A hepatoma cell line, huh7 jcrb0403, has been used extensively in various research fields and a number of studies using this line have been published continuously since it was established in 1982. To generate a reference genome for the tasmanian devil, we sequenced and assembled the genome of a 5yearold female tasmanian devil. Is there a karyotype database for human cell lines. The core of cosmic, an expertcurated database of somatic mutations. Apr 20, 2015 search pubmed for the cell line name and cross contamination. Although the vast majority of hesc lines have been derived for research purposes. Hello everybody, im a first year phd student on evolutionary biology. In some lines, the dms were in only some of the cells. The human pancreatic cancer cell line panc1 was purchased from the american type culture collection and validated by comparing with a reference database of short tandem repeat str profiles. It is an easy, low cost and reliable method for the authentication of human cell lines. This search will retrieve items that correspond to any of those words, ranking higher those with all or most of the keywords. Differences and homologies of chromosomal alterations within. Analysis of human cancer cells using this method identified gross chromosomal changes as.
To date, no genomic reference for this cell line has been released, and experiments have relied on the human reference genome. Singlecell sequencing reveals karyotype heterogeneity in. Is there any software to create a database of cell lines. German collection of microorganisms and cell cultures gmbh. Primary effusion lymphoma is a rare distinct large bcell neoplasm that is associated with kaposis sarcomaassociated herpesvirus kshv infection. This cell line may contribute to furthering our understanding of the pathogenesis of pel and kshv infection. A dynamic database of microarraycharacterized cell lines. All data required to generate the name are submitted to the database during cell line registration. Multispecies gband karyotyping analysis cell line genetics is recognized worldwide for its expertise in multispecies stem cell and cancer cell line karyotyping analysis. The genomic and transcriptomic landscape of a hela cell line.
As a screen when deriving a new cell line at the beginning of an experimental protocol to evaluate genomic stability during culture at the end of an experiment before publication to obtain highgrade karyotype images for publication. Im looking for the karyotype of a specific cell line. Aug 01, 20 hela is the most widely used model cell line for studying human cellular and molecular biology. A dynamic database of microarraycharacterized cell lines with various cytogenetic and genomic backgrounds zhenya tang coriell institute for medical research dorit s. Cell line authentication test recommendations abstract authentication of a cell line is the sum of the process by which a lines identity is verified and shown to be free of contamination from other cell lines and microbes.
The atlas is in open free access for readers, and there are no fees for. It detects genomic copy number variations at a higher resolution for level than conventional karyotyping or chromosomebased comparative genomic hybridization cgh. Many times i need to look up attributes of a cell line. Please note that for cancer cells and in any cases where very complex, unstable karyotypes are observed, the analysis consists only of a full karyotype for a single cell. This approach involves the isolation and enumeration of short sequence tags from specific genomic loci. Str dna profiling for human cell line authentication intraspeficic identification and detection of crosscontaminating cells str analysis can be performed in most laboratories that have the capabilities to execute molecular techniques. May 17, 2018 human cell lines represent a valuable resource as in vitro experimental models. Application performance management it asset management database management network monitoring help desk issue tracking. The jurkat cell line has an extensive history as a model of t cell signaling. The software enables automatic karyotyping of human chromosomes by band position, as well as karyotyping of chromosomes of animals and plants online.
Im looking to create a database of cell lines i use and their characterisitcs i. Chromosome abnormalities in 10 lung cancer cell lines of the. It serves as a preface for the following article and for others in this series offering detail on the characterization of cells and cell lines. Sequencing libraries were prepared from genomic dna extracted from a cell line derived from normal fibroblasts.
In summary, we report the first comprehensive karyotype of the ht. Based on conventional karyotyping and interphase fish analyses, mmlal was characterized by a hypodiploid composite karyotype, loss of chromosome, loss of chromosome 17 or del17p, with the absence of primary igh translocation and tp53 mutation. It was originally generated by immortalisation with the simian vacuolating virus 40 sv40 transforming t antigen and subsequent propagation in low serum conditions. Cell line chromosome analysis diagnostic cytogenetics. The contrast qc and mapd metrics generated by the software were used for. We provide multispecies characterization services and products for the stem cell and cancer cell cytogenetics. Introduction this article provides a strategy and summarizes steps for the authentication of cell line stocks. At least 10 metaphases were analyzed for each cell line, except ncih2126, where only 5 satisfactory metaphases were analyzed. Estimation of ploidy and dna content of kbm7 and the nearhaploid clone p155 by. Jimt1 cell line hms lincs database hms lincs project.
Is there any software to create a database of cell lines and their. Maintained in longterm culture, the cells grew as large mesenchymallike cells with a doubling time between 5 and 6 days. For complex mosaic karyotypes, fewer than 20 cells may be analyzed and additional karyogram images will be provided in the report. Guidelines for the use of cell lines in biomedical research.
Any variation from the standard karyotype may lead to developmental abnormalities. Genome sequencing and analysis of the tasmanian devil. Cancer cell lines are frequently used as in vitro tumour models. Establishing and characterizing a new primary effusion. Cosmic, the catalogue of somatic mutations in cancer, is the worlds largest and most comprehensive resource for exploring the impact of somatic mutations in human cancer. The fast and convenient routine karyotyping system. Karyotyping and fish metaclass image analysis system. Distinctive mutational spectrum and karyotype disruption in. Thus, we chose to use the humancytosnp12 array and karyostudio software.
In the example below, turning off channels a, b, and d highlights the derivative x chromosome. Application of this technology to human b cell leukaemias reveals different levels of karyotype heterogeneity in these cancers. Berlin coriell institute for medical research lorraine toji coriell institute for medical research gokce a. Define the terms karyotype, autosomal and sex chromosomes. To identify molecular lesions in this cell line in an unbiased fashion, we performed wholegenome and wholetranscriptome sequencing analysis. Cell line authentication why it matters as a biological resource center, atcc and other recognized cell banks comprehensively perform authentication and qualitycontrol tests on all distribution lots of cell lines. It is generally assumed that many cancer cell lines have relatively stable karyotypes over a long time of maintenance in steadystate culture conditions. Karyotype data cytogenetic data is perhaps the most basic information about a genome i. Longterm tmztreated tumour cells acquire tmz resistance by profound reprogramming of the transcriptome, proteome, kinome, metabolism, and demonstrate versatile and opposite changes in proliferation, invasion, in vivo growth, and drug crossresistance. Growth ratecorrected gr doseresponse metrics across a panel of 71 breast cancer cell lines treated with a library of small molecule and antibody perturbagens. After selecting a cell line in cell line view, in addition to common str profiling and other conventional methods, users can search its genomewide altered snps in amplicons and hds along the physical and cytogenetic locations of chromosomes figure 1.
All net chromosomal gains and losses implied by the karyotype are. Jun 18, 2001 the existence of ongoing structural and numerical chromosomal instability, as well as the rate of numerical instability, was established on cancer cell lines grown in culture. Jul 15, 2011 for instance, the karyotype data for the tanoue cell line has a chromosome modal number of 48 for the primary population of cells, but also 12% of the cell population was polyploid see additional file 1, table s2 for karyotype data. The chromosomal constitution of a cell is called karyotype. Cell lines project mutation profiles of over 1,000 cell lines used in cancer research. Thus the size of these chromosomes restricted the clarity of banding that one would. The flexible system architecture of neon and ikaros simplifies the adaptation of karyotyping workstations to any workflow. Whole genome and transcriptome analysis of a novel aml cell. Some karyotypes are well known, such as hela or some carcinomas, but some are very hard to find, such as lg2 b cells. Cell line was characterized for morphology, ultrastructure, doubling time, expression of epithelial markers, dna content, karyotyping, str markers, p53 mutations, hpv status, and tumorigenicity in scid mice with all trans. Revised karyotyping and gene mapping of the biomphalaria.
Cells were analyzed for dna content as described under materials and methods. A cell line resource derived from honey bee apis mellifera. Digital karyotyping was performed on dna from colorectal cancer cell lines difi and hx48, and from the lymphoblastoid cells of a normal individual gm12911, obtained from coriell cell repositories, camden, nj. Relative cell counts and normalized growth rate inhibition values across technical replicates. Evaluating cell lines as tumour models by comparison of. In genomic alteration profile of a selected cell line, user can continuously click on the. Highresolution genetic analysis of cancer cell lines with. This protocol works well for es cells, primary cultures, or longterm cultures. Temozolomide tmz is a first line drug for the treatment of glioblastoma. A hepatoma cell line, huh7 jcrb0403, has been used. Atlas of genetics and cytogenetics in oncology and haematology. Temozolomide promotes genomic and phenotypic changes in. Effective design and interpretation of molecular genetic studies performed using hela cells require accurate genomic information. This line was derived episomally from a healthy donor and has been fully sequenced, has a normal karyotype, differentiates into multiple cell types, and is amenable to gene editing.
Cell line genetics, inc is a leading stem cell research company. Systems management bundle can give you full application stack visibility for infrastructure performance and contextual software awareness. Jan 23, 2014 between 19 and 26 metaphases with good chromosome dispersion and morphology were analyzed for each cell line to define the structural and numerical alterations, and 100 metaphases cell line were analyzed to determine the level of ploidy. In an effort to obtain an endometriosis ex vivo model, we established the spontaneously growing them1 cell line from endometriotic implants in lung parenchyma from a woman with te. The rgb image demonstrates cytogenetic abnormalities in a cell from a secondary leukemia cell line. Karyotyping a cell line optimized by noranne enzer at mit. Dec 12, 20 we reported the establishment of a new human myeloma cell line, mmlal, which was derived from the pleural effusion of a chinese patient. Metaclass is an automatic karyotyping system that provides a good morphology and quality in the chromosome bands. The partial sequence for the mitochondrialencoded cytochrome c oxidase subunit i cox 1 gene in the cell line is identical to those from honey bee tissues and a consensus sequence for a. The pdxpc1 cell line was obtained after 80 serial passages over a period of 2 years, and aliquots were frozen in liquid nitrogen.
The skycgh database for spectral karyotyping and comparative genomic hybridization data 102 figure 1. All of these cell lines and dna samples are categorized into several. However, an accurate genome profile, which can be served as a reliable reference, has not been available. For human cytogenetically normal individuals the karyotype is composed of 46 chromosomes 23 pairs of autosomes and a pair of sexual ones, xx or xy. A method called digital karyotyping provides quantitative analysis of dna copy number at high resolution.
Pdf a bioinformatics analysis of the cell line nomenclature. Each individual cell line is described with patients clinical annotations, including tumor size, histopathologic features, gene mutation analysis, which will be part of a bioinformatics network with matched tumor tissue database under uobs labmatrix database system. Explain how many of each is present in a gamete and in a somatic cell. Cd cell line has been established from a poorly differentiated squamous cell carcinoma of tongue. Cell line genetics, inc cell line characterization. The search offers you access to our complete catalogue of dsmz human and animal cell lines. Creating a certified working cell bank for important cell. Karyotyping a cell line optimized by noranne enzer at mit, nov 2005 prep work. The molecular karyotype of 25 clinicalgrade human embryonic. Although this immortalized line is used in an increasing number of studies. The normal human karyotypes contain 22 pairs of autosomal chromosomes and one pair of sex chromosomes allosomes. High chromosome number in hematological cancer cell lines is. Is there any software to creat e a data base of cell lines and their characteristics.
Trisomy of chromosomes 8 and 18 can arise in extended cell cultures and seems to confer a proliferative advantage by an increased gene dosage effect. Normal karyotypes for females contain two x chromosomes and are denoted 46,xx. Stable karyotypes in epithelial cancer cell lines despite. Jul 01, 20 all investigators are encouraged to provide feedback regarding findings they obtained from analyzing any of the cell lines included in the database, regardless of the assay or platforms used, so that more information about each cell line can be added to the database and shared with the research community. Is there a database dedicated to karyotypes of human cell lines. Highresolution genetic analysis of cancer cell lines with near normal karyotypes cancer development is associated with multiple genetic alterations and genomic instability either at the chromosomal or base pair level is generally thought to underlie these changes. A total of 20 metaphases of each cell line were analyzed.
Gbanded karyotyping for human stem cell lines, progenitor cells, primary cell lines and cancer cell lines used for research purposes. Toruner umdnjnj medical school christine beiswanger. Arrows indicate some of the many chromosomal translocations in this cell line. Aug 17, 2016 a new kshvpositive and ebvnegative pel cell line, spel was established. The rate and type of chromosomal abnormalities for each cell line are shown in figure 1. The application of human embryonic stem cell hesc derivatives to regenerative medicine is now becoming a reality.
As part of our continuing efforts to characterize and authenticate the cell lines in the cell biology collection, atcc has developed a comprehensive database of short tandem repeat str dna profiles for all of our human cell lines. Ideally it needs to be a database that can be searched and added to. Establishment of a novel human cell line retaining the. Karyotyping is performed to identify the species as well as variation within the cell line. Cell types differentiated from these designated lines may be used as a cell. Recent molecular profiles of hundreds of cell lines from the cancer cell line encyclopedia and thousands of. Strs of the chromosomes are amplified, hybridised with fluorescent probes and run. The repository is managed using biofortis labmatrix v3. Comparison of the karyotype of bge 1 and 2 cell line isolates to the published karyotype of b. A dynamic database of microarraycharacterized cell lines with. Genetic characteristics of the human hepatic stellate cell.
Using standardized techniques, authentication enables communication among all users about. Optimized by noranne enzer from sorger labs protocol, updated 2006. Karyotype is a software development it company having everything under one umbrella, in order to create a master piece, every individual requires a proper plan and design in mind to make and give a name to it. The karyotype of the rpe1 cell line is known to have an additional piece of chromosome 10 at the end of the qarm of one of the x chromosomes. Prepare glass slides 5 per cell line by soaking overnight in etoh. A bioinformatics analysis of the cell line nomenclature.
Establishment and characterization of a stromal cell line. Print out each karyotype and count each chromosome by writing a. This cell line had a normal karyotype at passage 45 2020 metaphases, figure 3a and was further grown until passage 63, when it was analyzed in parallel by karyotype and gene expression. Chromosome analysis for stem cells is suggested for the following indications. Chromosome cytogenetic analysis is widely used for the detection of chromosome instability. Where fluorescence colors overlap at the junction between chromosomes, the spectral karyotyping software sometimes misidentifies the overlap as an irrelevant chromosome. When followed by gbanding and molecular techniques such as fluorescence in situ hybridization fish, this assay has the powerful ability to analyze individual cells for aberrations that involve gains or losses of portions of the genome and rearrangements involving one or more. Record all data relevant to the origin of the tissue when starting a new cell line and keep tissue for dna profiling. Repository and inventory of human renal tumor cell lines for. The tool will assign these data into an exclusive and understandable cell line name, answering the call for standardisation. The cell line ncih1770 had a long hsr of chromosome 2 material inserted into chromosome 12 figs. This is a first ever cell line established from an indian gutka chewer. Is one of the most widely used methods of human cell lines identification.
Spectral karyotype analysis of colon cancer cell lines of the tumor suppressor and mutator pathway. Virtual karyotype is the digital information reflecting a karyotype, resulting from the analysis of short sequences of dna from specific loci all over the genome, which are isolated and enumerated. Figure 1 a murine multicolor banding mcb was applied on chromosomes of the cmt93 cell line. We also have a master plan and a design to work together and get on to a wonderful platform. There is the possibility of training programs recognition of chromosomes, using his own chromosomes database. Karyotype service for human cells cell guidance systems. Authentication of human cell lines by str dna profiling. Check that all solutions are in stock and slides are prepped. Atcc a great repository that has cell line datasheets, references, images, and culturing info. A data portal for the cells, cell biology, data and tools made freely and publicly available by the allen institute for cell science. Establishment of a tongue squamous cell carcinoma cell line. As i work on the karyotyping of a species of earthworm, i would like to.
Isolation and characterization of a nearhaploid human. Hcc1954 cell line hms lincs database hms lincs project. Hela is the most widely used model cell line for studying human cellular and molecular biology. Chromosome abnormalities in 10 lung cancer cell lines of. Despite the fundamental nature of this data, many questions surrounding the evolution of genomes at this level remain unanswered. Establishment of a bortezomibresistant chinese human. Images lecturescourses karyotype online softwareinternet cancer support groups education resources fish. Creating a certified working cell bank for important cell lines in your research program introduction mutational changes, aging and evolution continually occur in all actively growing cell cultures. Karyotyping is a basic and indispensable test performed routinely to determine if the line has. The karyotype database karyotypedb contains karyotype and chromosome information like chromosome number, length, karyotype features, idiograms, physical localizations of dna sequences by fluorescence in situ hybridizion fish, and cell material for metaphase chromosomes and polytene chromosomes from different animal and plant species together with literature references and links.
As part of the cancer cell line encyclopedia 1, aml193 was. All cell lines except ncih95 had amplifications in the form of dms or hsrs. Alterations in the genetic content of a cell underlie many human diseases, including cancers. Most cells in the line are diploid 2n 32 and have the apis mellifera karyotype as revealed by giemsa stain. Spectral karyotype analysis of colon cancer cell lines of the. While numerous expression deficiencies have been described in jurkat, genetic explanations have only been provided for a handful of defects. A genomewide survey of mutations in the jurkat cell line. We are also able to make it available to the research community and sequence its genome.
Start using cosmic by searching for a gene, cancer type, mutation, etc. But at the turn of the 21st century, some expression irregularities were observed, raising doubts about how closely the cell line paralleled normal human t cells. For more info on why each of these steps is critical, see this page. The morphology of these chromosomes can be described in relation to other organisms such as homo sapiens, as being comparatively small and monomorphic. The allen institute for cell science presents the allen cell explorer. Single cell sequencing and aneufinder analysis reveals high levels of copy number heterogeneity in chromosome instabilitydriven murine t cell lymphoma samples, indicating ongoing chromosome instability. Check the database of international cell line authentication committee.
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