This site aggregates all the individual mybiocaddie datasets shared on GitHub
CTD contains manually curated data describing cross-species chemical-gene/protein interactions and chemical- and gene-disease relationships. The results provide insight into the molecular mechanisms underlying variable susceptibility and environmentally influenced diseases. These data will also provide insights into complex chemical-gene and protein interaction networks.
Background: The “fitness” of an infectious pathogen is defined as the ability of the pathogen to survive, reproduce, be transmitted, and cause disease. The fitness of multidrug-resistant tuberculosis (MDRTB) relative to drug-susceptible tuberculosis is cited as one of the most important determinants of MDRTB spread and epidemic size. To estimate the relative fitness of drug-resistant tuberculosis cases, we compared the incidence of tuberculosis disease among the household contacts of MDRTB index patients to that among the contacts of drug-susceptible index patients. Methods and Findings: This 3-y (2010–2013) prospective cohort household follow-up study in South Lima and Callao, Peru, measured the incidence of tuberculosis disease among 1,055 household contacts of 213 MDRTB index cases and 2,362 household contacts of 487 drug-susceptible index cases. A total of 35/1,055 (3.3%) household contacts of 213 MDRTB index cases developed tuberculosis disease, while 114/2,362 (4.8%) household contacts of 487 drug-susceptible index patients developed tuberculosis disease. The total follow-up time for drug-susceptible tuberculosis contacts was 2,620 person-years, while the total follow-up time for MDRTB contacts was 1,425 person-years. Using multivariate Cox regression to adjust for confounding variables including contact HIV status, contact age, socio-economic status, and index case sputum smear grade, the hazard ratio for tuberculosis disease among MDRTB household contacts was found to be half that for drug-susceptible contacts (hazard ratio 0.56, 95% CI 0.34–0.90, p = 0.017). The inference of transmission in this study was limited by the lack of genotyping data for household contacts. Capturing incident disease only among household contacts may also limit the extrapolation of these findings to the community setting. Conclusions: The low relative fitness of MDRTB estimated by this study improves the chances of controlling drug-resistant tuberculosis. However, fitter multidrug-resistant strains that emerge over time may make this increasingly difficult.
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ClinVar is a freely accessible, public archive of reports of the relationships among human variations and phenotypes, with supporting evidence. ClinVar thus facilitates access to and communication about the relationships asserted between human variation and observed health status, and the history of that interpretation. ClinVar processes submissions reporting variants found in patient samples, assertions made regarding their clinical significance, information about the submitter, and other supporting data. The alleles described in submissions are mapped to reference sequences, and reported according to the HGVS standard. ClinVar then presents the data for interactive users as well as those wishing to use ClinVar in daily workflows and other local applications. ClinVar works in collaboration with interested organizations to meet the needs of the medical genetics community as efficiently and effectively as possible.
Alzheimer’s disease is a neurodegenerative disorder accounting for more than 50% of cases of dementia. Diagnosis of Alzheimer’s disease relies on cognitive tests and analysis of amyloid beta, protein tau, and hyperphosphorylated tau in cerebrospinal fluid. Although these markers provide relatively high sensitivity and specificity for early disease detection, they are not suitable for monitor of disease progression. In the present study, authors used label-free shotgun mass spectrometry to analyse the cerebrospinal fluid proteome of Alzheimer’s disease patients and non-demented controls to identify potential biomarkers for Alzheimer’s disease. Authors processed the data using five programs (DecyderMS, Maxquant, OpenMS, PEAKS, and Sieve) and compared their results by means of reproducibility and peptide identification, including three different normalization methods. After depletion of high abundant proteins we found that Alzheimer’s disease patients had lower fraction of low-abundance proteins in cerebrospinal fluid compared to healthy controls (p<0.05). Consequently, global normalization was found to be less accurate compared to using spiked-in chicken ovalbumin for normalization. In addition, we determined that Sieve and OpenMS resulted in the highest reproducibility and PEAKS was the programs with the highest identification performance. Finally, authors successfully verified significantly lower levels (p<0.05) of eight proteins (A2GL, APOM, C1QB, C1QC, C1S, FBLN3, PTPRZ, and SEZ6) in Alzheimer’s disease compared to controls using an antibody-based detection method. These proteins are involved in different biological roles spanning from cell adhesion and migration, to regulation of the synapse and the immune system.
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MGI is the international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human health and disease. Data includes gene characterization, nomenclature, mapping, gene homologies among mammals, sequence links, phenotypes, allelic variants and mutants, and strain data.
From Analysis of protein-coding genetic variation in 60,706 humans Lek et al.: “ We have used this catalogue to calculate objective metrics of pathogenicity for sequence variants, and to identify genes subject to strong selection against various classes of mutation; identifying 3,230 genes with near-complete depletion of predicted protein-truncating variants, with 72% of these genes having no currently established human disease phenotype.”
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This Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house all publicly available QTL and trait mapping data (i.e. trait and genome location association data; collectively called “QTL data” on this site) on livestock animal species for easily locating and making comparisons within and between species. New database tools are continuely added to align the QTL and association data to other types of genome information, such as annotated genes, RH / SNP markers, and human genome maps. Besides the QTL data from species listed below, the QTLdb is open to house QTL/association date from other animal species where feasible. Note that the JAS along with other journals, now require that new QTL/association data be entered into a QTL database as part of their publication requirements.
BioGRID is an interaction repository with data compiled through comprehensive curation efforts. BioGRID currently holds over 980,000 interactions curated from both high-throughput datasets and individual focused studies, as derived from over 55,000 publications in the primary literature. Complete coverage of the entire literature is maintained for budding year (S. cerevisiae), fission yeast (S. pome), and thale cress (A. thaliana), and efforts to expand curation across multiple metazoan species are underway. All data are freely provided via the search index and available for download in standardized formats.
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“Gene Ontology” is a standard, specialising in the fields described under “scope and data types”, below. Until this entry is claimed, more information on this project can be found at http://purl.bioontology.org/ontology/GO. This text was generated automatically. If you work on the project responsible for “Gene Ontology” then please consider helping us by claiming this record and updating it appropriately.
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The Human Phenotype Ontology has been developed to provide a structured and controlled vocabulary for the phenotypic features encountered in human hereditary and other disease. The goal is to provide resource for the computational analysis of the human phenome, with a focus on monogenic diseases listed in the Online Mendelian Inheritance in Man (OMIM) and Orphanet databases, for which annotations are also provided.
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Online Mendelian Inheritance in Animals (OMIA) is a catalogue/compendium of inherited disorders, other (single-locus) traits, and genes in 218 animal species (other than human and mouse and rats, which have their own resources) authored by Professor Frank Nicholas of the University of Sydney, Australia, with help from many people over the years. OMIA information is stored in a database that contains textual information and references, as well as links to relevant PubMed and Gene records at the NCBI, and to OMIM and Ensembl.
OMIM is a comprehensive, authoritative compendium of human genes and genetic phenotypes that is freely available and updated daily. The full-text, referenced overviews in OMIM contain information on all known mendelian disorders and over 15,000 genes. OMIM focuses on the relationship between phenotype and genotype. It is updated daily, and the entries contain copious links to other genetics resources.
Orphanet is a database of information on rare diseases and orphan drugs for all publics. Its aim is to contribute to the improvement of the diagnosis, care and treatment of patients with rare diseases.
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ZFIN serves as the zebrafish model organism database. The long term goals for ZFIN are a) to be the community database resource for the laboratory use of zebrafish, b) to develop and support integrated zebrafish genetic, genomic and developmental information, c) to maintain the definitive reference data sets of zebrafish research information, d) to link this information extensively to corresponding data in other model organism and human databases, e) to facilitate the use of zebrafish as a model for human biology and f) to serve the needs of the research community. ZIRC is the Zebrafish International Resource Center, an independent NIH-funded facility providing a wide range of zebrafish lines, probes and health services. ZFIN works closely with ZIRC to connect our genetic data with available probes and fish lines.
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The cancer bioMarkers database is curated and maintained by several clinical and scientific experts in the field of precision oncology supported by the European Union’s Horizon 2020 funding. This database is currently being integrated with knowledge databases of other institutions in a collaborative effort of the Global Alliance for Genomics and Health. The contribution of the community is encouraged and proposals of edition or comments about the information contained in this database can be given by contacting us here or by using the feedback icon in the table.
FaceBase is a collaborative NIDCR-funded consortium to generate data in support of advancing research into craniofacial development and malformation. It serves as a community resource by generating large datasets of a variety of types and making them available to the wider research community via this website. Practices emphasize a comprehensive and multidisciplinary approach to understanding the developmental processes that create the face. The data offered spotlights high-throughput genetic, molecular, biological, imaging and computational techniques. One of the missions of this consortium is to facilitate cooperation and collaboration between projects.
FaceBase is a collaborative NIDCR-funded consortium to generate data in support of advancing research into craniofacial development and malformation. It serves as a community resource by generating large datasets of a variety of types and making them available to the wider research community via this website. Practices emphasize a comprehensive and multidisciplinary approach to understanding the developmental processes that create the face. The data offered spotlights high-throughput genetic, molecular, biological, imaging and computational techniques. One of the missions of this consortium is to facilitate cooperation and collaboration between projects.
Enhancer location: Mouse genome mm9, chr14:47230349-47231452; Name: mCF73 Vista Enhancer ID: mm387 Nearest craniofacial gene or locus: BMP4; Enhancer expression: positive Tissues where active: branchial arch, facial mesenchyme, nose, limbs, neural tube; Comment on OPT files: slightly damaged embryo;
Enhancer location: Mouse genome mm9, chr14:22932439-22935173; Name: mCF100; Nearest craniofacial gene or locus: ZFP503; Enhancer expression: positive; Tissues where active: branchial arch, eye, forebrain, limbs,midbrain
Enhancer location: Mouse genome mm9, chr14:24339368-24340818; Name: mCF103; Nearest craniofacial gene or locus: ZFP503; Enhancer expression: positive; Tissues where active: branchial arch; Comment on OPT files: signal lost?;
Enhancer location: Mouse genome mm9, chr2:4282958-4283735; Name: mCF106; Nearest craniofacial gene or locus: None; Enhancer expression: positive; Tissues where active: branchial arch; Comment on OPT files: damaged embryo / the signal is internal, see y sections for example
Enhancer location: Mouse genome mm9, chr2:4508633-4509808; Name: mCF109; Nearest craniofacial gene or locus: None; Enhancer expression: positive; Tissues where active: branchial arch, facial mesenchyme, nose, limbs; Comment on OPT files: no clip file
Enhancer location: Mouse genome mm9, chr5:38216912-38220459; Name: mCF112; Nearest craniofacial gene or locus: Msx1; Enhancer expression: positive; Tissues where active: branchial arch, ear, eye, facial mesenchyme, genital tubercle, hindbrain, limb, midbrain, nose, somite
Enhancer location: Mouse genome mm9, chr5:38292345-38293728; Name: mCF113; Nearest craniofacial gene or locus: Msx1; Enhancer expression: positive; Tissues where active: facial mesenchyme, nose; Comment on OPT files: no clip file
Enhancer location: Mouse genome mm9, chr5:38308981-38309832; Name: mCF114; Nearest craniofacial gene or locus: Msx1; Enhancer expression: positive; Tissues where active: branchial arch, facial mesenchyme, genital tubercle, limb; Comment on OPT files: slightly damaged embryo
Enhancer location: Mouse genome mm9, chr15:63025492-63026341; Name: mCF144; Nearest craniofacial gene or locus: NOG; Enhancer expression: positive; Tissues where active: branchial arch, limbs, other; Comment on OPT files: no clip file
Enhancer location: Mouse genome mm9, chr13:119304649-119305832; Name: mCF149; Nearest craniofacial gene or locus: FGF10; Enhancer expression: positive; Tissues where active: branchial arch; Comment on OPT files: embryo damaged during OPT. Has to be re-sent.
Enhancer location: Mouse genome mm9, chr14:46563519-46564802; Name: mCF70; Nearest craniofacial gene or locus: BMP4; Enhancer expression: positive; Tissues where active: branchial arch, facial mesenchyme, nose, limbs, neural tube; Comment on OPT files: slightly damaged embryo
The data preparation protocols for this study are described here. See Genome Browser Track Enhancer location: Mouse genome mm9, chr14:24305238-24305824; Name: mCF101; Vista Enhancer ID: mm415; Nearest craniofacial gene or locus: ZFP503; This data set includes the following: – Apdf file that summarizes the whole-mount data for the tested element. This file includes light microscopy whole-mount images of the LacZ reporter gene expression in mouse embryos, a summary of the annotation of the expression pattern, the DNA sequence of the tested element in Fasta format, and the sequences of the primers used to generate the test construct. To see this information in the Vista Enhancer Browser at Lawrence Berkeley Laboratory, click here. – Tested element.txt: A text file that includes information about the location, the proximal gene, and the tissues where the enhancer is active, if any, as stated above. Download text file only.
The data preparation protocols for this study are described here. See Genome Browser Track Enhancer location: Mouse genome mm9, chr14:24313049-24314033; Name: mCF102; Vista Enhancer ID: mm416; Nearest craniofacial gene or locus: ZFP503 This data set includes the following: – Apdf file that summarizes the whole-mount data for the tested element. This file includes light microscopy whole-mount images of the LacZ reporter gene expression in mouse embryos, a summary of the annotation of the expression pattern, the DNA sequence of the tested element in Fasta format, and the sequences of the primers used to generate the test construct. To see this information in the Vista Enhancer Browser at Lawrence Berkeley Laboratory, click here. – Tested element.txt: A text file that includes information about the location, the proximal gene, and the tissues where the enhancer is active, if any, as stated above. Download text file only.
The data preparation protocols for this study are described here. See Genome Browser Track Enhancer location: Mouse genome mm9, chr2:4269384-4270396; Name: mCF105; Vista Enhancer ID: mm419; Nearest craniofacial gene or locus: None; Enhancer Status: Other;This data set includes the following: – Apdf file that summarizes the whole-mount data for the tested element. This file includes light microscopy whole-mount images of the LacZ reporter gene expression in mouse embryos, a summary of the annotation of the expression pattern, the DNA sequence of the tested element in Fasta format, and the sequences of the primers used to generate the test construct. To see this information in the Vista Enhancer Browser at Lawrence Berkeley Laboratory, click here. – Tested element.txt: A text file that includes information about the location, the proximal gene, and the tissues where the enhancer is active, if any, as stated above. Download text file only.
The data preparation protocols for this study are described here. See Genome Browser Track Enhancer location: Mouse genome mm9, chr2:4477194-4478921; Name: mCF108; Vista Enhancer ID: mm422; Nearest craniofacial gene or locus: None; Enhancer Status: Other; This data set includes the following: – Apdf file that summarizes the whole-mount data for the tested element. This file includes light microscopy whole-mount images of the LacZ reporter gene expression in mouse embryos, a summary of the annotation of the expression pattern, the DNA sequence of the tested element in Fasta format, and the sequences of the primers used to generate the test construct. To see this information in the Vista Enhancer Browser at Lawrence Berkeley Laboratory, click here. – Tested element.txt: A text file that includes information about the location, the proximal gene, and the tissues where the enhancer is active, if any, as stated above. Download text file only.
The data preparation protocols for this study are described here. See Genome Browser Track Enhancer location: Mouse genome mm9, chr1:194615789-194617278; Name: mCF116; Vista Enhancer ID: mm430; Nearest craniofacial gene or locus: IRF6 This data set includes the following: – Apdf file that summarizes the whole-mount data for the tested element. This file includes light microscopy whole-mount images of the LacZ reporter gene expression in mouse embryos, a summary of the annotation of the expression pattern, the DNA sequence of the tested element in Fasta format, and the sequences of the primers used to generate the test construct. To see this information in the Vista Enhancer Browser at Lawrence Berkeley Laboratory, click here. – Tested element.txt: A text file that includes information about the location, the proximal gene, and the tissues where the enhancer is active, if any, as stated above. Download text file only.
The data preparation protocols for this study are described here. See Genome Browser Track Enhancer location: Mouse genome mm9, chr1:194677837-194678651; Name: mCF119; Vista Enhancer ID: mm433; Nearest craniofacial gene or locus: IRF6; This data set includes the following: – Apdf file that summarizes the whole-mount data for the tested element. This file includes light microscopy whole-mount images of the LacZ reporter gene expression in mouse embryos, a summary of the annotation of the expression pattern, the DNA sequence of the tested element in Fasta format, and the sequences of the primers used to generate the test construct. To see this information in the Vista Enhancer Browser at Lawrence Berkeley Laboratory, click here. – Tested element.txt: A text file that includes information about the location, the proximal gene, and the tissues where the enhancer is active, if any, as stated above. Download text file only.
The data preparation protocols for this study are described here. See Genome Browser Track Enhancer location: Mouse genome mm9, chr3:121656460-121657306; Name: mCF120; Vista Enhancer ID: mm433; Nearest craniofacial gene or locus: ABCA4; This data set includes the following: – Apdf file that summarizes the whole-mount data for the tested element. This file includes light microscopy whole-mount images of the LacZ reporter gene expression in mouse embryos, a summary of the annotation of the expression pattern, the DNA sequence of the tested element in Fasta format, and the sequences of the primers used to generate the test construct. To see this information in the Vista Enhancer Browser at Lawrence Berkeley Laboratory, click here. – Tested element.txt: A text file that includes information about the location, the proximal gene, and the tissues where the enhancer is active, if any, as stated above. Download text file only.
The data preparation protocols for this study are described here. See Genome Browser Track Enhancer location: Mouse genome mm9, chr11:87994053-87995154; Name: mCF124; Vista Enhancer ID: mm438; Nearest craniofacial gene or locus: NOG; Enhancer Status: Other; This data set includes the following: – Apdf file that summarizes the whole-mount data for the tested element. This file includes light microscopy whole-mount images of the LacZ reporter gene expression in mouse embryos, a summary of the annotation of the expression pattern, the DNA sequence of the tested element in Fasta format, and the sequences of the primers used to generate the test construct. o see this information in the Vista Enhancer Browser at Lawrence Berkeley Laboratory, click here. – Tested element.txt: A text file that includes information about the location, the proximal gene, and the tissues where the enhancer is active, if any, as stated above. Download text file only.
The data preparation protocols for this study are described here. See Genome Browser Track Enhancer location: Mouse genome mm9, chr11:88087585-88089577; Name: mCF125; Vista Enhancer ID: mm439; Nearest craniofacial gene or locus: NOG; Enhancer status: Other;This data set includes the following: – Apdf file that summarizes the whole-mount data for the tested element. This file includes light microscopy whole-mount images of the LacZ reporter gene expression in mouse embryos, a summary of the annotation of the expression pattern, the DNA sequence of the tested element in Fasta format, and the sequences of the primers used to generate the test construct. To see this information in the Vista Enhancer Browser at Lawrence Berkeley Laboratory, click here. – Tested element.txt: A text file that includes information about the location, the proximal gene, and the tissues where the enhancer is active, if any, as stated above. Download text file only.
The data preparation protocols for this study are described here. See Genome Browser Track Enhancer location: Mouse genome mm9, chr11:88341352-88342978; Name: mCF126; Vista Enhancer ID: mm440; Nearest craniofacial gene or locus: NOG; Enhancer Status: Other;This data set includes the following: – Apdf file that summarizes the whole-mount data for the tested element. This file includes light microscopy whole-mount images of the LacZ reporter gene expression in mouse embryos, a summary of the annotation of the expression pattern, the DNA sequence of the tested element in Fasta format, and the sequences of the primers used to generate the test construct. To see this information in the Vista Enhancer Browser at Lawrence Berkeley Laboratory, click here. – Tested element.txt: A text file that includes information about the location, the proximal gene, and the tissues where the enhancer is active, if any, as stated above. Download text file only.
The data preparation protocols for this study are described here. See Genome Browser Track Enhancer location: Mouse genome mm9, chr19:59341620-59342768; Name: mCF133; Vista Enhancer ID: mm447; Nearest craniofacial gene or locus: VAX1; Enhancer expression: Other; This data set includes the following: – Apdf file that summarizes the whole-mount data for the tested element. This file includes light microscopy whole-mount images of the LacZ reporter gene expression in mouse embryos, a summary of the annotation of the expression pattern, the DNA sequence of the tested element in Fasta format, and the sequences of the primers used to generate the test construct. To see this information in the Vista Enhancer Browser at Lawrence Berkeley Laboratory, click here. – Tested element.txt: A text file that includes information about the location, the proximal gene, and the tissues where the enhancer is active, if any, as stated above. Download text file only.
The data preparation protocols for this study are described here. See Genome Browser Track Enhancer location: Mouse genome mm9, chr19:60091349-60092721; Name: mCF135; Vista Enhancer ID: mm449; Nearest craniofacial gene or locus: VAX1; Enhancer expression: other; This data set includes the following: – Apdf file that summarizes the whole-mount data for the tested element. This file includes light microscopy whole-mount images of the LacZ reporter gene expression in mouse embryos, a summary of the annotation of the expression pattern, the DNA sequence of the tested element in Fasta format, and the sequences of the primers used to generate the test construct. To see this information in the Vista Enhancer Browser at Lawrence Berkeley Laboratory, click here. – Tested element.txt: A text file that includes information about the location, the proximal gene, and the tissues where the enhancer is active, if any, as stated above. Download text file only.
The data preparation protocols for this study are described here. See Genome Browser Track Enhancer location: Mouse genome mm9, chr6:143245796-143246980; Name: mCF136; Vista Enhancer ID: mm450; Nearest craniofacial gene or locus: NOG; Enhancer expression: negative; This data set includes the following: – Apdf file that summarizes the whole-mount data for the tested element. This file includes light microscopy whole-mount images of the LacZ reporter gene expression in mouse embryos, a summary of the annotation of the expression pattern, the DNA sequence of the tested element in Fasta format, and the sequences of the primers used to generate the test construct. To see this information in the Vista Enhancer Browser at Lawrence Berkeley Laboratory, click here. – Tested element.txt: A text file that includes information about the location, the proximal gene, and the tissues where the enhancer is active, if any, as stated above. Download text file only.
The data preparation protocols for this study are described here. See Genome Browser Track Enhancer location: Mouse genome mm9, chr6:143385863-143387546; Name: mCF137; Vista Enhancer ID: mm451; Nearest craniofacial gene or locus: Sox4; Enhancer expression: Other; This data set includes the following: – Apdf file that summarizes the whole-mount data for the tested element. This file includes light microscopy whole-mount images of the LacZ reporter gene expression in mouse embryos, a summary of the annotation of the expression pattern, the DNA sequence of the tested element in Fasta format, and the sequences of the primers used to generate the test construct. To see this information in the Vista Enhancer Browser at Lawrence Berkeley Laboratory, click here. – Tested element.txt: A text file that includes information about the location, the proximal gene, and the tissues where the enhancer is active, if any, as stated above. Download text file only.
The data preparation protocols for this study are described here. See Genome Browser Track Enhancer location: Mouse genome mm9, chr6:144893166-144894534; Name: mCF142; Vista Enhancer ID: mm456; Nearest craniofacial gene or locus: Sox5; Enhancer expression: Other; This data set includes the following: – Apdf file that summarizes the whole-mount data for the tested element. This file includes light microscopy whole-mount images of the LacZ reporter gene expression in mouse embryos, a summary of the annotation of the expression pattern, the DNA sequence of the tested element in Fasta format, and the sequences of the primers used to generate the test construct. To see this information in the Vista Enhancer Browser at Lawrence Berkeley Laboratory, click here. – Tested element.txt: A text file that includes information about the location, the proximal gene, and the tissues where the enhancer is active, if any, as stated above. Download text file only.
The data preparation protocols for this study are described here. See Genome Browser Track>; Enhancer location: Mouse genome mm9, chr15:62734249-62735453; Name: mCF143; Vista Enhancer ID: mm457; Nearest craniofacial gene or locus: 8q24; Enhancer expression: Negative; This data set includes the following: – Apdf file that summarizes the whole-mount data for the tested element. This file includes light microscopy whole-mount images of the LacZ reporter gene expression in mouse embryos, a summary of the annotation of the expression pattern, the DNA sequence of the tested element in Fasta format, and the sequences of the primers used to generate the test construct.To see this information in the Vista Enhancer Browser at Lawrence Berkeley Laboratory, click here. – Tested element.txt: A text file that includes information about the location, the proximal gene, and the tissues where the enhancer is active, if any, as stated above. Download text file only.
The data preparation protocols for this study are described here. See Genome Browser Track Enhancer location: Mouse genome mm9, chr14:46843672-46844634; Name: mCF71; Vista Enhancer ID: mm385; Nearest craniofacial gene or locus: BMP4; Enhancer expression: negative; This data set includes the following: – Apdf file that summarizes the whole-mount data for the tested element. This file includes light microscopy whole-mount images of the LacZ reporter gene expression in mouse embryos, a summary of the annotation of the expression pattern, the DNA sequence of the tested element in Fasta format, and the sequences of the primers used to generate the test construct. To see this information in the Vista Enhancer Browser at Lawrence Berkeley Laboratory, click here. – Tested element.txt: A text file that includes information about the location, the proximal gene, and the tissues where the enhancer is active, if any, as stated above. Download text file only.
The data preparation protocols for this study are described here. See Genome Browser Track Enhancer location: Mouse genome mm9, chr14:46867125-46868800; Name: mCF72; Vista Enhancer ID: mm386; Nearest craniofacial gene or locus: BMP4; Enhancer expression: negative; This data set includes the following: – Apdf file that summarizes the whole-mount data for the tested element. This file includes light microscopy whole-mount images of the LacZ reporter gene expression in mouse embryos, a summary of the annotation of the expression pattern, the DNA sequence of the tested element in Fasta format, and the sequences of the primers used to generate the test construct. To see this information in the Vista Enhancer Browser at Lawrence Berkeley Laboratory, click here. – Tested element.txt: A text file that includes information about the location, the proximal gene, and the tissues where the enhancer is active, if any, as stated above. Download text file only.
The data preparation protocols for this study are described here. See Genome Browser Track Enhancer location: Mouse genome mm9, chr5:19999596-20000707; Name: mCF75; Vista Enhancer ID: mm389; Nearest craniofacial gene or locus: None; Enhancer expression: other; This data set includes the following: – Apdf file that summarizes the whole-mount data for the tested element. This file includes light microscopy whole-mount images of the LacZ reporter gene expression in mouse embryos, the DNA sequence of the tested element in Fasta format, and the sequences of the primers used to generate the test construct. To see this information in the Vista Enhancer Browser at Lawrence Berkeley Laboratory, click here. – Tested element.txt: A text file that includes information about the location, the proximal gene, and the tissues where the enhancer is active, if any, as stated above. Download text file only.
The data preparation protocols for this study are described here See Genome Browser Track Enhancer location: Mouse genome mm9, chr5:20455843-20456804; Name: mCF76; Vista Enhancer ID: mm390; Nearest craniofacial gene or locus: none; Enhancer expression: negative; This data set includes the following: – Apdf file that summarizes the whole-mount data for the tested element. This file includes light microscopy whole-mount images of the LacZ reporter gene expression in mouse embryos, a summary of the annotation of the expression pattern, the DNA sequence of the tested element in Fasta format, and the sequences of the primers used to generate the test construct. To see this information in the Vista Enhancer Browser at Lawrence Berkeley Laboratory, click here. – Tested element.txt: A text file that includes information about the location, the proximal gene, and the tissues where the enhancer is active, if any, as stated above. Download text file only.
The data preparation protocols for this study are described here See Genome Browser Track Enhancer location: Mouse genome mm9, chr5:21001721-21003173; Name: mCF77; Vista Enhancer ID: mm391; Nearest craniofacial gene or locus: none; Enhancer expression: negative; This data set includes the following: – Apdf file that summarizes the whole-mount data for the tested element. This file includes light microscopy whole-mount images of the LacZ reporter gene expression in mouse embryos, a summary of the annotation of the expression pattern, the DNA sequence of the tested element in Fasta format, and the sequences of the primers used to generate the test construct. To see this information in the Vista Enhancer Browser at Lawrence Berkeley Laboratory, click here. – Tested element.txt: A text file that includes information about the location, the proximal gene, and the tissues where the enhancer is active, if any, as stated above. Download text file only.
The data preparation protocols for this study are described here. See Genome Browser Track Enhancer location: Mouse genome mm9, chr6: 4433466-4435322; Name: mCF84; Vista Enhancer ID: mm398; Nearest craniofacial gene or locus: Col1A2; Enhancer expression: other; This data set includes the following: – Apdf file that summarizes the whole-mount data for the tested element. This file includes light microscopy whole-mount images of the LacZ reporter gene expression in mouse embryos, a summary of the annotation of the expression pattern, the DNA sequence of the tested element in Fasta format, and the sequences of the primers used to generate the test construct. To see this information in the Vista Enhancer Browser at Lawrence Berkeley Laboratory, click here. – Tested element.txt: A text file that includes information about the location, the proximal gene, and the tissues where the enhancer is active, if any, as stated above. Download text file only.
The data preparation protocols for this study are described here. See Genome Browser Track Enhancer location: Mouse genome mm9, chr6: 4438997-4440635; Name: mCF85; Vista Enhancer ID: mm399; Nearest craniofacial gene or locus: Col1A2; Enhancer expression: negative; This data set includes the following: – Apdf file that summarizes the whole-mount data for the tested element. This file includes light microscopy whole-mount images of the LacZ reporter gene expression in mouse embryos, a summary of the annotation of the expression pattern, the DNA sequence of the tested element in Fasta format, and the sequences of the primers used to generate the test construct. To see this information in the Vista Enhancer Browser at Lawrence Berkeley Laboratory, click here. – Tested element.txt: A text file that includes information about the location, the proximal gene, and the tissues where the enhancer is active, if any, as stated above. Download text file only.
The data preparation protocols for this study are described here See Genome Browser Track Enhancer location: Mouse genome mm9, chr6:50760703-50761820; Name: mCF87; Vista Enhancer ID: mm401; Nearest craniofacial gene or locus: none; Enhancer expression: negative; This data set includes the following: – Apdf file that summarizes the whole-mount data for the tested element. This file includes light microscopy whole-mount images of the LacZ reporter gene expression in mouse embryos, a summary of the annotation of the expression pattern, the DNA sequence of the tested element in Fasta format, and the sequences of the primers used to generate the test construct. To see this information in the Vista Enhancer Browser at Lawrence Berkeley Laboratory, click here. – Tested element.txt: A text file that includes information about the location, the proximal gene, and the tissues where the enhancer is active, if any, as stated above. Download text file only.
Enhancer location: Mouse genome mm9, chr6:50771120-50773588; Name: mCF88; Vista Enhancer ID: mm402; Nearest craniofacial gene or locus: none; Enhancer expression: positive; Tissues where active: branchial arch, forebrain, hindbrain, midbrain, neural tube, other
The data preparation protocols for this study are described here The results are also presented as tracks on the FaceBase Genome Browser mirror. Enhancer location: Mouse genome mm9, chr6:50771120-50773588; Name: mCF88; Vista Enhancer ID: mm402; Nearest craniofacial gene or locus: none; Enhancer expression: positive; Tissues where active: branchial arch, forebrain, hindbrain, midbrain, neural tube, other; This data set includes the following: – Apdf file that summarizes the whole-mount data for the tested element. This file includes light microscopy whole-mount images of the LacZ reporter gene expression in mouse embryos, a summary of the annotation of the expression pattern, the DNA sequence of the tested element in Fasta format, and the sequences of the primers used to generate the test construct. To see this information in the Vista Enhancer Browser at Lawrence Berkeley Laboratory, click here. – Tested element.txt: A text file that includes information about the location, the proximal gene, and the tissues where the enhancer is active, if any, as stated above. Download text file only.
Enhancer location: Mouse genome mm9, chr6:50906958-50908237; Name: mCF90; Vista Enhancer ID: mm404; Nearest craniofacial gene or locus: none; Enhancer expression: positive; Tissues where active: branchial arch
The data preparation protocols for this study are described here. The results are also presented as tracks on the FaceBase Genome Browser mirror. Enhancer location: Mouse genome mm9, chr6:50906958-50908237; Name: mCF90; Vista Enhancer ID: mm404; Nearest craniofacial gene or locus: none; Enhancer expression: positive; Tissues where active: branchial arch; This data set includes the following: – Apdf file that summarizes the whole-mount data for the tested element. This file includes light microscopy whole-mount images of the LacZ reporter gene expression in mouse embryos, a summary of the annotation of the expression pattern, the DNA sequence of the tested element in Fasta format, and the sequences of the primers used to generate the test construct. To see this information in the Vista Enhancer Browser at Lawrence Berkeley Laboratory, click here. – Tested element.txt: A text file that includes information about the location, the proximal gene, and the tissues where the enhancer is active, if any, as stated above. Download text file only.
The data preparation protocols for this study are described here. See Genome Browser Track Enhancer location: Mouse genome mm9, chr6:51001775-51003272; Name: mCF93; Vista Enhancer ID: mm407; Nearest craniofacial gene or locus: none; Enhancer expression: other; This data set includes the following: – Apdf file that summarizes the whole-mount data for the tested element. This file includes light microscopy whole-mount images of the LacZ reporter gene expression in mouse embryos, a summary of the annotation of the expression pattern, the DNA sequence of the tested element in Fasta format, and the sequences of the primers used to generate the test construct. To see this information in the Vista Enhancer Browser at Lawrence Berkeley Laboratory, click here. – Tested element.txt: A text file that includes information about the location, the proximal gene, and the tissues where the enhancer is active, if any, as stated above. Download text file only.
The data preparation protocols for this study are described here See Genome Browser Track Enhancer location: Mouse genome mm9, chr6:51054237-51055194; Name: mCF94; Vista Enhancer ID: mm408; Nearest craniofacial gene or locus: none; Enhancer expression: negative; This data set includes the following: – Apdf file that summarizes the whole-mount data for the tested element. This file includes light microscopy whole-mount images of the LacZ reporter gene expression in mouse embryos, a summary of the annotation of the expression pattern, the DNA sequence of the tested element in Fasta format, and the sequences of the primers used to generate the test construct. To see this information in the Vista Enhancer Browser at Lawrence Berkeley Laboratory, click here. – Tested element.txt: A text file that includes information about the location, the proximal gene, and the tissues where the enhancer is active, if any, as stated above. Download text file only.
The data preparation protocols for this study are described here. See Genome Browser Track Enhancer location: Mouse genome mm9, chr6:51122426-51123469; Name: mCF95; Vista Enhancer ID: mm409; Nearest craniofacial gene or locus: none; Enhancer expression: negative; This data set includes the following: – Apdf file that summarizes the whole-mount data for the tested element. This file includes light microscopy whole-mount images of the LacZ reporter gene expression in mouse embryos, a summary of the annotation of the expression pattern, the DNA sequence of the tested element in Fasta format, and the sequences of the primers used to generate the test construct. To see this information in the Vista Enhancer Browser at Lawrence Berkeley Laboratory, click here. – Tested element.txt: A text file that includes information about the location, the proximal gene, and the tissues where the enhancer is active, if any, as stated above. Download text file only.
The data preparation protocols for this study are described here. See Genome Browser Track Enhancer location: Mouse genome mm9, chr6:51283777-51284475; Name: mCF96; Vista Enhancer ID: mm410; Nearest craniofacial gene or locus: none; Enhancer expression: negative; This data set includes the following: – Apdf file that summarizes the whole-mount data for the tested element. This file includes light microscopy whole-mount images of the LacZ reporter gene expression in mouse embryos, a summary of the annotation of the expression pattern, the DNA sequence of the tested element in Fasta format, and the sequences of the primers used to generate the test construct. To see this information in the Vista Enhancer Browser at Lawrence Berkeley Laboratory, click here. – Tested element.txt: A text file that includes information about the location, the proximal gene, and the tissues where the enhancer is active, if any, as stated above. Download text file only.
Enhancer location: Mouse genome mm9, chr5:38358865-38360435; Name: mCF115; Nearest craniofacial gene or locus: Msx1; Enhancer expression: positive; Tissues where active: branchial arch, facial mesenchyme, genital tubercle, limb
Enhancer location: Mouse genome mm9, chr6:50933970-50934809; Name: mCF92; Nearest craniofacial gene or locus: none; Enhancer expression: positive; Tissues where active: facial mesenchyme, limbs
Enhancer location: Mouse genome mm9, chr19:58446412-58447549; Name: mCF131; Nearest craniofacial gene or locus: VAX1; Enhancer expression: positive; Tissues where active: branchial arch, facial mesenchyme, nose, limbs, neural tube; Comment on OPT files: no clip file
Enhancer location: Mouse genome mm9, chr19:59497704-59500058; Name: mCF134; Nearest craniofacial gene or locus: VAX1; Enhancer expression: positive; Tissues where active: facial mesenchyme, nose, limbs; Comment on OPT files: slightly damaged embryo
Enhancer location: Mouse genome mm9, chr3:121750391-121752165 Name: mCF121; Nearest craniofacial gene or locus: ABCA4; Enhancer expression: positive; Tissues where active: nose, facial mesenchyme, forebrain; Comment on OPT files: damaged embryo
Enhancer location: Mouse genome mm9, chr6: 4503540-4505066; Name: mCF86; Nearest craniofacial gene or locus: Col1A2; Enhancer expression: positive; Tissues where active: branchial arch, facial mesenchyme, nose, limbs; Comment on OPT files: signal is internal
Enhancer location: Mouse genome mm9, chr6:50874551-50876236; Name: mCF89; Nearest craniofacial gene or locus: BMP4; Enhancer expression: positive; Tissues where active: branchial arch
Enhancer location: Mouse genome mm9, chr6:50931070-50932326; Name: mCF91; Nearest craniofacial gene or locus: none; Enhancer expression: positive; Tissues where active: branchial arch, facial mesenchyme, other, trigeminal V; Comment on OPT files: signal is internal
This dataset includes the results of ChIP-Seq analysis of p300 bound regions in E13.5 mouse palates. The results are also presented as tracks on the Genome Browser The data include the following information for each peak called: – ranking. Called peaks are ranked by maximum coverage, those with equal maximum coverage are then ranked by local p-value. – the location of the peak, shown as chromosome start and end positions (mouse genome build mm9) – peak length – position of the peak summit – tags: the number of reads in peaks (# reads in region, not maximum read coverage depth) – score: -(log(pvalue)) – fold enrichment: enrichment in peak vs input sample – FDR: false-discovery rate annotation based on post-peak calling filtering of peaks based on genome annotation To download the data, log in and click on the “Download dataset” button.
This dataset includes the results of RNA-Seq analysis in E13.5 mouse palates. The downloadable Excel file includes for each gene: – gene: official mouse gene symbol – gene length (bp, exons only) – RPKM (Reads per kb / million reads) in two replicate samples To download the data, log in and click on the "Download dataset" button. In addition to the tabulated Excel format, the same data can also be viewed as genome-wide coverage maps on the FaceBase Genome Browser mirror
This dataset includes the results of RNA-Seq analysis in E13.5 mouse palates. The downloadable Excel file includes for each gene: – gene: official mouse gene symbol – gene length (bp, exons only) – RPKM (Reads per kb / million reads) in two replicate samples To download the data, log in and click on the "Download dataset" button. In addition to the tabulated Excel format, the same data can also be viewed as genome-wide coverage maps on the Genome Browser
Enhancer location: Mouse genome mm9, chr16:15194506-15196207; Name: mCF69; Vista Enhancer ID: mm383; Nearest craniofacial gene or locus: Snai2; Enhancer expression: positive; Tissues where active: branchial arch, nose, facial mesenchyme, other; Comment on OPT files: none
Enhancer location: Mouse genome mm9, chr16: 15084685-15085804; Name: mCF152; Vista Enhancer ID: mm466; Nearest craniofacial gene or locus: Snai2; Enhancer expression: positive; Tissues where active: branchial arch, nose, tail, hindbrain, limb; Comment on OPT files: none
Enhancer location: Mouse genome mm9, chr8: 26453164-26454807; Name: mCF159; Vista Enhancer ID: mm610; Nearest craniofacial gene or locus: Fgfr1; Enhancer expression: positive; Tissues where active: branchial arch, facial mesenchyme, limb, other; Comment on OPT files: none
Enhancer location: Mouse genome mm9, chr8: 26550663-26552575; Name: mCF160; Vista Enhancer ID: mm919; Nearest craniofacial gene or locus: Fgfr1; Enhancer expression: positive; Tissues where active: facial mesenchyme, limb; Comment on OPT files: none
Enhancer location: Mouse genome mm9, chr1: 56343177-56344388; Name: mCF162; Vista Enhancer ID: mm613; Nearest craniofacial gene or locus: None; Enhancer expression: positive; Tissues where active: branchial arch, ear; Comment on OPT files: none
Enhancer location: Mouse genome mm9, chr8:26653487-26656234; Name: mCF161; Vista Enhancer ID: mm612; Nearest craniofacial gene or locus: Fgfr1; Enhancer expression: positive; Tissues where active: branchial arch, eye, nose, hindbrain, forebrain, limb, midbrain; Comment on OPT files: none
Enhancer location: Mouse genome mm9, chr5:112006329-112007316; Name: mCF170; Vista Enhancer ID: mm621; Nearest craniofacial gene or locus: Mn1; Enhancer expression: positive; Tissues where active: branchial arch; Comment on OPT files:
Enhancer location: Mouse genome mm9, chr5:112030286-112031759; Name: mCF171; Vista Enhancer ID: mm622; Nearest craniofacial gene or locus: Mn1; Enhancer expression: positive; Tissues where active: branchial arch; Comment on OPT files:
Enhancer location: Mouse genome mm9, chr5: 112104097-112105406; Name: mCF172; Vista Enhancer ID: mm921; Nearest craniofacial gene or locus: Mn1; Enhancer expression: positive; Tissues where active: facial mesenchyme, other; Comment on OPT files:
Enhancer location: Mouse genome mm9, chr13: 48874997-48876671; Name: mCF175; Vista Enhancer ID: mm922; Nearest craniofacial gene or locus: Barx1; Enhancer expression: positive; Tissues where active: branchial arch, hindbrain, midbrain; Comment on OPT files:
Enhancer location: Mouse genome mm9, chr15: 60684551-60685838; Name: mCF191; Vista Enhancer ID: mm642; Nearest craniofacial gene or locus: 8q24; Enhancer expression: positive; Tissues where active: branchial arch, ear, eye, heart, nose, facial mesenchyme, dorsal root ganglion, forebrain, limb, midbrain; Comment on OPT files:
Enhancer location: Mouse genome mm9, chr1: 194624291-194626894; Name: mCF195; Vista Enhancer ID: mm646; Nearest craniofacial gene or locus: Irf6; Enhancer expression: positive; Tissues where active: branchial arch, nose, facial mesenchyme, forebrain, limb, somite; Comment on OPT files:
Enhancer location: Mouse genome mm9, chr17: 44754669-44756591; Name: mCF205; Vista Enhancer ID: mm924; Nearest craniofacial gene or locus: Runx2; Enhancer expression: positive; Tissues where active: branchial arch, facial mesenchyme; Comment on OPT files:
Enhancer location: Mouse genome mm9, chr17: 44859063-44860738; Name: mCF206; Vista Enhancer ID: mm657; Nearest craniofacial gene or locus: Runx2; Enhancer expression: positive; Tissues where active: branchial arch; Comment on OPT files:
Enhancer location: Mouse genome mm9, chr13: 119639284-119640197; Name: mCF208; Vista Enhancer ID: mm605; Nearest craniofacial gene or locus: Fgf10; Enhancer expression: positive; Tissues where active: facial mesenchyme, trigeminal V (ganglion, cranial); Comment on OPT files:
Enhancer location: Mouse genome mm9, chr13: 116476829-116478253; Name: mCF219; Vista Enhancer ID: mm933; Nearest craniofacial gene or locus: Isl1; Enhancer expression: positive; Tissues where active: nose, cranial nerve, dorsal root ganglion; Comment on OPT files:
Enhancer location: Mouse genome mm9, chr7: 137569281-137570835; Name: mCF224; Vista Enhancer ID: mm938; Nearest craniofacial gene or locus: Fgfr2; Enhancer expression: positive; Tissues where active: eye, tail, other, limb; Comment on OPT files:
Enhancer location: Mouse genome mm9, chr5: 12505539-12509076; Name: mAN261; Vista Enhancer ID: mm832; Nearest craniofacial gene or locus: Sema3d; Enhancer expression: positive; Tissues where active: branchial arch, ear, nose; Comment on OPT files:
Enhancer location: Mouse genome mm9, chr1: 93859505-93862537; Name: mAN330; Vista Enhancer ID: mm901; Nearest craniofacial gene or locus: Twist2; Enhancer expression: positive; Tissues where active: branchial arch; Comment on OPT files:
Enhancer location: Mouse genome mm9, chr10: 36203387-36205893; Name: mAN32; Vista Enhancer ID: mm693; Nearest craniofacial gene or locus: none; Enhancer expression: positive; Tissues where active: nose, forebrain, limb, midbrain; Comment on OPT files:
Enhancer location: Mouse genome mm9, chr9: 87943415-87945786; Name: mAN327; Vista Enhancer ID: mm898; Nearest craniofacial gene or locus: none; Enhancer expression: positive; Tissues where active: branchial arch, limb; Comment on OPT files:
Enhancer location: Human genome hg19, chr4: 4522867-4524050; Name: UL198; Vista Enhancer ID: hs746; Nearest craniofacial gene or locus: Msx1; Enhancer expression: positive; Tissues where active: branchial arch; Comment on OPT files:
Enhancer location: Human genome hg19, chr5: 174160174-174161818; Name: CF6; Vista Enhancer ID: hs1256; Nearest craniofacial gene or locus: Msx2; Enhancer expression: positive; Tissues where active: nose, hindbrain, forebrain, limb; Comment on OPT files: no 3D movie available
This dataset includes the results of ChIP-Seq analysis of p300 bound regions in E14.5 mouse palates. The results are also presented as tracks on the Genome Browser The data include the following information for each peak called: – ranking. Called peaks are ranked by maximum coverage, those with equal maximum coverage are then ranked by local p-value. – the location of the peak, shown as chromosome start and end positions (mouse genome build mm9) – peak length – position of the peak summit – tags: the number of reads in peaks (# reads in region, not maximum read coverage depth) – score: -(log(pvalue)) – fold enrichment: enrichment in peak vs input sample – FDR: false-discovery rate annotation based on post-peak calling filtering of peaks based on genome annotation To download the data, log in and click on the "Download dataset" button.
This dataset includes the results of ChIP-Seq analysis of p300 bound regions in E15.5 mouse palates. The results are also presented as tracks on the Genome Browser The data include the following information for each peak called: – ranking. Called peaks are ranked by maximum coverage, those with equal maximum coverage are then ranked by local p-value. – the location of the peak, shown as chromosome start and end positions (mouse genome build mm9) – peak length – position of the peak summit – tags: the number of reads in peaks (# reads in region, not maximum read coverage depth) – score: -(log(pvalue)) – fold enrichment: enrichment in peak vs input sample – FDR: false-discovery rate annotation based on post-peak calling filtering of peaks based on genome annotation To download the data, log in and click on the "Download dataset" button.
Description goes here…
Description goes here…
As with most biomedical databases, the first step is to identify relevant data from the research community. The Monarch Initiative is focused primarily on phenotype-related resources. We bring in data associated with those phenotypes so that our users can begin to make connections among other biological entities of interest. We import data from a variety of data sources. With many resources integrated into a single database, we can join across the various data sources to produce integrated views. We have started with the big players including ClinVar and OMIM, but are equally interested in boutique databases (which you will see more of in the coming months). You can learn more about the sources of data that populate our system from our data sources page http://monarchinitiative.org/sources.
Digital Bee Collections Network, 2014 (and updates). Version: 2016-03-08. National Science Foundation grant DBI 0956388. Accessed at http://amnh.begoniasociety.org/dwc/AEC-DBCNet_DwC-A20160308.zip
Schriml, L. M., Arze, C., Nadendla, S., Ganapathy, A., Felix, V., Mahurkar, A., … Hall, N. (2009). GeMInA, Genomic Metadata for Infectious Agents, a geospatial surveillance pathogen database. Nucleic Acids Research, 38(Database), D754–D764. doi:10.1093/nar/gkp832
Sarah E Miller. 4/18/2016. Species associations from Wardeh, M. et al. Database of host-pathogen and related species interactions, and their global distribution. Sci. Data 2:150049 doi: 10.1038/sdata.2015.49 (2015). Accessed at https://raw.githubusercontent.com/millerse/Wardeh-et-al.-2015/c6e69d5a6f98f6d41161c1cfe6460f2abb777683/interactions.tsv on 07 Sep 2016.
This data set includes the following:
A .pdf file that summarizes the whole-mount data for the tested element. This file includes light microscopy whole-mount images of the LacZ reporter gene expression in mouse embryos, a summary of the annotation of the expression pattern, the DNA sequence of the tested element in Fasta format, and the sequences of the primers used to generate the test construct. Follow corresponding link in the External References section to see this information in the http://vista.lbl.gov at Lawrence Berkeley Laboratory
4 movie (.avi) files: A CLIP file that provides an overview of the 3-D model generated by Optical Projection Tomography (OPT). Thresholding-based false-color representation shows unstained regions of the embryo in green, LacZ signal in red. In addition, 3 movies representing a pass-through view of the OPT model in the coronal, sagittal, or transverse plane. See links in External Referece section to download the following movie files: Overview movie, Coronal plane movie, Sagittal plane movie, Transverse plane movie
4 files in .tgz format. Each of these corresponds to one of the .avi files and unzips to a set of .png files, each of which represents the individual frames of the movie (and, in case of the transverse/sagittal/coronal movies, can be used to retrieve individual virtual sections through features of interest in .png image format). [.tgz files can be unzipped with WinZip or Stuffit on a PC or Mac. On linux, treat the file as a gzipped .tar file: gunzip < file.tgz | tar xvf -