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Epidesigner

Manufactured by Agena
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EpiDesigner is a software tool designed for the design and visualization of epigenetic experiments. It provides a user-friendly interface for researchers to plan and optimize their epigenetic research projects.

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Lab products found in correlation

Mass array epityper1.2 suite, by Agena (2 mentions) Qiaamp dna mini kit, by Qiagen (2 mentions) Rnase one ribonuclease, by Promega (2 mentions) Hotstar polymerase, by Qiagen (1 mentions) Epitect bisulfite kit, by Qiagen (1 mentions) Epityper, by Agena (1 mentions) Allprep kit, by Qiagen (1 mentions) Ez dna methylation kit, by Zymo Research (1 mentions) Dna blood and tissue kit, by Qiagen (1 mentions) Ez dna methylation gold kit, by Zymo Research (1 mentions) Maldi tof ms, by CapitalBio (1 mentions)

7 protocols using epidesigner

1

DNA Methylation Analysis of GLS2 Promoter

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High molecular weight genomic DNA was isolated from breast cancer cells using QIAamp DNA Mini Kit (QIAGEN), and contaminating RNA was digested using RNase One Ribonuclease (Promega) followed by re-purification of DNA, elution with water, and adjustment of DNA concentration to 50 ng/μl. To assess DNA purity, UV/visible absorption spectra were measured, and for all samples the A260/280 ratio was >1.7 and the A260/230 ratio was >2.0. Samples were then submitted to the Epigenomics Core at Weill Cornell Medical College, where bisulfite conversion was carried out followed by DNA methylation analysis using Mass ARRAY EpiTYPER1.2 Suite (Agena Bioscience). The sequence of the CpG island in the GLS2 gene promoter was obtained from human reference genome GRCh38/hg38 using the UCSC Genome Browser (https://genome.ucsc.edu). Primers for DNA methylation analysis were designed using EpiDesigner (Agena Bioscience) and synthesized by Integrated DNA Technologies (Table S6). Relative methylation ratios at CpG sites are presented as a heatmap, generated using MORPHEUS (https://software.broadinstitute.org/morpheus).
Lukey M.J., Cluntun A.A., Katt W.P., Lin M.C., Druso J.E., Ramachandran S., Erickson J.W., Le H.H., Wang Z.E., Blank B., Greene K.S, & Cerione R.A. (2019). Liver-Type Glutaminase GLS2 Is a Druggable Metabolic Node in Luminal-Subtype Breast Cancer. Cell reports, 29(1), 76-88.e7.
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2

DNA Methylation Analysis of GLS2 Promoter

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High molecular weight genomic DNA was isolated from breast cancer cells using QIAamp DNA Mini Kit (QIAGEN), and contaminating RNA was digested using RNase One Ribonuclease (Promega) followed by re-purification of DNA, elution with water, and adjustment of DNA concentration to 50 ng/μl. To assess DNA purity, UV/visible absorption spectra were measured, and for all samples the A260/280 ratio was >1.7 and the A260/230 ratio was >2.0. Samples were then submitted to the Epigenomics Core at Weill Cornell Medical College, where bisulfite conversion was carried out followed by DNA methylation analysis using Mass ARRAY EpiTYPER1.2 Suite (Agena Bioscience). The sequence of the CpG island in the GLS2 gene promoter was obtained from human reference genome GRCh38/hg38 using the UCSC Genome Browser (https://genome.ucsc.edu). Primers for DNA methylation analysis were designed using EpiDesigner (Agena Bioscience) and synthesized by Integrated DNA Technologies (Table S6). Relative methylation ratios at CpG sites are presented as a heatmap, generated using MORPHEUS (https://software.broadinstitute.org/morpheus).
Lukey M.J., Cluntun A.A., Katt W.P., Lin M.C., Druso J.E., Ramachandran S., Erickson J.W., Le H.H., Wang Z.E., Blank B., Greene K.S, & Cerione R.A. (2019). Liver-Type Glutaminase GLS2 Is a Druggable Metabolic Node in Luminal-Subtype Breast Cancer. Cell reports, 29(1), 76-88.e7.
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3

Amplicon Bisulfite Sequencing for CXCL10 Methylation

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Amplicon bisulfite sequencing was used to measure methylation at 7 CpG sites in the promoter of the CXCL10 gene. Primers were designed using the EpiDesigner tool from Agena Biosciences (EpiDesigner.com">www.EpiDesigner.com). Genomic DNA was bisulfite converted, and amplicons were amplified using Qiagen HotStar polymerase. For each patient, amplicons were pooled at equimolar concentration before preparing libraries using the KAPA Hyper Prep library kit. Final libraries were quantified using the KAPA Library prep quantification kit, pooled at equimolar concentration, and sequenced on a MiSeq Nano V2 flow cell with PE-150 cycles. The data generated was trimmed of adapter sequences, mapped to the human genome (hg38) using Bismark, and methylation data was extracted using MethylDackel. The resulting files contain methylation data as beta values for each CpG site/sample. These were imported in R for analysis.
Zakharia Y., Singer E.A., Acharyya S., Garje R., Joshi M., Peace D., Baladandayuthapani V., Majumdar A., Li X., Lalancette C., Kryczek I., Zou W, & Alva A. (2024). Durvalumab and guadecitabine in advanced clear cell renal cell carcinoma: results from the phase Ib/II study BTCRC-GU16-043. Nature Communications, 15, 972.
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4

Methylation Analysis of CYP39A1 Gene

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Genomic DNA was extracted from peripheral blood samples of all participants by the GoldMag-Mini Purification Kit (GoldMag Co. Ltd. Xi’an, China). PCR primers for PCR amplification were designed by Agena Bioscience EpiDesigner (EpiDesigner.com/">http://www.EpiDesigner.com/), and are listed in Table S1. The genomic region of CpGs in CYP39A1 was chr6:46652805–46653452. The sequencing region for methylation was in the promoter region of CYP39A1. The prediction evaluation of each CpG site in different CYP39A1 gene fragments was shown in Figure S1. MassARRAY Epityper DNA platform and MALDI-TOF detection were performed to detect and analyze the methylation of CYP39A1.22 (link)
Wang P., Lu H., Rong H., Wang Y., Wang L., He X., Yuan D., He Y, & Jin T. (2023). The Association of Methylation Level in the CYP39A1 Gene with High Altitude Pulmonary Edema in the Chinese Population. Pharmacogenomics and Personalized Medicine, 16, 617-628.
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5

DNA Methylation Analysis of OXT Gene

Cited 1 time
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One microgram of DNA was treated with bisulfite using the EpiTect Bisulfite Kit (Qiagen, Hilden, Germany). DNA methylation of CpG sites in the promoter region of the OXT gene (chr20: 3,052,266–3,053,162; hg19 build) was analyzed using EpiTYPER (MassARRAY system; Agena Biosciences., San Diego, CA, USA) according to the manufacturer’s instructions. Forward (aggaagagagTTTTTTTGTTTTATTTTAGTGGTTTAGG) and reverse (cagtaatacgactcactatagggagaaggctTCTTACCTCCCAAAAAACAATTCTA) primers corresponding to chr20:3,052,009–3,052,392 were designed using EpiDesigner (Agena Bioscience, San Diego, CA, USA), and the spectrum characteristics were validated with RSeqMeth [28 (link)]. Further details were described in a previous study [22 (link)] where SN and AKS contributed as co-authors.
Nishitani S., Fujisawa T.X., Hiraoka D., Makita K., Takiguchi S., Hamamura S., Yao A., Shimada K., Smith A.K, & Tomoda A. (2021). A multi-modal MRI analysis of brain structure and function in relation to OXT methylation in maltreated children and adolescents. Translational Psychiatry, 11, 589.
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6

Quantitative DNA Methylation Analysis of Lung Tumors

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RNA and DNA was purified from resected lung tumors using the All-Prep kit (Qiagen). Analysis of DNA methylation of repetitive elements was performed using EpiTYPER MassARRAY(25 (link),35 (link)). Genomic DNA was prepared from resected lung tumors using the All-Prep kit (Qiagen), and 1.0 μg of genomic DNA was bisulfite convereted using the EZ DNA methylation kit (Zymo Research). Regions of interest were amplified from bisulfite-treated DNA by PCR using primers designed in EpiDesigner (Agena Biosciences). Matrix-assisted laser desorption/ionization-time of flight (MALDI-ToF) mass spectrometry was performed to quantitate CpG methylation. Data was analyzed using EpiTYPER software 1.2 (Agena Biosciences) and visualized using R package ggplot2. For primers and target CpGs see supplemental table 4.
Koenig M.J., Agana B.A., Kaufman J.M., Sharpnack M.F., Wang W.Z., Weigel C., Navarro F.C., Amann J.M., Cacciato N., Arasada R.R., Gerstein M.B., Wysocki V.H., Oakes C, & Carbone D.P. (2021). STK11/LKB1 loss of function is associated with global DNA hypomethylation and S-adenosyl-methionine depletion in human lung adenocarcinoma. Cancer research, 81(16), 4194-4204.
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7

Quantitative Analysis of RGS5 DNA Methylation

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Genomic DNA was extracted from HUVECs via a Blood and Tissue DNA Kit (provided by Qiagen Inc., Dusseldorf, Germany) based on the manufacturer’s protocols. The purity and concentration of the DNA were detected through measuring the absorbance at 280 and 260 nm. In total, 1.5 μg genomic DNA from each sample was treated with bisulfite using an EZ DNA Methylation-Gold Kit (provided by Zymo Research, Irvine, CA, America), in accordance with the manufacturer’s instructions. PCR primers were designed by using Epidesigner (Agena Bioscience, Inc., San Diego, CA, America). The methylation platform (CapitalBio Corp., Beijing, China), which included RNA base-specific cleavage and MALDI-TOF-MS (matrix-assisted laser desorption/ionization time-of-flight mass spectrometry), was employed for quantitative analysis on RGS5 methylation. The resulted methylation calls were analyzed by using EpiTyper 1.0 software (provided by Sequenom, San Diego, CA, America) to generate quantitative results for each CpG site or an aggregate of multiple CpG sites.
Zhang X., Tang N., Xi D., Feng Q., Liu Y., Wang L., Tang Y., Zhong H, & He F. (2020). Human cytomegalovirus promoting endothelial cell proliferation by targeting regulator of G-protein signaling 5 hypermethylation and downregulation. Scientific Reports, 10, 2252.
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