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Epidesigner beta software

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EpiDesigner beta software is a laboratory tool developed by Labcorp. It is a software application designed to assist researchers and scientists in the analysis and visualization of epigenetic data. The core function of EpiDesigner beta is to provide a platform for the processing, analysis, and interpretation of epigenetic information, such as DNA methylation patterns and histone modifications.

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Lab products found in correlation

Ez dna methylation kit, by Zymo Research (5 mentions) Epityper assay, by Labcorp (3 mentions) Gentra puregene cell kit, by Qiagen (2 mentions) Massarray assay, by Labcorp (1 mentions) Truseq protocol, by Illumina (1 mentions) Miseq machine, by Illumina (1 mentions) Epityper, by Labcorp (1 mentions) Purelink mini kit, by Thermo Fisher Scientific (1 mentions)

7 protocols using epidesigner beta software

1

Bisulfite-Sequenom DNA Methylation Analysis

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EpiTYPER assays (Sequenom) were performed on bisulfite-converted DNA from FL patients as previously described55 (link) after informed consent from all participants with the approval of the Institutional Review Boards of Weill Cornell Medical College. The primers were designed using Sequenom EpiDesigner beta software (http://www.epidesigner.com/). The primer sequences are available in (Supplementary Table 9).
Cimmino L., Dawlaty M.M., Ndiaye-Lobry D., Yap Y.S., Bakogianni S., Yu Y., Bhattacharyya S., Shaknovich R., Geng H., Lobry C., Mullenders J., King B., Trimarchi T., Aranda-Orgilles B., Liu C., Shen S., Verma A.K., Jaenisch R, & Aifantis I. (2015). Tet1 is a tumor suppressor of hematopoietic malignancy. Nature immunology, 16(6), 653-662.
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2

Validating DNA Methylation via ERRBS

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For validation of DNA methylation measured by ERRBS, single-locus quantitative DNA methylation was performed on bisulfite-converted DNA (EZ DNA Methylation Kit, Zymo Research) using MassArray assay (Sequenom, CA). Primers were designed to cover CpG dense areas of interest by using Sequenom EpiDesigner beta software (http://www.epidesigner.com/).
Pan H., Jiang Y., Boi M., Tabbò F., Redmond D., Nie K., Ladetto M., Chiappella A., Cerchietti L., Shaknovich R., Melnick A.M., Inghirami G.G., Tam W, & Elemento O. (2015). Epigenomic evolution in diffuse large B-cell lymphomas. Nature Communications, 6, 6921.
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3

Validating Intratumor DNA Methylation

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To validate intra-tumour DNA MH measured by ERRBS, we performed bisulfite-PCR on several loci of interest. Bisulfite conversion was performed using the EZ DNA Methylation Kit from Zymo Research. PCR primers were designed by using Sequenom EpiDesigner beta software. PCR products were gel purified, and then converted to sequencing libraries following Illumina TruSeq protocol. Pair-end sequencing (250 bp either end) was performed on Illumina MiSeq machine. In brief, bisulfite reads were aligned to the bisulife-converted hg19 reference genome using Bismark43 (link), with non-directional model.
Pan H., Jiang Y., Boi M., Tabbò F., Redmond D., Nie K., Ladetto M., Chiappella A., Cerchietti L., Shaknovich R., Melnick A.M., Inghirami G.G., Tam W, & Elemento O. (2015). Epigenomic evolution in diffuse large B-cell lymphomas. Nature Communications, 6, 6921.
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4

Quantifying DNA methylation with EpiTYPER

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EpiTYPER assays were performed on bisulfite-converted gDNA. For the biologic validation of the AID-dependent hypoDMRs in mouse B cells, primers were designed to cover CpG islands associated with the respective DMRs. All primers were designed using Sequenom EpiDesigner BETA software (http://www.epidesigner.com/). Primer sequences are shown in Supplemental Experimental Procedures.
Dominguez P.M., Teater M., Chambwe N., Kormaksson M., Redmond D., Ishii J., Vuong B., Chaudhuri J., Melnick A., Vasanthakumar A., Godley L.A., Papavasiliou F.N., Elemento O, & Shaknovich R. (2015). DNA Methylation Dynamics of Germinal Center B Cells Are Mediated by AID. Cell reports, 12(12), 2086-2098.
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5

Genome-wide DNA Methylation Analysis in Bladder Cancer

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Total genomic DNA was extracted from eight bladder cancer cells using the PureLink mini kit (Invitrogen). EpiTYPER assays (Sequenom, San Diego, CA, USA) were performed on bisulfite-converted DNA. Bisulfite conversion was performed using the EZ DNA Methylation kit from Zymo Research (Irvine, San Diego, CA, USA). EpiTYPER (Sequenom) primers were designed to cover CpG islands associated with the respective HpaII amplifiable fragments. All primers were designed using Sequenom EpiDesigner beta software. Primer sequences are shown in Table S3.
Xylinas E., Hassler M.R., Zhuang D., Krzywinski M., Erdem Z., Robinson B.D., Elemento O., Clozel T, & Shariat S.F. (2016). An Epigenomic Approach to Improving Response to Neoadjuvant Cisplatin Chemotherapy in Bladder Cancer. Biomolecules, 6(3), 37.
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6

Genome-wide DNA Methylation Analysis

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Total genomic DNA was extracted from 2 × 106 FaDu and FRII cells using the Gentra Puregene cell kit (Qiagen) and eluted in RNAse-free water. EpiTYPER assays (Sequenom, CA) were performed on bisulfite-converted DNA. Bisulfite conversion was performed using EZ DNA Methylation kit from Zymo Research (Irvine, CA). EpiTYPER primers were designed to cover 29 GLI1 CpGs (25 of them in CpG island) using Sequenom EpiDesigner beta software (http://www.epidesigner.com/). Primer sequences are below:
Zahreddine H.A., Culjkovic-Kraljacic B., Assouline S., Gendron P., Romeo A.A., Morris S.J., Cormack G., Jaquith J.B., Cerchietti L., Cocolakis E., Amri A., Bergeron J., Leber B., Becker M.W., Pei S., Jordan C.T., Miller WH J.r, & Borden K.L. (2014). The sonic hedgehog factor Gli1 imparts drug resistance through inducible glucuronidation. Nature, 511(7507), 90-93.
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7

Genome-wide DNA Methylation Analysis

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Total genomic DNA was extracted from 2 × 106 FaDu and FRII cells using the Gentra Puregene cell kit (Qiagen) and eluted in RNAse-free water. EpiTYPER assays (Sequenom, CA) were performed on bisulfite-converted DNA. Bisulfite conversion was performed using EZ DNA Methylation kit from Zymo Research (Irvine, CA). EpiTYPER primers were designed to cover 29 GLI1 CpGs (25 of them in CpG island) using Sequenom EpiDesigner beta software (http://www.epidesigner.com/). Primer sequences are below:
Zahreddine H.A., Culjkovic-Kraljacic B., Assouline S., Gendron P., Romeo A.A., Morris S.J., Cormack G., Jaquith J.B., Cerchietti L., Cocolakis E., Amri A., Bergeron J., Leber B., Becker M.W., Pei S., Jordan C.T., Miller WH J.r, & Borden K.L. (2014). The sonic hedgehog factor Gli1 imparts drug resistance through inducible glucuronidation. Nature, 511(7507), 90-93.
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