS. Interestingly, this heterozygous loss-of-function <i>BCL11A</i> mutation was also associated with a generalised idiopathic epilepsy and severe language delay observed in the patient. Moreover, our study showed that the combination of molecular genetic analyses with the monitoring of HbF was essential to make the final diagnosis of Dias-Logan syndrome. Because our patient suffered from well-controlled epilepsy, we propose to include the <i>BCL11A</i> gene in routinely used molecular genetic epilepsy-related gene panels. Additionally, many of the clinical features of IDS overlap with symptoms observed in patients with suspected alcohol spectrum disorders. Therefore, we also suggest monitoring HbF levels in patients with these syndromes to further facilitate clinical diagnosis.
DOI: 10.6084/m9.figshare.12533309.v1
title: Supplementary Material for: A Novel de novo Frameshift Mutation in the BCL11A Gene in a Patient with Intellectual Disability Syndrome and Epilepsy

description: Intellectual disability syndrome (IDS) associated with a hereditary persistence of fetal haemoglobin (HbF), also known as Dias-Logan syndrome, is commonly characterised by psychomotor developmental delay, intelectual disability, language delay, strabismus, thin upper lip, abnormalities of external ears, microcephaly, downslanting palpebral fissures. Sporadically, autism spectrum disorders and blue sclerae in infancy have been reported in IDS. Rarely, IDS-affected patients present with epilepsy and/or epileptic syndromes. It has been shown that a haploinsufficiency of the B cell leukaemia/lymphoma 11A gene (<i>BCL11A</i>) is responsible for IDS. Herein, we identified a novel de novo frameshift deletion (c.271delG; p.E91Afs*2) in the <i>BCL11A</i> gene in a boy affected with IDS. Interestingly, this heterozygous loss-of-function <i>BCL11A</i> mutation was also associated with a generalised idiopathic epilepsy and severe language delay observed in the patient. Moreover, our study showed that the combination of molecular genetic analyses with the monitoring of HbF was essential to make the final diagnosis of Dias-Logan syndrome. Because our patient suffered from well-controlled epilepsy, we propose to include the <i>BCL11A</i> gene in routinely used molecular genetic epilepsy-related gene panels. Additionally, many of the clinical features of IDS overlap with symptoms observed in patients with suspected alcohol spectrum disorders. Therefore, we also suggest monitoring HbF levels in patients with these syndromes to further facilitate clinical diagnosis.
DOI: 10.6084/m9.figshare.12533249
title: Table S6: Transcriptome-wide expression profiling of Sporothrix schenckii yeast and mycelial forms

description: GO terms associated with all up- and down-regulated genes
DOI: 10.6084/m9.figshare.12533228
title: Table S5: Transcriptome-wide expression profiling of Sporothrix schenckii yeast and mycelial forms

description: GO enrichment analysis of differentially expressed genes
DOI: 10.6084/m9.figshare.12533189
title: Table S4: Transcriptome-wide expression profiling of Sporothrix schenckii yeast and mycelial forms

description: List of differentially expressed lncRNAs overlapping protein-coding loci.
DOI: 10.6084/m9.figshare.12533189.v1
title: Table S4: Transcriptome-wide expression profiling of Sporothrix schenckii yeast and mycelial forms

description: List of differentially expressed lncRNAs overlapping protein-coding loci.
DOI: 10.6084/m9.figshare.12533228.v2
title: Table S5: Transcriptome-wide expression profiling of Sporothrix schenckii yeast and mycelial forms

description: GO enrichment analysis of differentially expressed genes
DOI: 10.6084/m9.figshare.12533249.v2
title: Table S6: Transcriptome-wide expression profiling of Sporothrix schenckii yeast and mycelial forms

description: GO terms associated with all up- and down-regulated genes
DOI: 10.6084/m9.figshare.12533174
title: Table S3: Transcriptome-wide expression profiling of Sporothrix schenckii yeast and mycelial forms

description: List of differentially expressed genes (yeast versus mold) and not regulated genes.
DOI: 10.6084/m9.figshare.12533171
title: Metadata record for: Liver transcriptome resources of four commercially exploited teleost species

description: This dataset contains key characteristics about the data described in the Data Descriptor Liver transcriptome resources of four commercially exploited teleost species. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format <br> <br> <br>
DOI: 10.6084/m9.figshare.12533228.v1
title: Table S5Transcriptome-wide expression profiling of Sporothrix schenckii yeast and mycelial forms

description: GO enrichment analysis of differentially expressed genes
DOI: 10.6084/m9.figshare.12533249.v1
title: Table S6Transcriptome-wide expression profiling of Sporothrix schenckii yeast and mycelial forms

description: GO terms associated with all up- and down-regulated genes
DOI: 10.6084/m9.figshare.12533069
title: Supplementary Material for: Truncated RUNX1 Generated by the Fusion of RUNX1 to Antisense GRIK2 via a Cryptic Chromosome Translocation Enhances Sensitivity to Granulocyte Colony-Stimulating Factor

description: Fusions of the Runt-related transcription factor 1 ( RUNX1 ) with different partner genes have been associated with various hematological disorders. Interestingly, the C-terminally truncated form of RUNX1 and RUNX1 fusion proteins are similarly considered important contributors to leukemogenesis. Here, we describe a 59-year-old male patient who was initially diagnosed with acute myeloid leukemia, inv(16)(p13;q22)/ CBFB-MYH11 (FAB classification M4Eo). He achieved complete remission and negative CBFB-MYH11 status with daunorubicin/cytarabine combination chemotherapy but relapsed 3 years later. Cytogenetic analysis of relapsed leukemia cells revealed CBFB-MYH11 negativity and complex chromosomal abnormalities without inv(16) (p13;q22). RNA-seq identified the glutamate receptor, ionotropic, kinase 2 ( GRIK2) gene on 6q16 as a novel fusion partner for RUNX1 in this case. Specifically, the fusion of RUNX1 to the GRIK2 antisense strand ( RUNX1-GRIK2as) generated multiple missplicing transcripts. Because extremely low levels of wild-type GRIK2 were detected in leukemia cells, <br> RUNX1-GRIK2as was thought to drive the pathogenesis associated with the RUNX1-GRIK2 fusion. The truncated RUNX1 generated from RUNX1-GRIK2as induced the expression of the granulocyte colony-stimulating factor (G-CSF) receptor on 32D myeloid leukemia cells and enhanced proliferation in response to G-CSF. In summary, the RUNX1-GRIK2as fusion emphasizes the importance of aberrantly truncated RUNX1 in leukemogenesis. <br>R
DOI: 10.6084/m9.figshare.12533096
title: Table S1: Transcriptome-wide expression profiling of Sporothrix schenckii yeast and mycelial forms

description: Oligonucleotide primers used for RT-qPCR analysis and list of new genes, overlapping sense-antisense regions and cis-SAS gene pairs
DOI: 10.6084/m9.figshare.12533162
title: Table S2: Transcriptome-wide expression profiling of Sporothrix schenckii yeast and mycelial forms

description: List of genes expressed in yeast and mold forms of <i>S. schenckii</i>
DOI: 10.6084/m9.figshare.12533171.v1
title: Metadata record for: Liver transcriptome resources of four commercially exploited teleost species

description: This dataset contains key characteristics about the data described in the Data Descriptor Liver transcriptome resources of four commercially exploited teleost species. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format <br> <br> <br>
DOI: 10.6084/m9.figshare.12532937
title: Supplementary Material for: 3-Hydroxyisobutyryl-CoA Hydrolase Deficiency in a Turkish Child with a Novel HIBCH Gene Mutation and Literature Review

description: 3-hydroxyisobutyryl-CoA hydrolase (HIBCH) deficiency (OMIM 250620) is an autosomal recessive inborn error of valine catabolism characterized by severely delayed psychomotor development, progressive neurodegeneration, recurrent metabolic attacks with intercurrent illness, increased lactic acid, cerebral atrophy, and brain lesions in the basal ganglia. <i>HIBCH</i> gene defect is a very rare organic aciduria and also might cause secondary mitochondrial dysfunction. We report a 12-month-old severely affected female infant with a novel homozygous c.556C&gt;G; p.R186G variant in the <i>HIBCH</i> gene presenting with axial hypotonia, severe developmental delay, and brain lesions in the basal ganglia and provide an overview of the literature. When suspected, newborn and selective screening with tandem mass analyses should include hydroxy-C4-carnitine to diagnose this disorder. However, in some cases, mostly in those with milder phenotype, diagnosis may be missed due to normal hydroxy-C4 carnitine levels.
DOI: 10.6084/m9.figshare.12533069.v1
title: Supplementary Material for: Truncated RUNX1 Generated by the Fusion of RUNX1 to Antisense GRIK2 via a Cryptic Chromosome Translocation Enhances Sensitivity to Granulocyte Colony-Stimulating Factor

description: Fusions of the Runt-related transcription factor 1 ( RUNX1 ) with different partner genes have been associated with various hematological disorders. Interestingly, the C-terminally truncated form of RUNX1 and RUNX1 fusion proteins are similarly considered important contributors to leukemogenesis. Here, we describe a 59-year-old male patient who was initially diagnosed with acute myeloid leukemia, inv(16)(p13;q22)/ CBFB-MYH11 (FAB classification M4Eo). He achieved complete remission and negative CBFB-MYH11 status with daunorubicin/cytarabine combination chemotherapy but relapsed 3 years later. Cytogenetic analysis of relapsed leukemia cells revealed CBFB-MYH11 negativity and complex chromosomal abnormalities without inv(16) (p13;q22). RNA-seq identified the glutamate receptor, ionotropic, kinase 2 ( GRIK2) gene on 6q16 as a novel fusion partner for RUNX1 in this case. Specifically, the fusion of RUNX1 to the GRIK2 antisense strand ( RUNX1-GRIK2as) generated multiple missplicing transcripts. Because extremely low levels of wild-type GRIK2 were detected in leukemia cells, <br> RUNX1-GRIK2as was thought to drive the pathogenesis associated with the RUNX1-GRIK2 fusion. The truncated RUNX1 generated from RUNX1-GRIK2as induced the expression of the granulocyte colony-stimulating factor (G-CSF) receptor on 32D myeloid leukemia cells and enhanced proliferation in response to G-CSF. In summary, the RUNX1-GRIK2as fusion emphasizes the importance of aberrantly truncated RUNX1 in leukemogenesis. <br>R
DOI: 10.6084/m9.figshare.12532847
title: Main Data (JAP).xlsx

description: Influence of Low Dose Acute Glutamine Supplementation on Gastrointestinal Barrier Integrity and Microbial Translocation in response to High Intensity Exertional-Heat Stress
DOI: 10.6084/m9.figshare.12533174.v2
title: Table S3: Transcriptome-wide expression profiling of Sporothrix schenckii yeast and mycelial forms

description: List of differentially expressed genes (yeast versus mold) and not regulated genes.
DOI: 10.6084/m9.figshare.12532847.v1
title: Main Data (JAP).xlsx

description: Influence of Low Dose Acute Glutamine Supplementation on Gastrointestinal Barrier Integrity and Microbial Translocation in response to High Intensity Exertional-Heat Stress
DOI: 10.6084/m9.figshare.12532937.v1
title: Supplementary Material for: 3-Hydroxyisobutyryl-CoA Hydrolase Deficiency in a Turkish Child with a Novel HIBCH Gene Mutation and Literature Review

description: 3-hydroxyisobutyryl-CoA hydrolase (HIBCH) deficiency (OMIM 250620) is an autosomal recessive inborn error of valine catabolism characterized by severely delayed psychomotor development, progressive neurodegeneration, recurrent metabolic attacks with intercurrent illness, increased lactic acid, cerebral atrophy, and brain lesions in the basal ganglia. <i>HIBCH</i> gene defect is a very rare organic aciduria and also might cause secondary mitochondrial dysfunction. We report a 12-month-old severely affected female infant with a novel homozygous c.556C&gt;G; p.R186G variant in the <i>HIBCH</i> gene presenting with axial hypotonia, severe developmental delay, and brain lesions in the basal ganglia and provide an overview of the literature. When suspected, newborn and selective screening with tandem mass analyses should include hydroxy-C4-carnitine to diagnose this disorder. However, in some cases, mostly in those with milder phenotype, diagnosis may be missed due to normal hydroxy-C4 carnitine levels.
DOI: 10.6084/m9.figshare.12533174.v1
title: Table S3Transcriptome-wide expression profiling of Sporothrix schenckii yeast and mycelial forms

description: List of differentially expressed genes (yeast versus mold) and not regulated genes.
DOI: 10.6084/m9.figshare.12532514
title: OTU data_bacterial communities among stress-sensitive and tolerant black tiger shrimp (Penaeus monodon) individuals.xls

description: Variation of bacterial communities among stress-sensitive and tolerant black tiger shrimp (<i>Penaues monodon</i>) individuals.
DOI: 10.5522/04/12532343
title: Severity of impulsivity, psychiatric morbidity and PD

description: SPSS file containing data for 85 subjects, with co-morbid Axis-I & -II disorders, and a sample of Axis-I disorders with no co-morbid PD were recruited at three general psychiatric mental health resource centers and then compared on a number of variables
DOI: 10.6084/m9.figshare.12533096.v2
title: Table S1: Transcriptome-wide expression profiling of Sporothrix schenckii yeast and mycelial forms

description: Oligonucleotide primers used for RT-qPCR analysis and list of new genes, overlapping sense-antisense regions and cis-SAS gene pairs
DOI: 10.5522/04/12532343.v1
title: Severity of impulsivity, psychiatric morbidity and PD

description: SPSS file containing data for 85 subjects, with co-morbid Axis-I & -II disorders, and a sample of Axis-I disorders with no co-morbid PD were recruited at three general psychiatric mental health resource centers and then compared on a number of variables
DOI: 10.6084/m9.figshare.12532514.v1
title: OTU data_bacterial communities among stress-sensitive and tolerant black tiger shrimp (Penaeus monodon) individuals.xls

description: Variation of bacterial communities among stress-sensitive and tolerant black tiger shrimp (<i>Penaues monodon</i>) individuals.
DOI: 10.6084/m9.figshare.12530627
title: Additional file 5 of Analysis of structural variants in four African cichlids highlights an association with developmental and immune related genes

description: Additional file 5: Supplementary file 4. Genes found inside PCR validated inversions. Each row corresponds to one gene. Genomic coordinates of the associated inversion, and the number of species carrying the inversion are indicated, along with the gene name and ncbi id.