genotyping

Robust, transferable genotyping assays are needed to screen many of the animal and cellular models during our production and validation cycles. NovoHelix can develop simple and robust genotyping protocols for all types of models in our portfolio including CRISPR models.  One of the core skills of the laboratory is the systematic collection of specimens for DNA/RNA extraction, and our team can isolate nucleic acid from skin, toes, tail, and many other tissues, organs, cell pellets, and embryos. We have experience genotyping various animal models including mice, rats, pigs, cows, goats, and multiple human pathology tissues and human cell lines.

NovoHelix also provides expert assay design and consultation to the client to ensure genotyping success.  Assay design costs are based on the number of alleles screened. In some cases, a synthetic positive control needs to be built for assay validation and these 'construction' costs will be passed on to the client. 

In addition to sample collection and genotyping, we provide pathogen detection services for mycoplasma and adventitious viruses.  We offer cell line expansion and cryopreservation and can authenticate these cell line resources to enhance reproducibility.  Indeed, NovoHelix has developed STR profiling and SNP assays to obviate cell line misidentification and contamination as mandated prior to publication in high-impact journals and encouraged by investigators funded by the NIH.  A detailed cost estimate can be developed based on your specific project through our online Quote Request.
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services

Service

Catalog Nr

Service Description

Price

Pathogen + Mycoplasma testing of client-provided ES cell lines/cell lines
MBGT001
A panel of over 20 viral pathogens are screened including coronavirus, reovirus and Sendai virus. This service also includes mycoplasma testing.
Mycoplasma testing of ES cell clones/cell lines provided by the client
MBGT002
 NovoHelix provides mycoplasma testing using a multiplex 16S rRNA gene assay to broadly determine adventitious mycoplasma species infection.  This service fee is per mouse ES cell (mESC) clone/cell line. The assay detects over 60 species of Mycoplasma, Acholeplasma, Spiroplasma and Ureaplasma including the eight species most likely to afflict cell cultures: M. arginini, M. fermentans, M. hominis, M.hyorhinis, M. orale, M. pirum, M. salivarium, and A. laidlawii.  
  Genotyping Assay Development
MBGT003
 Robust, transferable genotyping assays are needed to screen many of the animal and cellular models during our production and validation cycles. NovoHelix provides expert assay design and consultation to the client to ensure genotyping success.  Assay design costs are based on the number of alleles screened. In some cases, a synthetic positive control needs to be built for assay validation and these 'building' costs will be passed on to the client.
 Sample Genotyping
MBGT004
 Genotyping includes DNA extraction and purification services with a minimum charge of 10 samples. Samples that require additional genotyping validation such as Sanger sequencing of frameshifting mutants or point mutations will incur additional fee schedules (sequencing costs, etc). Genotyping is $15 per sample per allele screened.   
technology
references
Huang J, Mirel D, Pugh E, Xing C, Robinson PN, Pertsemlidis A, Ding L, Kozlitina J, Maher J, Rios J, Story M, Marthandan N, Scheuermann RH. Minimum Information about a Genotyping Experiment (MIGEN). Stand Genomic Sci. 2011 Nov 30;5(2):224-9. doi: 10.4056/sigs.1994602. Epub 2011 Nov 22. PubMed PMID: 22180825; PubMed Central PMCID: PMC3235517.



Truett GE, Heeger P, Mynatt RL, Truett AA, Walker JA, Warman ML. Preparation of PCR-quality mouse genomic DNA with hot sodium hydroxide and tris (HotSHOT). Biotechniques. 2000 Jul;29(1):52, 54. PubMed PMID: 10907076.


Tunster SJ. Genetic sex determination of mice by simplex PCR. Biol Sex Differ. 2017 Oct 17;8(1):31. doi: 10.1186/s13293-017-0154-6. PubMed PMID: 29041956; PubMed Central PMCID: PMC5645908.


Hrovatin K, Kunej T. Genetic sex determination assays in 53 mammalian species: Literature analysis and guidelines for reporting standardization. Ecol Evol. 2017 Dec 13;8(2):1009-1018. doi: 10.1002/ece3.3707. eCollection 2018 Jan. PubMed PMID: 29375774; PubMed Central PMCID: PMC5773321.


Strah R, Kunej T. Molecular sexing assays in 114 mammalian species: In silico  sequence reanalysis and a unified graphical visualization of diagnostic tests. Ecol Evol. 2019 Apr 8;9(8):5018-5028. doi: 10.1002/ece3.5093. eCollection 2019 Apr. Review. PubMed PMID: 31031962; PubMed Central PMCID: PMC6476764.


Green MR, Sambrook J. One-Tube Isolation of DNA from Mouse Tails. Cold Spring  Harb Protoc. 2018 Feb 1;2018(2). doi: 10.1101/pdb.prot093534. PubMed PMID: 29438056.


Weeks DP, Beerman N, Griffith OM. A small-scale five-hour procedure for isolating multiple samples of CsCl-purified DNA: application to isolations from mammalian, insect, higher plant, algal, yeast, and bacterial sources. Anal Biochem. 1986 Feb 1;152(2):376-85. PubMed PMID: 3963370.


Gemmell NJ, Akiyama S. An efficient method for the extraction of DNA from vertebrate tissues. Trends Genet. 1996 Sep;12(9):338-9. PubMed PMID: 8855658.


Strauss WM. Preparation of genomic DNA from mammalian tissue. Curr Protoc Mol Biol. 2001 May;Chapter 2:Unit2.2. doi: 10.1002/0471142727.mb0202s42. PubMed PMID:18265182.

Behringer R, Gertsenstein M, Nagy KV, Nagy A. Isolation of High-Molecular-Weight DNA from Mouse Tail Tips. Cold Spring Harb Protoc. 2019 Apr 1;2019(4). doi: 10.1101/pdb.prot092692. PubMed PMID: 30936380.

Yu M, Selvaraj SK, Liang-Chu MM, Aghajani S, Busse M, Yuan J, Lee G, Peale F, Klijn C, Bourgon R, Kaminker JS, Neve RM. A resource for cell line authentication, annotation and quality control. Nature. 2015 Apr 16;520(7547):307-11. doi: 10.1038/nature14397. PubMed PMID: 25877200.

Beermann F, Hummler E, Schmid E, Schütz G. Perinatal activation of a tyrosine  aminotransferase fusion gene does not occur in albino lethal mice. Mech Dev. 1993 Jul;42(1-2):59-65. PubMed PMID: 8103668.
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