allprep dna rna ffpe kit  (Qiagen)


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    Name:
    AllPrep DNA/RNA FFPE Kit
    Description:
    For simultaneous purification of genomic DNA and total RNA (including small RNAs) from formalin-fixed, paraffin-embedded tissue sections. Kit contents: Qiagen AllPrep DNA/RNA FFPE Kit, 50 preps, FFPE Tissue Sample, RNA: 14 to 30L. DNA: 30 to 100L Elution Volume, Silica Technology, Manual Processing, For Simultaneous Purification of Genomic DNA and Total RNA from Formalin-fixed, Paraffin-embedded Tissue Sections, Ideal for PCR, qPCR, Real-time RT-PCR, Microarray, Includes 50 RNeasy minElute Spin Columns, 50 QIAamp minElute Spin Columns, Collection Tubes, RNase-free Reagents and Buffers. Benefits: Maximum output with minimal sample consumption. Releases DNA/RNA without compromising integrity. Effectively separates RNA and DNA. Comprehensive DNA and RNA analysis of the same FFPE sam
    Catalog Number:
    80234
    Price:
    None
    Category:
    AllPrep DNA/RNA FFPE Kit
    Score:
    85
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    Structured Review

    Qiagen allprep dna rna ffpe kit
    AllPrep DNA/RNA FFPE Kit
    For simultaneous purification of genomic DNA and total RNA (including small RNAs) from formalin-fixed, paraffin-embedded tissue sections. Kit contents: Qiagen AllPrep DNA/RNA FFPE Kit, 50 preps, FFPE Tissue Sample, RNA: 14 to 30L. DNA: 30 to 100L Elution Volume, Silica Technology, Manual Processing, For Simultaneous Purification of Genomic DNA and Total RNA from Formalin-fixed, Paraffin-embedded Tissue Sections, Ideal for PCR, qPCR, Real-time RT-PCR, Microarray, Includes 50 RNeasy minElute Spin Columns, 50 QIAamp minElute Spin Columns, Collection Tubes, RNase-free Reagents and Buffers. Benefits: Maximum output with minimal sample consumption. Releases DNA/RNA without compromising integrity. Effectively separates RNA and DNA. Comprehensive DNA and RNA analysis of the same FFPE sam
    https://www.bioz.com/result/allprep dna rna ffpe kit/product/Qiagen
    Average 99 stars, based on 66 article reviews
    Price from $9.99 to $1999.99
    allprep dna rna ffpe kit - by Bioz Stars, 2019-12
    99/100 stars

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    Related Articles

    Amplification:

    Article Title: A Hot-spot of In-frame Duplications Activates the Oncoprotein AKT1 in Juvenile Granulosa Cell Tumors
    Article Snippet: We isolated genomic DNA and RNA from FFPE tumors using the AllPrep DNA/RNA FFPE Kit (Qiagen) and the frozen ones were processed using standard procedures. .. Sequencing of exon 8 of the Gαs gene, potentially harboring the activating mutations R201C and R201H, was performed as described ( ).

    Article Title: Short telomere length in IPF lung associates with fibrotic lesions and predicts survival
    Article Snippet: DNA was isolated from FFPE tissue sections using an AllPrep DNA/RNA FFPE Kit (Qiagen, Hilden, Germany) according to manufacturer instructions. .. To measure whole lung biopsy and white blood TL, monochrome multiplex qPCR (MMqPCR) was performed as described earlier [ , ].

    Article Title: Somatic alterations of targetable oncogenes are frequently observed in BRCA1/2 mutation negative male breast cancers
    Article Snippet: The expression of ER, PR, and Ki67/MIB1 was scored based on the percentages of positive nuclei (ER/PR positive if > 10%; Ki67/MIB1 high if > 20%) over the total number of counted cancer cell nuclei HER2 positivity was defined as a score of 3+ using immunohistochemistry (IHC) test, or amplification shown by fluorescence in situ hybridization (FISH), in equivocal cases [ – ]. .. DNA from FFPE sections was extracted using DNA/RNA FFPE kit (Qiagen Inc., Venlo, Netherlands) according to the manufacturer's instructions.

    Polymerase Chain Reaction:

    Article Title: Nucleic acid extraction from formalin-fixed paraffin-embedded cancer cell line samples: a trade off between quantity and quality?
    Article Snippet: The percentage of samples assigned a RIN value varies between the kits tested: 69% of samples were assigned a RIN value for the Arcturus Paradise Plus RNA kit, 13% for the Maxwell 16 LEV RNA FFPE kit, 64% for the AllPrep DNA/RNA FFPE kit and 71% for the Qiagen RNeasy FFPE kit. .. The percentage of samples assigned a RIN value varies between the kits tested: 69% of samples were assigned a RIN value for the Arcturus Paradise Plus RNA kit, 13% for the Maxwell 16 LEV RNA FFPE kit, 64% for the AllPrep DNA/RNA FFPE kit and 71% for the Qiagen RNeasy FFPE kit.

    Blocking Assay:

    Article Title: Evidence of disrupted high-risk human papillomavirus DNA in morphologically normal cervices of older women
    Article Snippet: To avoid cross contamination, the microtome blades were changed between the cutting of each block. .. DNA was extracted using AllPrep DNA/RNA FFPE (formalin fixed paraffin embedded) kit, according to manufacturer’s instructions (Qiagen) and stored at −20 °C.

    Article Title: Morphological and Molecular Characteristics of Mixed Epithelial Ovarian Cancers
    Article Snippet: When different histotypes were present on the same block, distinct regions were separated by macrodissection using the H & E slide as a guide after having been marked by an expert pathologist (CBG). .. DNA and RNA were extracted using the Qiagen AllPrep FFPE kit, according to the manufacturers recommended protocols, with the following exceptions: deparaffinization was done using xylene, with digestion of tissue prior to RNA extraction for 30min, and use of RBC buffer (Qiagen RNeasy FFPE kit) rather than buffer FRN.

    TaqMan RNAsep Assay:

    Article Title: Characterization of FGFR1 Locus in sqNSCLC Reveals a Broad and Heterogeneous Amplicon
    Article Snippet: Genomic DNA was extracted from 2 x 5μM FFPE sections/sample using Qiagen AllPrep (Qiagen, Cat nr 80234) according to the manufacturer's instructions. .. Genomic DNA was extracted from 2 x 5μM FFPE sections/sample using Qiagen AllPrep (Qiagen, Cat nr 80234) according to the manufacturer's instructions.

    Real-time Polymerase Chain Reaction:

    Article Title: Short telomere length in IPF lung associates with fibrotic lesions and predicts survival
    Article Snippet: DNA was isolated from FFPE tissue sections using an AllPrep DNA/RNA FFPE Kit (Qiagen, Hilden, Germany) according to manufacturer instructions. .. DNA was isolated from FFPE tissue sections using an AllPrep DNA/RNA FFPE Kit (Qiagen, Hilden, Germany) according to manufacturer instructions.

    Article Title: Characterization of FGFR1 Locus in sqNSCLC Reveals a Broad and Heterogeneous Amplicon
    Article Snippet: Genomic DNA was extracted from 2 x 5μM FFPE sections/sample using Qiagen AllPrep (Qiagen, Cat nr 80234) according to the manufacturer's instructions. .. Genomic DNA was extracted from 2 x 5μM FFPE sections/sample using Qiagen AllPrep (Qiagen, Cat nr 80234) according to the manufacturer's instructions.

    Multiplex Assay:

    Article Title: Short telomere length in IPF lung associates with fibrotic lesions and predicts survival
    Article Snippet: DNA was isolated from FFPE tissue sections using an AllPrep DNA/RNA FFPE Kit (Qiagen, Hilden, Germany) according to manufacturer instructions. .. DNA was isolated from FFPE tissue sections using an AllPrep DNA/RNA FFPE Kit (Qiagen, Hilden, Germany) according to manufacturer instructions.

    Article Title: Nucleic acid extraction from formalin-fixed paraffin-embedded cancer cell line samples: a trade off between quantity and quality?
    Article Snippet: The assigned RNA integrity number (RIN) values were compared to the in house multiplex RT-PCR assay as an assessment of amplifiable RNA. .. The percentage of samples assigned a RIN value varies between the kits tested: 69% of samples were assigned a RIN value for the Arcturus Paradise Plus RNA kit, 13% for the Maxwell 16 LEV RNA FFPE kit, 64% for the AllPrep DNA/RNA FFPE kit and 71% for the Qiagen RNeasy FFPE kit.

    Incubation:

    Article Title: Heterogeneous patterns of DNA methylation-based field effects in histologically normal prostate tissue from cancer patients
    Article Snippet: Tissue sections were scraped into 1.5 ml tubes and genomic DNA extracted using the QIAamp DNA FFPE Tissue Kit (Qiagen) with the following modifications: Deparaffination was performed as described above and incubation in ATL buffer with proteinase K at 56 °C was extended from 1 to 16 hours. .. The Veritas Microdissection Instrument (Arcturus) was used for LMD of individual DAN/PAN/CAN areas from 10–20 serial sections and genomic DNA extracted using the Allprep DNA/RNA FFPE Kit (Qiagen) or the QIAamp DNA FFPE Tissue Kit (Qiagen).

    Formalin-fixed Paraffin-Embedded:

    Article Title: Quantity and quality of nucleic acids extracted from archival formalin fixed paraffin embedded prostate biopsies
    Article Snippet: The study was approved by the Ethical committee in Stockholm, Sweden (Approval number 2012/1586–31/1). .. The study material, consisting of 30 FFPE prostate biopsies with normal histology, was randomly divided into three different groups; 1) ten biopsies for comparison between the High Pure FFPE RNA Micro Kit (Roche Diagnostics, West Sussex, UK) and the RNeasy® FFPE kit (Qiagen, Hilden, Germany), 2) ten biopsies for comparison between the High Pure DNA FFPET Isolation Kit (Roche Diagnostics, West Sussex, UK) and the QIAamp® DNA FFPE Tissue kit (Qiagen, Hilden, Germany), and 3) ten biopsies for comparison of the best performing DNA and RNA kits from the two previous steps to the AllPrep® DNA/RNA FFPE kit (Qiagen, Hilden, Germany). .. In order to minimize the risk of variation due to different operators, the same operator performed all extractions with one kit (e.g. all extractions using the RNeasy® FFPE kit).

    Article Title: piRNA-8041 is downregulated in human glioblastoma and suppresses tumor growth in vitro and in vivo
    Article Snippet: Subjects providing tumor specimens had not undergone radio- or chemotherapy at the time of resection. .. RNA was isolated from sections corresponding to approximately 8-10 mg of tissue from each specimen using the AllPrep DNA/RNA FFPE Kit (QIAGEN). .. The study was approved by the institutional review board (IRB) of Yale University (HIC Protocol #: 1212011202).

    Article Title: A Hot-spot of In-frame Duplications Activates the Oncoprotein AKT1 in Juvenile Granulosa Cell Tumors
    Article Snippet: Four tumors were obtained as frozen samples (T13–T16). .. We isolated genomic DNA and RNA from FFPE tumors using the AllPrep DNA/RNA FFPE Kit (Qiagen) and the frozen ones were processed using standard procedures. .. To assess the somatic status of the mutations, we extracted DNA from manually isolated peritumoral tissue fragments (only available for 8 samples).

    Article Title: Heterogeneous patterns of DNA methylation-based field effects in histologically normal prostate tissue from cancer patients
    Article Snippet: Tissue sections (5 μm) were mounted on polyethylene naphthalate membrane glass, deparaffinised and rehydrated in xylene/EtOH, and stained with a 0.25% w/v solution of cresyl violet (Sigma-Aldrich) in 99.99% EtOH. .. The Veritas Microdissection Instrument (Arcturus) was used for LMD of individual DAN/PAN/CAN areas from 10–20 serial sections and genomic DNA extracted using the Allprep DNA/RNA FFPE Kit (Qiagen) or the QIAamp DNA FFPE Tissue Kit (Qiagen). .. The full procedure is described in .

    Article Title: Short telomere length in IPF lung associates with fibrotic lesions and predicts survival
    Article Snippet: All images were taken at fixed time points between 1 to 3 days after staining to circumvent data variability by DAPI fluorescence fading. .. DNA was isolated from FFPE tissue sections using an AllPrep DNA/RNA FFPE Kit (Qiagen, Hilden, Germany) according to manufacturer instructions. .. The paraffin was removed using paraffin dissolver (Macherey-Nagel, Düren, Germany).

    Article Title: Evaluation of commercial DNA and RNA extraction methods for high-throughput sequencing of FFPE samples
    Article Snippet: For DNA, the AllPrep DNA/RNA FFPE Kit, GeneRead DNA FFPE Kit and QIAamp DNA FFPE Tissue Kit from QIAGEN and truXTRAC FFPE DNA Kit from Covaris were used. .. For RNA, the AllPrep DNA/RNA FFPE Kit and RNeasy FFPE Kit from QIAGEN, Agencourt FormaPure Kit from Beckman Coulter and truXTRAC FFPE RNA Kit from Covaris were used. .. For the AllPrep DNA/RNA FFPE Kit, simultaneous extraction of DNA and RNA was done.

    Article Title: Prevalence of Mouse Mammary Tumor Virus (MMTV)-like sequences in human breast cancer tissues and adjacent normal breast tissues in Saudi Arabia
    Article Snippet: To avoid cross contamination, each sample was processed separately and the microtome blade was brushed and cleaned with alcohol before each use. .. Extraction of DNA and RNA was done using Allprep DNA/RNA FFPE kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. .. The kit allows simultaneous extraction of DNA and RNA in separate tubes.

    Article Title: Phase I Trial of Seneca Valley Virus (NTX-010) in Children with Relapsed / Refractory Solid Tumors: A Report of the Children’s Oncology Group
    Article Snippet: Of the 23 samples collected from 19 patients, 7 patients were excluded due to inadequate tissue/poor quality RNA. .. Consecutive slides were then macro-dissected and RNA was extracted using the AllPrep DNA/RNA FFPE Kit (Qiagen). .. Additional normal controls for adult muscle and adrenal tissue were obtained from Agilent Technologies.

    Article Title: Cell of origin of transformed follicular lymphoma
    Article Snippet: The Hans algorithm was used for COO assignment by IHC. .. RNA was extracted from 10 μm FFPET sections and cut to a surface of ≥1 cm2 using the AllPrep DNA/RNA FFPE Kit (Qiagen). .. Two hundred nanograms of FFPET-derived RNA were used for the Lymph2Cx assay, a digital gene expression (NanoString)-based test that assesses the expression of 20 genes (8 genes that are overexpressed in ABC-DLBCL, 7 genes that are overexpressed in GCB-DLBCL, and 5 housekeeping genes), as described by Scott et al. For each case, the linear predictor score (LPS) was calculated and the likelihood of that sample belonging to either COO subgroup was determined using Bayes’ rule, as described in Wright et al. Calibration between the lot of NanoString reagents used in this study and the lot used in Scott et al was achieved by determining the LPS for 30 RNA samples from that study on the current reagent lot.

    Article Title: A Druggable TCF4 and BRD4 dependent Transcriptional Network Sustains Malignancy in Blastic Plasmacytoid Dendritic Cell Neoplasm
    Article Snippet: Pair-end sequencing was performed on a HiSeq 2000 sequencer with v3 sequencing reagents (2×101bp reads). .. For RNA-Seq on the FFPE samples, RNA was extracted with the AllPrep DNA/RNA FFPE Kit (QIAGEN) and libraries were generated with the TruSeq RNA Access kit (Illumina) according to the manufacturer’s instruction. .. Pair-end sequencing was performed on a NextSeq 500 sequencer with v2 sequencing reagents.

    Article Title: Characterization of FGFR1 Locus in sqNSCLC Reveals a Broad and Heterogeneous Amplicon
    Article Snippet: The aCGH data was analyzed using CGH Analytics 3.4 software (Agilent). .. Genomic DNA was extracted from 2 x 5μM FFPE sections/sample using Qiagen AllPrep (Qiagen, Cat nr 80234) according to the manufacturer's instructions. .. Macrodissection ensured DNA was only extracted from tumour regions.

    Article Title: Association Between Programmed Death-Ligand 1 Expression and the Vascular Endothelial Growth Factor Pathway in Angiosarcoma
    Article Snippet: Slides were evaluated at ×400 magnification for the presence of TILs and if present, scored semi-quantitatively as either brisk or non-brisk using the protocol used by the College of American Pathologists ( ). .. Total RNA was isolated from three slides per tumor at 10-µm sections of tumor-rich areas of FFPE tissue blocks using the AllPrep DNA/RNA FFPE kit reagents (Qiagen) following vendor’s standard protocols. .. Isolated FFPE RNA was treated with 20 units DNase I. RNA concentration was measured and purity analyzed on a NanoDrop ND-2000c Spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA).

    Article Title: Evidence of disrupted high-risk human papillomavirus DNA in morphologically normal cervices of older women
    Article Snippet: To avoid cross contamination, the microtome blades were changed between the cutting of each block. .. DNA was extracted using AllPrep DNA/RNA FFPE (formalin fixed paraffin embedded) kit, according to manufacturer’s instructions (Qiagen) and stored at −20 °C. .. The INFORM HPVIII Family 16 Probe(B) which is capable of detecting 12 oncogenic HPV genotypes (Ventana Medical Systems) was used to stain cervical tissues.

    Article Title: Morphological and Molecular Characteristics of Mixed Epithelial Ovarian Cancers
    Article Snippet: When different histotypes were present on the same block, distinct regions were separated by macrodissection using the H & E slide as a guide after having been marked by an expert pathologist (CBG). .. DNA and RNA were extracted using the Qiagen AllPrep FFPE kit, according to the manufacturers recommended protocols, with the following exceptions: deparaffinization was done using xylene, with digestion of tissue prior to RNA extraction for 30min, and use of RBC buffer (Qiagen RNeasy FFPE kit) rather than buffer FRN. .. Mixed-type cases with RNA extraction yields of sufficient quantity ( > 400ng) and purity (OD 260/280 1.7–2.5) were selected for expression analysis.

    Article Title: A benchmark for microRNA quantification algorithms using the OpenArray platform
    Article Snippet: These anonymized human samples were used based on an exemption from the Institutional Review Board of Johns Hopkins Hospital. .. We extracted RNA from FFPE sections of kidney, placenta, skeletal muscle, and brain using the AllPrep DNA/RNA FFPE protocol (Qiagen). .. Xylene was chosen for deparaffinization.

    Article Title: The expression pattern of matrix-producing tumor stroma is of prognostic importance in breast cancer
    Article Snippet: Sections of archived formalin-fixed paraffin-embedded breast tumor samples (5 μm) were mounted onto polyethylene terephthalate (PET) membrane slides (Leica Microsystems, Wetzlar, Germany) as described previously [ ] and stained with cresyl violet LCM staining kit (Ambion, part of Thermo Fisher Scientific, Waltham, MA, USA) to optimize RNA quality. .. Tumor compartments were isolated with laser microdissection on a Leica LMD6500 and collected in AllPrep RNA/DNA FFPE kit lysis buffer (Qiagen, Hilden, Germany) with Proteinase K (Additional file : Figure S2). .. Total RNA was extracted and evaluated as described previously [ ].

    Article Title: Somatic alterations of targetable oncogenes are frequently observed in BRCA1/2 mutation negative male breast cancers
    Article Snippet: Genomic DNA was isolated from microdissected formalin fixed paraffin-embedded (FFPE) and fresh frozen tumor sections. .. DNA from FFPE sections was extracted using DNA/RNA FFPE kit (Qiagen Inc., Venlo, Netherlands) according to the manufacturer's instructions. .. DNA from fresh frozen samples was extracted by following standard phenol-chloroform extraction protocol.

    Article Title: Comparative Characteristics of Porous Bioceramics for an Osteogenic Response In Vitro and In Vivo
    Article Snippet: RNA/protein extraction was performed from formalin fixed paraffin-embedded (FFPE) muscular and femur tissues. .. RNA was extracted using an All prep DNA/RNA FFPE kit (QIAGEN, Hilden, Germany) for RT-PCR, and protein extraction was carried out using a Q proteome FFPE tissue kit (QIAGEN) following manufacturer's instructions for immunoblotting. .. Statistical analysis was performed using Prism 4.02 (GraphPad Software, San Diego, CA, USA).

    Article Title: Nucleic acid extraction from formalin-fixed paraffin-embedded cancer cell line samples: a trade off between quantity and quality?
    Article Snippet: The RNA samples fell into two groups, those obtained from FFPE cell line pellets generated < 6 months prior to commencing the study and those obtained from FFPE cell line pellets generated > 2 years prior to commencing the study. .. The percentage of samples assigned a RIN value varies between the kits tested: 69% of samples were assigned a RIN value for the Arcturus Paradise Plus RNA kit, 13% for the Maxwell 16 LEV RNA FFPE kit, 64% for the AllPrep DNA/RNA FFPE kit and 71% for the Qiagen RNeasy FFPE kit. .. However, the assigned RIN values failed to show any significant differences in the quality of the RNA released (Fig. ).

    Expressing:

    Article Title: Phase I Trial of Seneca Valley Virus (NTX-010) in Children with Relapsed / Refractory Solid Tumors: A Report of the Children’s Oncology Group
    Article Snippet: Available tumor tissue (archival) was submitted for evaluation of markers of neuroendocrine expression including synaptophysin, chromogranin A, NSE, neural cell adhesion molecule, insulin-like growth factor 2, Bcl-2 and gastrin releasing peptide. .. Consecutive slides were then macro-dissected and RNA was extracted using the AllPrep DNA/RNA FFPE Kit (Qiagen).

    Article Title: Association Between Programmed Death-Ligand 1 Expression and the Vascular Endothelial Growth Factor Pathway in Angiosarcoma
    Article Snippet: Total RNA was isolated from three slides per tumor at 10-µm sections of tumor-rich areas of FFPE tissue blocks using the AllPrep DNA/RNA FFPE kit reagents (Qiagen) following vendor’s standard protocols. .. Total RNA was isolated from three slides per tumor at 10-µm sections of tumor-rich areas of FFPE tissue blocks using the AllPrep DNA/RNA FFPE kit reagents (Qiagen) following vendor’s standard protocols.

    Article Title: Somatic alterations of targetable oncogenes are frequently observed in BRCA1/2 mutation negative male breast cancers
    Article Snippet: The expression of ER, PR, and Ki67/MIB1 was scored based on the percentages of positive nuclei (ER/PR positive if > 10%; Ki67/MIB1 high if > 20%) over the total number of counted cancer cell nuclei HER2 positivity was defined as a score of 3+ using immunohistochemistry (IHC) test, or amplification shown by fluorescence in situ hybridization (FISH), in equivocal cases [ – ]. .. DNA from FFPE sections was extracted using DNA/RNA FFPE kit (Qiagen Inc., Venlo, Netherlands) according to the manufacturer's instructions.

    Modification:

    Article Title: Early Molecular Stratification of High-risk Primary Biliary Cholangitis
    Article Snippet: 2.4 mRNA was extracted from 10 μm FFPE curls using AllPrep kit (Qiagen, Hilden, Germany). .. 2.4 mRNA was extracted from 10 μm FFPE curls using AllPrep kit (Qiagen, Hilden, Germany).

    Derivative Assay:

    Article Title: Short telomere length in IPF lung associates with fibrotic lesions and predicts survival
    Article Snippet: DNA was isolated from FFPE tissue sections using an AllPrep DNA/RNA FFPE Kit (Qiagen, Hilden, Germany) according to manufacturer instructions. .. To measure whole lung biopsy and white blood TL, monochrome multiplex qPCR (MMqPCR) was performed as described earlier [ , ].

    Intra Assay:

    Article Title: Nucleic acid extraction from formalin-fixed paraffin-embedded cancer cell line samples: a trade off between quantity and quality?
    Article Snippet: The percentage of samples assigned a RIN value varies between the kits tested: 69% of samples were assigned a RIN value for the Arcturus Paradise Plus RNA kit, 13% for the Maxwell 16 LEV RNA FFPE kit, 64% for the AllPrep DNA/RNA FFPE kit and 71% for the Qiagen RNeasy FFPE kit. .. To allow for a more sensitive, quantitative assessment of RNA quality isolated from FFPE samples, we developed a multiplex PCR assay in house targeting 3 housekeeping genes ActB, RPL19 and RPLP0 to asses RNA quality based on the ability to amplify targets.

    Generated:

    Article Title: A Druggable TCF4 and BRD4 dependent Transcriptional Network Sustains Malignancy in Blastic Plasmacytoid Dendritic Cell Neoplasm
    Article Snippet: Pair-end sequencing was performed on a HiSeq 2000 sequencer with v3 sequencing reagents (2×101bp reads). .. For RNA-Seq on the FFPE samples, RNA was extracted with the AllPrep DNA/RNA FFPE Kit (QIAGEN) and libraries were generated with the TruSeq RNA Access kit (Illumina) according to the manufacturer’s instruction. .. Pair-end sequencing was performed on a NextSeq 500 sequencer with v2 sequencing reagents.

    Article Title: Nucleic acid extraction from formalin-fixed paraffin-embedded cancer cell line samples: a trade off between quantity and quality?
    Article Snippet: The RNA samples fell into two groups, those obtained from FFPE cell line pellets generated < 6 months prior to commencing the study and those obtained from FFPE cell line pellets generated > 2 years prior to commencing the study. .. The percentage of samples assigned a RIN value varies between the kits tested: 69% of samples were assigned a RIN value for the Arcturus Paradise Plus RNA kit, 13% for the Maxwell 16 LEV RNA FFPE kit, 64% for the AllPrep DNA/RNA FFPE kit and 71% for the Qiagen RNeasy FFPE kit.

    Reverse Transcription Polymerase Chain Reaction:

    Article Title: Comparative Characteristics of Porous Bioceramics for an Osteogenic Response In Vitro and In Vivo
    Article Snippet: RNA/protein extraction was performed from formalin fixed paraffin-embedded (FFPE) muscular and femur tissues. .. RNA was extracted using an All prep DNA/RNA FFPE kit (QIAGEN, Hilden, Germany) for RT-PCR, and protein extraction was carried out using a Q proteome FFPE tissue kit (QIAGEN) following manufacturer's instructions for immunoblotting. .. Statistical analysis was performed using Prism 4.02 (GraphPad Software, San Diego, CA, USA).

    Article Title: Nucleic acid extraction from formalin-fixed paraffin-embedded cancer cell line samples: a trade off between quantity and quality?
    Article Snippet: Paragraph title: RNA quality assessment: Agilent vs RT-PCR ... The percentage of samples assigned a RIN value varies between the kits tested: 69% of samples were assigned a RIN value for the Arcturus Paradise Plus RNA kit, 13% for the Maxwell 16 LEV RNA FFPE kit, 64% for the AllPrep DNA/RNA FFPE kit and 71% for the Qiagen RNeasy FFPE kit.

    DNA Extraction:

    Article Title: Quantity and quality of nucleic acids extracted from archival formalin fixed paraffin embedded prostate biopsies
    Article Snippet: The study material, consisting of 30 FFPE prostate biopsies with normal histology, was randomly divided into three different groups; 1) ten biopsies for comparison between the High Pure FFPE RNA Micro Kit (Roche Diagnostics, West Sussex, UK) and the RNeasy® FFPE kit (Qiagen, Hilden, Germany), 2) ten biopsies for comparison between the High Pure DNA FFPET Isolation Kit (Roche Diagnostics, West Sussex, UK) and the QIAamp® DNA FFPE Tissue kit (Qiagen, Hilden, Germany), and 3) ten biopsies for comparison of the best performing DNA and RNA kits from the two previous steps to the AllPrep® DNA/RNA FFPE kit (Qiagen, Hilden, Germany). .. The study material, consisting of 30 FFPE prostate biopsies with normal histology, was randomly divided into three different groups; 1) ten biopsies for comparison between the High Pure FFPE RNA Micro Kit (Roche Diagnostics, West Sussex, UK) and the RNeasy® FFPE kit (Qiagen, Hilden, Germany), 2) ten biopsies for comparison between the High Pure DNA FFPET Isolation Kit (Roche Diagnostics, West Sussex, UK) and the QIAamp® DNA FFPE Tissue kit (Qiagen, Hilden, Germany), and 3) ten biopsies for comparison of the best performing DNA and RNA kits from the two previous steps to the AllPrep® DNA/RNA FFPE kit (Qiagen, Hilden, Germany).

    Article Title: Characterization of FGFR1 Locus in sqNSCLC Reveals a Broad and Heterogeneous Amplicon
    Article Snippet: Paragraph title: DNA extraction ... Genomic DNA was extracted from 2 x 5μM FFPE sections/sample using Qiagen AllPrep (Qiagen, Cat nr 80234) according to the manufacturer's instructions.

    RNA Sequencing Assay:

    Article Title: A Druggable TCF4 and BRD4 dependent Transcriptional Network Sustains Malignancy in Blastic Plasmacytoid Dendritic Cell Neoplasm
    Article Snippet: Pair-end sequencing was performed on a HiSeq 2000 sequencer with v3 sequencing reagents (2×101bp reads). .. For RNA-Seq on the FFPE samples, RNA was extracted with the AllPrep DNA/RNA FFPE Kit (QIAGEN) and libraries were generated with the TruSeq RNA Access kit (Illumina) according to the manufacturer’s instruction. .. Pair-end sequencing was performed on a NextSeq 500 sequencer with v2 sequencing reagents.

    Fluorescence:

    Article Title: Somatic alterations of targetable oncogenes are frequently observed in BRCA1/2 mutation negative male breast cancers
    Article Snippet: The expression of ER, PR, and Ki67/MIB1 was scored based on the percentages of positive nuclei (ER/PR positive if > 10%; Ki67/MIB1 high if > 20%) over the total number of counted cancer cell nuclei HER2 positivity was defined as a score of 3+ using immunohistochemistry (IHC) test, or amplification shown by fluorescence in situ hybridization (FISH), in equivocal cases [ – ]. .. DNA from FFPE sections was extracted using DNA/RNA FFPE kit (Qiagen Inc., Venlo, Netherlands) according to the manufacturer's instructions.

    Isolation:

    Article Title: Quantity and quality of nucleic acids extracted from archival formalin fixed paraffin embedded prostate biopsies
    Article Snippet: The study was approved by the Ethical committee in Stockholm, Sweden (Approval number 2012/1586–31/1). .. The study material, consisting of 30 FFPE prostate biopsies with normal histology, was randomly divided into three different groups; 1) ten biopsies for comparison between the High Pure FFPE RNA Micro Kit (Roche Diagnostics, West Sussex, UK) and the RNeasy® FFPE kit (Qiagen, Hilden, Germany), 2) ten biopsies for comparison between the High Pure DNA FFPET Isolation Kit (Roche Diagnostics, West Sussex, UK) and the QIAamp® DNA FFPE Tissue kit (Qiagen, Hilden, Germany), and 3) ten biopsies for comparison of the best performing DNA and RNA kits from the two previous steps to the AllPrep® DNA/RNA FFPE kit (Qiagen, Hilden, Germany). .. In order to minimize the risk of variation due to different operators, the same operator performed all extractions with one kit (e.g. all extractions using the RNeasy® FFPE kit).

    Article Title: piRNA-8041 is downregulated in human glioblastoma and suppresses tumor growth in vitro and in vivo
    Article Snippet: Subjects providing tumor specimens had not undergone radio- or chemotherapy at the time of resection. .. RNA was isolated from sections corresponding to approximately 8-10 mg of tissue from each specimen using the AllPrep DNA/RNA FFPE Kit (QIAGEN). .. The study was approved by the institutional review board (IRB) of Yale University (HIC Protocol #: 1212011202).

    Article Title: A Hot-spot of In-frame Duplications Activates the Oncoprotein AKT1 in Juvenile Granulosa Cell Tumors
    Article Snippet: Four tumors were obtained as frozen samples (T13–T16). .. We isolated genomic DNA and RNA from FFPE tumors using the AllPrep DNA/RNA FFPE Kit (Qiagen) and the frozen ones were processed using standard procedures. .. To assess the somatic status of the mutations, we extracted DNA from manually isolated peritumoral tissue fragments (only available for 8 samples).

    Article Title: Short telomere length in IPF lung associates with fibrotic lesions and predicts survival
    Article Snippet: All images were taken at fixed time points between 1 to 3 days after staining to circumvent data variability by DAPI fluorescence fading. .. DNA was isolated from FFPE tissue sections using an AllPrep DNA/RNA FFPE Kit (Qiagen, Hilden, Germany) according to manufacturer instructions. .. The paraffin was removed using paraffin dissolver (Macherey-Nagel, Düren, Germany).

    Article Title: Association Between Programmed Death-Ligand 1 Expression and the Vascular Endothelial Growth Factor Pathway in Angiosarcoma
    Article Snippet: Slides were evaluated at ×400 magnification for the presence of TILs and if present, scored semi-quantitatively as either brisk or non-brisk using the protocol used by the College of American Pathologists ( ). .. Total RNA was isolated from three slides per tumor at 10-µm sections of tumor-rich areas of FFPE tissue blocks using the AllPrep DNA/RNA FFPE kit reagents (Qiagen) following vendor’s standard protocols. .. Isolated FFPE RNA was treated with 20 units DNase I. RNA concentration was measured and purity analyzed on a NanoDrop ND-2000c Spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA).

    Article Title: The expression pattern of matrix-producing tumor stroma is of prognostic importance in breast cancer
    Article Snippet: Sections of archived formalin-fixed paraffin-embedded breast tumor samples (5 μm) were mounted onto polyethylene terephthalate (PET) membrane slides (Leica Microsystems, Wetzlar, Germany) as described previously [ ] and stained with cresyl violet LCM staining kit (Ambion, part of Thermo Fisher Scientific, Waltham, MA, USA) to optimize RNA quality. .. Tumor compartments were isolated with laser microdissection on a Leica LMD6500 and collected in AllPrep RNA/DNA FFPE kit lysis buffer (Qiagen, Hilden, Germany) with Proteinase K (Additional file : Figure S2). .. Total RNA was extracted and evaluated as described previously [ ].

    Article Title: Somatic alterations of targetable oncogenes are frequently observed in BRCA1/2 mutation negative male breast cancers
    Article Snippet: Genomic DNA was isolated from microdissected formalin fixed paraffin-embedded (FFPE) and fresh frozen tumor sections. .. DNA from FFPE sections was extracted using DNA/RNA FFPE kit (Qiagen Inc., Venlo, Netherlands) according to the manufacturer's instructions.

    Article Title: Early Molecular Stratification of High-risk Primary Biliary Cholangitis
    Article Snippet: 2.4 mRNA was extracted from 10 μm FFPE curls using AllPrep kit (Qiagen, Hilden, Germany). .. 2.4 mRNA was extracted from 10 μm FFPE curls using AllPrep kit (Qiagen, Hilden, Germany).

    Article Title: Nucleic acid extraction from formalin-fixed paraffin-embedded cancer cell line samples: a trade off between quantity and quality?
    Article Snippet: The percentage of samples assigned a RIN value varies between the kits tested: 69% of samples were assigned a RIN value for the Arcturus Paradise Plus RNA kit, 13% for the Maxwell 16 LEV RNA FFPE kit, 64% for the AllPrep DNA/RNA FFPE kit and 71% for the Qiagen RNeasy FFPE kit. .. The percentage of samples assigned a RIN value varies between the kits tested: 69% of samples were assigned a RIN value for the Arcturus Paradise Plus RNA kit, 13% for the Maxwell 16 LEV RNA FFPE kit, 64% for the AllPrep DNA/RNA FFPE kit and 71% for the Qiagen RNeasy FFPE kit.

    Immunohistochemistry:

    Article Title: Evidence of disrupted high-risk human papillomavirus DNA in morphologically normal cervices of older women
    Article Snippet: Paraffin embedded blocks were sectioned every 4 μm and one section stained with haematoxylin and eosin; sequential sections were used for routine immunohistochemical staining and in situ analyses with the last of these sections used for HPV DNA testing. .. DNA was extracted using AllPrep DNA/RNA FFPE (formalin fixed paraffin embedded) kit, according to manufacturer’s instructions (Qiagen) and stored at −20 °C.

    Article Title: Somatic alterations of targetable oncogenes are frequently observed in BRCA1/2 mutation negative male breast cancers
    Article Snippet: The expression of ER, PR, and Ki67/MIB1 was scored based on the percentages of positive nuclei (ER/PR positive if > 10%; Ki67/MIB1 high if > 20%) over the total number of counted cancer cell nuclei HER2 positivity was defined as a score of 3+ using immunohistochemistry (IHC) test, or amplification shown by fluorescence in situ hybridization (FISH), in equivocal cases [ – ]. .. DNA from FFPE sections was extracted using DNA/RNA FFPE kit (Qiagen Inc., Venlo, Netherlands) according to the manufacturer's instructions.

    Purification:

    Article Title: Early Molecular Stratification of High-risk Primary Biliary Cholangitis
    Article Snippet: Paragraph title: RNA Purification ... 2.4 mRNA was extracted from 10 μm FFPE curls using AllPrep kit (Qiagen, Hilden, Germany).

    Sequencing:

    Article Title: A Hot-spot of In-frame Duplications Activates the Oncoprotein AKT1 in Juvenile Granulosa Cell Tumors
    Article Snippet: Paragraph title: Nucleic Acid Extraction and Sequencing ... We isolated genomic DNA and RNA from FFPE tumors using the AllPrep DNA/RNA FFPE Kit (Qiagen) and the frozen ones were processed using standard procedures.

    Article Title: A Druggable TCF4 and BRD4 dependent Transcriptional Network Sustains Malignancy in Blastic Plasmacytoid Dendritic Cell Neoplasm
    Article Snippet: Pair-end sequencing was performed on a HiSeq 2000 sequencer with v3 sequencing reagents (2×101bp reads). .. For RNA-Seq on the FFPE samples, RNA was extracted with the AllPrep DNA/RNA FFPE Kit (QIAGEN) and libraries were generated with the TruSeq RNA Access kit (Illumina) according to the manufacturer’s instruction.

    Protein Extraction:

    Article Title: Comparative Characteristics of Porous Bioceramics for an Osteogenic Response In Vitro and In Vivo
    Article Snippet: RNA/protein extraction was performed from formalin fixed paraffin-embedded (FFPE) muscular and femur tissues. .. RNA was extracted using an All prep DNA/RNA FFPE kit (QIAGEN, Hilden, Germany) for RT-PCR, and protein extraction was carried out using a Q proteome FFPE tissue kit (QIAGEN) following manufacturer's instructions for immunoblotting. .. Statistical analysis was performed using Prism 4.02 (GraphPad Software, San Diego, CA, USA).

    Staining:

    Article Title: Heterogeneous patterns of DNA methylation-based field effects in histologically normal prostate tissue from cancer patients
    Article Snippet: Tissue sections (5 μm) were mounted on polyethylene naphthalate membrane glass, deparaffinised and rehydrated in xylene/EtOH, and stained with a 0.25% w/v solution of cresyl violet (Sigma-Aldrich) in 99.99% EtOH. .. The Veritas Microdissection Instrument (Arcturus) was used for LMD of individual DAN/PAN/CAN areas from 10–20 serial sections and genomic DNA extracted using the Allprep DNA/RNA FFPE Kit (Qiagen) or the QIAamp DNA FFPE Tissue Kit (Qiagen).

    Article Title: Phase I Trial of Seneca Valley Virus (NTX-010) in Children with Relapsed / Refractory Solid Tumors: A Report of the Children’s Oncology Group
    Article Snippet: Consecutive slides were then macro-dissected and RNA was extracted using the AllPrep DNA/RNA FFPE Kit (Qiagen). .. Consecutive slides were then macro-dissected and RNA was extracted using the AllPrep DNA/RNA FFPE Kit (Qiagen).

    Article Title: Evidence of disrupted high-risk human papillomavirus DNA in morphologically normal cervices of older women
    Article Snippet: Paraffin embedded blocks were sectioned every 4 μm and one section stained with haematoxylin and eosin; sequential sections were used for routine immunohistochemical staining and in situ analyses with the last of these sections used for HPV DNA testing. .. DNA was extracted using AllPrep DNA/RNA FFPE (formalin fixed paraffin embedded) kit, according to manufacturer’s instructions (Qiagen) and stored at −20 °C.

    Article Title: The expression pattern of matrix-producing tumor stroma is of prognostic importance in breast cancer
    Article Snippet: Paragraph title: Tissue preparation, staining and laser microdissection ... Tumor compartments were isolated with laser microdissection on a Leica LMD6500 and collected in AllPrep RNA/DNA FFPE kit lysis buffer (Qiagen, Hilden, Germany) with Proteinase K (Additional file : Figure S2).

    In Situ Hybridization:

    Article Title: Somatic alterations of targetable oncogenes are frequently observed in BRCA1/2 mutation negative male breast cancers
    Article Snippet: The expression of ER, PR, and Ki67/MIB1 was scored based on the percentages of positive nuclei (ER/PR positive if > 10%; Ki67/MIB1 high if > 20%) over the total number of counted cancer cell nuclei HER2 positivity was defined as a score of 3+ using immunohistochemistry (IHC) test, or amplification shown by fluorescence in situ hybridization (FISH), in equivocal cases [ – ]. .. DNA from FFPE sections was extracted using DNA/RNA FFPE kit (Qiagen Inc., Venlo, Netherlands) according to the manufacturer's instructions.

    RNA Extraction:

    Article Title: Evaluation of commercial DNA and RNA extraction methods for high-throughput sequencing of FFPE samples
    Article Snippet: Paragraph title: DNA and RNA extraction methods ... For RNA, the AllPrep DNA/RNA FFPE Kit and RNeasy FFPE Kit from QIAGEN, Agencourt FormaPure Kit from Beckman Coulter and truXTRAC FFPE RNA Kit from Covaris were used.

    Article Title: Prevalence of Mouse Mammary Tumor Virus (MMTV)-like sequences in human breast cancer tissues and adjacent normal breast tissues in Saudi Arabia
    Article Snippet: Paragraph title: DNA and RNA extraction ... Extraction of DNA and RNA was done using Allprep DNA/RNA FFPE kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.

    Article Title: Morphological and Molecular Characteristics of Mixed Epithelial Ovarian Cancers
    Article Snippet: When different histotypes were present on the same block, distinct regions were separated by macrodissection using the H & E slide as a guide after having been marked by an expert pathologist (CBG). .. DNA and RNA were extracted using the Qiagen AllPrep FFPE kit, according to the manufacturers recommended protocols, with the following exceptions: deparaffinization was done using xylene, with digestion of tissue prior to RNA extraction for 30min, and use of RBC buffer (Qiagen RNeasy FFPE kit) rather than buffer FRN. .. Mixed-type cases with RNA extraction yields of sufficient quantity ( > 400ng) and purity (OD 260/280 1.7–2.5) were selected for expression analysis.

    Article Title: A benchmark for microRNA quantification algorithms using the OpenArray platform
    Article Snippet: Paragraph title: RNA extraction ... We extracted RNA from FFPE sections of kidney, placenta, skeletal muscle, and brain using the AllPrep DNA/RNA FFPE protocol (Qiagen).

    Positron Emission Tomography:

    Article Title: The expression pattern of matrix-producing tumor stroma is of prognostic importance in breast cancer
    Article Snippet: Sections of archived formalin-fixed paraffin-embedded breast tumor samples (5 μm) were mounted onto polyethylene terephthalate (PET) membrane slides (Leica Microsystems, Wetzlar, Germany) as described previously [ ] and stained with cresyl violet LCM staining kit (Ambion, part of Thermo Fisher Scientific, Waltham, MA, USA) to optimize RNA quality. .. Tumor compartments were isolated with laser microdissection on a Leica LMD6500 and collected in AllPrep RNA/DNA FFPE kit lysis buffer (Qiagen, Hilden, Germany) with Proteinase K (Additional file : Figure S2).

    Sample Prep:

    Article Title: A Druggable TCF4 and BRD4 dependent Transcriptional Network Sustains Malignancy in Blastic Plasmacytoid Dendritic Cell Neoplasm
    Article Snippet: For RNA-Seq on the BPDCN cell lines Cal-1 and Gen2.2, total RNA was extracted with the AllPrep DNA/RNA kit (QIAGEN) and libraries were generated with the TruSeq RNA Sample Prep Kit-v2 (Illumina) according to the manufacturer’s instruction. .. For RNA-Seq on the FFPE samples, RNA was extracted with the AllPrep DNA/RNA FFPE Kit (QIAGEN) and libraries were generated with the TruSeq RNA Access kit (Illumina) according to the manufacturer’s instruction.

    In Situ:

    Article Title: Evidence of disrupted high-risk human papillomavirus DNA in morphologically normal cervices of older women
    Article Snippet: Paraffin embedded blocks were sectioned every 4 μm and one section stained with haematoxylin and eosin; sequential sections were used for routine immunohistochemical staining and in situ analyses with the last of these sections used for HPV DNA testing. .. DNA was extracted using AllPrep DNA/RNA FFPE (formalin fixed paraffin embedded) kit, according to manufacturer’s instructions (Qiagen) and stored at −20 °C.

    Laser Capture Microdissection:

    Article Title: Heterogeneous patterns of DNA methylation-based field effects in histologically normal prostate tissue from cancer patients
    Article Snippet: Tissue sections (5 μm) were mounted on polyethylene naphthalate membrane glass, deparaffinised and rehydrated in xylene/EtOH, and stained with a 0.25% w/v solution of cresyl violet (Sigma-Aldrich) in 99.99% EtOH. .. The Veritas Microdissection Instrument (Arcturus) was used for LMD of individual DAN/PAN/CAN areas from 10–20 serial sections and genomic DNA extracted using the Allprep DNA/RNA FFPE Kit (Qiagen) or the QIAamp DNA FFPE Tissue Kit (Qiagen). .. The full procedure is described in .

    Article Title: The expression pattern of matrix-producing tumor stroma is of prognostic importance in breast cancer
    Article Snippet: Sections of archived formalin-fixed paraffin-embedded breast tumor samples (5 μm) were mounted onto polyethylene terephthalate (PET) membrane slides (Leica Microsystems, Wetzlar, Germany) as described previously [ ] and stained with cresyl violet LCM staining kit (Ambion, part of Thermo Fisher Scientific, Waltham, MA, USA) to optimize RNA quality. .. Tumor compartments were isolated with laser microdissection on a Leica LMD6500 and collected in AllPrep RNA/DNA FFPE kit lysis buffer (Qiagen, Hilden, Germany) with Proteinase K (Additional file : Figure S2). .. Total RNA was extracted and evaluated as described previously [ ].

    Spectrophotometry:

    Article Title: Phase I Trial of Seneca Valley Virus (NTX-010) in Children with Relapsed / Refractory Solid Tumors: A Report of the Children’s Oncology Group
    Article Snippet: Consecutive slides were then macro-dissected and RNA was extracted using the AllPrep DNA/RNA FFPE Kit (Qiagen). .. Consecutive slides were then macro-dissected and RNA was extracted using the AllPrep DNA/RNA FFPE Kit (Qiagen).

    Article Title: Early Molecular Stratification of High-risk Primary Biliary Cholangitis
    Article Snippet: 2.4 mRNA was extracted from 10 μm FFPE curls using AllPrep kit (Qiagen, Hilden, Germany). .. 2.4 mRNA was extracted from 10 μm FFPE curls using AllPrep kit (Qiagen, Hilden, Germany).

    Concentration Assay:

    Article Title: Nucleic acid extraction from formalin-fixed paraffin-embedded cancer cell line samples: a trade off between quantity and quality?
    Article Snippet: RNA samples with a concentration ≥5 ng/μl (limit of detection of the Agilent nano assay), obtained using four different extraction kits, were analysed for quality using the Agilent RNA 6000 nano assay. .. The percentage of samples assigned a RIN value varies between the kits tested: 69% of samples were assigned a RIN value for the Arcturus Paradise Plus RNA kit, 13% for the Maxwell 16 LEV RNA FFPE kit, 64% for the AllPrep DNA/RNA FFPE kit and 71% for the Qiagen RNeasy FFPE kit.

    DNA Purification:

    Article Title: Heterogeneous patterns of DNA methylation-based field effects in histologically normal prostate tissue from cancer patients
    Article Snippet: Paragraph title: DNA Purification from Tissue ... The Veritas Microdissection Instrument (Arcturus) was used for LMD of individual DAN/PAN/CAN areas from 10–20 serial sections and genomic DNA extracted using the Allprep DNA/RNA FFPE Kit (Qiagen) or the QIAamp DNA FFPE Tissue Kit (Qiagen).

    Preserving:

    Article Title: Early Molecular Stratification of High-risk Primary Biliary Cholangitis
    Article Snippet: 2.4 mRNA was extracted from 10 μm FFPE curls using AllPrep kit (Qiagen, Hilden, Germany). .. 2.4 mRNA was extracted from 10 μm FFPE curls using AllPrep kit (Qiagen, Hilden, Germany).

    Lysis:

    Article Title: The expression pattern of matrix-producing tumor stroma is of prognostic importance in breast cancer
    Article Snippet: Sections of archived formalin-fixed paraffin-embedded breast tumor samples (5 μm) were mounted onto polyethylene terephthalate (PET) membrane slides (Leica Microsystems, Wetzlar, Germany) as described previously [ ] and stained with cresyl violet LCM staining kit (Ambion, part of Thermo Fisher Scientific, Waltham, MA, USA) to optimize RNA quality. .. Tumor compartments were isolated with laser microdissection on a Leica LMD6500 and collected in AllPrep RNA/DNA FFPE kit lysis buffer (Qiagen, Hilden, Germany) with Proteinase K (Additional file : Figure S2). .. Total RNA was extracted and evaluated as described previously [ ].

    Fluorescence In Situ Hybridization:

    Article Title: Somatic alterations of targetable oncogenes are frequently observed in BRCA1/2 mutation negative male breast cancers
    Article Snippet: The expression of ER, PR, and Ki67/MIB1 was scored based on the percentages of positive nuclei (ER/PR positive if > 10%; Ki67/MIB1 high if > 20%) over the total number of counted cancer cell nuclei HER2 positivity was defined as a score of 3+ using immunohistochemistry (IHC) test, or amplification shown by fluorescence in situ hybridization (FISH), in equivocal cases [ – ]. .. DNA from FFPE sections was extracted using DNA/RNA FFPE kit (Qiagen Inc., Venlo, Netherlands) according to the manufacturer's instructions.

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    Qiagen ffpe rna extraction kit
    Fraction of reads mapping to various parts of the genome. Ribosomal <t>RNA-depleted</t> total RNA library preparation for <t>FFPE</t> RNA resulted in larger fraction of reads mapping to intronic regions (both absolute and relative fraction) compared to mRNA library preparation for FF RNA.
    Ffpe Rna Extraction Kit, supplied by Qiagen, used in various techniques. Bioz Stars score: 99/100, based on 17 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Fraction of reads mapping to various parts of the genome. Ribosomal RNA-depleted total RNA library preparation for FFPE RNA resulted in larger fraction of reads mapping to intronic regions (both absolute and relative fraction) compared to mRNA library preparation for FF RNA.

    Journal: Scientific Reports

    Article Title: Robust gene expression and mutation analyses of RNA-sequencing of formalin-fixed diagnostic tumor samples

    doi: 10.1038/srep12335

    Figure Lengend Snippet: Fraction of reads mapping to various parts of the genome. Ribosomal RNA-depleted total RNA library preparation for FFPE RNA resulted in larger fraction of reads mapping to intronic regions (both absolute and relative fraction) compared to mRNA library preparation for FF RNA.

    Article Snippet: RNA and DNA from FFPE tumor samples were extracted using Qiagen FFPE All-Prep kit.

    Techniques: Formalin-fixed Paraffin-Embedded

    Clustered heat map to visualize correlation matrix. Heat map of clustered correlation matrix (RNA-seq NanoString data sets from paired FF FFPE samples) shows strong correlation in gene expression between paired FF and FFPE samples. Color key was adjusted to minimal and maximal values to differentiate the differences. Dendrogram illustrates the relationship-distance between samples. Associated samples (e.g. FF2474 and FFPE2474) from the data sets produced with the same technology (either RNA sequencing or NanoString) are highlighted with a white frame, whereas associated samples from different technologies are highlighted with a blue frame. Sample NS_FF3356r1.NS_FF4079r1 was a replicate sample that was mislabeled as FF3356r1 during NanoString analysis. However, clustering analysis correctly identified it as FF4079r1. Note that correctly labeled FF3356r1 clustered with other FF3356 and FFPE3356 replicates.

    Journal: Scientific Reports

    Article Title: Robust gene expression and mutation analyses of RNA-sequencing of formalin-fixed diagnostic tumor samples

    doi: 10.1038/srep12335

    Figure Lengend Snippet: Clustered heat map to visualize correlation matrix. Heat map of clustered correlation matrix (RNA-seq NanoString data sets from paired FF FFPE samples) shows strong correlation in gene expression between paired FF and FFPE samples. Color key was adjusted to minimal and maximal values to differentiate the differences. Dendrogram illustrates the relationship-distance between samples. Associated samples (e.g. FF2474 and FFPE2474) from the data sets produced with the same technology (either RNA sequencing or NanoString) are highlighted with a white frame, whereas associated samples from different technologies are highlighted with a blue frame. Sample NS_FF3356r1.NS_FF4079r1 was a replicate sample that was mislabeled as FF3356r1 during NanoString analysis. However, clustering analysis correctly identified it as FF4079r1. Note that correctly labeled FF3356r1 clustered with other FF3356 and FFPE3356 replicates.

    Article Snippet: RNA and DNA from FFPE tumor samples were extracted using Qiagen FFPE All-Prep kit.

    Techniques: RNA Sequencing Assay, Formalin-fixed Paraffin-Embedded, Expressing, Produced, Labeling

    Variant allele frequencies and FFPE artifacts. Panel A, B and D show the comparison of variant allele fraction in FF or FFPE RNA (left y-axis) and FF DNA (right y-axis). Each line represents the relationship of one variant in comparison. The color code indicates whether the mutations is concordant (green), discordant (red), or ambiguous (black) because of low DNA coverage. Panel A shows the comparison between RNA with DNA from fresh frozen sample (2474). Most of the variants detected in RNA samples are concordant with variant calls from DNA. No discordant calls were observed. Eighteen variant calls from RNA sequence data were considered ambiguous because the same variants were not called in DNA due to low coverage. Panel B shows the comparison of variant allele fraction in RNA and DNA from paired FFPE and FF samples (2474), respectively. High degree of discordant calls were observed. Panel C shows the distribution of various substitutions in FF and FFPE samples. Substitutions that are concordant between paired FF and FFPE samples are indicated by green and discordant substitutions are indicated by red. The majority of discordant calls are observed as C > T or G > A substitutions, suggesting a documented FFPE artifact. Results from Panel D indicate that a small fraction of discordant calls remained after removing the C > T or G > A substitutions present at

    Journal: Scientific Reports

    Article Title: Robust gene expression and mutation analyses of RNA-sequencing of formalin-fixed diagnostic tumor samples

    doi: 10.1038/srep12335

    Figure Lengend Snippet: Variant allele frequencies and FFPE artifacts. Panel A, B and D show the comparison of variant allele fraction in FF or FFPE RNA (left y-axis) and FF DNA (right y-axis). Each line represents the relationship of one variant in comparison. The color code indicates whether the mutations is concordant (green), discordant (red), or ambiguous (black) because of low DNA coverage. Panel A shows the comparison between RNA with DNA from fresh frozen sample (2474). Most of the variants detected in RNA samples are concordant with variant calls from DNA. No discordant calls were observed. Eighteen variant calls from RNA sequence data were considered ambiguous because the same variants were not called in DNA due to low coverage. Panel B shows the comparison of variant allele fraction in RNA and DNA from paired FFPE and FF samples (2474), respectively. High degree of discordant calls were observed. Panel C shows the distribution of various substitutions in FF and FFPE samples. Substitutions that are concordant between paired FF and FFPE samples are indicated by green and discordant substitutions are indicated by red. The majority of discordant calls are observed as C > T or G > A substitutions, suggesting a documented FFPE artifact. Results from Panel D indicate that a small fraction of discordant calls remained after removing the C > T or G > A substitutions present at

    Article Snippet: RNA and DNA from FFPE tumor samples were extracted using Qiagen FFPE All-Prep kit.

    Techniques: Variant Assay, Formalin-fixed Paraffin-Embedded, Sequencing

    GC content distribution before and after applying filter on FF and FFPE samples. The GC-content distribution indicates abnormal GC peak (blue line) in FFPE (A) but not in FF (B) samples. The GC content of the human reference genome is plotted in red line. To understand why GC content in FFPE sample show an abnormal peak, mapped reads were visualized by SeqMonk. The representative chromosome view shows three rows of data tracks for each sample: (1) mRNA.only contains only reads in mRNA regions, (2) not.mRNA contains all reads that did not align to exons, (3) total contains all reads. Strand information is shown in red and blue. FFPE RNA sequencing produces reads that also map to intronic regions. When reads mapping to intronic regions in both FF and FFPE were filtered out, abnormal GC peak in FFPE samples were removed (D) without affecting the GC-content distribution of FF samples (E).

    Journal: Scientific Reports

    Article Title: Robust gene expression and mutation analyses of RNA-sequencing of formalin-fixed diagnostic tumor samples

    doi: 10.1038/srep12335

    Figure Lengend Snippet: GC content distribution before and after applying filter on FF and FFPE samples. The GC-content distribution indicates abnormal GC peak (blue line) in FFPE (A) but not in FF (B) samples. The GC content of the human reference genome is plotted in red line. To understand why GC content in FFPE sample show an abnormal peak, mapped reads were visualized by SeqMonk. The representative chromosome view shows three rows of data tracks for each sample: (1) mRNA.only contains only reads in mRNA regions, (2) not.mRNA contains all reads that did not align to exons, (3) total contains all reads. Strand information is shown in red and blue. FFPE RNA sequencing produces reads that also map to intronic regions. When reads mapping to intronic regions in both FF and FFPE were filtered out, abnormal GC peak in FFPE samples were removed (D) without affecting the GC-content distribution of FF samples (E).

    Article Snippet: RNA and DNA from FFPE tumor samples were extracted using Qiagen FFPE All-Prep kit.

    Techniques: Gas Chromatography, Formalin-fixed Paraffin-Embedded, RNA Sequencing Assay

    A . Overlay of representative Experion-generated electropherograms and gels for total extracted FFPE RNA from either the -mH or +mH RNA extraction methods. L, - and + in the gels indicates lanes for the ladder, -mH and +mH sample preparation methods. B . RNA extracted from FFPE tumor samples using these two methods was reverse transcribed to cDNA and analyzed by qPCR in triplicate using βactin-specific primers that generate increasing length amplicons. βactin Ct values were normalized relative to the HPRT1 and POLR2A house-keeping genes and plotted as relative quantification (RQ) fold change compared to the FFPE samples processed without the mH-based method. * indicates a Student's t-test p value

    Journal: Oncotarget

    Article Title: A novel method for RNA extraction from FFPE samples reveals significant differences in biomarker expression between orthotopic and subcutaneous pancreatic cancer patient-derived xenografts

    doi: 10.18632/oncotarget.11809

    Figure Lengend Snippet: A . Overlay of representative Experion-generated electropherograms and gels for total extracted FFPE RNA from either the -mH or +mH RNA extraction methods. L, - and + in the gels indicates lanes for the ladder, -mH and +mH sample preparation methods. B . RNA extracted from FFPE tumor samples using these two methods was reverse transcribed to cDNA and analyzed by qPCR in triplicate using βactin-specific primers that generate increasing length amplicons. βactin Ct values were normalized relative to the HPRT1 and POLR2A house-keeping genes and plotted as relative quantification (RQ) fold change compared to the FFPE samples processed without the mH-based method. * indicates a Student's t-test p value

    Article Snippet: RNA yield and purity were measured for PDAC FFPE samples processed using the Qiagen FFPE RNA purification kit according the manufacturer recommendations, with or without the mH.

    Techniques: Generated, Formalin-fixed Paraffin-Embedded, RNA Extraction, Sample Prep, Real-time Polymerase Chain Reaction

    A . FFPE samples are usually used for hematoxylin and eosin (H E) and/or immunohistochemistry (IHC) stains. To overcome hurdles associated with gene expression analyses of tissue in FFPE samples, we show that the mH can increase the purification of high-quality RNA for downstream applications. B . H E staining of the four xenograft FFPE samples (BxPC3 [B] and FG [F]) or patient (MDA-AC2 [M]) xenografts (S = subcutaneous, O = orthotopic). C . Nucleic acid (RNA) concentrations (ng/uL) for the four FFPE samples of PDAC using either the standard Qiagen FFPE RNA extraction (-mH) or our mH-modified protocol (+mH). Measurements were made using Nanodrop, Qubit and Experion Bioanalyzer assays. D . Average +/- standard error mean (SEM) RNA 260/280 ratios for the same samples described in (A). *, **, *** indicate student t-test p values

    Journal: Oncotarget

    Article Title: A novel method for RNA extraction from FFPE samples reveals significant differences in biomarker expression between orthotopic and subcutaneous pancreatic cancer patient-derived xenografts

    doi: 10.18632/oncotarget.11809

    Figure Lengend Snippet: A . FFPE samples are usually used for hematoxylin and eosin (H E) and/or immunohistochemistry (IHC) stains. To overcome hurdles associated with gene expression analyses of tissue in FFPE samples, we show that the mH can increase the purification of high-quality RNA for downstream applications. B . H E staining of the four xenograft FFPE samples (BxPC3 [B] and FG [F]) or patient (MDA-AC2 [M]) xenografts (S = subcutaneous, O = orthotopic). C . Nucleic acid (RNA) concentrations (ng/uL) for the four FFPE samples of PDAC using either the standard Qiagen FFPE RNA extraction (-mH) or our mH-modified protocol (+mH). Measurements were made using Nanodrop, Qubit and Experion Bioanalyzer assays. D . Average +/- standard error mean (SEM) RNA 260/280 ratios for the same samples described in (A). *, **, *** indicate student t-test p values

    Article Snippet: RNA yield and purity were measured for PDAC FFPE samples processed using the Qiagen FFPE RNA purification kit according the manufacturer recommendations, with or without the mH.

    Techniques: Formalin-fixed Paraffin-Embedded, Immunohistochemistry, Expressing, Purification, Staining, Multiple Displacement Amplification, RNA Extraction, Modification

    A . Previously published expression patterns for ITGB6, SYK and CDH1 genes (Nakamura et al.) in FG cells grown under 2D in vitro , subcutaneous in vivo and orthotopic in vivo microenvironment conditions. RNA was processed from fresh/frozen samples. B and C . qPCR analysis for these same three genes in RNA extracts from FG cells grown in vitro or FFPE samples of FG cell xenografts. RNA was isolated using the standard Qiagen FFPE RNA kit protocol (B) or our mH-modified protocol (C). Relative quantification (RQ) values for gene expression were normalized to house-keeping genes (GAPDH and/or POLR2A) and calculated relative to gene expression levels in cells grown in vitro .

    Journal: Oncotarget

    Article Title: A novel method for RNA extraction from FFPE samples reveals significant differences in biomarker expression between orthotopic and subcutaneous pancreatic cancer patient-derived xenografts

    doi: 10.18632/oncotarget.11809

    Figure Lengend Snippet: A . Previously published expression patterns for ITGB6, SYK and CDH1 genes (Nakamura et al.) in FG cells grown under 2D in vitro , subcutaneous in vivo and orthotopic in vivo microenvironment conditions. RNA was processed from fresh/frozen samples. B and C . qPCR analysis for these same three genes in RNA extracts from FG cells grown in vitro or FFPE samples of FG cell xenografts. RNA was isolated using the standard Qiagen FFPE RNA kit protocol (B) or our mH-modified protocol (C). Relative quantification (RQ) values for gene expression were normalized to house-keeping genes (GAPDH and/or POLR2A) and calculated relative to gene expression levels in cells grown in vitro .

    Article Snippet: RNA yield and purity were measured for PDAC FFPE samples processed using the Qiagen FFPE RNA purification kit according the manufacturer recommendations, with or without the mH.

    Techniques: Expressing, In Vitro, In Vivo, Real-time Polymerase Chain Reaction, Formalin-fixed Paraffin-Embedded, Isolation, Modification

    A and B . qPCR analysis of ITGB6, SYK, CDH1, PEAK1 and MST1R in FG (A, KRas mutant G12D line) or BxPC3 (B, KRas wild type line) PDAC cells grown under the indicated microenvironmental conditions. All RNA was extracted using our mH-modified Qiagen FFPE kit protocol and relative quantification (RQ) values for gene expression were normalized to house-keeping genes (GAPDH and/or POLR2A).

    Journal: Oncotarget

    Article Title: A novel method for RNA extraction from FFPE samples reveals significant differences in biomarker expression between orthotopic and subcutaneous pancreatic cancer patient-derived xenografts

    doi: 10.18632/oncotarget.11809

    Figure Lengend Snippet: A and B . qPCR analysis of ITGB6, SYK, CDH1, PEAK1 and MST1R in FG (A, KRas mutant G12D line) or BxPC3 (B, KRas wild type line) PDAC cells grown under the indicated microenvironmental conditions. All RNA was extracted using our mH-modified Qiagen FFPE kit protocol and relative quantification (RQ) values for gene expression were normalized to house-keeping genes (GAPDH and/or POLR2A).

    Article Snippet: RNA yield and purity were measured for PDAC FFPE samples processed using the Qiagen FFPE RNA purification kit according the manufacturer recommendations, with or without the mH.

    Techniques: Real-time Polymerase Chain Reaction, Mutagenesis, Modification, Formalin-fixed Paraffin-Embedded, Expressing