cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5104741.v1
title: Table 1 - Non-specific sgRNAs GeCKO v2 library (human).xlsx

description: <b>Table 1 - Non-specific sgRNAs GeCKO v2 (human).</b> This table represents the total of 5664 sgRNAs within the entire human GeCKO v2 library (half-libraries A and B combined) that recognise at least two identical target sites (20 bp protospacer + NGG PAM) within the reference genome. For the analysis, sgRNA target sites were aligned against the human reference genome (GRCh38/hg19 – primary assembly) using BLAT (v36) after optimisation of the algorithm for short length queries (-tileSize=6, -stepSize=3). A raw threshold of 95% minimum identity was applied during the analysis and the resulted alignments were further filtered to only include perfect matches and unique targets (exclusion of hits on alternative assemblies). Analysis was performed using R (v3.2.3) in R studio (v1.0.136) using Ubuntu.<br><b>Table 2 - Flagged genes GeCKO v2 (human).</b> This table represents the total of 775 genes for which more than half the corresponding sgRNAs within the entire human GeCKO v2 library (half-libraries A and B combined) are non-specific, i.e. recognise at least two identical target sites (20 bp protospacer + NGG PAM) within the reference genome. A threshold of &gt;50% non-specific sgRNAs per gene (e.g. 4 out of 6 for protein coding genes; 3 out of 4 for miRNA genes) was set in order to flag a group of sgRNAs. Analysis was performed using R (v3.2.3) in R studio (v1.0.136) using Ubuntu.
DOI: 10.6084/m9.figshare.5104714
title: Supplementary Material for: Comparison of mealybug <i>(Planococcus lilacinus)</i> and fruit fly genomes: isolation and analysis of conserved sequences and their utility in studying synteny in the mealybug

description: By using ligation-mediated PCR products from mealybug DNA as tester and biotinylated fly DNA as driver, we recovered a fraction of the tester that remains hybridized to driver following high-stringency washing conditions. This fraction is expected to contain mealybug sequences conserved in the fly (MCF). Reciprocal experiments enabled the isolation of fly sequences conserved in the mealybug (FCM). Coding sequences among MCF show amino acid identities &gt;40% with fly proteins, allowing a reliable identification of orthologs. Three sequences from the fly cytogenetic positions 98–99 were hybridized onto mealybug chromosomes and the results identified differences in synteny between the two species. Taken together, our results present a method for direct isolation of sequences conserved between an ‘orphan’ (mealybug) genome and a ‘reference’ (fly) genome and showed that these sequences can be used to study chromosome synteny in the mealybug.
DOI: 10.6084/m9.figshare.5104717
title: Supplementary Material for: Genome-Wide Profiling of Antigen-Induced Time Course Expression Using Murine Models for Acute and Chronic Asthma

description: <i>Background:</i> Asthma is a complex-trait disease caused by complicated interactions among multiple genetic and environmental risk factors. The clinical symptoms of asthma, such as periodic airway obstruction, hyperresponsiveness and mucus hypersecretion, are mediated by acute and chronic bronchial inflammation. <i>Methods:</i> To better understand the mechanisms by which allergen-induced acute inflammation leads to chronic asthma accompanied by irreversible airway remodeling, we analyzed time course transcriptional responses in the lungs of model mice that were exposed to aerosolized ovalbumin for up to 9 weeks after an initial sensitization. <i>Results:</i> We observed increased levels of total plasma IgE and histological changes in lung tissues from the ovalbumin-treated mice, which is consistent with the typical inflammatory phenotypes of asthma pathogenesis. Our oligonucleotide microarray analyses revealed a total of 776 differentially expressed genes induced by antigenic challenge (≧1.5-fold change, p &lt; 0.05). Of these genes, most of the immune-responsive genes were transiently up-regulated in the early phase of the allergen treatment (within a week) with a concomitant up-regulation of genes involved in mucus production. These genes were not differentially regulated in the mice challenged for a longer period of time (up to 6 weeks). We also identified some of the genes implicated in extracellular matrix remodeling, for which the time course expression did not necessarily coincide with the expression patterns of immune-responsive genes. <i>Conclusion:</i> Our data suggest that there is a complex interregulatory genetic network associated with the structural changes that accompany the progression of the allergic inflammatory reaction in chronic asthma.
DOI: 10.6084/m9.figshare.5104723.v1
title: Supplementary Material for: Maternal Footprints of Southeast Asians in North India

description: We have analyzed 7,137 samples from 125 different caste, tribal and religious groups of India and 99 samples from three populations of Nepal for the length variation in the COII/tRNA<sup>Lys</sup> region of mtDNA. Samples showing length variation were subjected to detailed phylogenetic analysis based on HVS-I and informative coding region sequence variation. The overall frequencies of the 9-bp deletion and insertion variants in South Asia were 1.9 and 0.6%, respectively. We have also defined a novel deep-rooting haplogroup M43 and identified the rare haplogroup H14 in Indian populations carrying the 9-bp deletion by complete mtDNA sequencing. Moreover, we redefined haplogroup M6 and dissected it into two well-defined subclades. The presence of haplogroups F1 and B5a in Uttar Pradesh suggests minor maternal contribution from Southeast Asia to Northern India. The occurrence of haplogroup F1 in the Nepalese sample implies that Nepal might have served as a bridge for the flow of eastern lineages to India. The presence of R6 in the Nepalese, on the other hand, suggests that the gene flow between India and Nepal has been reciprocal.
DOI: 10.6084/m9.figshare.5104708
title: Supplementary Material for: A chromosome inversion near the <i>KIT</i> gene and the Tobiano spotting pattern in horses

description: Tobiano is a white spotting pattern in horses caused by a dominant gene, <i>Tobiano</i><i>(TO)</i>. Here, we report <i>TO</i> associated with a large paracentric chromosome inversion on horse chromosome 3. DNA sequences flanking the inversion were identified and a PCR test was developed to detect the inversion. The inversion was only found in horses with the tobiano pattern, including horses with diverse genetic backgrounds, which indicated a common genetic origin thousands of years ago. The inversion does not interrupt any annotated genes, but begins approximately 100 kb downstream of the <i>KIT</i> gene. This inversion may disrupt regulatory sequences for the <i>KIT</i> gene and cause the white spotting pattern. This manuscript is accompanied by supplemental figures S1, S2 and S3, as well as supplemental Tables S1 and S2 (www.karger.com/doi/10.1159/000112065). The DNA sequence generated in this work has been submitted to GenBank under the following accession number: EF442014.
DOI: 10.6084/m9.figshare.5104705
title: Supplementary Material for: Specific transcriptional changes in human fetuses with autosomal trisomies

description: Among full autosomal trisomies, only trisomies of chromosome 21 (Down syndrome), 18 (Edwards syndrome) and 13 (Patau syndrome) are compatible with postnatal survival. But the mechanisms, how a supernumerary chromosome disrupts the normal development and causes specific phenotypes, are still not fully explained. As an alternative to gene dosage effect due to the trisomic chromosome a genome-wide transcriptional dysregulation has been postulated. The aim of this study was to define the transcriptional changes in trisomy 13, 18, and 21 during early fetal development in order to obtain more insights into the molecular etiopathology of aneuploidy. Using oligonucleotide microarrays, we analyzed whole genome expression profiles in cultured amniocytes (AC) and chorionic villus cells (CV) from pregnancies with a normal karyotype and with trisomies of human chromosomes 13, 18 and 21. We observed a low to moderate up-regulation for a subset of genes of the trisomic chromosomes. Transcriptional levels of most of the genes on the supernumerary chromosome appeared similar to the respective chromosomal pair in normal karyotypes. A subset of chromosome 21 genes including the <i>DSCR1</i> gene involved in fetal heart development was consistently up-regulated in different prenatal tissues (AC, CV) of trisomy 21 fetuses whereas only minor changes were found for genes of all other chromosomes. In contrast, in trisomy 18 vigorous downstream transcriptional changes were found. Global transcriptome analysis for autosomal trisomies 13, 18, and 21 supported a combination of the two major hypotheses.
DOI: 10.6084/m9.figshare.5104711
title: Supplementary Material for: Characterization of a balanced reciprocal translocation, rcp(9;11)(q27;q11) in cattle

description: Cytogenetic analysis of a phenotypically normal young bull from Marchigiana breed revealed the presence of an abnormal karyotype. The observation of longer and smaller chromosomes than BTA1 and BTA29, respectively in all metaphases suggested the presence of a reciprocal translocation. RBG-banding confirmed this hypothesis revealing the involvement of BTA9 and BTA11. FISH analyses using cattle-specific BAC clones (474A12 and 293G09 for BTA9; 035D03 for BTA11) identified rcp(9;11)(q27;q11) in the two regions affected. Moreover analyses performed on both parents established the ‘de novo’ origin of the anomaly. Comparison with human homologue sequences (HSA6q24.3→q25.3 for BTA9q27 and HSA2q11.1→q12.1 for BTA11q11) revealed that both breakpoint regions are gene rich as up to date at least 200 genes have been localized in these regions. Thus, further analyses are required to identify the sequences disrupted by the breakpoints and to verify their consequences on rcp carrier phenotype.
DOI: 10.6084/m9.figshare.5104714.v1
title: Supplementary Material for: Comparison of mealybug <i>(Planococcus lilacinus)</i> and fruit fly genomes: isolation and analysis of conserved sequences and their utility in studying synteny in the mealybug

description: By using ligation-mediated PCR products from mealybug DNA as tester and biotinylated fly DNA as driver, we recovered a fraction of the tester that remains hybridized to driver following high-stringency washing conditions. This fraction is expected to contain mealybug sequences conserved in the fly (MCF). Reciprocal experiments enabled the isolation of fly sequences conserved in the mealybug (FCM). Coding sequences among MCF show amino acid identities &gt;40% with fly proteins, allowing a reliable identification of orthologs. Three sequences from the fly cytogenetic positions 98–99 were hybridized onto mealybug chromosomes and the results identified differences in synteny between the two species. Taken together, our results present a method for direct isolation of sequences conserved between an ‘orphan’ (mealybug) genome and a ‘reference’ (fly) genome and showed that these sequences can be used to study chromosome synteny in the mealybug.
DOI: 10.6084/m9.figshare.5104717.v1
title: Supplementary Material for: Genome-Wide Profiling of Antigen-Induced Time Course Expression Using Murine Models for Acute and Chronic Asthma

description: <i>Background:</i> Asthma is a complex-trait disease caused by complicated interactions among multiple genetic and environmental risk factors. The clinical symptoms of asthma, such as periodic airway obstruction, hyperresponsiveness and mucus hypersecretion, are mediated by acute and chronic bronchial inflammation. <i>Methods:</i> To better understand the mechanisms by which allergen-induced acute inflammation leads to chronic asthma accompanied by irreversible airway remodeling, we analyzed time course transcriptional responses in the lungs of model mice that were exposed to aerosolized ovalbumin for up to 9 weeks after an initial sensitization. <i>Results:</i> We observed increased levels of total plasma IgE and histological changes in lung tissues from the ovalbumin-treated mice, which is consistent with the typical inflammatory phenotypes of asthma pathogenesis. Our oligonucleotide microarray analyses revealed a total of 776 differentially expressed genes induced by antigenic challenge (≧1.5-fold change, p &lt; 0.05). Of these genes, most of the immune-responsive genes were transiently up-regulated in the early phase of the allergen treatment (within a week) with a concomitant up-regulation of genes involved in mucus production. These genes were not differentially regulated in the mice challenged for a longer period of time (up to 6 weeks). We also identified some of the genes implicated in extracellular matrix remodeling, for which the time course expression did not necessarily coincide with the expression patterns of immune-responsive genes. <i>Conclusion:</i> Our data suggest that there is a complex interregulatory genetic network associated with the structural changes that accompany the progression of the allergic inflammatory reaction in chronic asthma.
DOI: 10.6084/m9.figshare.5104705.v1
title: Supplementary Material for: Specific transcriptional changes in human fetuses with autosomal trisomies

description: Among full autosomal trisomies, only trisomies of chromosome 21 (Down syndrome), 18 (Edwards syndrome) and 13 (Patau syndrome) are compatible with postnatal survival. But the mechanisms, how a supernumerary chromosome disrupts the normal development and causes specific phenotypes, are still not fully explained. As an alternative to gene dosage effect due to the trisomic chromosome a genome-wide transcriptional dysregulation has been postulated. The aim of this study was to define the transcriptional changes in trisomy 13, 18, and 21 during early fetal development in order to obtain more insights into the molecular etiopathology of aneuploidy. Using oligonucleotide microarrays, we analyzed whole genome expression profiles in cultured amniocytes (AC) and chorionic villus cells (CV) from pregnancies with a normal karyotype and with trisomies of human chromosomes 13, 18 and 21. We observed a low to moderate up-regulation for a subset of genes of the trisomic chromosomes. Transcriptional levels of most of the genes on the supernumerary chromosome appeared similar to the respective chromosomal pair in normal karyotypes. A subset of chromosome 21 genes including the <i>DSCR1</i> gene involved in fetal heart development was consistently up-regulated in different prenatal tissues (AC, CV) of trisomy 21 fetuses whereas only minor changes were found for genes of all other chromosomes. In contrast, in trisomy 18 vigorous downstream transcriptional changes were found. Global transcriptome analysis for autosomal trisomies 13, 18, and 21 supported a combination of the two major hypotheses.
DOI: 10.6084/m9.figshare.5104693
title: Supplementary Material for: Clinical MRI Cutoff Points for Predicting Lacunar Stroke May Not Exist: Need for a Grading rather than a Dichotomizing System

description: <i>Background:</i> Lacunar stroke has been defined as an infarct &lt;15 mm in diameter in the presence of symptoms of lacunar syndromes. We investigated a new approach in predicting whether a deep infarct is caused by small arterial occlusion. <i>Methods:</i> A total of 319 consecutive patients with acute symptomatic infarcts within the striatocapsular territory underwent diffusion-weighted imaging (DWI) and diagnostic workups, including vascular and cardiological studies. Predictors for nonlacunar mechanisms were evaluated by logistic regression analysis, with the size of infarct (1-mm increase) and stroke syndrome (traditional vs. atypical lacunar syndrome vs. cortical syndrome) graded rather than dichotomized. <i>Results:</i> Amongst the 171 patients who did not meet the established criteria for lacunar stroke, that is, deep infarct of ≧15 mm or presenting symptoms of nontraditional lacunar syndrome, a documented etiology could not be determined in 97 (56.7%) patients. In contrast, amongst the 148 patients who met the criteria, 27 (18.2%) had nonlacunar mechanisms. Logistic regression analysis identified the variables that predicted nonlacunar stroke mechanisms with statistical significance as nontraditional lacunar syndromes (OR 2.19 for atypical lacunar syndrome, and OR 6.72 for cortical syndrome), infarct size on DWI (OR 1.05 per 1-mm increase), and unilateral multiple deep infarcts on DWI (OR 2.22, p &lt; 0.05 in all cases). Receiver operating characteristic curves showed that discrimination power of the model derived from logistic regression analysis (grading system) was better than that of the previously established dichotomizing criterion in predicting nonlacunar mechanisms (p = 0.004). <i>Conclusions: </i>A clinically significant proportion of clinical MRI lacunae are associated with underlying nonlacunar mechanisms. Decisions regarding the extent of diagnostic procedures in patients with subcortical infarcts can be guided by the point value in terms of the stroke syndrome and infarct patterns, as well as the size of infarct.
DOI: 10.6084/m9.figshare.5104696
title: Supplementary Material for: Manganese Affects <i>Streptococcus mutans</i> Virulence Gene Expression

description: <i>Background/Aims:</i> Studies of trace metals in drinking water and tooth enamel have suggested a caries-promoting potential for manganese (Mn). Additionally, Mn has been shown to be essential for the expression of mutans streptococci virulence factors such as the glucan-binding lectin (GBL) of <i>Streptococcus sobrinus</i>. The <i>Streptococcus mutans</i> glucan-binding protein (Gbp) GbpC is the functional analogue of the <i>S. sobrinus</i> GBL. <i>S. mutans</i> Gbps have been shown to contribute to biofilm architecture and virulence. This study was undertaken to examine the effects of Mn on the transcription of genes encoding <i>S. mutans</i> Gbps, including <i>gbpC</i>, along with other critical <i>S. mutans</i> virulence genes. <i>Methods:</i> Microarray analyses suggested the potential for an Mn effect on Gbp genes. Further investigation of the Mn effects on selected genes was undertaken by performing Northern blots, Western blots, and RT-PCR under conditions of planktonic and biofilm growth in Mn-depleted media or in media containing 50 µ<i>M</i> Mn. <i>Results:</i> Mn resulted in increased expression of <i>gbpC</i> and <i>gtfB</i>, and decreased expression of <i>wapA</i>, in both planktonic and biofilm cultures. The expression levels of <i>gbpA</i> and <i>gbpD</i> were also decreased in the presence of Mn, but only in biofilms. The expression of <i>gtfC</i> was increased in the presence of Mn only in planktonic cultures. The <i>spaP</i> gene was expressed more highly in Mn-supplemented planktonic cultures but less in Mn-supplemented biofilms. <i>Conclusion:</i> Mn availability affects the expression of multiple <i>S. mutans</i> genes involved in adhesion and biofilm formation. Furthermore, these effects depend on the growth state of the organism.
DOI: 10.6084/m9.figshare.5104699
title: Supplementary Material for: The Ig1/2 Domain of MuSK Binds to Muscle Surface and Is Involved in Acetylcholine Receptor Clustering

description: The neuromuscular junction, the synapse between motor neurons and muscle cells, serves as an excellent model for studying synapse formation. Agrin is believed to be released by motor neurons to induce postsynaptic differentiation at the neuromuscular junction. MuSK, a receptor tyrosine kinase, appears to be a key component of the agrin receptor complex. However, how agrin activates MuSK remains unclear. To address this question, we characterized the binding of the MuSK extracellular region to the muscle cell surface. The MuSK ectodomain was found to bind to muscle cells in a manner dependent on stimulation with neural agrin. Moreover, the binding was myotube specific and appeared to be mediated by two regions in the MuSK: one region containing the first and second immunoglobin domains and the other containing the cysteine-rich domain. Importantly, recombinant proteins containing the binding activity can block full-length MuSK binding to muscle cells and agrin-induced AChR clustering. These results suggest that the Ig1/2 domain of MuSK is involved in AChR clustering by binding to the muscle surface.
DOI: 10.6084/m9.figshare.5104702
title: Supplementary Material for: Gene Expression Profiling of Hypothalamic Hamartomas: A Search for Genes Associated with Central Precocious Puberty

description: <i>Background:</i> Hypothalamic hamartomas (HHs) are congenital lesions composed of neurons and astroglia. Frequently, HHs cause central precocious puberty (CPP) and/or gelastic seizures. Because HHs might express genes similar to those required for the initiation of normal puberty, we used cDNA arrays to compare the gene expression profile of an HH associated with CPP with three HHs not accompanied by sexual precocity. <i>Methods:</i> Global changes in gene expression were detected using Affymetrix arrays. The results were confirmed by semiquantitative PCR, which also served to examine the expression of selected genes in the hypothalamus of female monkeys undergoing puberty. <i>Results:</i> All HHs were associated with seizures. Ten genes whose expression was increased in the HH with CPP were identified. They encode proteins involved in three key cellular processes: transcriptional regulation, cell-cell signaling, and cell adhesiveness. They include <i>IA-1</i> and <i>MEF2A</i>, two transcription factors required for neuronal development; <i>mGluR1</i> and<i> VILIP-1</i>, which encode proteins involved in neuronal communication, and <i>TSG-6 </i>that encodes a protein involved in cell adhesiveness. Of these, expression of <i>mGluR1</i> also increases in the female monkey hypothalamus at puberty. <i>Conclusions:</i> Increased expression of these genes in HHs may be relevant to the ability of some HHs to induce sexual precocity.
DOI: 10.6084/m9.figshare.5104711.v1
title: Supplementary Material for: Characterization of a balanced reciprocal translocation, rcp(9;11)(q27;q11) in cattle

description: Cytogenetic analysis of a phenotypically normal young bull from Marchigiana breed revealed the presence of an abnormal karyotype. The observation of longer and smaller chromosomes than BTA1 and BTA29, respectively in all metaphases suggested the presence of a reciprocal translocation. RBG-banding confirmed this hypothesis revealing the involvement of BTA9 and BTA11. FISH analyses using cattle-specific BAC clones (474A12 and 293G09 for BTA9; 035D03 for BTA11) identified rcp(9;11)(q27;q11) in the two regions affected. Moreover analyses performed on both parents established the ‘de novo’ origin of the anomaly. Comparison with human homologue sequences (HSA6q24.3→q25.3 for BTA9q27 and HSA2q11.1→q12.1 for BTA11q11) revealed that both breakpoint regions are gene rich as up to date at least 200 genes have been localized in these regions. Thus, further analyses are required to identify the sequences disrupted by the breakpoints and to verify their consequences on rcp carrier phenotype.