cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12873509
title: Additional file 10 of Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae)

description: Additional file 10:Annotation results in GFF3. All the annotation results (ORFS, introns, descriptions, GO terms, Arabidopsis and melon orthologs, SNVs and SSRs) are provided also in the standard format GFF3 of The Sequence Ontology Resources [100] that facilitate annotations uploading, representation and analysis. (ZIP 4 MB)
DOI: 10.6084/m9.figshare.12873506.v14
title: Additional file of Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae)

description: Additional file of Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae)
DOI: 10.6084/m9.figshare.12873533.v1
title: Additional file 3 of Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae)

description: Additional file 3:Blast Hits and GO terms. Descriptions build from the blast hit obtained by a sequential blast search of 3 protein databases [60–62] and GO annotations for the whole Cucurbita unigene collection are compiled. (XLS 5 MB)
DOI: 10.6084/m9.figshare.12873506
title: Additional file of Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae)

description: Additional file of Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae)
DOI: 10.6084/m9.figshare.12873536
title: Additional file 4 of Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae)

description: Additional file 4:Arabidopsis and melon orthologs. Orthologs found by reciprocal search with Arabidopsis and melon databases [12, 61] are indicated. (XLS 2 MB)
DOI: 10.6084/m9.figshare.12873509.v1
title: Additional file 10 of Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae)

description: Additional file 10:Annotation results in GFF3. All the annotation results (ORFS, introns, descriptions, GO terms, Arabidopsis and melon orthologs, SNVs and SSRs) are provided also in the standard format GFF3 of The Sequence Ontology Resources [100] that facilitate annotations uploading, representation and analysis. (ZIP 4 MB)
DOI: 10.6084/m9.figshare.12873542.v1
title: Additional file 6 of Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae)

description: Additional file 6:Cucurbita SSRs. The table provides the list of SSRs identified from the Cucurbita unigene dataset, their length, motif sequences, position in the unigene, and scores. (XLSX 101 KB)
DOI: 10.6084/m9.figshare.12873527.v1
title: Additional file 1 of Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae)

description: Additional file 1:Cucurbita unigenes. The fasta sequence of the 49,610 Cucurbita unigenes assembled from 454 ESTs is included. (ZIP 10 MB)
DOI: 10.6084/m9.figshare.12873539.v1
title: Additional file 5 of Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae)

description: Additional file 5:Genes potentially encoding pathogen resistance, flowering, fruit and root traits. Genes were identified in the Cucurbita data set by comparison with the Arabidopsis and melon databases [12, 61]. A brief description and the corresponding Arabidopsis and melon locus are given for each unigene. (XLSX 16 KB)
DOI: 10.6084/m9.figshare.12873545
title: Additional file 7 of Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae)

description: Additional file 7:Validated Cucurbita SSRs. The table provides the list of Cucurbita SSRs experimentally validated using a collection of C. pepo. Primers used for validation, number of alleles, and polymorphism detected between the sequenced genotypes, within subspecies, and within the zucchini morphotypes are included. Also transference to C. moschata is indicated. (XLSX 14 KB)
DOI: 10.6084/m9.figshare.7987754
title: Identification of erosion-prone areas using modified morphometric prioritization method and sediment production rate: a remote sensing and GIS approach

description: Watersheds from semiarid zones are sensitive to land degradation processes wherein the morphometric investigation is an important aspect to unwrap the susceptible areas. Hence it is a prerequisite for the assessment of erosional pattern of the watershed. Thus, based on the response to erosional processes, prioritization task has been undertaken for fourteen sub-watersheds from basaltic region of Western Ghats of India. A morphometry-based framework using weighted sum analysis (WSA) coupled with the remote sensing data, field data and topographical maps were generated on geographical information system (GIS) platform to estimate the soil erosion susceptibility. The study also evaluates the performance of this new methodology by considering the sediment production rate (SPR) of these sub-watersheds. The resultant WSA-SPR model has prioritized the study area into high, moderate low and very low categories. The high and moderate priority areas lie in the proximity of outlet, upper elevated and undulating terrain of the watershed. It represents 41.38% of the total area covering SW1, 3, 13 and 14 sub-watersheds. This study proposes a useful tool to define areas for planning the strategies to control soil erosion and promote soil conservation.
DOI: 10.6084/m9.figshare.12873545.v1
title: Additional file 7 of Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae)

description: Additional file 7:Validated Cucurbita SSRs. The table provides the list of Cucurbita SSRs experimentally validated using a collection of C. pepo. Primers used for validation, number of alleles, and polymorphism detected between the sequenced genotypes, within subspecies, and within the zucchini morphotypes are included. Also transference to C. moschata is indicated. (XLSX 14 KB)
DOI: 10.6084/m9.figshare.12873548
title: Additional file 8 of Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae)

description: Additional file 8:Cucurbita SNPs and INDELs. The file provides the list of SNPs and INDELs (SNVs) identified from the Cucurbita unigene dataset, their position, the nucleotide change (or I or D for insertion and deletion in INDELs), the quality of the polymorphic base, and additional information about allele number and frequency. The different filters applied for the in silico selection of the SNVs are also indicated: VKS (is not an SNPs, is an INDEL), HVR4 (SNV is in a region with more than 4 SNVs per 100 bp), CS60 (SNV is closer than 60 bp to another SNV), I60 (SNV is located closer than 60 bp to an intron), CL60 (SNV is closer than 60 bp to the sequence end), NVSM1 (SNV is variable within UPV196, or not sequenced in this genotype), NVSM2 (SNV is variable within MU16, or not sequenced in this genotype), CEF (SNV does not alter a restriction target and cannot be detected as a CAPS). The VCF (Variant Call Format) version 4.0 has been used for this file [108]. (VCF 2 MB)
DOI: 10.6084/m9.figshare.12873548.v1
title: Additional file 8 of Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae)

description: Additional file 8:Cucurbita SNPs and INDELs. The file provides the list of SNPs and INDELs (SNVs) identified from the Cucurbita unigene dataset, their position, the nucleotide change (or I or D for insertion and deletion in INDELs), the quality of the polymorphic base, and additional information about allele number and frequency. The different filters applied for the in silico selection of the SNVs are also indicated: VKS (is not an SNPs, is an INDEL), HVR4 (SNV is in a region with more than 4 SNVs per 100 bp), CS60 (SNV is closer than 60 bp to another SNV), I60 (SNV is located closer than 60 bp to an intron), CL60 (SNV is closer than 60 bp to the sequence end), NVSM1 (SNV is variable within UPV196, or not sequenced in this genotype), NVSM2 (SNV is variable within MU16, or not sequenced in this genotype), CEF (SNV does not alter a restriction target and cannot be detected as a CAPS). The VCF (Variant Call Format) version 4.0 has been used for this file [108]. (VCF 2 MB)
DOI: 10.6084/m9.figshare.12873551.v1
title: Additional file 9 of Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae)

description: Additional file 9:Cucurbita SNPs validated as CAPS. The table provides the list of SNPs that affected restriction targets and were validated via CAPS, their position, location, primers used for validation and the occurrence of polymorphism between the two sequenced varieties. (XLSX 13 KB)
DOI: 10.6084/m9.figshare.12873536.v1
title: Additional file 4 of Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae)

description: Additional file 4:Arabidopsis and melon orthologs. Orthologs found by reciprocal search with Arabidopsis and melon databases [12, 61] are indicated. (XLS 2 MB)
DOI: 10.6084/m9.figshare.7987754.v1
title: Identification of erosion-prone areas using modified morphometric prioritization method and sediment production rate: a remote sensing and GIS approach

description: Watersheds from semiarid zones are sensitive to land degradation processes wherein the morphometric investigation is an important aspect to unwrap the susceptible areas. Hence it is a prerequisite for the assessment of erosional pattern of the watershed. Thus, based on the response to erosional processes, prioritization task has been undertaken for fourteen sub-watersheds from basaltic region of Western Ghats of India. A morphometry-based framework using weighted sum analysis (WSA) coupled with the remote sensing data, field data and topographical maps were generated on geographical information system (GIS) platform to estimate the soil erosion susceptibility. The study also evaluates the performance of this new methodology by considering the sediment production rate (SPR) of these sub-watersheds. The resultant WSA-SPR model has prioritized the study area into high, moderate low and very low categories. The high and moderate priority areas lie in the proximity of outlet, upper elevated and undulating terrain of the watershed. It represents 41.38% of the total area covering SW1, 3, 13 and 14 sub-watersheds. This study proposes a useful tool to define areas for planning the strategies to control soil erosion and promote soil conservation.
DOI: 10.6084/m9.figshare.12873530.v1
title: Additional file 2 of Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae)

description: Additional file 2:Annotation of ORFs and introns. Unigene length and predicted position of ORFs and introns is indicated for the whole Cucurbita unigene collection. (XLSX 4 MB)
DOI: 10.6084/m9.figshare.12873527
title: Additional file 1 of Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae)

description: Additional file 1:Cucurbita unigenes. The fasta sequence of the 49,610 Cucurbita unigenes assembled from 454 ESTs is included. (ZIP 10 MB)
DOI: 10.6084/m9.figshare.12873533
title: Additional file 3 of Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae)

description: Additional file 3:Blast Hits and GO terms. Descriptions build from the blast hit obtained by a sequential blast search of 3 protein databases [60–62] and GO annotations for the whole Cucurbita unigene collection are compiled. (XLS 5 MB)
DOI: 10.6084/m9.figshare.12873539
title: Additional file 5 of Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae)

description: Additional file 5:Genes potentially encoding pathogen resistance, flowering, fruit and root traits. Genes were identified in the Cucurbita data set by comparison with the Arabidopsis and melon databases [12, 61]. A brief description and the corresponding Arabidopsis and melon locus are given for each unigene. (XLSX 16 KB)
DOI: 10.6084/m9.figshare.12873551
title: Additional file 9 of Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae)

description: Additional file 9:Cucurbita SNPs validated as CAPS. The table provides the list of SNPs that affected restriction targets and were validated via CAPS, their position, location, primers used for validation and the occurrence of polymorphism between the two sequenced varieties. (XLSX 13 KB)
DOI: 10.6084/m9.figshare.12873542
title: Additional file 6 of Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae)

description: Additional file 6:Cucurbita SSRs. The table provides the list of SSRs identified from the Cucurbita unigene dataset, their length, motif sequences, position in the unigene, and scores. (XLSX 101 KB)
DOI: 10.6084/m9.figshare.12873530
title: Additional file 2 of Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae)

description: Additional file 2:Annotation of ORFs and introns. Unigene length and predicted position of ORFs and introns is indicated for the whole Cucurbita unigene collection. (XLSX 4 MB)
DOI: 10.6084/m9.figshare.7987439
title: Prevalence of Orientia tsutsugamushi, Anaplasma phagocytophilum and Leptospira interrogans in striped field mice in Gwangju, Republic of Korea

description: This study investigated the prevalence of <i>Orientia tsutsugamushi, Anaplasma phagocytophilum, </i>and <i>Leptospira interrogans</i> in wild rodents through molecular detection using organ samples and through serological assay using blood samples of mice collected from two distinct sites in Gwangju Metropolitan City, Republic of Korea (ROK). A total of 47 wild rodents, identified as <i>Apodemus agrarius (A. agrarius)</i>, were captured from June to August 2016. The seroprevalence of antibodies against bacterial pathogens in <i>A. agrarius</i> sera was analyzed; 17.4% (8/46) were identified as <i>O. tsutsugamushi</i> through indirect immunofluorescence assay and 2.2% (1/46) were identified as <i>Leptospira</i> species through passive hemagglutination assay. Using polymerase chain reaction, the spleen, kidney and blood samples were investigated for the presence of <i>O. tsutsugamushi</i>, <i>A. phagocytophilum</i>, and <i>L. interrogans</i>. Out of the 47 <i>A. agrarius</i>, 19.1% (9/47) were positive for <i>A. phagocytophilum </i>and 6.4% (3/47) were positive for <i>L. interrogans</i>, while none were positive for <i>O. tsutsugamushi</i>. Four out of 46 (8.7%) blood samples, six out of 45 (13.3%) spleen samples, and one out of 47 (2.1%) kidney samples were positive for <i>A. phagocytophilum.</i> Three out of 47 (6.4%) kidney samples were positive for <i>L. interrogans</i>. The sequencing results of PCR positive samples demonstrated &gt; 99% similarity with <i>A. phagocytophilum</i> and <i>L. interrogans </i>sequences. <i>A. phagocytophilum</i> was mostly detected in the spleen, whereas <i>L. interrogans</i> was mostly detected in the kidneys. Notably, <i>A. phagocytophilum</i> and <i>L. interrogans</i> were detected in <i>A. agrarius</i> living in close proximity to humans in the metropolitan suburban areas. The results of this study indicate that rodent-borne bacteria may be present in wild rodents in the metropolitan suburban areas of ROK.
DOI: 10.6084/m9.figshare.7987439.v1
title: Prevalence of Orientia tsutsugamushi, Anaplasma phagocytophilum and Leptospira interrogans in striped field mice in Gwangju, Republic of Korea

description: This study investigated the prevalence of <i>Orientia tsutsugamushi, Anaplasma phagocytophilum, </i>and <i>Leptospira interrogans</i> in wild rodents through molecular detection using organ samples and through serological assay using blood samples of mice collected from two distinct sites in Gwangju Metropolitan City, Republic of Korea (ROK). A total of 47 wild rodents, identified as <i>Apodemus agrarius (A. agrarius)</i>, were captured from June to August 2016. The seroprevalence of antibodies against bacterial pathogens in <i>A. agrarius</i> sera was analyzed; 17.4% (8/46) were identified as <i>O. tsutsugamushi</i> through indirect immunofluorescence assay and 2.2% (1/46) were identified as <i>Leptospira</i> species through passive hemagglutination assay. Using polymerase chain reaction, the spleen, kidney and blood samples were investigated for the presence of <i>O. tsutsugamushi</i>, <i>A. phagocytophilum</i>, and <i>L. interrogans</i>. Out of the 47 <i>A. agrarius</i>, 19.1% (9/47) were positive for <i>A. phagocytophilum </i>and 6.4% (3/47) were positive for <i>L. interrogans</i>, while none were positive for <i>O. tsutsugamushi</i>. Four out of 46 (8.7%) blood samples, six out of 45 (13.3%) spleen samples, and one out of 47 (2.1%) kidney samples were positive for <i>A. phagocytophilum.</i> Three out of 47 (6.4%) kidney samples were positive for <i>L. interrogans</i>. The sequencing results of PCR positive samples demonstrated &gt; 99% similarity with <i>A. phagocytophilum</i> and <i>L. interrogans </i>sequences. <i>A. phagocytophilum</i> was mostly detected in the spleen, whereas <i>L. interrogans</i> was mostly detected in the kidneys. Notably, <i>A. phagocytophilum</i> and <i>L. interrogans</i> were detected in <i>A. agrarius</i> living in close proximity to humans in the metropolitan suburban areas. The results of this study indicate that rodent-borne bacteria may be present in wild rodents in the metropolitan suburban areas of ROK.
DOI: 10.6084/m9.figshare.12873593.v2
title: Additional file of Applicability of RNA standards for evaluating RT-qPCR assays and platforms

description: Additional file of Applicability of RNA standards for evaluating RT-qPCR assays and platforms
DOI: 10.6084/m9.figshare.7987313
title: A new specimen of <i>Platypterygius sachicarum</i> (Reptilia, Ichthyosauria) from the Early Cretaceous of Colombia and its phylogenetic implications

description: <i>Platypterygius sachicarum</i> is one of the few Lower Cretaceous ichthyosaurian species described from the Hauterivian–Aptian-aged Paja Formation, the most complete Lower Cretaceous sedimentary sequence in northern South America. To date, <i>P. sachicarum</i> has been described only from a single skull, limiting morphological, stratigraphic, and phylogenetic comparisons. Here, we describe a new skull and associated postcranium of upper Barremian age from Villa de Leyva, Colombia, which represent the first documented postcranial remains of this species and enable detailed comparison with other Early Cretaceous ophthalmosaurid ichthyosaurs. <i>Platypterygius sachicarum</i> shares many morphological similarities with contemporaneous taxa from Europe but differs in both skull and tooth morphology from coeval South American species from northern South America and from the eastern Pacific. The additional data provide new diagnostic characters for this species and resolve the position of <i>P. sachicarum</i> as part of a polytomy of other species historically referred to <i>Platypterygius</i>. However, as with previous analyses, all recovered clades are poorly supported. The rich vertebrate fossil record of the Paja Formation provides an unparalleled opportunity to explore paleobiogeographic and paleoecological questions pertaining to Cretaceous marine reptiles; however, in most cases, a robust stratigraphic and phylogenetic framework remains elusive.
DOI: 10.6084/m9.figshare.7987319
title: AJPEM_Omentin_Suppl Tab.2

description: List of 56 potential upstream regulators and 3 potential inhibitors of the omentin-induced secretion profile<br>
DOI: 10.6084/m9.figshare.7987319.v1
title: AJPEM_Omentin_Suppl Tab.2

description: List of 56 potential upstream regulators and 3 potential inhibitors of the omentin-induced secretion profile<br>
DOI: 10.6084/m9.figshare.7987313.v2
title: A new specimen of <i>Platypterygius sachicarum</i> (Reptilia, Ichthyosauria) from the Early Cretaceous of Colombia and its phylogenetic implications

description: <i>Platypterygius sachicarum</i> is one of the few Lower Cretaceous ichthyosaurian species described from the Hauterivian–Aptian-aged Paja Formation, the most complete Lower Cretaceous sedimentary sequence in northern South America. To date, <i>P. sachicarum</i> has been described only from a single skull, limiting morphological, stratigraphic, and phylogenetic comparisons. Here, we describe a new skull and associated postcranium of upper Barremian age from Villa de Leyva, Colombia, which represent the first documented postcranial remains of this species and enable detailed comparison with other Early Cretaceous ophthalmosaurid ichthyosaurs. <i>Platypterygius sachicarum</i> shares many morphological similarities with contemporaneous taxa from Europe but differs in both skull and tooth morphology from coeval South American species from northern South America and from the eastern Pacific. The additional data provide new diagnostic characters for this species and resolve the position of <i>P. sachicarum</i> as part of a polytomy of other species historically referred to <i>Platypterygius</i>. However, as with previous analyses, all recovered clades are poorly supported. The rich vertebrate fossil record of the Paja Formation provides an unparalleled opportunity to explore paleobiogeographic and paleoecological questions pertaining to Cretaceous marine reptiles; however, in most cases, a robust stratigraphic and phylogenetic framework remains elusive.
DOI: 10.6084/m9.figshare.12873599
title: Additional file 2 of Applicability of RNA standards for evaluating RT-qPCR assays and platforms

description: Additional file 2:MIQE Additional Information. Microsoft Excel file containing further information on RNA preparation, purity, PCR efficiency and negative control data complying with the MIQE guidelines. (XLS 2 MB)
DOI: 10.6084/m9.figshare.12873599.v1
title: Additional file 2 of Applicability of RNA standards for evaluating RT-qPCR assays and platforms

description: Additional file 2:MIQE Additional Information. Microsoft Excel file containing further information on RNA preparation, purity, PCR efficiency and negative control data complying with the MIQE guidelines. (XLS 2 MB)