Allprep dna rna ffpe isolation kit

Manufactured by Qiagen

The AllPrep DNA/RNA FFPE isolation kit is a laboratory product designed to extract and purify both DNA and RNA from formalin-fixed, paraffin-embedded (FFPE) tissue samples. It is a tool for researchers working with FFPE samples in various applications.

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Lab products found in correlation

Qubit 3.0 fluorometer, by Thermo Fisher Scientific (3 mentions) Qubit dsdna hs assay kit, by Thermo Fisher Scientific (2 mentions) Allprep dna rna mirna universal isolation kit, by Qiagen (1 mentions) 4200 tapestation system, by Agilent Technologies (1 mentions) Rneasy ffpe kit, by Qiagen (1 mentions) Reliaprep ffpe total rna miniprep kit, by Promega (1 mentions) Qubit rna xr assay kit, by Thermo Fisher Scientific (1 mentions) High pure ffpe rna isolation kit, by Roche (1 mentions) Tapestation, by Agilent Technologies (1 mentions) Qiaamp dna mini kit, by Qiagen (1 mentions) Superscript 3 reverse transcriptase, by Thermo Fisher Scientific (1 mentions) Qiacube, by Qiagen (1 mentions)

Close spelling variants of this product

AllPrep DNA/RNA FFPE Kit AllPrep DNA/RNA isolation kit AllPrep DNA/RNA FFPE AllPrep DNA FFPE Kit Allprep RNA isolation kit FFPE RNA isolation kit FFPE DNA isolation kit AllPrep FFPE kit Allprep RNA/DNA AllPrep Isolation Kit

7 protocols using allprep dna rna ffpe isolation kit

DCIS Microdissection and Nucleic Acid Isolation

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The pathologist scored the tumor percentage and indicated the DCIS regions for isolation on a H&E slide.
From 5 to 15 (depending on the DCIS area size) FFPE 10 μm slides, the DCIS regions were dissected by scraping the areas off under a stereomicroscope using a needle. The scraped off tissue was stored in PKD digestion buffer (Qiagen, #80234) and stored at 4 ⁰C for up to a week. DNA and RNA was isolated simultaneously with the Allprep DNA/RNA FFPE isolation kit (Qiagen, #80234) by using the QIAcube, according to manufacturer’s protocol.

Hutten S.J., de Bruijn R., Lutz C., Badoux M., Eijkman T., Chao X., Ciwinska M., Sheinman M., Messal H., Herencia-Ropero A., Kristel P., Mulder L., van der Waal R., Sanders J., Almekinders M.M., Llop-Guevara A., Davies H.R., van Haren M.J., Martin N.I., Behbod F., Nik-Zainal S., Serra V., van Rheenen J., Lips E.H., Wessels L.F., Wesseling J., Scheele C.L, & Jonkers J. (2023). A living biobank of patient-derived ductal carcinoma in situ mouse-intraductal xenografts identifies risk factors for invasive progression. Cancer Cell, 41(5), 986-1002.e9.

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Extracting DNA and RNA from FFPE Tissue

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Tumor DNA and RNA was isolated from formalin-fixed, paraffin-embedded (FFPE) sections. A pathologist scored the tumor percentage and indicated the most tumor-dense region on a H&E stain slide for subsequent DNA/RNA isolation. A total of 5–10 FFPE slides (10 µm) were used for simultaneous isolation of DNA and RNA using the AllPrep DNA/RNA FFPE isolation kit (Qiagen, 80234) and the QIAcube, according to the manufacturer’s protocol.
Germline DNA was isolated from peripheral blood mononuclear cells using AllPrep DNA/RNA/miRNA Universal isolation kit (Qiagen, 80224) and the QIAcube, according to the manufacturer’s protocol.

Hoefsmit E.P., Rozeman E.A., Van T.M., Dimitriadis P., Krijgsman O., Conway J.W., Pires da Silva I., van der Wal J.E., Ketelaars S.L., Bresser K., Broeks A., Kerkhoven R.M., Reeves J.W., Warren S., Kvistborg P., Scolyer R.A., Kapiteijn E.W., Peeper D.S., Long G.V., Schumacher T.N, & Blank C.U. (2020). Comprehensive analysis of cutaneous and uveal melanoma liver metastases. Journal for Immunotherapy of Cancer, 8(2), e001501.

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DNA Extraction from FFPE Tumor Samples

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One pathologist (J.V.) evaluated hematoxylin and eosin–stained sections of the tumor and adjacent mucosa in order to distinguish between carcinoma tissue and adjacent, non-dysplastic mucosa. After macro-dissection from 10-µm FFPE sections, DNA was isolated using the AllPrep DNA/RNA FFPE isolation kit (Qiagen). Briefly, slides were deparaffinized in series of xylene and ethanol, after which either of the 2 different conditions (cancer mucosa or adjacent mucosa) were scratched out from the tissue sections. DNA was isolated after incubation with proteinase K (20 mg/ml) at 56 °C in lysis buffer for an overnight incubation period. Small samples were incubated for a 6-day incubation period. DNA concentrations and purity were measured with a Nanodrop ND-1000 spectrophotometer (Isogen), as well as with a Qubit 3.0 Fluorometer (Thermo Fisher Scientific) using the Qubit dsDNA HS Assay Kit to measure double-stranded DNA.

de Krijger M., Carvalho B., Rausch C., Bolijn A.S., Delis-van Diemen P.M., Tijssen M., van Engeland M., Mostafavi N., Bogie R.M., Dekker E., Masclee A.A., Verheij J., Meijer G.A, & Ponsioen C.Y. (2022). Genetic Profiling of Colorectal Carcinomas of Patients with Primary Sclerosing Cholangitis and Inflammatory Bowel Disease. Inflammatory Bowel Diseases, 28(9), 1309-1320.

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Comparison of FFPE-RNA Isolation Kits

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We compared three different FFPE-RNA isolation procedures on RNA quality, as estimated with the DV₂₀₀, determined by the 4200 TapeStation System (Agilent). We compared the RNeasy FFPE kit (QIAGEN), the ReliaPrep FFPE total RNA miniprep kit (Promega) and the AllPrep DNA/RNA FFPE isolation kit (QIAGEN). For the FFPE-RNA application cohort, total RNA and genomic DNA were isolated from FFPE samples with QIAGEN’s QIAcube classic (cat. no. 9001293; QIAGEN). A DV₂₀₀>15% was deemed sufficient for RNA-seq.

de Back T.R., Wu T., Schafrat P.J., ten Hoorn S., Tan M., He L., van Hooff S.R., Koster J., Nijman L.E., Vink G.R., Beumer I.J., Elbers C.C., Lenos K.J., Sommeijer D.W., Wang X, & Vermeulen L. (2024). A consensus molecular subtypes classification strategy for clinical colorectal cancer tissues. Life Science Alliance, 7(8), e202402730.

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NanoString PanCancer IO 360 Analysis

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RNA of pretreatment FFPE samples from the NKI-AVL cohorts were isolated with the AllPrep DNA/RNA FFPE isolation kit (No. 80234, Qiagen) according to the manufacturer's recommendations and quantified by Tapestation (Agilent). RNA from the CERTIM cohort was extracted with High Pure FFPE RNA Isolation Kit (Roche Diagnostics) according to the manufacturer's recommendations and quantified using fluorimetry with Qubit RNA XR Assay Kit (Invitrogen, Thermo Fisher Scientific). A total of 200- to 300-ng RNA from the NKI-AVL cohorts and 30- to 100-ng RNA from the CERTIM cohort were hybridized to NanoString PanCancer IO 360 Panel code set (NanoString), according to the manufacturer's recommendations. After hybridization, nonbound probes were washed off, and the RNA–probe complex was bound to the cartridge on the NanoString Flex Prep Station (NanoString) according to manufacturing protocol. The cartridge was sealed and transferred to the digital analyzer for imaging.

Hummelink K., Tissier R., Bosch L.J., Krijgsman O., van den Heuvel M.M., Theelen W.S., Damotte D., Goldwasser F., Leroy K., Smit E.F., Meijer G.A., Thommen D.S, & Monkhorst K. (2023). A Dysfunctional T-cell Gene Signature for Predicting Nonresponse to PD-1 Blockade in Non–small Cell Lung Cancer That Is Suitable for Routine Clinical Diagnostics. Clinical Cancer Research, 30(4), 814-823.

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DNA and RNA Extraction from FFPE Tissue

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DNA and RNA were extracted from four 20 μm-thick formalin-fixed, paraffin-embedded tissue scrolls from a lesional skin biopsy using the Allprep DNA/RNA FFPE isolation kit (Qiagen) as per the manufacturer’s instructions. DNA and RNA amounts were measured using a BioDrop spectrophotometer (Denville Scientific Inc.). For fresh frozen samples from the validation set, DNA was isolated from thirty cryosections of 10 μm thickness. DNA extraction was carried out using the QIAamp DNA Mini Kit (Qiagen) kit as per manufacturer’s instructions with overnight tissue digestion.

De Masson A., O’Malley J.T., Elco C.P., Garcia S.S., Divito S.J., Lowry E.L., Tawa M., Fisher D.C., Devlin P.M., Teague J.E., Leboeuf N.R., Kirsch I.R., Robins H., Clark R.A, & Kupper T.S. (2018). High-Throughput Sequencing of the T cell Receptor β gene identifies aggressive early-stage Mycosis Fungoides. Science translational medicine, 10(440), eaar5894.

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FFPE RNA and DNA Isolation

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Prior to RNA isolation, FFPE material was pathologically assessed. The expert pathologist scored tumor cell percentage and indicated most tumor-dense regions for isolation on a hematoxylin and eosin (H&E) slide. RNA and DNA from FFPE material were simultaneously isolated from 3-10 sections (depending on tumor size) of 10 μm using the AllPrep DNA/RNA FFPE isolation kit (80234, Qiagen) and the QIAcube according to the manufacturer’s instructions. cDNA was synthesized from 250 ng RNA using SuperScript III Reverse Transcriptase (Invitrogen) with random hexamer primers.

Linder S., Hoogstraat M., Stelloo S., Eickhoff N., Schuurman K., de Barros H., Alkemade M., Bekers E.M., Severson T.M., Sanders J., Huang C.C., Morova T., Altintas U.B., Hoekman L., Kim Y., Baca S.C., Sjöström M., Zaalberg A., Hintzen D.C., de Jong J., Kluin R.J., de Rink I., Giambartolomei C., Seo J.H., Pasaniuc B., Altelaar M., Medema R.H., Feng F.Y., Zoubeidi A., Freedman M.L., Wessels L.F., Butler L.M., Lack N.A., van der Poel H., Bergman A.M, & Zwart W. (2022). Drug-induced epigenomic plasticity reprograms circadian rhythm regulation to drive prostate cancer towards androgen-independence. Cancer discovery, 12(9), 2074-2097.

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