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. The purpose of choosing a particular type of tissue is for disease or protein assessment, or retroviral vector production and cell culture support. Cancer program scientific tools and resources broad. Gxd collects and integrates the gene expression information in mgi. Clicking an individual cell in either matrix view opens a summary window of the data represented in that cell shown in the tissuebygene matrix by the white arrow. The genome of c57bl6j eve, the mother of the laboratory mouse genome reference strain. This is the resource identification portal, supporting guidelines for rigor and transparency in scientific publications.
We evaluate the human and mouse archs4 data sets by comparing them to coexpression matrices created in the same way from the cancer cell line encyclopedia ccle and. 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. Its primary emphasis is on endogenous gene expression during mouse development. We use an old access database to keep track of our cell lines, however, our uni does not. Database institute organization alteration types primary source processed data organisms cell lines public data restricted data. Ideally i would need a database which will tell me. There are many conserved alleles between the three balbcderived samples. However, i am on the 7th page of the new document and am not cutting and pasting from the old document and i am finding that it is beginning to do the same thing using the mouse to select one cell will select more than one cell. Our first job is to listen to and observe what our customers need, and meet those needs with quality products and services. Sigmaaldrich has partnered with the european collection of cell cultures, ecacc, a world leader and recognized expert in the maintenance, cultivation and distribution of authenticated cell lines. 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. What software do you use for your cell line database. We demonstrate here the generation of primordial germ cell like cells pgclcs in mice with robust capacity for spermatogenesis. Mouse strains and cell lines available from the international mouse strain resource carrying this mutation.
All of our human cell line authentication report options include a single mouse marker for the detection of mouse dna contamination, especially helpful for researchers who are using mouse human xenograft models andor human and mouse cell lines simultaneously. Antibodies, model organisms, cell lines, plasmids, and other tools software, databases, services. The consortium for mouse cell line authentication was formed to validate short tandem repeat str markers for intraspecies identification of mouse cell lines. Transfection of p73 into the sknas cell line suppresses its tumorigenic phenotype. Determining differentially required genes between p53 wt or mutant cell lines from sirna data and making a heatmap. Cell concentration should be carefully controlled in microwellseq. The mutation data table displays a list of mutations specifics to the cell line or gene. Apr 15, 2015 b, c, pcrbased detection of human left panel and mouse right panel cytochrome b oxidase i cox1 in cell lines b and in titrated mixtures of human molt4 and mouse stv2 cell lines c to. The consortium was developed in collaboration with american type culture collection atcc.
Neuroblastoma cell lines center for cancer research. Hms lincs project library of integrated networkbased cellular signatures. To view a cell lines information, search for it from the front page. The cell atlas provides highresolution insights into the expression and spatiotemporal distribution of proteins within human cells. Atcc was entrusted with its first cell line in 1962 and has consistently attained the highest standards and used the most reliable procedures to verify every cell line since. The mouse tumor biology database pubmed central pmc. Some repositories and journals have heeded calls for mandatory authentication of human cell lines, yet misidentification of mouse cell lines has received little publicity despite their importance in sponsored research. When selecting a single cell in excel 10 with the mouse. Using a panel of 64 cell lines to represent various cell populations in. Was originally considered to be a breast cancer cell line but has since been identified as a melanoma cell line.
Using microwellseq, we constructed a first stage mouse cell atlas with more than 400 k singlecell transcriptomic profiles from 51 mouse tissues, organs, and cell cultures. Can anyone recommend a mouse colony management software system. These data are synchronized with the corresponding data held in the mouse genome database. Our first job is to listen to and observe what our.
If you are an author, please find your key resources. The genehero cas9 stable cell lines are available premade in many human, mouse, and rat cell line backgrounds. Cell lines project mutation profiles of over 1,000 cell lines used in cancer research. 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. The cellosaurus is a knowledge resource on cell lines. If you or your institution hold mice, cryopreserved gametes or embryos, or es cell lines. The problem of cell line misidentification and contamination has plagued cell biology for decades. Interlaboratory study to validate a str profiling method for. Cosmic, the catalogue of somatic mutations in cancer, is the worlds largest and most comprehensive resource for exploring the impact of somatic mutations in.
Development of mouse cell line str multiplex assays and a consortium for validation of the measurement method. 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. Hi, i am trying to find a good solution for linking together information about. The resulting map covers more than 800 major cell types and potentially more than 1,000 cell subtypes in the mouse system. The mtb database does not currently include data on tumour cell lines or human. Companion mouse strains created using deltagens es cell lines are also available via the jackson laboratory repository. There are a number of other cell line repositories or cell banks as they are also known around the world. Syngeneic cell line reference database taconic biosciences.
Murine embryo fibroblast cell lines 3t3l1 1 murine embryo fibroblast cell line. Mouse cell lines are established from mouse tissue that originates from liver, neural segments, blood, tumorigenic cells, and fibroblasts. Panel of mouse cell lines cls cell lines service part of the cls cell bank table 1. A mouse click on any row shows the mutation plot on gene coordinate. Other databases on the pathobiology of cancer that provide. All havana biotypes and encode principal isoforms for the three organisms are also included. There is a growing movement to require the validation of all cell lines. To obtain fastq files, we implemented an automated program using the ncbi. Mousemine now includes sequence data for 19 mouse inbred strains. Origin and general characteristics name of cell line cell type organism strain age gender tissue disease morphology growth properties cls order no.
It is part of a multiyear project to create a census of cells in the mammalian brain. Contributing repositories a summary of institutions, organizations, and individuals contributing mouse resource information to the imsr database. Mousemine is funded through a grant from the nihnhgri. Use the menu bar at the left to access the overview of the project, methods, quality control summary for 54 es cell lines that are ready for distribution, microarray data, information on the use of es cell bank for chipseq, analysis of protein complexes, and development of transgenic mice. Transcriptomics overview the complexity of a cells function can, at some level, be described by its transcriptional signature. Is there any software to create a database of 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. Are there leukemia cell lines, especially aml cells, derived from the c57bl6 mice. The consortium has been developed in collaboration with american type culture collection atcc. Is there an online tool or database that can show which genes have been found to be expressed in different cell types. Many nb cell lines such as chp212, smskan and sknbe2 are. The human cell in cell line the human protein atlas. The generation of properly functioning gametes in vitro requires reconstitution of the multistepped pathway of germ cell development. 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.
Whats new gene expression database news gxd now includes rnaseq data gxd has been expanded to include rnaseq data. Pgclcs were generated from embryonic stem cells escs and induced pluripotent stem cells ipscs through epiblastlike cells epilcs. Contributing repositories international mouse strain. Feb 22, 20 the majority of mouse cell lines are derived from inbred mice resulting in alleles that are mostly homozygous in nature green 1968.
A immortal human breastderived cell line cell that has the characteristics. We are looking for new software to house our database. Imsr contributing repositories international mouse strain. Take advantage of the convenience of having your husbandry, sourcing, and efficacy evaluation needs met by jax. The test can also be used to confirm that a mouse cell line. Snp array profiling of mouse cell lines identifies their. It is designed to analyze mirna and gene isoforms lists under a common and consistent space of annotations. Data collected by nist will be used to develop a public str profile database for mouse cell lines. The database contains, for each of the 100 examples. The core of cosmic, an expertcurated database of somatic mutations.
May 23, 20 in the older document, the selection of a single cell via the mouse would always select more than one cell. Antibodies, model organisms, cell lines, plasmids, and other tools software. If you find this doesnt work for your specific cell type, then you can look to our cell. The mutation data table displays a list of mutations specifics to the cell line. One database for cell lines, one for plasmids, one for primers and one for reagents.
Atcc stands ready to support our customers needs during the coronavirus pandemic. This brain cell database contains a survey of biological features derived from single cell data, from both human and mouse. Multiple alleles present at each locus could indicate a mixed population of cells. Both cell and bead concentrations were estimated by hemocytometer. Is there a database linking cell lines and mutations. Microarray, sage and other gene expression databases hsls.
Is there a database to find out which genes are expressed in which cell lines. Including all existing 3 utr and the entirely known mirnas. We set up a filemaker pro database system to track information in the lab. Gemiccl gene expression and mutations in cancer cell lines is an online database of human cancer cell lines that provides genotype and expression information.
These products became available after 2005, when the nih announced an agreement allowing the distribution of mutant mice and frozen embryos from two private collections of knockout ko mice. Massive mining of publicly available rnaseq data from. Nist patents first dna method to authenticate mouse cell lines. The purpose of choosing a particular type of tissue is for disease or protein assessment, or retroviral vector production and cell. It is very flexible as you can custom any entry on the preformed lists or you add your own.
You may have been redirected here from the broad cancer program resource gateway, which is no longer active. Atcc signs crada with nist to validate genetic identification. A summary of institutions, organizations, and individuals contributing mouse resource information to the imsr database. Jax mice are the most published and well characterized mouse models in the world, and include the only fully sequenced strain, c57bl6j. Mgimouse genome informaticsthe international database. Certain cell lines have been deposited by their inventor the cell line. Use the database of published references below to help you identify tumor cell lines. 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. Data and scientific tools from many of our cancer research projects can now be accessed via broad data, software and tools. The mouse tumor biology mtb database provides integrated access to data on the pathobiology and genetics of cancers in mouse models of human disease. Evenly distributed cell suspension were pipetted onto microwell array 5 min10 min and extra cells. The goal of the imsr is to assist the international scientific community in locating and obtaining mouse resources for research. The proper cell concentration is 170,000 cells ml 10% wells will be occupied by single cells.
Invitrogen lipofectamine transfection reagent protocols have been optimized for efficiency, viability, and reproducibility across a broad range of cell types. Is there a database to find out which genes are expressed in. Search for gene expression data based studies of a range of macrophage cell types following treatment with pathogens and immune modulators. Gxa gene expression database find information about gene expression in different cell types, organism parts, developmental stages, disease states, sample treatments and other biologicalexperimental. Nov 23, 2011 here we report the generation and characterization of 84 mouse es cell lines with doxycyclinecontrollable transcription factors tfs which, together with the previous 53 lines, cover 710% of. Human cell lines have been authenticated by short tandem repeat profiling.
Cnv data from three representative databases on cell linescancer cell line. Nih3t3 str profile electropherogram and cell image. This software is really helpful, it is like you have a virtual mice colony on your screen. 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. Human cell line derived from breast adenocarcinoma. All data are attributed to a source, either published or personal submission. Human cell lines, mouse cell lines, cancer cell lines and more are available.
In this study, mouse cell lines registered with the jcrb cell. 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. Taconic biosciences inbred mice and gems on defined genetic backgrounds are widely used for syngeneic tumor studies, in which mouse tumor cells are engrafted into hosts from the same genetic background. The mutation, gene expression, and copy number variation cnv data were collected from three representative databases on cell lines ccle cancer cell line. 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 contaminated cell lines in advance. This is often the best place to start, especially in a new cell line.
Please see below for a partial list of resources or refer to the list of cancerrelated data, software and tools. Cell line data base cell line data base cldb, the first database set up within the interlab project, contains detailed information on human and animal cell lines that are available in many italian laboratories and in some of the most important european cell banks and cell culture collections. This cell line was established from nude mouse xenograft tumor dr. List of databases for oncogenomic research wikipedia.
For decades, misidentified and contaminated cell lines have been a highprofile cause of wasted research effort and funding, and false claims in the literature. Using the mouse multiplex assay, unique profiles were obtained for the mouse cell lines listed in table 5 with the capability of distinguishing between three balbcderived cell lines. Listed below are other resources available online that offer data. Cancer cell lines are essential components for biomedical research. Use the menu bar at the left to access the overview of the project, methods, quality control summary for 54 es cell lines that are ready for distribution, microarray data, information on the use of es cell bank. The goal of the imsr is to assist the international scientific community in locating and obtaining mouse. Please note that cell line data are also included in the dataset od somatic mutations. Is there a database to find out which genes are expressed. Publish a written consensus standard for mouse cell line authentication by identity testing.
The cell line name and lineage are listed at the top of the cell line page. The atcc cell biology collection is one of the largest bioresources in the world, and offers a complex array of human, animal, insect, fish and stem cell lines from which to choose. Our first job is to listen to and observe what our customers need, and meet those needs with quality products and. The atcc cell biology collection is one of the largest bioresources in the world, and offers a complex array of human, animal, insect, fish and stem cell lines. In recent analyses of human and mouse cell lines, at least % and 4% of samples, respectively, were falsely identified 4, 5. Ecacc primary cell lines are offered from a variety of mammalian sources. Filemaker pro lets you view in various formats and is highly customizable and pretty, but if you want simple, just use an excel spreadsheet. Transformed cancer cell lines rnaseq database hi, i am trying to find a database which has rnaseq data for cancer cell lines transformed from.
A immortal human liverderived cell line cell that has the characteristics. Recent technical advances in rna sequencing rnaseq allow the creation of a transcriptomic inventory at the cellular level. The international mouse phenotyping consortium project is systematically phenotyping knockout mice from the mutant es cells produced by the international mouse. Deposit str profiles for mouse cell lines into the ncbi public database. Reconstitution of the mouse germ cell specification pathway. The search offers you access to our complete catalogue of dsmz human and animal cell lines. Catalogue german collection of microorganisms and cell. 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. Evenly distributed cell suspension were pipetted onto microwell array 5 min10 min and extra cells were washed. Be aware that many cell lines may have different tp53 status according to different studies.