The cell line name and lineage are listed at the top of the cell line page. The purpose of choosing a particular type of tissue is for disease or protein assessment, or retroviral vector production and cell culture support. A immortal human mouthderived cell line cell that has the characteristics. Oct 31, 2012 the celllinenavigator database, freely available at, is a webbased workbench for large scale comparisons of a large collection of diverse cell lines. The jackson laboratory makes no representation about the suitability or accuracy of this software or data for any purpose, and makes no warranties, either express or implied, including merchantability and fitness for a particular purpose or that the use of this software or data will not. Microarray, sage and other gene expression databases hsls. Search for gene expression data based studies of a range of macrophage cell types following treatment with pathogens and immune modulators. To obtain fastq files, we implemented an automated program using the ncbi. Mouse nfatc2nfat1 luciferase lucporter stable reporter. In keeping with gxds scope, these data are from experiments that examine endogenous gene expression in wildtype and mutant mice during the embryonic stages andor postnatal life. Atcc stands ready to support our customers needs during the coronavirus pandemic. A immortal mouse cell line cell that has the characteristics.
What software do you use for your cell line database. Take advantage of the convenience of having your husbandry, sourcing, and efficacy evaluation needs met by jax. Cell lines project mutation profiles of over 1,000 cell lines used in cancer research. Mouse bindings line displays the current mouse button settings. Acknowledgments the authors express appreciation for the expert advice and direction of michael coble, margaret kline, peter vallone, erica butts, and john butler nist, applied genetics group. If you would like to schedule a remote interactive session to learn to use mgi, contact user support to discuss the details.
An overview of the hyperlopit workflow is shown in fig. These settings change as you move the mouse in and out of windows and start and stop commands. Multiple alleles present at each locus could indicate a mixed population of cells. Adoption of this assay would increase confidence in studies using mouse cell lines and could ultimately save time and reduce costs by identifying misidentified or. Violet, pink, orange, turquoise, blue, yellow, and green lines indicate. This page contains references to known 2d page database servers, as well as to 2d page related servers and services. Oracle exadata storage server is a highly optimized storage server that runs oracle exadata system software to store and access oracle database data with traditional storage, data is transferred to the database server for processing. The consortium will collaborate to obtain concordant short tandem repeat str profiles for mouse cell lines, draft consensus standards for mouse cell line authentication, and create a public database of str profiles for mouse cell lines. Antibodies, model organisms, cell lines, plasmids, and other tools software, databases, services. Other mgi data resources include the gene expression database gxd, the mouse tumor biology database mtb, the gene ontology project go, mouse mine and the mousecyc database of biochemical pathways. Cell line authentication can verify whether the genotype of the cell line in question is identical to the genotype of the presumed parental cells. Deposit str profiles for mouse cell lines into the ncbi public database. A draft map of the mouse pluripotent stem cell spatial.
Is there a database to find out which genes are expressed in. Mice have been the most popular laboratory animal, widely used for genetic and basic research studies, resulting in mouse cell lines being the most numerous and important cell lines second to human cell lines. It aims to support experimental design in the fields of genomics, systems biology and translational. Publish a written consensus standard for mouse cell line authentication by identity testing.
You may also find related information in the proteomics links page of the swiss proteomics society for a reference to federated 2d page database, see appel et al. Workflow description language wdl, python3 and r scripts. Oh alright, i was under the illusion that the mice had the receptor knocked out. Mouse genome database 2016 nucleic acids research oxford. A summary of institutions, organizations, and individuals contributing mouse resource information to the imsr database. Development of mouse cell line str multiplex assays and a consortium for validation of the measurement method. The research community has responded to this problem with validated methods for human cell line identification.
Karyotyping is most often used for detection of gross abnormalities in chromosomes, but chromosome number was the basis of early reports of cell line. Search for cell lines at the american type culture collection atcc mouse or rat cell lines at the european cell line database cldb search for cell lines, from the european collection of animal cell cultures ecacc developmental studies hybridoma bank at the. Comprehensive assessment of the quality of cell lines. The mirnas were mined from mirbase, phenomir, mir2disease etc and their respective sequences were obtained from mirbase. Altex 27, 210 105 pancreatic beta cell lines and their applications in diabetes mellitus research 1 1 1,2 1faculty of medicine, university of maribor, slovenia. The biosample database contains descriptions of biological source materials used in experimental assays.
The goal of the imsr is to assist the international scientific community in locating and obtaining mouse resources for research. Getting started with the cadence software input line is where you type in cadence skill language expressions or type numeric values for commands instead of clicking on points. The cell atlas provides highresolution insights into the expression and spatiotemporal distribution of proteins within human cells. Cooperative research and development agreement crada are in place between nist and consortium members. An efficient pipeline for brainwide imaging and morphological reconstruction of individual neurons, including longrange projection neurons, is presented along with a searchable database containing more than 1,000 fully reconstructed neurons in the mouse neocortex, hippocampus, thalamus, and hypothalamus. A listing of epigenetic tools and databases that enable epigenomics research, which. The core of cosmic, an expertcurated database of somatic mutations.
The consortium has been developed in collaboration with american type culture collection atcc. The consortium for mouse cell line authentication was formed to validate short tandem repeat str markers for intraspecies identification of mouse cell lines. Other databases on the pathobiology of cancer that provide. Our data showing widespread crosscontamination served to refocus attention onto the need to verify cell line authenticity, leading ultimately to joint efforts by major cell banks to. In addition, the database contains about 36 000 single cell images and zstack movies. In contrast, oracle exadata system software provides databaseaware storage services, such as the ability to offload sql and other. These data are synchronized with the corresponding data held in the mouse genome database. Pancreatic beta cell lines and their applications in. Msms and searching the data against the corresponding database. Interlaboratory study to validate a str profiling method for. Peptides in mouse astrocytic cell lines and rat primary cultured astrocytes were identi. It is part of a multiyear project to create a census of cells in the mammalian brain. A mouse cell line ltkaprt which is resistant to the antiviral effects of interferon also has a reduced ability to synthesize metallothionein on exposure to cadmium.
The intrinsic activities of selected dopamine d1 receptor agonists were compared in three distinct molecular expression systems, c6, ltk, and gh4 cells transfected with. Does anybody know anything about mouse ltk cell lines. A reference epigenome project for human cells and not the typical stem cell lines. Jan 12, 2016 biochemical fractionation of mouse es cells. Cell line, established from a metastasis of 63 year old black male with androgenindependent adenocarcinoma of the prostate. Classification of mouse b cell types using surfaceome. Mgimouse genome informaticsthe international database.
Imsr contributing repositories international mouse strain. The proposed kit, combined with a consensus standard and a cell line database, would provide researchers worldwide with the tools needed to ensure the identity of their mouse cell lines. Explore a new public biomedical resource complementing the cell surface protein atlas cspa and use it to uncover cellular phenotypes and new surfaceome markers. To create a method fit for the purpose of capturing cell wide proteome localization data, we. The mouse tumor biology database pubmed central pmc. Identification of metastasisassociated receptor tyrosine kinases in nonsmall cell lung cancer.
Oncomirdbb is an integrated database consisting of the mirnas of human and mouse genomes, their sequences, chromosome and gene locations, respective targets and their description, pathways it regulates in breast cancer. Search for cell lines at the american type culture collection atcc mouse or rat cell lines at the european cell line database cldb search for cell lines, from the european collection of animal cell cultures ecacc. The mutation, gene expression, and copy number variation cnv data were collected from three representative databases on cell lines ccle cancer cell line encyclopedia, cosmic. The majority of mouse cell lines are derived from inbred mice resulting in alleles that are mostly homozygous in nature green 1968. Cell line authentication, cell line identification company. These resources are tightly integrated and can be accessed as a single data resource, the mgi database. Database provides dna methylation profiles from humans and mice.
A database of gene expression in mouse haematopoiesis. Is there a database to find out which genes are expressed. Are there leukemia cell lines, especially aml cells, derived from the c57bl6 mice. News 20181101 new the in silico human surfaceome website is online now. Interlaboratory study to validate a str profiling method. We are looking for new software to house our database. Peptidomic analyses of mouse astrocytic cell lines and rat. The final database contains 4741 bulk and 5847 single cell ec transcriptomes from six different model organisms homo sapiens human, mus musculus mouse, rattus norvegicus rat, bos taurus cow, danio rerio zebrafish, sus scrofa pig, generated using a variety of technologies microarrays, single cell rna sequencing and platforms. Overall, the database covers 78 human cell types supplementary figure s2 and 119 mouse cell types supplementary figure s3. Mousemine is funded through a grant from the nihnhgri. An open source and flexible pipeline to analyze dnbelab c series tm single cell rna datasets.
Our first job is to listen to and observe what our customers need, and meet those needs with quality products and services. Using a panel of 64 cell lines to represent various cell populations in different organs and tissues of the human body, the mrna expression of all human genes are characterized by deep rnasequencing. The mutation data table displays a list of mutations specifics to the cell line or gene. With success in mouse cell line experiments, we then moved our analysis to more complex organs, including adult mouse mammary gland, kidney, lung, and e14.
An organized mouse cell line authentication consortium in partnership with nist was created. The str profiling method is a multiplex polymerase chain reaction pcr assay comprised of primers targeting 19 mouse str markers and two human str markers for interspecies contamination screening. Nist patents first dna method to authenticate mouse cell lines. Human cell line derived from oral squamous cell carcinoma occurred in 69yo, male patient. If you are an author, please find your key resources. The proposed kit, combined with a consensus standard and a cell line database, would provide researchers worldwide with the tools needed to ensure.
Genemania software was employed to generate networks to the mouse a or human b proteinprotein interaction database. In order to detect cell line contaminants, primers for two human str markers were incorporated into the multiplex assay to facilitate detection of human and african green monkey dna. There are a number of methods available that provide relevant data on the quality of cell lines, and some of the more commonly used methods appear in table 1. Can anyone recommend a mouse colony management software system. Is there a database to find out which genes are expressed in which cell lines. The mouse cell line authentication consortium mclac selected murine cell lines because of their widespread use in both biomanufacturing and preclinical research. The mtb database does not currently include data on tumour cell lines or human. We use an old access database to keep track of our cell lines, however, our uni does not. Can anyone recommend a mouse colony management software. If the parental cells genotypes have been determined by a recognized repository atcc, dsmz, or jcrb, the genotype of the submitted cells can be compared to genotypes in the database. Gemiccl gene expression and mutations in cancer cell lines is an online database of human cancer cell lines that provides genotype and expression information. This is the resource identification portal, supporting guidelines for rigor and transparency in scientific publications.
Each crada is identical, so that every laboratory is working under the exact same conditions in the agreement and is protected equally. If you or your institution hold mice, cryopreserved gametes or embryos, or es cell lines that you distribute to other researchers, please consider listing them in the imsr catalog to make them more widely known. Gxa gene expression database find information about gene expression in different cell types, organism parts, developmental stages, disease states, sample treatments and other biologicalexperimental. A typical mgi workshop includes a brief presentation and a handson, interactive tutorial. The requirement of cell line authentication is becoming more routine, and this assay provides a reliable method to genotype mouse cell lines. Contributing repositories international mouse strain. Mouse cell lines are established from mouse tissue that originates from liver, neural segments, blood, tumorigenic cells, and fibroblasts. Mclac will also need to generate a mouse cell line database, establish an algorithm for comparing str profiles, and define matching criterion. The consortium was developed in collaboration with american type culture collection atcc. It is very flexible as you can custom any entry on the preformed lists or you add your own. The database contains, for each of the 100 examples. Cell types are typically identified and classified using selected cellsurface proteins as this subproteome reflects the maturity and functional state of a.
This brain cell database contains a survey of biological features derived from single cell data, from both human and mouse. Gxd collects and integrates the gene expression information in mgi. Apr 21, 2020 dnbelab tm c series single cell rna analysis software introduction. Mouse aml cell lines, human aml cell lines, imef cell line, 3t3 cell line and human sarcoma cell line were infected with virus encoding cas9 addgene 52962 followed with blastcitidin selection to generate cas9 cell lines. The web use is free for everyone including commercial. The mammary gland provides a unique model for studying organ tissue specification, as it is the only glandular organ that reaches full development after birth. Reconstruction of 1,000 projection neurons reveals new cell. Mouse nfatc2nfat1 luciferase lucporter stable reporter cell line summary description the nfat lucporter reporter cell line can be used for screening of agonists, antagonists or signaling inhibitors related with the nfatinvolved signaling pathways. The imsr is a searchable online database of mouse strains, stocks, and mutant es cell lines available worldwide, including inbred, mutant, and genetically engineered strains. Jax mice are the most published and well characterized mouse models in the world, and include the only fully sequenced strain, c57bl6j.
At the time of this publication, the database contains 67 146 transcriptomics profiles of human and mouse cells with curated metadata. The mouse tumor biology mtb database adheres to the official nomenclature for genes, alleles and strains as determined by the guidelines of the international committee on standardized genetic nomenclature for mice 16. Reconstruction of 1,000 projection neurons reveals. Its primary emphasis is on endogenous gene expression during mouse development. To view a cell lines information, search for it from the front page. Our collaboration with nist will provide the research community with a validated authentication assay for mouse identification along with a database for mouse cell lines.