Ffpe dna kit

Manufactured by Omega Bio-Tek

Sourced in United States

The FFPE DNA kit is a laboratory product designed to extract and purify DNA from formalin-fixed, paraffin-embedded (FFPE) tissue samples. The kit utilizes a proprietary technology to efficiently recover DNA from these challenging samples.

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Lab products found in correlation

Nanodrop spectrophotometer, by Thermo Fisher Scientific (2 mentions) Nanodrop, by Thermo Fisher Scientific (2 mentions) Qsep100 bioanalyzer, by Bioptic (1 mentions) Epitect fast dna bisulfite kit, by Qiagen (1 mentions) Tissue dna kit, by Omega Bio-Tek (1 mentions) Quan it picogreen dsdna assay, by Thermo Fisher Scientific (1 mentions) Ez 96 dna methylation kit, by Zymo Research (1 mentions)

Close spelling variants of this product

EZNA FFPE DNA Kit (8 citations) E.Z.N.A FFPE DNA Isolation kit (2 citations) E.Z.N.A™ FFPE DNA extraction kit (2 citations)

6 protocols using ffpe dna kit

Extracting DNA from FFPE Samples

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The study was approved by the Ethics Committee of the Central Hospital of Wuhan in China (WHZXKYL2022-047). We recruited 59 PCa patients admitted to our hospital from January 2019 to December 2020. Formalin-fixed, paraffin-embedded (FFPE) tissue blocks were examined by an experienced pathologist to select tumor samples with malignant cell purities over 70% and adjacent normal tissues. All patients provided signed informed consent before enrollment.
For each FFPE sample, DNA was extracted using E.A.N., an FFPE DNA Kit (Omega Biotek) according to the manufacturer’s protocol. The DNA concentration was quantified using a Qubit 4.0 Fluorometer. The fragment length and degradation were assessed by a Qsep100 bioanalyzer (BIOptic). The DNA was stored at – 20 °C before use.

Lang B., Cao C., Zhao X., Wang Y., Cao Y., Zhou X., Zhao T., Wang Y., Liu T., Liang W., Hu Z., Tian X., Zhang J, & Yan Y. (2023). Genomic alterations related to HPV infection status in a cohort of Chinese prostate cancer patients. European Journal of Medical Research, 28, 239.

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Tissue Fixation, Paraffin Embedding, and DNA Extraction

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Surgically removed tissue was fixed in 10% buffered formalin for 24 h at room temperature and embedded in paraffin. Hematoxylin and eosin-stained tumor tissues (stained for 5 min and 30 sec at room temperature, respectively) were independently reviewed by two pathologists. DNA was extracted using the FFPE DNA kit (Omega Bio-Tek, Inc., Norcross, GA, USA), according to the manufacturer's protocol. The DNA concentration was determined using a NanoDrop 2000 instrument and the 260/280 nm ratio was calculated to evaluate the quality of DNA. The sample concentration was adjusted to 200–300 ng/µl, and DNA was stored at −80°C.

Zhang Y., Dong J., Shi R., Feng L., Li Y., Cheng C., Zhang L., Song B., Bi Y., Huang H., Kong P., Guo J, & Liu J. (2019). Mps1 is associated with the BRAFV600E mutation and predicts poor outcome in patients with colorectal cancer. Oncology Letters, 17(3), 2809-2817.

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BRAF and IDH1/2 Mutation Analysis

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Five 10-µm sections from each selected FFPE block were subjected to genomic DNA extraction. DNA was isolated using E.Z.N.A.® FFPE DNA kit (D3399-02; Omega Bio-tek, US) according to the manufacturer’s instructions. Next, the genomic DNA was amplified by polymerase chain reaction (PCR) and the PCR products were purified. The purified products were sequenced and then analyzed using Chromas Lite software. Compared with the reference sequence, the BRAF^V600E mutation and IDH1/2 alterations in the hotspot codons R132H and R172K were obtained.

Yan J., Cheng J., Liu F, & Liu X. (2018). Pleomorphic xanthoastrocytomas of adults: MRI features, molecular markers, and clinical outcomes. Scientific Reports, 8, 14275.

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FFPE DNA Extraction and Quantification

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Total DNA was extracted from formalin-fixed, paraffin-embedded tissues using the E.Z.N.A.^® FFPE DNA kit (Omega Bio-Tek, Inc., Norcross, GA, USA), according to the manufacturer's protocol. The isolated DNA was eluted in 100 µl Tris-EDTA buffer included in the E.Z.N.A.^® FFPE DNA kit and stored at −20°C until required. The quality of the isolated DNA was assessed by NanoDrop spectrophotometer (NanoDrop Technologies, Thermo Fisher Scientific, Inc., Wilmington, DE, USA). The optical density values of all samples ranged from 1.8 to 2.0.

Qi Y., Wei Y., Wang Q., Xu H., Wang Y., Yao A., Yang H., Gao Y, & Zhou F. (2016). Heteroplasmy of mutant mitochondrial DNA A10398G and analysis of its prognostic value in non-small cell lung cancer. Oncology Letters, 12(5), 3081-3088.

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Genomic DNA Extraction and Bisulfite Modification

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Genomic DNA from the samples of GC and normal adjacent tissue and FFPE samples were isolated using a Tissue DNA Kit and an FFPE DNA kit (Omega Bio-Tek, USA), respectively. Next, 1 μg DNA was bisulfite-modified using the EpiTect Fast DNA Bisulfite kit (Qiagen, Germany), according to the manufacturer’s protocol.

Wang H., Duan X.L., Qi X.L., Meng L., Xu Y.S., Wu T, & Dai P.G. (2017). Concurrent Hypermethylation of SFRP2 and DKK2 Activates the Wnt/β-Catenin Pathway and Is Associated with Poor Prognosis in Patients with Gastric Cancer. Molecules and Cells, 40(1), 45-53.

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DNA Extraction and Purification from Fresh-Frozen and FFPE Tissues

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DNA from fresh-frozen (FF) tissue samples was isolated using a standard phenol-chloroform/proteinase-k protocol, whereas paraffin samples (FFPE) (10 sections of 14 μm) were processed using the E.Z.N.A. FFPE DNA kit (Omega Bio-Tek, Norcross, GA, USA), with a xylene wash to remove the paraffin. For each sample of tumor tissue, subsequent sections were stained with hematoxylin and eosin for histologic confirmation of the presence (>50%) of tumor cells. The obtained DNA was treated with RNase A for 1 h at 45ºC. All DNA samples were quantified using the fluorometric method (Quan-iT PicoGreen DsDNA Assay, Life Technologies) and were assessed for purity using a NanoDrop (Thermo Scientific) with 260/280 and 260/230 ratio measurements. The integrity of the FF DNA was verified by electrophoresis in a 1.3% agarose gel. FF DNA (600 ng) and FFPE DNA (300 ng) were processed using the EZ-96 DNA Methylation kit (Zymo Research Corp, Irvine, CA, USA) following the manufacturer's recommendations for Infinium assays.

Crujeiras A.B., Diaz-Lagares A., Stefansson O.A., Macias-Gonzalez M., Sandoval J., Cueva J., Lopez-Lopez R., Moran S., Jonasson J.G., Tryggvadottir L., Olafsdottir E., Tinahones F.J., Carreira M.C., Casanueva F.F, & Esteller M. (2017). Obesity and menopause modify the epigenomic profile of breast cancer. Endocrine-related cancer, 24(7).

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