allprep dna rna ffpe kit  (Qiagen)


Bioz Verified Symbol Qiagen is a verified supplier
Bioz Manufacturer Symbol Qiagen manufactures this product  
  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 99
    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:
    660
    Category:
    AllPrep DNA RNA FFPE Kit
    Buy from Supplier


    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 26825 article reviews
    Price from $9.99 to $1999.99
    allprep dna rna ffpe kit - by Bioz Stars, 2020-04
    99/100 stars

    Images

    1) Product Images from "Evaluation of commercial DNA and RNA extraction methods for high-throughput sequencing of FFPE samples"

    Article Title: Evaluation of commercial DNA and RNA extraction methods for high-throughput sequencing of FFPE samples

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0197456

    Yield and amplifiability of extracted DNA and RNA. (A) Average total amount of DNA. (B) Average total amount of RNA. (C) Amplifiable DNA quantified with the FFPE QC kit from Illumina. (D) Amplifiable RNA quantified with the PreSeq QC assay from ArcherDx. The average total amount and average delta Ct values for the different samples and extraction methods are shown. The standard deviation is shown as vertical bars. Methods with significant differences in yield are marked as connected with horizontal bars (p
    Figure Legend Snippet: Yield and amplifiability of extracted DNA and RNA. (A) Average total amount of DNA. (B) Average total amount of RNA. (C) Amplifiable DNA quantified with the FFPE QC kit from Illumina. (D) Amplifiable RNA quantified with the PreSeq QC assay from ArcherDx. The average total amount and average delta Ct values for the different samples and extraction methods are shown. The standard deviation is shown as vertical bars. Methods with significant differences in yield are marked as connected with horizontal bars (p

    Techniques Used: Formalin-fixed Paraffin-Embedded, Standard Deviation

    2) Product Images from "Demodifying RNA for Transcriptomic Analyses of Archival Formalin-Fixed Paraffin-Embedded Samples"

    Article Title: Demodifying RNA for Transcriptomic Analyses of Archival Formalin-Fixed Paraffin-Embedded Samples

    Journal: Toxicological sciences : an official journal of the Society of Toxicology

    doi: 10.1093/toxsci/kfx278

    Effects of formalin, fixation, and demodification on total RNA, amplifiable RNA, and RNA integrity. A) Total RNA yield as assessed by Nanodrop spectrophotometer and Qubit fluorometer. B) RNA integrity number as measured by Bioanalyzer. C) Amplifiable Actb RNA as measured by reverse transcriptase quantitative PCR of three amplicons across the gene body. *The results of a statistical comparison between OH, 18F, and 3F vs. FR with a p-value
    Figure Legend Snippet: Effects of formalin, fixation, and demodification on total RNA, amplifiable RNA, and RNA integrity. A) Total RNA yield as assessed by Nanodrop spectrophotometer and Qubit fluorometer. B) RNA integrity number as measured by Bioanalyzer. C) Amplifiable Actb RNA as measured by reverse transcriptase quantitative PCR of three amplicons across the gene body. *The results of a statistical comparison between OH, 18F, and 3F vs. FR with a p-value

    Techniques Used: Spectrophotometry, Real-time Polymerase Chain Reaction

    3) Product Images from "Multiscale, multimodal analysis of tumor heterogeneity in IDH1 mutant vs wild-type diffuse gliomas"

    Article Title: Multiscale, multimodal analysis of tumor heterogeneity in IDH1 mutant vs wild-type diffuse gliomas

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0219724

    Comprehensive rendering of multiscale measurements in gliomas. Multiscale modalities depicted include: 1) clinical information (red), 2) IDH1 mutational status (blue), 3) MRI derived variables (green), 4) RNA expression level of genes involved in the “inducing angiogenesis” hallmark (black), and 5) MxIF angiogenesis markers or cell clusters (magenta). The data is binned in low, medium and high categories. Across the treatment-naïve gliomas (a) and the recurrent (post-treatment) glioblastoma* (b) cohorts, it can be observed that IDHmt patients have low angiogenesis according to RNA expression levels and expression of S100A4 and VEGRF. Those subjects also have high fraction of cells in clusters 1 and 2 (low angiogenesis markers), and low fraction of cells in cluster 4 and 5 (high angiogenesis markers ( S8 Fig , cluster profiles of angiogenesis clusters). Moreover, MR Images for the same subjects have lower normalized enhancing cores volumes and measure higher intensities on T1 post contrast. *Recurrent GBM (5 subjects are not shown since they were missing MxIF).
    Figure Legend Snippet: Comprehensive rendering of multiscale measurements in gliomas. Multiscale modalities depicted include: 1) clinical information (red), 2) IDH1 mutational status (blue), 3) MRI derived variables (green), 4) RNA expression level of genes involved in the “inducing angiogenesis” hallmark (black), and 5) MxIF angiogenesis markers or cell clusters (magenta). The data is binned in low, medium and high categories. Across the treatment-naïve gliomas (a) and the recurrent (post-treatment) glioblastoma* (b) cohorts, it can be observed that IDHmt patients have low angiogenesis according to RNA expression levels and expression of S100A4 and VEGRF. Those subjects also have high fraction of cells in clusters 1 and 2 (low angiogenesis markers), and low fraction of cells in cluster 4 and 5 (high angiogenesis markers ( S8 Fig , cluster profiles of angiogenesis clusters). Moreover, MR Images for the same subjects have lower normalized enhancing cores volumes and measure higher intensities on T1 post contrast. *Recurrent GBM (5 subjects are not shown since they were missing MxIF).

    Techniques Used: Magnetic Resonance Imaging, Derivative Assay, RNA Expression, Expressing

    4) Product Images from "Evaluation of commercial DNA and RNA extraction methods for high-throughput sequencing of FFPE samples"

    Article Title: Evaluation of commercial DNA and RNA extraction methods for high-throughput sequencing of FFPE samples

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0197456

    Yield and amplifiability of extracted DNA and RNA. (A) Average total amount of DNA. (B) Average total amount of RNA. (C) Amplifiable DNA quantified with the FFPE QC kit from Illumina. (D) Amplifiable RNA quantified with the PreSeq QC assay from ArcherDx. The average total amount and average delta Ct values for the different samples and extraction methods are shown. The standard deviation is shown as vertical bars. Methods with significant differences in yield are marked as connected with horizontal bars (p
    Figure Legend Snippet: Yield and amplifiability of extracted DNA and RNA. (A) Average total amount of DNA. (B) Average total amount of RNA. (C) Amplifiable DNA quantified with the FFPE QC kit from Illumina. (D) Amplifiable RNA quantified with the PreSeq QC assay from ArcherDx. The average total amount and average delta Ct values for the different samples and extraction methods are shown. The standard deviation is shown as vertical bars. Methods with significant differences in yield are marked as connected with horizontal bars (p

    Techniques Used: Formalin-fixed Paraffin-Embedded, Standard Deviation

    5) Product Images from "Organocatalytic Removal of Formaldehyde Adducts from RNA and DNA Bases"

    Article Title: Organocatalytic Removal of Formaldehyde Adducts from RNA and DNA Bases

    Journal: Nature chemistry

    doi: 10.1038/nchem.2307

    Enhancement in recovery of RNAs from formalin-fixed, paraffin-embedded cell specimens using catalyst 3 (20 mM) as compared with different incubation and isolation conditions. Amplifiable RNA yield is plotted for eight amplicons, and quantity is determined with a standard curve. Lane 1 employs incubation conditions from a commercial kit (Qiagen AllPrep ® DNA/RNA FFPE kit), which uses an 80 °C, 0.25 h incubation step without catalyst (“no cat”) and a spin column for isolation, with the addition of catalyst to these conditions shown in lane 2 (“cat. 3”). Optimized incubation conditions (55 °C, 18 h) followed by a spin column RNA isolation are shown in lanes 3–4. A common literature procedure is shown in lane 5 (“PCI”) 28 . Addition of the catalyst to the optimized incubation conditions results in a ~2 fold increase in detectable RNA, and more substantial increases relative to the catalyst-free commercial kit protocol (see enhancements in red) or the literature protocol. The means of three independent experiments are shown, error bars indicating the standard deviation of variation in the qRT-PCR yield. SC: spin column isolation. PCI: Masuda protocol of phenol-chloroform-isoamyl alcohol extraction followed by heating in buffer. 28 A.U.: arbitrary units. Significance for pairwise comparisons shown was tested using a 1-tailed paired samples t-test. *: P
    Figure Legend Snippet: Enhancement in recovery of RNAs from formalin-fixed, paraffin-embedded cell specimens using catalyst 3 (20 mM) as compared with different incubation and isolation conditions. Amplifiable RNA yield is plotted for eight amplicons, and quantity is determined with a standard curve. Lane 1 employs incubation conditions from a commercial kit (Qiagen AllPrep ® DNA/RNA FFPE kit), which uses an 80 °C, 0.25 h incubation step without catalyst (“no cat”) and a spin column for isolation, with the addition of catalyst to these conditions shown in lane 2 (“cat. 3”). Optimized incubation conditions (55 °C, 18 h) followed by a spin column RNA isolation are shown in lanes 3–4. A common literature procedure is shown in lane 5 (“PCI”) 28 . Addition of the catalyst to the optimized incubation conditions results in a ~2 fold increase in detectable RNA, and more substantial increases relative to the catalyst-free commercial kit protocol (see enhancements in red) or the literature protocol. The means of three independent experiments are shown, error bars indicating the standard deviation of variation in the qRT-PCR yield. SC: spin column isolation. PCI: Masuda protocol of phenol-chloroform-isoamyl alcohol extraction followed by heating in buffer. 28 A.U.: arbitrary units. Significance for pairwise comparisons shown was tested using a 1-tailed paired samples t-test. *: P

    Techniques Used: Formalin-fixed Paraffin-Embedded, Incubation, Isolation, Standard Deviation, Quantitative RT-PCR

    6) Product Images from "A comparative analysis of RNA sequencing methods with ribosome RNA depletion for degraded and low-input total RNA from formalin-fixed and paraffin-embedded samples"

    Article Title: A comparative analysis of RNA sequencing methods with ribosome RNA depletion for degraded and low-input total RNA from formalin-fixed and paraffin-embedded samples

    Journal: BMC Genomics

    doi: 10.1186/s12864-019-6166-3

    Genome alignment profiles of four RNA-seq kits with paired FFPE and FF samples. For FF RNA from GM 12878 cell line, all the four kits got similar alignment profiles while the input RNA of TaKaRa kit was 10 ng and it of the others was 100 ng. For FFPE RNA from GM 12878 cell line, the library with TaKaRa kit produced more exon profiles with 10 ng total RNA input
    Figure Legend Snippet: Genome alignment profiles of four RNA-seq kits with paired FFPE and FF samples. For FF RNA from GM 12878 cell line, all the four kits got similar alignment profiles while the input RNA of TaKaRa kit was 10 ng and it of the others was 100 ng. For FFPE RNA from GM 12878 cell line, the library with TaKaRa kit produced more exon profiles with 10 ng total RNA input

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

    Comparison of transcripts quantification in FFPE and FF samples across four kits. High concordance in transcript quantifications were got between FF and FFPE samples using any kit. For either FFPE or FF RNA from GM 12878, the Pearson R between TaKaRa kit and the other three kits were lower and higher similarity was got among KAPA, Vazyme and QIAGEN kits
    Figure Legend Snippet: Comparison of transcripts quantification in FFPE and FF samples across four kits. High concordance in transcript quantifications were got between FF and FFPE samples using any kit. For either FFPE or FF RNA from GM 12878, the Pearson R between TaKaRa kit and the other three kits were lower and higher similarity was got among KAPA, Vazyme and QIAGEN kits

    Techniques Used: Formalin-fixed Paraffin-Embedded

    The distribution of transcripts of four RNA-seq kits with paired FFPE and FF samples. For FF RNA from GM 12878 cell line, more low-expressed transcripts were detected in the library of TaKaRa with only 10 ng total RNA input. For FFPE RNA from GM 12878 cell line, similar transcripts were detected while the input RNA of TaKaRa kit was 10 ng and it of the others was 100 ng
    Figure Legend Snippet: The distribution of transcripts of four RNA-seq kits with paired FFPE and FF samples. For FF RNA from GM 12878 cell line, more low-expressed transcripts were detected in the library of TaKaRa with only 10 ng total RNA input. For FFPE RNA from GM 12878 cell line, similar transcripts were detected while the input RNA of TaKaRa kit was 10 ng and it of the others was 100 ng

    Techniques Used: RNA Sequencing Assay, Formalin-fixed Paraffin-Embedded

    7) Product Images from "Quantity and quality of nucleic acids extracted from archival formalin fixed paraffin embedded prostate biopsies"

    Article Title: Quantity and quality of nucleic acids extracted from archival formalin fixed paraffin embedded prostate biopsies

    Journal: BMC Medical Research Methodology

    doi: 10.1186/s12874-018-0628-1

    Bland-Altman plots for investigation of level of agreements between DNA extraction kits. Each plot shows the differences between the two kits against the averages of the two kits. The lines represent the mean differences and upper and lower limits of agreement (LOA, mean differences ±1.96SD). a Comparison of DNA yield (ng/μl) of samples extracted with High Pure FFPET DNA Isolation kit and QIAamp® DNA FFPE Tissue kit. b Comparison of purity (A260/A280) of DNA samples extracted with High Pure FFPET DNA Isolation kit and QIAamp® DNA FFPE Tissue kit. c Comparison of DNA yield (ng/μl) of samples extracted with QIAamp® DNA FFPE Tissue kit and AllPrep® DNA/RNA FFPE kit. d Comparison of purity (A260/A280) of samples extracted with QIAamp® DNA FFPE Tissue kit and AllPrep® DNA/RNA FFPE kit
    Figure Legend Snippet: Bland-Altman plots for investigation of level of agreements between DNA extraction kits. Each plot shows the differences between the two kits against the averages of the two kits. The lines represent the mean differences and upper and lower limits of agreement (LOA, mean differences ±1.96SD). a Comparison of DNA yield (ng/μl) of samples extracted with High Pure FFPET DNA Isolation kit and QIAamp® DNA FFPE Tissue kit. b Comparison of purity (A260/A280) of DNA samples extracted with High Pure FFPET DNA Isolation kit and QIAamp® DNA FFPE Tissue kit. c Comparison of DNA yield (ng/μl) of samples extracted with QIAamp® DNA FFPE Tissue kit and AllPrep® DNA/RNA FFPE kit. d Comparison of purity (A260/A280) of samples extracted with QIAamp® DNA FFPE Tissue kit and AllPrep® DNA/RNA FFPE kit

    Techniques Used: DNA Extraction, Formalin-fixed Paraffin-Embedded

    Bland-Altman plots for investigating the level of agreement between RNA extraction kits. Each plot shows the differences between the two kits against the averages of the two kits. The lines represent the mean differences and upper and lower limits of agreement (LOA, mean differences ±1.96SD). a Comparison of RNA yield (ng/μl) of samples extracted with High Pure FFPE RNA Micro Kit and RNeasy® FFPE kit. b Comparison of purity (A260/A280) of samples extracted with High Pure FFPE RNA Micro kit and RNeasy® FFPE kit. c Comparison of RIN-values of samples extracted with High Pure FFPE RNA Micro kit and RNeasy® FFPE kit. d Comparison of RNA yield (ng/μl) of samples extracted with RNeasy® FFPE kit and AllPrep® DNA/RNA FFPE kit. e Comparison of purity (A260/A280) of samples extracted with RNeasy® FFPE kit and AllPrep® DNA/RNA FFPE kit. f Comparison of RIN-values of samples extracted with RNeasy® FFPE kit and AllPrep® DNA/RNA FFPE kit
    Figure Legend Snippet: Bland-Altman plots for investigating the level of agreement between RNA extraction kits. Each plot shows the differences between the two kits against the averages of the two kits. The lines represent the mean differences and upper and lower limits of agreement (LOA, mean differences ±1.96SD). a Comparison of RNA yield (ng/μl) of samples extracted with High Pure FFPE RNA Micro Kit and RNeasy® FFPE kit. b Comparison of purity (A260/A280) of samples extracted with High Pure FFPE RNA Micro kit and RNeasy® FFPE kit. c Comparison of RIN-values of samples extracted with High Pure FFPE RNA Micro kit and RNeasy® FFPE kit. d Comparison of RNA yield (ng/μl) of samples extracted with RNeasy® FFPE kit and AllPrep® DNA/RNA FFPE kit. e Comparison of purity (A260/A280) of samples extracted with RNeasy® FFPE kit and AllPrep® DNA/RNA FFPE kit. f Comparison of RIN-values of samples extracted with RNeasy® FFPE kit and AllPrep® DNA/RNA FFPE kit

    Techniques Used: RNA Extraction, Formalin-fixed Paraffin-Embedded

    8) Product Images from "Effective DNA/RNA Co-Extraction for Analysis of MicroRNAs, mRNAs, and Genomic DNA from Formalin-Fixed Paraffin-Embedded Specimens"

    Article Title: Effective DNA/RNA Co-Extraction for Analysis of MicroRNAs, mRNAs, and Genomic DNA from Formalin-Fixed Paraffin-Embedded Specimens

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0034683

    MicroRNA expression analysis of matched fresh and FFPE RNA from MCF10A cells using different RNA extraction methods. The upper panel displays a graphic representation of quantitative RT-PCR (Taqman® miRNA assays). Measurements obtain for miR-10a, miR-196b, miR-135b, miR-32a and miR-21 using matched fresh and FFPE RNA from MCF10A cells. MiRNAs were quantified using FFPE RNA extracted with TRIzol (TRI), Qiagen AllPrep DNA/RNA FFPE (QDR), AMBion RecoverAll™ Total Nucleic Acid Isolation (AMB) kits and compared to control RNA extracted from fresh cells with TRIzol (TRI-Fr). Results are represented as ΔδC t (δC t target miRNA - δC t miR-10a (least expressed miRNA)). The lower panels show the comparison of global miRNA quantification obtained between fresh and FFPE RNA samples using the Illumina miRNA platform. Comparisons were performed between triplicate RNA extractions obtained from matched fresh (TRI-Fr1, TRI-Fr2, TRI-Fr3) and FFPE (TRI1-3, QDR1-3, and AMB1-3) cells. The correlation coefficient (r) between matched fresh and FFPE RNAs is displayed in each graph.
    Figure Legend Snippet: MicroRNA expression analysis of matched fresh and FFPE RNA from MCF10A cells using different RNA extraction methods. The upper panel displays a graphic representation of quantitative RT-PCR (Taqman® miRNA assays). Measurements obtain for miR-10a, miR-196b, miR-135b, miR-32a and miR-21 using matched fresh and FFPE RNA from MCF10A cells. MiRNAs were quantified using FFPE RNA extracted with TRIzol (TRI), Qiagen AllPrep DNA/RNA FFPE (QDR), AMBion RecoverAll™ Total Nucleic Acid Isolation (AMB) kits and compared to control RNA extracted from fresh cells with TRIzol (TRI-Fr). Results are represented as ΔδC t (δC t target miRNA - δC t miR-10a (least expressed miRNA)). The lower panels show the comparison of global miRNA quantification obtained between fresh and FFPE RNA samples using the Illumina miRNA platform. Comparisons were performed between triplicate RNA extractions obtained from matched fresh (TRI-Fr1, TRI-Fr2, TRI-Fr3) and FFPE (TRI1-3, QDR1-3, and AMB1-3) cells. The correlation coefficient (r) between matched fresh and FFPE RNAs is displayed in each graph.

    Techniques Used: Expressing, Formalin-fixed Paraffin-Embedded, RNA Extraction, Quantitative RT-PCR, Isolation

    Summary of sequential recovery of DNA and RNA from MCF10A Fresh and FFPE samples using different extraction methods. (A) Schematic representation of cell culture and DNA/RNA extraction methods used with matched fresh and 1 month-old formalin-fixed paraffin-embedded (FFPE) human mammary epithelial MCF10A cells. FFPE DNA and RNA extractions (QD, TRI, QDR, AMB) were performed in triplicate using three 10 µm sections for each replicate. (B) Analysis of RNA extracted from matched fresh and FFPE MCF10A cells. Total RNA extracted from fresh cells using TRIzol (TRI-Fr; Lane 2), and total RNA extracted from FFPE cells using TRIzol (TRI; lane 3), Qiagen QIAamp DNA/RNA extraction kit (QDR; lane 4), and AMBion RecoverAll™ Total Nucleic Acid Isolation kit (AMB; lane 5) was analyzed and quantified using an Agilent 2100 Bioanalyzer 6000 Nanochip (size ladder in lane 1). The bar graph placed above the Bioanalyzer image displays total amounts of RNA recovered from three consecutive 10 µm sections, in triplicate experiments, using the three different methods (TRI, QDR, AMB). (C) Analysis of genomic DNA extracted from matched fresh and FFPE MCF10A cells. DNA was extracted from fresh cells using a phenol/chloroform based method (PC-Fr; lane 2), and TRIzol (TRI-Fr lane 3); and from FFPE cells using Qiagen QIAamp DNA FFPE kit (QD; lane 4), TRIzol DNA/RNA extraction method (TRI; lane 5), Qiagen AllPrep DNA/RNA FFPE kit (QDR; lane 6), and AMBion RecoverAll™ Total Nucleic Acid Isolation kit (AMB; lane 7) was analyzed on a 1% agarose gel (size ladder in lane 1). The bar graph placed above the agarose gel displays total amounts of DNA recovered alone (QD), simultaneously with RNA (TRI, QDR), or separately from RNA (AMB), using three consecutive 10 µm sections, in triplicate experiments for each method.
    Figure Legend Snippet: Summary of sequential recovery of DNA and RNA from MCF10A Fresh and FFPE samples using different extraction methods. (A) Schematic representation of cell culture and DNA/RNA extraction methods used with matched fresh and 1 month-old formalin-fixed paraffin-embedded (FFPE) human mammary epithelial MCF10A cells. FFPE DNA and RNA extractions (QD, TRI, QDR, AMB) were performed in triplicate using three 10 µm sections for each replicate. (B) Analysis of RNA extracted from matched fresh and FFPE MCF10A cells. Total RNA extracted from fresh cells using TRIzol (TRI-Fr; Lane 2), and total RNA extracted from FFPE cells using TRIzol (TRI; lane 3), Qiagen QIAamp DNA/RNA extraction kit (QDR; lane 4), and AMBion RecoverAll™ Total Nucleic Acid Isolation kit (AMB; lane 5) was analyzed and quantified using an Agilent 2100 Bioanalyzer 6000 Nanochip (size ladder in lane 1). The bar graph placed above the Bioanalyzer image displays total amounts of RNA recovered from three consecutive 10 µm sections, in triplicate experiments, using the three different methods (TRI, QDR, AMB). (C) Analysis of genomic DNA extracted from matched fresh and FFPE MCF10A cells. DNA was extracted from fresh cells using a phenol/chloroform based method (PC-Fr; lane 2), and TRIzol (TRI-Fr lane 3); and from FFPE cells using Qiagen QIAamp DNA FFPE kit (QD; lane 4), TRIzol DNA/RNA extraction method (TRI; lane 5), Qiagen AllPrep DNA/RNA FFPE kit (QDR; lane 6), and AMBion RecoverAll™ Total Nucleic Acid Isolation kit (AMB; lane 7) was analyzed on a 1% agarose gel (size ladder in lane 1). The bar graph placed above the agarose gel displays total amounts of DNA recovered alone (QD), simultaneously with RNA (TRI, QDR), or separately from RNA (AMB), using three consecutive 10 µm sections, in triplicate experiments for each method.

    Techniques Used: Formalin-fixed Paraffin-Embedded, Cell Culture, RNA Extraction, Isolation, Agarose Gel Electrophoresis

    DNA/RNA extractions using archived human specimens. Four different methods were tested on seven different archived tissues: (A) Qiagen QIAamp DNA FFPE kit for DNA (QD), (B) TRIzol DNA/RNA extraction method for DNA and RNA (TRI), (C) Qiagen AllPrep DNA/RNA FFPE kit for DNA and RNA (QDR), and (D) Ambion RecoverAll™ Total Nucleic Acid Isolation (AMB) for DNA and for RNA. Each nucleic acid extraction was done in triplicate to determine technical reproducibility.
    Figure Legend Snippet: DNA/RNA extractions using archived human specimens. Four different methods were tested on seven different archived tissues: (A) Qiagen QIAamp DNA FFPE kit for DNA (QD), (B) TRIzol DNA/RNA extraction method for DNA and RNA (TRI), (C) Qiagen AllPrep DNA/RNA FFPE kit for DNA and RNA (QDR), and (D) Ambion RecoverAll™ Total Nucleic Acid Isolation (AMB) for DNA and for RNA. Each nucleic acid extraction was done in triplicate to determine technical reproducibility.

    Techniques Used: Formalin-fixed Paraffin-Embedded, RNA Extraction, Isolation

    Methylation analysis of CpG regions in genes of interest using matched fresh and FFPE genomic DNA obtained by different extraction methods. Representative 2% agarose gel electrophoresis images of PCR products for (A) ESR1 and (B) CCND2 genes. Graphs depict methylation values as a percentage for CpG dinucleotide rich regions in (C) ESR1, (D) CCND2, (E) GHSR, and (F) ARID3A as assayed via the MassARRAY system (Sequenom). Data were analyzed and confirmed using the MassArray R script statistical package. Methylation values for fresh MCF10A DNA isolated with control methods (DNA from fresh cells recovered by phenol/chloroform (PC-Fr) and from FFPE cells using the Qiagen QIAamp DNA FFPE kit (QD)) are compared against methods used for matched FFPE DNA (TRIzol extraction (TRI), Qiagen AllPrep DNA/RNA FFPE (QDR), and AMBion RecoverAll™ Total Nucleic Acid Isolation (AMB)). The bar graphs display the correlation between DNA methylation measurements obtained from fresh genomic DNA and each FFPE genomic DNA recovered by the different extraction methods.
    Figure Legend Snippet: Methylation analysis of CpG regions in genes of interest using matched fresh and FFPE genomic DNA obtained by different extraction methods. Representative 2% agarose gel electrophoresis images of PCR products for (A) ESR1 and (B) CCND2 genes. Graphs depict methylation values as a percentage for CpG dinucleotide rich regions in (C) ESR1, (D) CCND2, (E) GHSR, and (F) ARID3A as assayed via the MassARRAY system (Sequenom). Data were analyzed and confirmed using the MassArray R script statistical package. Methylation values for fresh MCF10A DNA isolated with control methods (DNA from fresh cells recovered by phenol/chloroform (PC-Fr) and from FFPE cells using the Qiagen QIAamp DNA FFPE kit (QD)) are compared against methods used for matched FFPE DNA (TRIzol extraction (TRI), Qiagen AllPrep DNA/RNA FFPE (QDR), and AMBion RecoverAll™ Total Nucleic Acid Isolation (AMB)). The bar graphs display the correlation between DNA methylation measurements obtained from fresh genomic DNA and each FFPE genomic DNA recovered by the different extraction methods.

    Techniques Used: Methylation, Formalin-fixed Paraffin-Embedded, Agarose Gel Electrophoresis, Polymerase Chain Reaction, Isolation, DNA Methylation Assay

    Optimized TRIzol extraction of DNA from archived specimens. (A) Schematic representation of DNA recovery from the lower phase of TRIzol (upper phase yields RNA). In step 1 (yellow bullet), tissue digestion is performed following the procedure described in Loudig et al. 2007. In step 2 (yellow bullet), using TRIzol RNA and DNA are separated into the upper and lower phases, respectively. The DNA is recovered from the lower phase, using our optimized approach described in the materials and methods . The four steps describing optimization of DNA recovery from the lower phase of TRIzol include: a. Precipitate DNA; b. Process DNA pellet (using reagents from Qiagen DNA FFPE kit for steps b to d); c. Purify DNA; d. Bind, wash, and elute DNA. (B) Analysis of DNA from FFPE tissue recovered from the lower phase of TRIzol. The upper panel shows the histogram of DNA recovery. The lower panel shows a 1.5% agarose gel electrophoresis image of fresh DNA recovered from a TRIzol treatment lower phase (lane 1), FFPE DNA recovered from a TRIzol lower phase (lanes 2–6), and the size ladder (lane 7). For DNA, precipitation was tested for 600 µl (lane 2 and lane 4), 1000 µl (lane 3 and lane 5), and 1200 µl of Ethanol (lane 6). Proteinase K (PK) treatment was performed for 24 (lanes 2–3) or 48 hours (lanes 4–6). Electrophoresis reveals integrity of the extracted DNA samples. The histogram and agarose gel show that precipitation with a combination of 1200 µl ethanol and 48 hours of PK treatment gives the best quality and quantity of DNA. 500 ng of DNA was loaded per well of the gel.
    Figure Legend Snippet: Optimized TRIzol extraction of DNA from archived specimens. (A) Schematic representation of DNA recovery from the lower phase of TRIzol (upper phase yields RNA). In step 1 (yellow bullet), tissue digestion is performed following the procedure described in Loudig et al. 2007. In step 2 (yellow bullet), using TRIzol RNA and DNA are separated into the upper and lower phases, respectively. The DNA is recovered from the lower phase, using our optimized approach described in the materials and methods . The four steps describing optimization of DNA recovery from the lower phase of TRIzol include: a. Precipitate DNA; b. Process DNA pellet (using reagents from Qiagen DNA FFPE kit for steps b to d); c. Purify DNA; d. Bind, wash, and elute DNA. (B) Analysis of DNA from FFPE tissue recovered from the lower phase of TRIzol. The upper panel shows the histogram of DNA recovery. The lower panel shows a 1.5% agarose gel electrophoresis image of fresh DNA recovered from a TRIzol treatment lower phase (lane 1), FFPE DNA recovered from a TRIzol lower phase (lanes 2–6), and the size ladder (lane 7). For DNA, precipitation was tested for 600 µl (lane 2 and lane 4), 1000 µl (lane 3 and lane 5), and 1200 µl of Ethanol (lane 6). Proteinase K (PK) treatment was performed for 24 (lanes 2–3) or 48 hours (lanes 4–6). Electrophoresis reveals integrity of the extracted DNA samples. The histogram and agarose gel show that precipitation with a combination of 1200 µl ethanol and 48 hours of PK treatment gives the best quality and quantity of DNA. 500 ng of DNA was loaded per well of the gel.

    Techniques Used: Formalin-fixed Paraffin-Embedded, Agarose Gel Electrophoresis, Electrophoresis

    Messenger RNA expression analysis of matched fresh and FFPE RNA using different RNA extraction methods. The upper panel displays a graphic representation of quantitative RT-PCR (Taqman® mRNA assays) Measurements obtained for ESR1, CCND2 and KRT14 genes using matched fresh and FFPE RNA from MCF10A cells. The three genes were quantified using matched fresh RNA recovered with TRIzol (TRI-Fr), and FFPE RNA recovered with TRIzol (TRI), with Qiagen AllPrep DNA/RNA FFPE (QDR), with AMBion RecoverAll™ Total Nucleic Acid Isolation (AMB) and with the Roche RNA FFPE (Roche) kits. The results are represented as fold changes. The lower panels show the comparison of global mRNA quantifications obtained between fresh and FFPE RNA samples using the Illumina whole-Genome DASL platform. The different panels display comparison between triplicate RNA extractions from matched fresh (TRI-Fr1, TRI-Fr2, TRI-Fr3 (bottom to top panel)) and FFPE (TRI1-3, QDR1-3, AMB1-3 and Roche1-3 (from left to right panel)) cells. The correlation coefficient (r) between matched fresh and FFPE RNAs is displayed in each graph.
    Figure Legend Snippet: Messenger RNA expression analysis of matched fresh and FFPE RNA using different RNA extraction methods. The upper panel displays a graphic representation of quantitative RT-PCR (Taqman® mRNA assays) Measurements obtained for ESR1, CCND2 and KRT14 genes using matched fresh and FFPE RNA from MCF10A cells. The three genes were quantified using matched fresh RNA recovered with TRIzol (TRI-Fr), and FFPE RNA recovered with TRIzol (TRI), with Qiagen AllPrep DNA/RNA FFPE (QDR), with AMBion RecoverAll™ Total Nucleic Acid Isolation (AMB) and with the Roche RNA FFPE (Roche) kits. The results are represented as fold changes. The lower panels show the comparison of global mRNA quantifications obtained between fresh and FFPE RNA samples using the Illumina whole-Genome DASL platform. The different panels display comparison between triplicate RNA extractions from matched fresh (TRI-Fr1, TRI-Fr2, TRI-Fr3 (bottom to top panel)) and FFPE (TRI1-3, QDR1-3, AMB1-3 and Roche1-3 (from left to right panel)) cells. The correlation coefficient (r) between matched fresh and FFPE RNAs is displayed in each graph.

    Techniques Used: RNA Expression, Formalin-fixed Paraffin-Embedded, RNA Extraction, Quantitative RT-PCR, Isolation

    9) Product Images from "Effective DNA/RNA Co-Extraction for Analysis of MicroRNAs, mRNAs, and Genomic DNA from Formalin-Fixed Paraffin-Embedded Specimens"

    Article Title: Effective DNA/RNA Co-Extraction for Analysis of MicroRNAs, mRNAs, and Genomic DNA from Formalin-Fixed Paraffin-Embedded Specimens

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0034683

    MicroRNA expression analysis of matched fresh and FFPE RNA from MCF10A cells using different RNA extraction methods. The upper panel displays a graphic representation of quantitative RT-PCR (Taqman® miRNA assays). Measurements obtain for miR-10a, miR-196b, miR-135b, miR-32a and miR-21 using matched fresh and FFPE RNA from MCF10A cells. MiRNAs were quantified using FFPE RNA extracted with TRIzol (TRI), Qiagen AllPrep DNA/RNA FFPE (QDR), AMBion RecoverAll™ Total Nucleic Acid Isolation (AMB) kits and compared to control RNA extracted from fresh cells with TRIzol (TRI-Fr). Results are represented as ΔδC t (δC t target miRNA - δC t miR-10a (least expressed miRNA)). The lower panels show the comparison of global miRNA quantification obtained between fresh and FFPE RNA samples using the Illumina miRNA platform. Comparisons were performed between triplicate RNA extractions obtained from matched fresh (TRI-Fr1, TRI-Fr2, TRI-Fr3) and FFPE (TRI1-3, QDR1-3, and AMB1-3) cells. The correlation coefficient (r) between matched fresh and FFPE RNAs is displayed in each graph.
    Figure Legend Snippet: MicroRNA expression analysis of matched fresh and FFPE RNA from MCF10A cells using different RNA extraction methods. The upper panel displays a graphic representation of quantitative RT-PCR (Taqman® miRNA assays). Measurements obtain for miR-10a, miR-196b, miR-135b, miR-32a and miR-21 using matched fresh and FFPE RNA from MCF10A cells. MiRNAs were quantified using FFPE RNA extracted with TRIzol (TRI), Qiagen AllPrep DNA/RNA FFPE (QDR), AMBion RecoverAll™ Total Nucleic Acid Isolation (AMB) kits and compared to control RNA extracted from fresh cells with TRIzol (TRI-Fr). Results are represented as ΔδC t (δC t target miRNA - δC t miR-10a (least expressed miRNA)). The lower panels show the comparison of global miRNA quantification obtained between fresh and FFPE RNA samples using the Illumina miRNA platform. Comparisons were performed between triplicate RNA extractions obtained from matched fresh (TRI-Fr1, TRI-Fr2, TRI-Fr3) and FFPE (TRI1-3, QDR1-3, and AMB1-3) cells. The correlation coefficient (r) between matched fresh and FFPE RNAs is displayed in each graph.

    Techniques Used: Expressing, Formalin-fixed Paraffin-Embedded, RNA Extraction, Quantitative RT-PCR, Isolation

    Summary of sequential recovery of DNA and RNA from MCF10A Fresh and FFPE samples using different extraction methods. (A) Schematic representation of cell culture and DNA/RNA extraction methods used with matched fresh and 1 month-old formalin-fixed paraffin-embedded (FFPE) human mammary epithelial MCF10A cells. FFPE DNA and RNA extractions (QD, TRI, QDR, AMB) were performed in triplicate using three 10 µm sections for each replicate. (B) Analysis of RNA extracted from matched fresh and FFPE MCF10A cells. Total RNA extracted from fresh cells using TRIzol (TRI-Fr; Lane 2), and total RNA extracted from FFPE cells using TRIzol (TRI; lane 3), Qiagen QIAamp DNA/RNA extraction kit (QDR; lane 4), and AMBion RecoverAll™ Total Nucleic Acid Isolation kit (AMB; lane 5) was analyzed and quantified using an Agilent 2100 Bioanalyzer 6000 Nanochip (size ladder in lane 1). The bar graph placed above the Bioanalyzer image displays total amounts of RNA recovered from three consecutive 10 µm sections, in triplicate experiments, using the three different methods (TRI, QDR, AMB). (C) Analysis of genomic DNA extracted from matched fresh and FFPE MCF10A cells. DNA was extracted from fresh cells using a phenol/chloroform based method (PC-Fr; lane 2), and TRIzol (TRI-Fr lane 3); and from FFPE cells using Qiagen QIAamp DNA FFPE kit (QD; lane 4), TRIzol DNA/RNA extraction method (TRI; lane 5), Qiagen AllPrep DNA/RNA FFPE kit (QDR; lane 6), and AMBion RecoverAll™ Total Nucleic Acid Isolation kit (AMB; lane 7) was analyzed on a 1% agarose gel (size ladder in lane 1). The bar graph placed above the agarose gel displays total amounts of DNA recovered alone (QD), simultaneously with RNA (TRI, QDR), or separately from RNA (AMB), using three consecutive 10 µm sections, in triplicate experiments for each method.
    Figure Legend Snippet: Summary of sequential recovery of DNA and RNA from MCF10A Fresh and FFPE samples using different extraction methods. (A) Schematic representation of cell culture and DNA/RNA extraction methods used with matched fresh and 1 month-old formalin-fixed paraffin-embedded (FFPE) human mammary epithelial MCF10A cells. FFPE DNA and RNA extractions (QD, TRI, QDR, AMB) were performed in triplicate using three 10 µm sections for each replicate. (B) Analysis of RNA extracted from matched fresh and FFPE MCF10A cells. Total RNA extracted from fresh cells using TRIzol (TRI-Fr; Lane 2), and total RNA extracted from FFPE cells using TRIzol (TRI; lane 3), Qiagen QIAamp DNA/RNA extraction kit (QDR; lane 4), and AMBion RecoverAll™ Total Nucleic Acid Isolation kit (AMB; lane 5) was analyzed and quantified using an Agilent 2100 Bioanalyzer 6000 Nanochip (size ladder in lane 1). The bar graph placed above the Bioanalyzer image displays total amounts of RNA recovered from three consecutive 10 µm sections, in triplicate experiments, using the three different methods (TRI, QDR, AMB). (C) Analysis of genomic DNA extracted from matched fresh and FFPE MCF10A cells. DNA was extracted from fresh cells using a phenol/chloroform based method (PC-Fr; lane 2), and TRIzol (TRI-Fr lane 3); and from FFPE cells using Qiagen QIAamp DNA FFPE kit (QD; lane 4), TRIzol DNA/RNA extraction method (TRI; lane 5), Qiagen AllPrep DNA/RNA FFPE kit (QDR; lane 6), and AMBion RecoverAll™ Total Nucleic Acid Isolation kit (AMB; lane 7) was analyzed on a 1% agarose gel (size ladder in lane 1). The bar graph placed above the agarose gel displays total amounts of DNA recovered alone (QD), simultaneously with RNA (TRI, QDR), or separately from RNA (AMB), using three consecutive 10 µm sections, in triplicate experiments for each method.

    Techniques Used: Formalin-fixed Paraffin-Embedded, Cell Culture, RNA Extraction, Isolation, Agarose Gel Electrophoresis

    DNA/RNA extractions using archived human specimens. Four different methods were tested on seven different archived tissues: (A) Qiagen QIAamp DNA FFPE kit for DNA (QD), (B) TRIzol DNA/RNA extraction method for DNA and RNA (TRI), (C) Qiagen AllPrep DNA/RNA FFPE kit for DNA and RNA (QDR), and (D) Ambion RecoverAll™ Total Nucleic Acid Isolation (AMB) for DNA and for RNA. Each nucleic acid extraction was done in triplicate to determine technical reproducibility.
    Figure Legend Snippet: DNA/RNA extractions using archived human specimens. Four different methods were tested on seven different archived tissues: (A) Qiagen QIAamp DNA FFPE kit for DNA (QD), (B) TRIzol DNA/RNA extraction method for DNA and RNA (TRI), (C) Qiagen AllPrep DNA/RNA FFPE kit for DNA and RNA (QDR), and (D) Ambion RecoverAll™ Total Nucleic Acid Isolation (AMB) for DNA and for RNA. Each nucleic acid extraction was done in triplicate to determine technical reproducibility.

    Techniques Used: Formalin-fixed Paraffin-Embedded, RNA Extraction, Isolation

    Methylation analysis of CpG regions in genes of interest using matched fresh and FFPE genomic DNA obtained by different extraction methods. Representative 2% agarose gel electrophoresis images of PCR products for (A) ESR1 and (B) CCND2 genes. Graphs depict methylation values as a percentage for CpG dinucleotide rich regions in (C) ESR1, (D) CCND2, (E) GHSR, and (F) ARID3A as assayed via the MassARRAY system (Sequenom). Data were analyzed and confirmed using the MassArray R script statistical package. Methylation values for fresh MCF10A DNA isolated with control methods (DNA from fresh cells recovered by phenol/chloroform (PC-Fr) and from FFPE cells using the Qiagen QIAamp DNA FFPE kit (QD)) are compared against methods used for matched FFPE DNA (TRIzol extraction (TRI), Qiagen AllPrep DNA/RNA FFPE (QDR), and AMBion RecoverAll™ Total Nucleic Acid Isolation (AMB)). The bar graphs display the correlation between DNA methylation measurements obtained from fresh genomic DNA and each FFPE genomic DNA recovered by the different extraction methods.
    Figure Legend Snippet: Methylation analysis of CpG regions in genes of interest using matched fresh and FFPE genomic DNA obtained by different extraction methods. Representative 2% agarose gel electrophoresis images of PCR products for (A) ESR1 and (B) CCND2 genes. Graphs depict methylation values as a percentage for CpG dinucleotide rich regions in (C) ESR1, (D) CCND2, (E) GHSR, and (F) ARID3A as assayed via the MassARRAY system (Sequenom). Data were analyzed and confirmed using the MassArray R script statistical package. Methylation values for fresh MCF10A DNA isolated with control methods (DNA from fresh cells recovered by phenol/chloroform (PC-Fr) and from FFPE cells using the Qiagen QIAamp DNA FFPE kit (QD)) are compared against methods used for matched FFPE DNA (TRIzol extraction (TRI), Qiagen AllPrep DNA/RNA FFPE (QDR), and AMBion RecoverAll™ Total Nucleic Acid Isolation (AMB)). The bar graphs display the correlation between DNA methylation measurements obtained from fresh genomic DNA and each FFPE genomic DNA recovered by the different extraction methods.

    Techniques Used: Methylation, Formalin-fixed Paraffin-Embedded, Agarose Gel Electrophoresis, Polymerase Chain Reaction, Isolation, DNA Methylation Assay

    Optimized TRIzol extraction of DNA from archived specimens. (A) Schematic representation of DNA recovery from the lower phase of TRIzol (upper phase yields RNA). In step 1 (yellow bullet), tissue digestion is performed following the procedure described in Loudig et al. 2007. In step 2 (yellow bullet), using TRIzol RNA and DNA are separated into the upper and lower phases, respectively. The DNA is recovered from the lower phase, using our optimized approach described in the materials and methods . The four steps describing optimization of DNA recovery from the lower phase of TRIzol include: a. Precipitate DNA; b. Process DNA pellet (using reagents from Qiagen DNA FFPE kit for steps b to d); c. Purify DNA; d. Bind, wash, and elute DNA. (B) Analysis of DNA from FFPE tissue recovered from the lower phase of TRIzol. The upper panel shows the histogram of DNA recovery. The lower panel shows a 1.5% agarose gel electrophoresis image of fresh DNA recovered from a TRIzol treatment lower phase (lane 1), FFPE DNA recovered from a TRIzol lower phase (lanes 2–6), and the size ladder (lane 7). For DNA, precipitation was tested for 600 µl (lane 2 and lane 4), 1000 µl (lane 3 and lane 5), and 1200 µl of Ethanol (lane 6). Proteinase K (PK) treatment was performed for 24 (lanes 2–3) or 48 hours (lanes 4–6). Electrophoresis reveals integrity of the extracted DNA samples. The histogram and agarose gel show that precipitation with a combination of 1200 µl ethanol and 48 hours of PK treatment gives the best quality and quantity of DNA. 500 ng of DNA was loaded per well of the gel.
    Figure Legend Snippet: Optimized TRIzol extraction of DNA from archived specimens. (A) Schematic representation of DNA recovery from the lower phase of TRIzol (upper phase yields RNA). In step 1 (yellow bullet), tissue digestion is performed following the procedure described in Loudig et al. 2007. In step 2 (yellow bullet), using TRIzol RNA and DNA are separated into the upper and lower phases, respectively. The DNA is recovered from the lower phase, using our optimized approach described in the materials and methods . The four steps describing optimization of DNA recovery from the lower phase of TRIzol include: a. Precipitate DNA; b. Process DNA pellet (using reagents from Qiagen DNA FFPE kit for steps b to d); c. Purify DNA; d. Bind, wash, and elute DNA. (B) Analysis of DNA from FFPE tissue recovered from the lower phase of TRIzol. The upper panel shows the histogram of DNA recovery. The lower panel shows a 1.5% agarose gel electrophoresis image of fresh DNA recovered from a TRIzol treatment lower phase (lane 1), FFPE DNA recovered from a TRIzol lower phase (lanes 2–6), and the size ladder (lane 7). For DNA, precipitation was tested for 600 µl (lane 2 and lane 4), 1000 µl (lane 3 and lane 5), and 1200 µl of Ethanol (lane 6). Proteinase K (PK) treatment was performed for 24 (lanes 2–3) or 48 hours (lanes 4–6). Electrophoresis reveals integrity of the extracted DNA samples. The histogram and agarose gel show that precipitation with a combination of 1200 µl ethanol and 48 hours of PK treatment gives the best quality and quantity of DNA. 500 ng of DNA was loaded per well of the gel.

    Techniques Used: Formalin-fixed Paraffin-Embedded, Agarose Gel Electrophoresis, Electrophoresis

    Messenger RNA expression analysis of matched fresh and FFPE RNA using different RNA extraction methods. The upper panel displays a graphic representation of quantitative RT-PCR (Taqman® mRNA assays) Measurements obtained for ESR1, CCND2 and KRT14 genes using matched fresh and FFPE RNA from MCF10A cells. The three genes were quantified using matched fresh RNA recovered with TRIzol (TRI-Fr), and FFPE RNA recovered with TRIzol (TRI), with Qiagen AllPrep DNA/RNA FFPE (QDR), with AMBion RecoverAll™ Total Nucleic Acid Isolation (AMB) and with the Roche RNA FFPE (Roche) kits. The results are represented as fold changes. The lower panels show the comparison of global mRNA quantifications obtained between fresh and FFPE RNA samples using the Illumina whole-Genome DASL platform. The different panels display comparison between triplicate RNA extractions from matched fresh (TRI-Fr1, TRI-Fr2, TRI-Fr3 (bottom to top panel)) and FFPE (TRI1-3, QDR1-3, AMB1-3 and Roche1-3 (from left to right panel)) cells. The correlation coefficient (r) between matched fresh and FFPE RNAs is displayed in each graph.
    Figure Legend Snippet: Messenger RNA expression analysis of matched fresh and FFPE RNA using different RNA extraction methods. The upper panel displays a graphic representation of quantitative RT-PCR (Taqman® mRNA assays) Measurements obtained for ESR1, CCND2 and KRT14 genes using matched fresh and FFPE RNA from MCF10A cells. The three genes were quantified using matched fresh RNA recovered with TRIzol (TRI-Fr), and FFPE RNA recovered with TRIzol (TRI), with Qiagen AllPrep DNA/RNA FFPE (QDR), with AMBion RecoverAll™ Total Nucleic Acid Isolation (AMB) and with the Roche RNA FFPE (Roche) kits. The results are represented as fold changes. The lower panels show the comparison of global mRNA quantifications obtained between fresh and FFPE RNA samples using the Illumina whole-Genome DASL platform. The different panels display comparison between triplicate RNA extractions from matched fresh (TRI-Fr1, TRI-Fr2, TRI-Fr3 (bottom to top panel)) and FFPE (TRI1-3, QDR1-3, AMB1-3 and Roche1-3 (from left to right panel)) cells. The correlation coefficient (r) between matched fresh and FFPE RNAs is displayed in each graph.

    Techniques Used: RNA Expression, Formalin-fixed Paraffin-Embedded, RNA Extraction, Quantitative RT-PCR, Isolation

    10) Product Images from "Effective DNA/RNA Co-Extraction for Analysis of MicroRNAs, mRNAs, and Genomic DNA from Formalin-Fixed Paraffin-Embedded Specimens"

    Article Title: Effective DNA/RNA Co-Extraction for Analysis of MicroRNAs, mRNAs, and Genomic DNA from Formalin-Fixed Paraffin-Embedded Specimens

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0034683

    MicroRNA expression analysis of matched fresh and FFPE RNA from MCF10A cells using different RNA extraction methods. The upper panel displays a graphic representation of quantitative RT-PCR (Taqman® miRNA assays). Measurements obtain for miR-10a, miR-196b, miR-135b, miR-32a and miR-21 using matched fresh and FFPE RNA from MCF10A cells. MiRNAs were quantified using FFPE RNA extracted with TRIzol (TRI), Qiagen AllPrep DNA/RNA FFPE (QDR), AMBion RecoverAll™ Total Nucleic Acid Isolation (AMB) kits and compared to control RNA extracted from fresh cells with TRIzol (TRI-Fr). Results are represented as ΔδC t (δC t target miRNA - δC t miR-10a (least expressed miRNA)). The lower panels show the comparison of global miRNA quantification obtained between fresh and FFPE RNA samples using the Illumina miRNA platform. Comparisons were performed between triplicate RNA extractions obtained from matched fresh (TRI-Fr1, TRI-Fr2, TRI-Fr3) and FFPE (TRI1-3, QDR1-3, and AMB1-3) cells. The correlation coefficient (r) between matched fresh and FFPE RNAs is displayed in each graph.
    Figure Legend Snippet: MicroRNA expression analysis of matched fresh and FFPE RNA from MCF10A cells using different RNA extraction methods. The upper panel displays a graphic representation of quantitative RT-PCR (Taqman® miRNA assays). Measurements obtain for miR-10a, miR-196b, miR-135b, miR-32a and miR-21 using matched fresh and FFPE RNA from MCF10A cells. MiRNAs were quantified using FFPE RNA extracted with TRIzol (TRI), Qiagen AllPrep DNA/RNA FFPE (QDR), AMBion RecoverAll™ Total Nucleic Acid Isolation (AMB) kits and compared to control RNA extracted from fresh cells with TRIzol (TRI-Fr). Results are represented as ΔδC t (δC t target miRNA - δC t miR-10a (least expressed miRNA)). The lower panels show the comparison of global miRNA quantification obtained between fresh and FFPE RNA samples using the Illumina miRNA platform. Comparisons were performed between triplicate RNA extractions obtained from matched fresh (TRI-Fr1, TRI-Fr2, TRI-Fr3) and FFPE (TRI1-3, QDR1-3, and AMB1-3) cells. The correlation coefficient (r) between matched fresh and FFPE RNAs is displayed in each graph.

    Techniques Used: Expressing, Formalin-fixed Paraffin-Embedded, RNA Extraction, Quantitative RT-PCR, Isolation

    Summary of sequential recovery of DNA and RNA from MCF10A Fresh and FFPE samples using different extraction methods. (A) Schematic representation of cell culture and DNA/RNA extraction methods used with matched fresh and 1 month-old formalin-fixed paraffin-embedded (FFPE) human mammary epithelial MCF10A cells. FFPE DNA and RNA extractions (QD, TRI, QDR, AMB) were performed in triplicate using three 10 µm sections for each replicate. (B) Analysis of RNA extracted from matched fresh and FFPE MCF10A cells. Total RNA extracted from fresh cells using TRIzol (TRI-Fr; Lane 2), and total RNA extracted from FFPE cells using TRIzol (TRI; lane 3), Qiagen QIAamp DNA/RNA extraction kit (QDR; lane 4), and AMBion RecoverAll™ Total Nucleic Acid Isolation kit (AMB; lane 5) was analyzed and quantified using an Agilent 2100 Bioanalyzer 6000 Nanochip (size ladder in lane 1). The bar graph placed above the Bioanalyzer image displays total amounts of RNA recovered from three consecutive 10 µm sections, in triplicate experiments, using the three different methods (TRI, QDR, AMB). (C) Analysis of genomic DNA extracted from matched fresh and FFPE MCF10A cells. DNA was extracted from fresh cells using a phenol/chloroform based method (PC-Fr; lane 2), and TRIzol (TRI-Fr lane 3); and from FFPE cells using Qiagen QIAamp DNA FFPE kit (QD; lane 4), TRIzol DNA/RNA extraction method (TRI; lane 5), Qiagen AllPrep DNA/RNA FFPE kit (QDR; lane 6), and AMBion RecoverAll™ Total Nucleic Acid Isolation kit (AMB; lane 7) was analyzed on a 1% agarose gel (size ladder in lane 1). The bar graph placed above the agarose gel displays total amounts of DNA recovered alone (QD), simultaneously with RNA (TRI, QDR), or separately from RNA (AMB), using three consecutive 10 µm sections, in triplicate experiments for each method.
    Figure Legend Snippet: Summary of sequential recovery of DNA and RNA from MCF10A Fresh and FFPE samples using different extraction methods. (A) Schematic representation of cell culture and DNA/RNA extraction methods used with matched fresh and 1 month-old formalin-fixed paraffin-embedded (FFPE) human mammary epithelial MCF10A cells. FFPE DNA and RNA extractions (QD, TRI, QDR, AMB) were performed in triplicate using three 10 µm sections for each replicate. (B) Analysis of RNA extracted from matched fresh and FFPE MCF10A cells. Total RNA extracted from fresh cells using TRIzol (TRI-Fr; Lane 2), and total RNA extracted from FFPE cells using TRIzol (TRI; lane 3), Qiagen QIAamp DNA/RNA extraction kit (QDR; lane 4), and AMBion RecoverAll™ Total Nucleic Acid Isolation kit (AMB; lane 5) was analyzed and quantified using an Agilent 2100 Bioanalyzer 6000 Nanochip (size ladder in lane 1). The bar graph placed above the Bioanalyzer image displays total amounts of RNA recovered from three consecutive 10 µm sections, in triplicate experiments, using the three different methods (TRI, QDR, AMB). (C) Analysis of genomic DNA extracted from matched fresh and FFPE MCF10A cells. DNA was extracted from fresh cells using a phenol/chloroform based method (PC-Fr; lane 2), and TRIzol (TRI-Fr lane 3); and from FFPE cells using Qiagen QIAamp DNA FFPE kit (QD; lane 4), TRIzol DNA/RNA extraction method (TRI; lane 5), Qiagen AllPrep DNA/RNA FFPE kit (QDR; lane 6), and AMBion RecoverAll™ Total Nucleic Acid Isolation kit (AMB; lane 7) was analyzed on a 1% agarose gel (size ladder in lane 1). The bar graph placed above the agarose gel displays total amounts of DNA recovered alone (QD), simultaneously with RNA (TRI, QDR), or separately from RNA (AMB), using three consecutive 10 µm sections, in triplicate experiments for each method.

    Techniques Used: Formalin-fixed Paraffin-Embedded, Cell Culture, RNA Extraction, Isolation, Agarose Gel Electrophoresis

    DNA/RNA extractions using archived human specimens. Four different methods were tested on seven different archived tissues: (A) Qiagen QIAamp DNA FFPE kit for DNA (QD), (B) TRIzol DNA/RNA extraction method for DNA and RNA (TRI), (C) Qiagen AllPrep DNA/RNA FFPE kit for DNA and RNA (QDR), and (D) Ambion RecoverAll™ Total Nucleic Acid Isolation (AMB) for DNA and for RNA. Each nucleic acid extraction was done in triplicate to determine technical reproducibility.
    Figure Legend Snippet: DNA/RNA extractions using archived human specimens. Four different methods were tested on seven different archived tissues: (A) Qiagen QIAamp DNA FFPE kit for DNA (QD), (B) TRIzol DNA/RNA extraction method for DNA and RNA (TRI), (C) Qiagen AllPrep DNA/RNA FFPE kit for DNA and RNA (QDR), and (D) Ambion RecoverAll™ Total Nucleic Acid Isolation (AMB) for DNA and for RNA. Each nucleic acid extraction was done in triplicate to determine technical reproducibility.

    Techniques Used: Formalin-fixed Paraffin-Embedded, RNA Extraction, Isolation

    Methylation analysis of CpG regions in genes of interest using matched fresh and FFPE genomic DNA obtained by different extraction methods. Representative 2% agarose gel electrophoresis images of PCR products for (A) ESR1 and (B) CCND2 genes. Graphs depict methylation values as a percentage for CpG dinucleotide rich regions in (C) ESR1, (D) CCND2, (E) GHSR, and (F) ARID3A as assayed via the MassARRAY system (Sequenom). Data were analyzed and confirmed using the MassArray R script statistical package. Methylation values for fresh MCF10A DNA isolated with control methods (DNA from fresh cells recovered by phenol/chloroform (PC-Fr) and from FFPE cells using the Qiagen QIAamp DNA FFPE kit (QD)) are compared against methods used for matched FFPE DNA (TRIzol extraction (TRI), Qiagen AllPrep DNA/RNA FFPE (QDR), and AMBion RecoverAll™ Total Nucleic Acid Isolation (AMB)). The bar graphs display the correlation between DNA methylation measurements obtained from fresh genomic DNA and each FFPE genomic DNA recovered by the different extraction methods.
    Figure Legend Snippet: Methylation analysis of CpG regions in genes of interest using matched fresh and FFPE genomic DNA obtained by different extraction methods. Representative 2% agarose gel electrophoresis images of PCR products for (A) ESR1 and (B) CCND2 genes. Graphs depict methylation values as a percentage for CpG dinucleotide rich regions in (C) ESR1, (D) CCND2, (E) GHSR, and (F) ARID3A as assayed via the MassARRAY system (Sequenom). Data were analyzed and confirmed using the MassArray R script statistical package. Methylation values for fresh MCF10A DNA isolated with control methods (DNA from fresh cells recovered by phenol/chloroform (PC-Fr) and from FFPE cells using the Qiagen QIAamp DNA FFPE kit (QD)) are compared against methods used for matched FFPE DNA (TRIzol extraction (TRI), Qiagen AllPrep DNA/RNA FFPE (QDR), and AMBion RecoverAll™ Total Nucleic Acid Isolation (AMB)). The bar graphs display the correlation between DNA methylation measurements obtained from fresh genomic DNA and each FFPE genomic DNA recovered by the different extraction methods.

    Techniques Used: Methylation, Formalin-fixed Paraffin-Embedded, Agarose Gel Electrophoresis, Polymerase Chain Reaction, Isolation, DNA Methylation Assay

    Optimized TRIzol extraction of DNA from archived specimens. (A) Schematic representation of DNA recovery from the lower phase of TRIzol (upper phase yields RNA). In step 1 (yellow bullet), tissue digestion is performed following the procedure described in Loudig et al. 2007. In step 2 (yellow bullet), using TRIzol RNA and DNA are separated into the upper and lower phases, respectively. The DNA is recovered from the lower phase, using our optimized approach described in the materials and methods . The four steps describing optimization of DNA recovery from the lower phase of TRIzol include: a. Precipitate DNA; b. Process DNA pellet (using reagents from Qiagen DNA FFPE kit for steps b to d); c. Purify DNA; d. Bind, wash, and elute DNA. (B) Analysis of DNA from FFPE tissue recovered from the lower phase of TRIzol. The upper panel shows the histogram of DNA recovery. The lower panel shows a 1.5% agarose gel electrophoresis image of fresh DNA recovered from a TRIzol treatment lower phase (lane 1), FFPE DNA recovered from a TRIzol lower phase (lanes 2–6), and the size ladder (lane 7). For DNA, precipitation was tested for 600 µl (lane 2 and lane 4), 1000 µl (lane 3 and lane 5), and 1200 µl of Ethanol (lane 6). Proteinase K (PK) treatment was performed for 24 (lanes 2–3) or 48 hours (lanes 4–6). Electrophoresis reveals integrity of the extracted DNA samples. The histogram and agarose gel show that precipitation with a combination of 1200 µl ethanol and 48 hours of PK treatment gives the best quality and quantity of DNA. 500 ng of DNA was loaded per well of the gel.
    Figure Legend Snippet: Optimized TRIzol extraction of DNA from archived specimens. (A) Schematic representation of DNA recovery from the lower phase of TRIzol (upper phase yields RNA). In step 1 (yellow bullet), tissue digestion is performed following the procedure described in Loudig et al. 2007. In step 2 (yellow bullet), using TRIzol RNA and DNA are separated into the upper and lower phases, respectively. The DNA is recovered from the lower phase, using our optimized approach described in the materials and methods . The four steps describing optimization of DNA recovery from the lower phase of TRIzol include: a. Precipitate DNA; b. Process DNA pellet (using reagents from Qiagen DNA FFPE kit for steps b to d); c. Purify DNA; d. Bind, wash, and elute DNA. (B) Analysis of DNA from FFPE tissue recovered from the lower phase of TRIzol. The upper panel shows the histogram of DNA recovery. The lower panel shows a 1.5% agarose gel electrophoresis image of fresh DNA recovered from a TRIzol treatment lower phase (lane 1), FFPE DNA recovered from a TRIzol lower phase (lanes 2–6), and the size ladder (lane 7). For DNA, precipitation was tested for 600 µl (lane 2 and lane 4), 1000 µl (lane 3 and lane 5), and 1200 µl of Ethanol (lane 6). Proteinase K (PK) treatment was performed for 24 (lanes 2–3) or 48 hours (lanes 4–6). Electrophoresis reveals integrity of the extracted DNA samples. The histogram and agarose gel show that precipitation with a combination of 1200 µl ethanol and 48 hours of PK treatment gives the best quality and quantity of DNA. 500 ng of DNA was loaded per well of the gel.

    Techniques Used: Formalin-fixed Paraffin-Embedded, Agarose Gel Electrophoresis, Electrophoresis

    Messenger RNA expression analysis of matched fresh and FFPE RNA using different RNA extraction methods. The upper panel displays a graphic representation of quantitative RT-PCR (Taqman® mRNA assays) Measurements obtained for ESR1, CCND2 and KRT14 genes using matched fresh and FFPE RNA from MCF10A cells. The three genes were quantified using matched fresh RNA recovered with TRIzol (TRI-Fr), and FFPE RNA recovered with TRIzol (TRI), with Qiagen AllPrep DNA/RNA FFPE (QDR), with AMBion RecoverAll™ Total Nucleic Acid Isolation (AMB) and with the Roche RNA FFPE (Roche) kits. The results are represented as fold changes. The lower panels show the comparison of global mRNA quantifications obtained between fresh and FFPE RNA samples using the Illumina whole-Genome DASL platform. The different panels display comparison between triplicate RNA extractions from matched fresh (TRI-Fr1, TRI-Fr2, TRI-Fr3 (bottom to top panel)) and FFPE (TRI1-3, QDR1-3, AMB1-3 and Roche1-3 (from left to right panel)) cells. The correlation coefficient (r) between matched fresh and FFPE RNAs is displayed in each graph.
    Figure Legend Snippet: Messenger RNA expression analysis of matched fresh and FFPE RNA using different RNA extraction methods. The upper panel displays a graphic representation of quantitative RT-PCR (Taqman® mRNA assays) Measurements obtained for ESR1, CCND2 and KRT14 genes using matched fresh and FFPE RNA from MCF10A cells. The three genes were quantified using matched fresh RNA recovered with TRIzol (TRI-Fr), and FFPE RNA recovered with TRIzol (TRI), with Qiagen AllPrep DNA/RNA FFPE (QDR), with AMBion RecoverAll™ Total Nucleic Acid Isolation (AMB) and with the Roche RNA FFPE (Roche) kits. The results are represented as fold changes. The lower panels show the comparison of global mRNA quantifications obtained between fresh and FFPE RNA samples using the Illumina whole-Genome DASL platform. The different panels display comparison between triplicate RNA extractions from matched fresh (TRI-Fr1, TRI-Fr2, TRI-Fr3 (bottom to top panel)) and FFPE (TRI1-3, QDR1-3, AMB1-3 and Roche1-3 (from left to right panel)) cells. The correlation coefficient (r) between matched fresh and FFPE RNAs is displayed in each graph.

    Techniques Used: RNA Expression, Formalin-fixed Paraffin-Embedded, RNA Extraction, Quantitative RT-PCR, Isolation

    11) Product Images from "Nucleic acid extraction from formalin-fixed paraffin-embedded cancer cell line samples: a trade off between quantity and quality?"

    Article Title: Nucleic acid extraction from formalin-fixed paraffin-embedded cancer cell line samples: a trade off between quantity and quality?

    Journal: BMC Clinical Pathology

    doi: 10.1186/s12907-016-0039-3

    Investigating the relationship between DNA concentration and the input tissue amount: Geometric mean increase in DNA concentration across 6 different FFPE blocks when combining 5 μm sections in a linear fashion and associated standard error of geomean, line of Y = X/5 represents a linear relationship a Qiagen AllPrep DNA/RNA FFPE, b Qiagen QIAmp DNA FFPE tissue, c Arcturus PicoPure DNA extraction kit, d Maxwell 16 FFPE Tissue LEV DNA Purification Kit
    Figure Legend Snippet: Investigating the relationship between DNA concentration and the input tissue amount: Geometric mean increase in DNA concentration across 6 different FFPE blocks when combining 5 μm sections in a linear fashion and associated standard error of geomean, line of Y = X/5 represents a linear relationship a Qiagen AllPrep DNA/RNA FFPE, b Qiagen QIAmp DNA FFPE tissue, c Arcturus PicoPure DNA extraction kit, d Maxwell 16 FFPE Tissue LEV DNA Purification Kit

    Techniques Used: Concentration Assay, Formalin-fixed Paraffin-Embedded, DNA Extraction, DNA Purification

    Investigating the relationship between RNA concentration and the input amount of tissue: Geometric mean increase in RNA concentration ( n = 6) when combining 5 μm sections in a linear fashion and associated standard error of mean, line of Y = X/5 represents a linear relationship a Qiagen AllPrep DNA/RNA FFPE kit, b Qiagen RNeasy, c Arcturus Paradise plus FFPE RNA isolation kit, d Maxwell 16 LEV RNA FFPE Purification kit
    Figure Legend Snippet: Investigating the relationship between RNA concentration and the input amount of tissue: Geometric mean increase in RNA concentration ( n = 6) when combining 5 μm sections in a linear fashion and associated standard error of mean, line of Y = X/5 represents a linear relationship a Qiagen AllPrep DNA/RNA FFPE kit, b Qiagen RNeasy, c Arcturus Paradise plus FFPE RNA isolation kit, d Maxwell 16 LEV RNA FFPE Purification kit

    Techniques Used: Concentration Assay, Formalin-fixed Paraffin-Embedded, Isolation, Purification

    12) Product Images from "Evaluation of commercial DNA and RNA extraction methods for high-throughput sequencing of FFPE samples"

    Article Title: Evaluation of commercial DNA and RNA extraction methods for high-throughput sequencing of FFPE samples

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0197456

    Yield and amplifiability of extracted DNA and RNA. (A) Average total amount of DNA. (B) Average total amount of RNA. (C) Amplifiable DNA quantified with the FFPE QC kit from Illumina. (D) Amplifiable RNA quantified with the PreSeq QC assay from ArcherDx. The average total amount and average delta Ct values for the different samples and extraction methods are shown. The standard deviation is shown as vertical bars. Methods with significant differences in yield are marked as connected with horizontal bars (p
    Figure Legend Snippet: Yield and amplifiability of extracted DNA and RNA. (A) Average total amount of DNA. (B) Average total amount of RNA. (C) Amplifiable DNA quantified with the FFPE QC kit from Illumina. (D) Amplifiable RNA quantified with the PreSeq QC assay from ArcherDx. The average total amount and average delta Ct values for the different samples and extraction methods are shown. The standard deviation is shown as vertical bars. Methods with significant differences in yield are marked as connected with horizontal bars (p

    Techniques Used: Formalin-fixed Paraffin-Embedded, Standard Deviation

    13) Product Images from "Effective DNA/RNA Co-Extraction for Analysis of MicroRNAs, mRNAs, and Genomic DNA from Formalin-Fixed Paraffin-Embedded Specimens"

    Article Title: Effective DNA/RNA Co-Extraction for Analysis of MicroRNAs, mRNAs, and Genomic DNA from Formalin-Fixed Paraffin-Embedded Specimens

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0034683

    MicroRNA expression analysis of matched fresh and FFPE RNA from MCF10A cells using different RNA extraction methods. The upper panel displays a graphic representation of quantitative RT-PCR (Taqman® miRNA assays). Measurements obtain for miR-10a, miR-196b, miR-135b, miR-32a and miR-21 using matched fresh and FFPE RNA from MCF10A cells. MiRNAs were quantified using FFPE RNA extracted with TRIzol (TRI), Qiagen AllPrep DNA/RNA FFPE (QDR), AMBion RecoverAll™ Total Nucleic Acid Isolation (AMB) kits and compared to control RNA extracted from fresh cells with TRIzol (TRI-Fr). Results are represented as ΔδC t (δC t target miRNA - δC t miR-10a (least expressed miRNA)). The lower panels show the comparison of global miRNA quantification obtained between fresh and FFPE RNA samples using the Illumina miRNA platform. Comparisons were performed between triplicate RNA extractions obtained from matched fresh (TRI-Fr1, TRI-Fr2, TRI-Fr3) and FFPE (TRI1-3, QDR1-3, and AMB1-3) cells. The correlation coefficient (r) between matched fresh and FFPE RNAs is displayed in each graph.
    Figure Legend Snippet: MicroRNA expression analysis of matched fresh and FFPE RNA from MCF10A cells using different RNA extraction methods. The upper panel displays a graphic representation of quantitative RT-PCR (Taqman® miRNA assays). Measurements obtain for miR-10a, miR-196b, miR-135b, miR-32a and miR-21 using matched fresh and FFPE RNA from MCF10A cells. MiRNAs were quantified using FFPE RNA extracted with TRIzol (TRI), Qiagen AllPrep DNA/RNA FFPE (QDR), AMBion RecoverAll™ Total Nucleic Acid Isolation (AMB) kits and compared to control RNA extracted from fresh cells with TRIzol (TRI-Fr). Results are represented as ΔδC t (δC t target miRNA - δC t miR-10a (least expressed miRNA)). The lower panels show the comparison of global miRNA quantification obtained between fresh and FFPE RNA samples using the Illumina miRNA platform. Comparisons were performed between triplicate RNA extractions obtained from matched fresh (TRI-Fr1, TRI-Fr2, TRI-Fr3) and FFPE (TRI1-3, QDR1-3, and AMB1-3) cells. The correlation coefficient (r) between matched fresh and FFPE RNAs is displayed in each graph.

    Techniques Used: Expressing, Formalin-fixed Paraffin-Embedded, RNA Extraction, Quantitative RT-PCR, Isolation

    Summary of sequential recovery of DNA and RNA from MCF10A Fresh and FFPE samples using different extraction methods. (A) Schematic representation of cell culture and DNA/RNA extraction methods used with matched fresh and 1 month-old formalin-fixed paraffin-embedded (FFPE) human mammary epithelial MCF10A cells. FFPE DNA and RNA extractions (QD, TRI, QDR, AMB) were performed in triplicate using three 10 µm sections for each replicate. (B) Analysis of RNA extracted from matched fresh and FFPE MCF10A cells. Total RNA extracted from fresh cells using TRIzol (TRI-Fr; Lane 2), and total RNA extracted from FFPE cells using TRIzol (TRI; lane 3), Qiagen QIAamp DNA/RNA extraction kit (QDR; lane 4), and AMBion RecoverAll™ Total Nucleic Acid Isolation kit (AMB; lane 5) was analyzed and quantified using an Agilent 2100 Bioanalyzer 6000 Nanochip (size ladder in lane 1). The bar graph placed above the Bioanalyzer image displays total amounts of RNA recovered from three consecutive 10 µm sections, in triplicate experiments, using the three different methods (TRI, QDR, AMB). (C) Analysis of genomic DNA extracted from matched fresh and FFPE MCF10A cells. DNA was extracted from fresh cells using a phenol/chloroform based method (PC-Fr; lane 2), and TRIzol (TRI-Fr lane 3); and from FFPE cells using Qiagen QIAamp DNA FFPE kit (QD; lane 4), TRIzol DNA/RNA extraction method (TRI; lane 5), Qiagen AllPrep DNA/RNA FFPE kit (QDR; lane 6), and AMBion RecoverAll™ Total Nucleic Acid Isolation kit (AMB; lane 7) was analyzed on a 1% agarose gel (size ladder in lane 1). The bar graph placed above the agarose gel displays total amounts of DNA recovered alone (QD), simultaneously with RNA (TRI, QDR), or separately from RNA (AMB), using three consecutive 10 µm sections, in triplicate experiments for each method.
    Figure Legend Snippet: Summary of sequential recovery of DNA and RNA from MCF10A Fresh and FFPE samples using different extraction methods. (A) Schematic representation of cell culture and DNA/RNA extraction methods used with matched fresh and 1 month-old formalin-fixed paraffin-embedded (FFPE) human mammary epithelial MCF10A cells. FFPE DNA and RNA extractions (QD, TRI, QDR, AMB) were performed in triplicate using three 10 µm sections for each replicate. (B) Analysis of RNA extracted from matched fresh and FFPE MCF10A cells. Total RNA extracted from fresh cells using TRIzol (TRI-Fr; Lane 2), and total RNA extracted from FFPE cells using TRIzol (TRI; lane 3), Qiagen QIAamp DNA/RNA extraction kit (QDR; lane 4), and AMBion RecoverAll™ Total Nucleic Acid Isolation kit (AMB; lane 5) was analyzed and quantified using an Agilent 2100 Bioanalyzer 6000 Nanochip (size ladder in lane 1). The bar graph placed above the Bioanalyzer image displays total amounts of RNA recovered from three consecutive 10 µm sections, in triplicate experiments, using the three different methods (TRI, QDR, AMB). (C) Analysis of genomic DNA extracted from matched fresh and FFPE MCF10A cells. DNA was extracted from fresh cells using a phenol/chloroform based method (PC-Fr; lane 2), and TRIzol (TRI-Fr lane 3); and from FFPE cells using Qiagen QIAamp DNA FFPE kit (QD; lane 4), TRIzol DNA/RNA extraction method (TRI; lane 5), Qiagen AllPrep DNA/RNA FFPE kit (QDR; lane 6), and AMBion RecoverAll™ Total Nucleic Acid Isolation kit (AMB; lane 7) was analyzed on a 1% agarose gel (size ladder in lane 1). The bar graph placed above the agarose gel displays total amounts of DNA recovered alone (QD), simultaneously with RNA (TRI, QDR), or separately from RNA (AMB), using three consecutive 10 µm sections, in triplicate experiments for each method.

    Techniques Used: Formalin-fixed Paraffin-Embedded, Cell Culture, RNA Extraction, Isolation, Agarose Gel Electrophoresis

    DNA/RNA extractions using archived human specimens. Four different methods were tested on seven different archived tissues: (A) Qiagen QIAamp DNA FFPE kit for DNA (QD), (B) TRIzol DNA/RNA extraction method for DNA and RNA (TRI), (C) Qiagen AllPrep DNA/RNA FFPE kit for DNA and RNA (QDR), and (D) Ambion RecoverAll™ Total Nucleic Acid Isolation (AMB) for DNA and for RNA. Each nucleic acid extraction was done in triplicate to determine technical reproducibility.
    Figure Legend Snippet: DNA/RNA extractions using archived human specimens. Four different methods were tested on seven different archived tissues: (A) Qiagen QIAamp DNA FFPE kit for DNA (QD), (B) TRIzol DNA/RNA extraction method for DNA and RNA (TRI), (C) Qiagen AllPrep DNA/RNA FFPE kit for DNA and RNA (QDR), and (D) Ambion RecoverAll™ Total Nucleic Acid Isolation (AMB) for DNA and for RNA. Each nucleic acid extraction was done in triplicate to determine technical reproducibility.

    Techniques Used: Formalin-fixed Paraffin-Embedded, RNA Extraction, Isolation

    Methylation analysis of CpG regions in genes of interest using matched fresh and FFPE genomic DNA obtained by different extraction methods. Representative 2% agarose gel electrophoresis images of PCR products for (A) ESR1 and (B) CCND2 genes. Graphs depict methylation values as a percentage for CpG dinucleotide rich regions in (C) ESR1, (D) CCND2, (E) GHSR, and (F) ARID3A as assayed via the MassARRAY system (Sequenom). Data were analyzed and confirmed using the MassArray R script statistical package. Methylation values for fresh MCF10A DNA isolated with control methods (DNA from fresh cells recovered by phenol/chloroform (PC-Fr) and from FFPE cells using the Qiagen QIAamp DNA FFPE kit (QD)) are compared against methods used for matched FFPE DNA (TRIzol extraction (TRI), Qiagen AllPrep DNA/RNA FFPE (QDR), and AMBion RecoverAll™ Total Nucleic Acid Isolation (AMB)). The bar graphs display the correlation between DNA methylation measurements obtained from fresh genomic DNA and each FFPE genomic DNA recovered by the different extraction methods.
    Figure Legend Snippet: Methylation analysis of CpG regions in genes of interest using matched fresh and FFPE genomic DNA obtained by different extraction methods. Representative 2% agarose gel electrophoresis images of PCR products for (A) ESR1 and (B) CCND2 genes. Graphs depict methylation values as a percentage for CpG dinucleotide rich regions in (C) ESR1, (D) CCND2, (E) GHSR, and (F) ARID3A as assayed via the MassARRAY system (Sequenom). Data were analyzed and confirmed using the MassArray R script statistical package. Methylation values for fresh MCF10A DNA isolated with control methods (DNA from fresh cells recovered by phenol/chloroform (PC-Fr) and from FFPE cells using the Qiagen QIAamp DNA FFPE kit (QD)) are compared against methods used for matched FFPE DNA (TRIzol extraction (TRI), Qiagen AllPrep DNA/RNA FFPE (QDR), and AMBion RecoverAll™ Total Nucleic Acid Isolation (AMB)). The bar graphs display the correlation between DNA methylation measurements obtained from fresh genomic DNA and each FFPE genomic DNA recovered by the different extraction methods.

    Techniques Used: Methylation, Formalin-fixed Paraffin-Embedded, Agarose Gel Electrophoresis, Polymerase Chain Reaction, Isolation, DNA Methylation Assay

    Optimized TRIzol extraction of DNA from archived specimens. (A) Schematic representation of DNA recovery from the lower phase of TRIzol (upper phase yields RNA). In step 1 (yellow bullet), tissue digestion is performed following the procedure described in Loudig et al. 2007. In step 2 (yellow bullet), using TRIzol RNA and DNA are separated into the upper and lower phases, respectively. The DNA is recovered from the lower phase, using our optimized approach described in the materials and methods . The four steps describing optimization of DNA recovery from the lower phase of TRIzol include: a. Precipitate DNA; b. Process DNA pellet (using reagents from Qiagen DNA FFPE kit for steps b to d); c. Purify DNA; d. Bind, wash, and elute DNA. (B) Analysis of DNA from FFPE tissue recovered from the lower phase of TRIzol. The upper panel shows the histogram of DNA recovery. The lower panel shows a 1.5% agarose gel electrophoresis image of fresh DNA recovered from a TRIzol treatment lower phase (lane 1), FFPE DNA recovered from a TRIzol lower phase (lanes 2–6), and the size ladder (lane 7). For DNA, precipitation was tested for 600 µl (lane 2 and lane 4), 1000 µl (lane 3 and lane 5), and 1200 µl of Ethanol (lane 6). Proteinase K (PK) treatment was performed for 24 (lanes 2–3) or 48 hours (lanes 4–6). Electrophoresis reveals integrity of the extracted DNA samples. The histogram and agarose gel show that precipitation with a combination of 1200 µl ethanol and 48 hours of PK treatment gives the best quality and quantity of DNA. 500 ng of DNA was loaded per well of the gel.
    Figure Legend Snippet: Optimized TRIzol extraction of DNA from archived specimens. (A) Schematic representation of DNA recovery from the lower phase of TRIzol (upper phase yields RNA). In step 1 (yellow bullet), tissue digestion is performed following the procedure described in Loudig et al. 2007. In step 2 (yellow bullet), using TRIzol RNA and DNA are separated into the upper and lower phases, respectively. The DNA is recovered from the lower phase, using our optimized approach described in the materials and methods . The four steps describing optimization of DNA recovery from the lower phase of TRIzol include: a. Precipitate DNA; b. Process DNA pellet (using reagents from Qiagen DNA FFPE kit for steps b to d); c. Purify DNA; d. Bind, wash, and elute DNA. (B) Analysis of DNA from FFPE tissue recovered from the lower phase of TRIzol. The upper panel shows the histogram of DNA recovery. The lower panel shows a 1.5% agarose gel electrophoresis image of fresh DNA recovered from a TRIzol treatment lower phase (lane 1), FFPE DNA recovered from a TRIzol lower phase (lanes 2–6), and the size ladder (lane 7). For DNA, precipitation was tested for 600 µl (lane 2 and lane 4), 1000 µl (lane 3 and lane 5), and 1200 µl of Ethanol (lane 6). Proteinase K (PK) treatment was performed for 24 (lanes 2–3) or 48 hours (lanes 4–6). Electrophoresis reveals integrity of the extracted DNA samples. The histogram and agarose gel show that precipitation with a combination of 1200 µl ethanol and 48 hours of PK treatment gives the best quality and quantity of DNA. 500 ng of DNA was loaded per well of the gel.

    Techniques Used: Formalin-fixed Paraffin-Embedded, Agarose Gel Electrophoresis, Electrophoresis

    Messenger RNA expression analysis of matched fresh and FFPE RNA using different RNA extraction methods. The upper panel displays a graphic representation of quantitative RT-PCR (Taqman® mRNA assays) Measurements obtained for ESR1, CCND2 and KRT14 genes using matched fresh and FFPE RNA from MCF10A cells. The three genes were quantified using matched fresh RNA recovered with TRIzol (TRI-Fr), and FFPE RNA recovered with TRIzol (TRI), with Qiagen AllPrep DNA/RNA FFPE (QDR), with AMBion RecoverAll™ Total Nucleic Acid Isolation (AMB) and with the Roche RNA FFPE (Roche) kits. The results are represented as fold changes. The lower panels show the comparison of global mRNA quantifications obtained between fresh and FFPE RNA samples using the Illumina whole-Genome DASL platform. The different panels display comparison between triplicate RNA extractions from matched fresh (TRI-Fr1, TRI-Fr2, TRI-Fr3 (bottom to top panel)) and FFPE (TRI1-3, QDR1-3, AMB1-3 and Roche1-3 (from left to right panel)) cells. The correlation coefficient (r) between matched fresh and FFPE RNAs is displayed in each graph.
    Figure Legend Snippet: Messenger RNA expression analysis of matched fresh and FFPE RNA using different RNA extraction methods. The upper panel displays a graphic representation of quantitative RT-PCR (Taqman® mRNA assays) Measurements obtained for ESR1, CCND2 and KRT14 genes using matched fresh and FFPE RNA from MCF10A cells. The three genes were quantified using matched fresh RNA recovered with TRIzol (TRI-Fr), and FFPE RNA recovered with TRIzol (TRI), with Qiagen AllPrep DNA/RNA FFPE (QDR), with AMBion RecoverAll™ Total Nucleic Acid Isolation (AMB) and with the Roche RNA FFPE (Roche) kits. The results are represented as fold changes. The lower panels show the comparison of global mRNA quantifications obtained between fresh and FFPE RNA samples using the Illumina whole-Genome DASL platform. The different panels display comparison between triplicate RNA extractions from matched fresh (TRI-Fr1, TRI-Fr2, TRI-Fr3 (bottom to top panel)) and FFPE (TRI1-3, QDR1-3, AMB1-3 and Roche1-3 (from left to right panel)) cells. The correlation coefficient (r) between matched fresh and FFPE RNAs is displayed in each graph.

    Techniques Used: RNA Expression, Formalin-fixed Paraffin-Embedded, RNA Extraction, Quantitative RT-PCR, Isolation

    14) Product Images from "Multiplex genomic profiling of non-small cell lung cancers from the LETS phase III trial of first-line S-1/carboplatin versus paclitaxel/carboplatin: results of a West Japan Oncology Group study"

    Article Title: Multiplex genomic profiling of non-small cell lung cancers from the LETS phase III trial of first-line S-1/carboplatin versus paclitaxel/carboplatin: results of a West Japan Oncology Group study

    Journal: Oncotarget

    doi:

    CONSORT diagram for the study Of the FFPE specimens obtained from 304 advanced NSCLC patients (54%) enrolled in the LETS study, 9 specimens contained no tumor cells and the remaining 295 specimens were subjected to extraction of DNA and RNA. In addition, 229 FFPE specimens were analyzed for MET amplification by FISH.
    Figure Legend Snippet: CONSORT diagram for the study Of the FFPE specimens obtained from 304 advanced NSCLC patients (54%) enrolled in the LETS study, 9 specimens contained no tumor cells and the remaining 295 specimens were subjected to extraction of DNA and RNA. In addition, 229 FFPE specimens were analyzed for MET amplification by FISH.

    Techniques Used: Formalin-fixed Paraffin-Embedded, Amplification, Fluorescence In Situ Hybridization

    15) Product Images from "Nucleic acid extraction from formalin-fixed paraffin-embedded cancer cell line samples: a trade off between quantity and quality?"

    Article Title: Nucleic acid extraction from formalin-fixed paraffin-embedded cancer cell line samples: a trade off between quantity and quality?

    Journal: BMC Clinical Pathology

    doi: 10.1186/s12907-016-0039-3

    Investigating the relationship between DNA concentration and the input tissue amount: Geometric mean increase in DNA concentration across 6 different FFPE blocks when combining 5 μm sections in a linear fashion and associated standard error of geomean, line of Y = X/5 represents a linear relationship a Qiagen AllPrep DNA/RNA FFPE, b Qiagen QIAmp DNA FFPE tissue, c Arcturus PicoPure DNA extraction kit, d Maxwell 16 FFPE Tissue LEV DNA Purification Kit
    Figure Legend Snippet: Investigating the relationship between DNA concentration and the input tissue amount: Geometric mean increase in DNA concentration across 6 different FFPE blocks when combining 5 μm sections in a linear fashion and associated standard error of geomean, line of Y = X/5 represents a linear relationship a Qiagen AllPrep DNA/RNA FFPE, b Qiagen QIAmp DNA FFPE tissue, c Arcturus PicoPure DNA extraction kit, d Maxwell 16 FFPE Tissue LEV DNA Purification Kit

    Techniques Used: Concentration Assay, Formalin-fixed Paraffin-Embedded, DNA Extraction, DNA Purification

    Investigating the relationship between RNA concentration and the input amount of tissue: Geometric mean increase in RNA concentration ( n = 6) when combining 5 μm sections in a linear fashion and associated standard error of mean, line of Y = X/5 represents a linear relationship a Qiagen AllPrep DNA/RNA FFPE kit, b Qiagen RNeasy, c Arcturus Paradise plus FFPE RNA isolation kit, d Maxwell 16 LEV RNA FFPE Purification kit
    Figure Legend Snippet: Investigating the relationship between RNA concentration and the input amount of tissue: Geometric mean increase in RNA concentration ( n = 6) when combining 5 μm sections in a linear fashion and associated standard error of mean, line of Y = X/5 represents a linear relationship a Qiagen AllPrep DNA/RNA FFPE kit, b Qiagen RNeasy, c Arcturus Paradise plus FFPE RNA isolation kit, d Maxwell 16 LEV RNA FFPE Purification kit

    Techniques Used: Concentration Assay, Formalin-fixed Paraffin-Embedded, Isolation, Purification

    16) Product Images from "Reliability and performance of commercial RNA and DNA extraction kits for FFPE tissue cores"

    Article Title: Reliability and performance of commercial RNA and DNA extraction kits for FFPE tissue cores

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0179732

    Comparison of DNA and RNA yields and quality across labs and sample age. ( A) Bar graph (mean ± SD) comparing the yields of DNA and RNA extracted from 12 FFPE samples (circles) in three independent laboratories, using the AllPrep kit. (B) Correlation plot of DNA and RNA yield from the same 12 samples, as a function of age of sample. Each data point represents the yield for a given sample, extracted at a given laboratory, superimposed on a linear regression line. Correlation of sample age with MS-PCR amplification cycle thresholds (C) or total mRNA counts in a NanoString assay (D), based on a representative set of genes assayed in each case. Each data point represents the Cq value or the total mRNA count for a given sample, extracted at a given laboratory, superimposed on a linear regression line. Detailed data and statistical analyses are presented in the supplementary S2 Table .
    Figure Legend Snippet: Comparison of DNA and RNA yields and quality across labs and sample age. ( A) Bar graph (mean ± SD) comparing the yields of DNA and RNA extracted from 12 FFPE samples (circles) in three independent laboratories, using the AllPrep kit. (B) Correlation plot of DNA and RNA yield from the same 12 samples, as a function of age of sample. Each data point represents the yield for a given sample, extracted at a given laboratory, superimposed on a linear regression line. Correlation of sample age with MS-PCR amplification cycle thresholds (C) or total mRNA counts in a NanoString assay (D), based on a representative set of genes assayed in each case. Each data point represents the Cq value or the total mRNA count for a given sample, extracted at a given laboratory, superimposed on a linear regression line. Detailed data and statistical analyses are presented in the supplementary S2 Table .

    Techniques Used: Formalin-fixed Paraffin-Embedded, Mass Spectrometry, Polymerase Chain Reaction, Amplification

    17) Product Images from "Quantity and quality of nucleic acids extracted from archival formalin fixed paraffin embedded prostate biopsies"

    Article Title: Quantity and quality of nucleic acids extracted from archival formalin fixed paraffin embedded prostate biopsies

    Journal: BMC Medical Research Methodology

    doi: 10.1186/s12874-018-0628-1

    Bland-Altman plots for investigation of level of agreements between DNA extraction kits. Each plot shows the differences between the two kits against the averages of the two kits. The lines represent the mean differences and upper and lower limits of agreement (LOA, mean differences ±1.96SD). a Comparison of DNA yield (ng/μl) of samples extracted with High Pure FFPET DNA Isolation kit and QIAamp® DNA FFPE Tissue kit. b Comparison of purity (A260/A280) of DNA samples extracted with High Pure FFPET DNA Isolation kit and QIAamp® DNA FFPE Tissue kit. c Comparison of DNA yield (ng/μl) of samples extracted with QIAamp® DNA FFPE Tissue kit and AllPrep® DNA/RNA FFPE kit. d Comparison of purity (A260/A280) of samples extracted with QIAamp® DNA FFPE Tissue kit and AllPrep® DNA/RNA FFPE kit
    Figure Legend Snippet: Bland-Altman plots for investigation of level of agreements between DNA extraction kits. Each plot shows the differences between the two kits against the averages of the two kits. The lines represent the mean differences and upper and lower limits of agreement (LOA, mean differences ±1.96SD). a Comparison of DNA yield (ng/μl) of samples extracted with High Pure FFPET DNA Isolation kit and QIAamp® DNA FFPE Tissue kit. b Comparison of purity (A260/A280) of DNA samples extracted with High Pure FFPET DNA Isolation kit and QIAamp® DNA FFPE Tissue kit. c Comparison of DNA yield (ng/μl) of samples extracted with QIAamp® DNA FFPE Tissue kit and AllPrep® DNA/RNA FFPE kit. d Comparison of purity (A260/A280) of samples extracted with QIAamp® DNA FFPE Tissue kit and AllPrep® DNA/RNA FFPE kit

    Techniques Used: DNA Extraction, Formalin-fixed Paraffin-Embedded

    Bland-Altman plots for investigating the level of agreement between RNA extraction kits. Each plot shows the differences between the two kits against the averages of the two kits. The lines represent the mean differences and upper and lower limits of agreement (LOA, mean differences ±1.96SD). a Comparison of RNA yield (ng/μl) of samples extracted with High Pure FFPE RNA Micro Kit and RNeasy® FFPE kit. b Comparison of purity (A260/A280) of samples extracted with High Pure FFPE RNA Micro kit and RNeasy® FFPE kit. c Comparison of RIN-values of samples extracted with High Pure FFPE RNA Micro kit and RNeasy® FFPE kit. d Comparison of RNA yield (ng/μl) of samples extracted with RNeasy® FFPE kit and AllPrep® DNA/RNA FFPE kit. e Comparison of purity (A260/A280) of samples extracted with RNeasy® FFPE kit and AllPrep® DNA/RNA FFPE kit. f Comparison of RIN-values of samples extracted with RNeasy® FFPE kit and AllPrep® DNA/RNA FFPE kit
    Figure Legend Snippet: Bland-Altman plots for investigating the level of agreement between RNA extraction kits. Each plot shows the differences between the two kits against the averages of the two kits. The lines represent the mean differences and upper and lower limits of agreement (LOA, mean differences ±1.96SD). a Comparison of RNA yield (ng/μl) of samples extracted with High Pure FFPE RNA Micro Kit and RNeasy® FFPE kit. b Comparison of purity (A260/A280) of samples extracted with High Pure FFPE RNA Micro kit and RNeasy® FFPE kit. c Comparison of RIN-values of samples extracted with High Pure FFPE RNA Micro kit and RNeasy® FFPE kit. d Comparison of RNA yield (ng/μl) of samples extracted with RNeasy® FFPE kit and AllPrep® DNA/RNA FFPE kit. e Comparison of purity (A260/A280) of samples extracted with RNeasy® FFPE kit and AllPrep® DNA/RNA FFPE kit. f Comparison of RIN-values of samples extracted with RNeasy® FFPE kit and AllPrep® DNA/RNA FFPE kit

    Techniques Used: RNA Extraction, Formalin-fixed Paraffin-Embedded

    18) Product Images from "Distinct tumor microenvironments of lytic and blastic bone metastases in prostate cancer patients"

    Article Title: Distinct tumor microenvironments of lytic and blastic bone metastases in prostate cancer patients

    Journal: Journal for Immunotherapy of Cancer

    doi: 10.1186/s40425-019-0753-3

    Gene expression from decalcified FFPE prostate cancer in bone. a 16 FFPE derived RNA samples (6 lytic and 10 blastic) were analyzed on an Agilent Tape Station for concentration and integrity to produce RNA Integrity Scores (RIN). b 3 lytic and 4 blastic samples contained sufficient RNA (25-100 ng) to endure adequate probe coverage of the NanoString Human Immune Oncology 360 gene expression panel. Differential expression revealed a list of significantly upregulated (moving right) and downregulated genes (moving left) in lytic prostate cancer metastases compared to blastic types. c Blastic samples were enriched for JAK-STAT pathway genes while ( d ) Lytic samples were enriched for PI3K-AKT gene expression. e , f Lytic samples based on gene expression demonstrate increased immune cell populations relative to blastic samples. Graphs created using Advanced Analysis module from NanoString nSolver application
    Figure Legend Snippet: Gene expression from decalcified FFPE prostate cancer in bone. a 16 FFPE derived RNA samples (6 lytic and 10 blastic) were analyzed on an Agilent Tape Station for concentration and integrity to produce RNA Integrity Scores (RIN). b 3 lytic and 4 blastic samples contained sufficient RNA (25-100 ng) to endure adequate probe coverage of the NanoString Human Immune Oncology 360 gene expression panel. Differential expression revealed a list of significantly upregulated (moving right) and downregulated genes (moving left) in lytic prostate cancer metastases compared to blastic types. c Blastic samples were enriched for JAK-STAT pathway genes while ( d ) Lytic samples were enriched for PI3K-AKT gene expression. e , f Lytic samples based on gene expression demonstrate increased immune cell populations relative to blastic samples. Graphs created using Advanced Analysis module from NanoString nSolver application

    Techniques Used: Expressing, Formalin-fixed Paraffin-Embedded, Derivative Assay, Concentration Assay

    Related Articles

    Amplification:

    Article Title: Nucleic acid extraction from formalin-fixed paraffin-embedded cancer cell line samples: a trade off between quantity and quality?
    Article Snippet: Investigating the linearity of the multiplex PCR assay: relationship between cDNA concentration and mean Cq value for serial dilutions of a 10 ng/μl RNA sample ran in the multiplex PCR assay. (PDF 28 kb) Comparison of the Nanodrop and Qubit for RNA quantification: Correlation plot between RNA concentrations measured using the Nanodrop absorbance based assay and the Qubit fluorescence based assay, r2 represents the correlation coefficient, (a) Qiagen AllPrep DNA/RNA FFPE kit n = 30, (b) Qiagen RNeasy FFPE kit, n = 30, (c) Arcturus paradise plus FFPE RNA isolation kit, n = 25, (d) Maxwell 16 LEV RNA FFPE Purification kit, n = 30. (PDF 49 kb) Investigating the relationship between elution volume, RNA concentration and yield: Geometric mean RNA yield (orange bars) and geometric mean RNA concentration (black line) across four FFPE blocks when processing 5 μm of tissue using the RNeasy FFPE kit using varied elution volumes, error bars represent the standard error of geomean. (PDF 13 kb) Validation of the in house multiplex PCR assay: Correlation between the Cq values for each housekeeping gene for samples ran in both the single and multiplex PCR assay, r2 represents the correlation coefficient (PDF 24 kb) Assessing intra assay variation of the multiplex PCR assay: Correlation between the Cq values of technical replicates for each housekeeping gene for samples ran in the multiplex PCR assay, r2 represents the correlation coefficient. (PDF 34 kb) Properties of the three primers and probes used in the in house multiplex PCR assay to asses RNA quality. .. Roche LightCycler480 PCR machine conditions: 1 pre incubation cycle at 95 °C for 10 min followed by 45 amplification cycles at 95 °C for 10 s, 60 °C for 30 s, 72 °C for 1 s before cooling to 40 °C for 30 s. (PDF 81 kb)

    Blocking Assay:

    Article Title: Evaluation of commercial DNA and RNA extraction methods for high-throughput sequencing of FFPE samples
    Article Snippet: The QIAamp DNA FFPE Tissue Kit, miRNeasy FFPE Kit and AllPrep DNA/RNA FFPE Kit from QIAGEN have been shown to perform well in comparison with other DNA and RNA protocols in previous studies [ , , ]. .. Equal amount of starting material and a randomized order of the consecutive FFPE block sections were used for all methods of extraction.

    SYBR Green Assay:

    Article Title: Organocatalytic Removal of Formaldehyde Adducts from RNA and DNA Bases
    Article Snippet: RNA recovery from FFPE specimens RNA was extracted from a FFPE Raji cell pellet using either the spin-column-based AllPrep® DNA/RNA FFPE kit (Qiagen), according to the manufacturer’s protocol, or a phenol-chloroform-isoamyl alcohol (PCI) extraction procedure. .. 200 ng RNA was used to synthesize cDNA using the Invitrogen SuperScript® III First-Strand Synthesis System for RT-PCR (Life Technologies). qPCR was performed in 384-well plates using SYBR® Green dye.

    Incubation:

    Article Title: Nucleic acid extraction from formalin-fixed paraffin-embedded cancer cell line samples: a trade off between quantity and quality?
    Article Snippet: Investigating the linearity of the multiplex PCR assay: relationship between cDNA concentration and mean Cq value for serial dilutions of a 10 ng/μl RNA sample ran in the multiplex PCR assay. (PDF 28 kb) Comparison of the Nanodrop and Qubit for RNA quantification: Correlation plot between RNA concentrations measured using the Nanodrop absorbance based assay and the Qubit fluorescence based assay, r2 represents the correlation coefficient, (a) Qiagen AllPrep DNA/RNA FFPE kit n = 30, (b) Qiagen RNeasy FFPE kit, n = 30, (c) Arcturus paradise plus FFPE RNA isolation kit, n = 25, (d) Maxwell 16 LEV RNA FFPE Purification kit, n = 30. (PDF 49 kb) Investigating the relationship between elution volume, RNA concentration and yield: Geometric mean RNA yield (orange bars) and geometric mean RNA concentration (black line) across four FFPE blocks when processing 5 μm of tissue using the RNeasy FFPE kit using varied elution volumes, error bars represent the standard error of geomean. (PDF 13 kb) Validation of the in house multiplex PCR assay: Correlation between the Cq values for each housekeeping gene for samples ran in both the single and multiplex PCR assay, r2 represents the correlation coefficient (PDF 24 kb) Assessing intra assay variation of the multiplex PCR assay: Correlation between the Cq values of technical replicates for each housekeeping gene for samples ran in the multiplex PCR assay, r2 represents the correlation coefficient. (PDF 34 kb) Properties of the three primers and probes used in the in house multiplex PCR assay to asses RNA quality. .. Roche LightCycler480 PCR machine conditions: 1 pre incubation cycle at 95 °C for 10 min followed by 45 amplification cycles at 95 °C for 10 s, 60 °C for 30 s, 72 °C for 1 s before cooling to 40 °C for 30 s. (PDF 81 kb)

    Formalin-fixed Paraffin-Embedded:

    Article Title: Evaluation of commercial DNA and RNA extraction methods for high-throughput sequencing of FFPE samples
    Article Snippet: .. 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: Evaluation of commercial DNA and RNA extraction methods for high-throughput sequencing of FFPE samples
    Article Snippet: .. The QIAamp DNA FFPE Tissue Kit, miRNeasy FFPE Kit and AllPrep DNA/RNA FFPE Kit from QIAGEN have been shown to perform well in comparison with other DNA and RNA protocols in previous studies [ , , ]. .. Equal amount of starting material and a randomized order of the consecutive FFPE block sections were used for all methods of extraction.

    Article Title: Nucleic acid extraction from formalin-fixed paraffin-embedded cancer cell line samples: a trade off between quantity and quality?
    Article Snippet: .. Investigating the linearity of the multiplex PCR assay: relationship between cDNA concentration and mean Cq value for serial dilutions of a 10 ng/μl RNA sample ran in the multiplex PCR assay. (PDF 28 kb) Comparison of the Nanodrop and Qubit for RNA quantification: Correlation plot between RNA concentrations measured using the Nanodrop absorbance based assay and the Qubit fluorescence based assay, r2 represents the correlation coefficient, (a) Qiagen AllPrep DNA/RNA FFPE kit n = 30, (b) Qiagen RNeasy FFPE kit, n = 30, (c) Arcturus paradise plus FFPE RNA isolation kit, n = 25, (d) Maxwell 16 LEV RNA FFPE Purification kit, n = 30. (PDF 49 kb) Investigating the relationship between elution volume, RNA concentration and yield: Geometric mean RNA yield (orange bars) and geometric mean RNA concentration (black line) across four FFPE blocks when processing 5 μm of tissue using the RNeasy FFPE kit using varied elution volumes, error bars represent the standard error of geomean. (PDF 13 kb) Validation of the in house multiplex PCR assay: Correlation between the Cq values for each housekeeping gene for samples ran in both the single and multiplex PCR assay, r2 represents the correlation coefficient (PDF 24 kb) Assessing intra assay variation of the multiplex PCR assay: Correlation between the Cq values of technical replicates for each housekeeping gene for samples ran in the multiplex PCR assay, r2 represents the correlation coefficient. (PDF 34 kb) Properties of the three primers and probes used in the in house multiplex PCR assay to asses RNA quality. .. Roche LightCycler480 PCR machine conditions: 1 pre incubation cycle at 95 °C for 10 min followed by 45 amplification cycles at 95 °C for 10 s, 60 °C for 30 s, 72 °C for 1 s before cooling to 40 °C for 30 s. (PDF 81 kb)

    Article Title: Quantity and quality of nucleic acids extracted from archival formalin fixed paraffin embedded prostate biopsies
    Article Snippet: .. In the second trial of comparisons, the RNeasy® FFPE kit was compared to the RNA fraction of the samples extracted with Qiagen’s AllPrep® DNA/RNA FFPE kit. .. There was no evidence of difference in yields (11.4 ng/μl versus 12.6 ng/μl), A260/A280 ratios (1.47 versus 1.50) or CT -values (27.4 versus 28.0) between these two kits, although higher RIN-values were seen for samples extracted with the RNeasy® FFPE kit (2.2 versus 1.2, p = 0.006)(Table ).

    Article Title: Effective DNA/RNA Co-Extraction for Analysis of MicroRNAs, mRNAs, and Genomic DNA from Formalin-Fixed Paraffin-Embedded Specimens
    Article Snippet: .. Our analyses demonstrated that the two co-extraction methods tested (optimized TRIzol method (TRI), and Qiagen AllPrep DNA/RNA FFPE kit (QDR)) provided higher yields as well as more reliable material for molecular studies than the separate extraction method (Ambion RecoverAll™ kit (AMB)). .. On one side, the QDR has a short pK digestion (15 minutes), and might be automated, but it might not provide the highest amounts of FFPE DNA and RNA.

    Article Title: Effective DNA/RNA Co-Extraction for Analysis of MicroRNAs, mRNAs, and Genomic DNA from Formalin-Fixed Paraffin-Embedded Specimens
    Article Snippet: .. Analysis of 200 ng of genomic DNA recovered from 8, 13, 20, 27 and 31 year-old BBD tissue specimens using the TRIzol-based optimized method (TRI) and the Qiagen AllPrep DNA/RNA FFPE (QDR) kit. .. For each specimen 5× 10 µm sections were used for each method and the total amounts of genomic DNA recovered are displayed below the image of the agarose gel, showing that TRI provides at least twice the amount of DNA than QDR.

    Article Title: Effective DNA/RNA Co-Extraction for Analysis of MicroRNAs, mRNAs, and Genomic DNA from Formalin-Fixed Paraffin-Embedded Specimens
    Article Snippet: .. For co-extraction of FFPE-DNA and -RNA we used the Qiagen AllPrep DNA/RNA FFPE kit following manufacturer's instructions. .. We used the RecoverAll™ Total Nucleic Acid Isolation kit (Ambion, TX, USA) to extract FFPE-DNA or -RNA, and following manufacturers' instructions the pK digested FFPE tissue solution was separated into two halves, with one half subjected to DNase for FFPE-RNA purification, and the other half left at 55°C for 16 hours before RNase treatment and DNA purification.

    Article Title: Multiplex genomic profiling of non-small cell lung cancers from the LETS phase III trial of first-line S-1/carboplatin versus paclitaxel/carboplatin: results of a West Japan Oncology Group study
    Article Snippet: .. DNA and RNA were purified with the use of an Allprep DNA/RNA FFPE Kit (Qiagen, Valencia, CA). .. The isolated RNA was subjected to reverse transcription with the use of a High Capacity cDNA Reverse Transcription Kit (Applied Biosystems, Foster City, CA).

    Article Title: Organocatalytic Removal of Formaldehyde Adducts from RNA and DNA Bases
    Article Snippet: .. RNA recovery from FFPE specimens RNA was extracted from a FFPE Raji cell pellet using either the spin-column-based AllPrep® DNA/RNA FFPE kit (Qiagen), according to the manufacturer’s protocol, or a phenol-chloroform-isoamyl alcohol (PCI) extraction procedure. ..

    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.

    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. ..

    Article Title: Effective DNA/RNA Co-Extraction for Analysis of MicroRNAs, mRNAs, and Genomic DNA from Formalin-Fixed Paraffin-Embedded Specimens
    Article Snippet: .. Using a series of seven different archived specimens, we evaluated the total amounts of genomic DNA and total RNA recovered by our TRIzol-based co-extraction method and compared our results with those from two commercial kits, the Qiagen AllPrep DNA/RNA FFPE kit, for co-extraction, and the Ambion RecoverAll™ Total Nucleic Acid Isolation kit, for separate extraction of FFPE-DNA and -RNA. .. Then, to accurately assess the quality of DNA and RNA co-extracted from a single FFPE specimen, we used qRT-PCR, gene expression profiling and methylation assays to analyze microRNAs, mRNAs, and genomic DNA recovered from matched fresh and FFPE MCF10A cells.

    Expressing:

    Article Title: Multiplex genomic profiling of non-small cell lung cancers from the LETS phase III trial of first-line S-1/carboplatin versus paclitaxel/carboplatin: results of a West Japan Oncology Group study
    Article Snippet: DNA and RNA were purified with the use of an Allprep DNA/RNA FFPE Kit (Qiagen, Valencia, CA). .. The DNA and RNA samples were analyzed in the following order of priority: (1) multiplex analysis of somatic gene mutations (LungCarta Panel; Sequenom, San Diego, CA), (2) quantitative analysis of gene expression (results to be described elsewhere), and (3) characterization of ALK , ROS1 , and RET fusion genes (LungFusion Panel).

    Article Title: Effective DNA/RNA Co-Extraction for Analysis of MicroRNAs, mRNAs, and Genomic DNA from Formalin-Fixed Paraffin-Embedded Specimens
    Article Snippet: Using a series of seven different archived specimens, we evaluated the total amounts of genomic DNA and total RNA recovered by our TRIzol-based co-extraction method and compared our results with those from two commercial kits, the Qiagen AllPrep DNA/RNA FFPE kit, for co-extraction, and the Ambion RecoverAll™ Total Nucleic Acid Isolation kit, for separate extraction of FFPE-DNA and -RNA. .. Then, to accurately assess the quality of DNA and RNA co-extracted from a single FFPE specimen, we used qRT-PCR, gene expression profiling and methylation assays to analyze microRNAs, mRNAs, and genomic DNA recovered from matched fresh and FFPE MCF10A cells.

    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: .. Investigating the linearity of the multiplex PCR assay: relationship between cDNA concentration and mean Cq value for serial dilutions of a 10 ng/μl RNA sample ran in the multiplex PCR assay. (PDF 28 kb) Comparison of the Nanodrop and Qubit for RNA quantification: Correlation plot between RNA concentrations measured using the Nanodrop absorbance based assay and the Qubit fluorescence based assay, r2 represents the correlation coefficient, (a) Qiagen AllPrep DNA/RNA FFPE kit n = 30, (b) Qiagen RNeasy FFPE kit, n = 30, (c) Arcturus paradise plus FFPE RNA isolation kit, n = 25, (d) Maxwell 16 LEV RNA FFPE Purification kit, n = 30. (PDF 49 kb) Investigating the relationship between elution volume, RNA concentration and yield: Geometric mean RNA yield (orange bars) and geometric mean RNA concentration (black line) across four FFPE blocks when processing 5 μm of tissue using the RNeasy FFPE kit using varied elution volumes, error bars represent the standard error of geomean. (PDF 13 kb) Validation of the in house multiplex PCR assay: Correlation between the Cq values for each housekeeping gene for samples ran in both the single and multiplex PCR assay, r2 represents the correlation coefficient (PDF 24 kb) Assessing intra assay variation of the multiplex PCR assay: Correlation between the Cq values of technical replicates for each housekeeping gene for samples ran in the multiplex PCR assay, r2 represents the correlation coefficient. (PDF 34 kb) Properties of the three primers and probes used in the in house multiplex PCR assay to asses RNA quality. .. Roche LightCycler480 PCR machine conditions: 1 pre incubation cycle at 95 °C for 10 min followed by 45 amplification cycles at 95 °C for 10 s, 60 °C for 30 s, 72 °C for 1 s before cooling to 40 °C for 30 s. (PDF 81 kb)

    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 multiplex PCR assay showed good concordance with single-plex PCR assays for each housekeeping gene (Additional file : Figure S4) and little intra-assay variation was seen, demonstrated by the strong correlation (R2 value of 0.985) between technical replicates (Additional file : Figure S5).

    Generated:

    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.

    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: .. Investigating the linearity of the multiplex PCR assay: relationship between cDNA concentration and mean Cq value for serial dilutions of a 10 ng/μl RNA sample ran in the multiplex PCR assay. (PDF 28 kb) Comparison of the Nanodrop and Qubit for RNA quantification: Correlation plot between RNA concentrations measured using the Nanodrop absorbance based assay and the Qubit fluorescence based assay, r2 represents the correlation coefficient, (a) Qiagen AllPrep DNA/RNA FFPE kit n = 30, (b) Qiagen RNeasy FFPE kit, n = 30, (c) Arcturus paradise plus FFPE RNA isolation kit, n = 25, (d) Maxwell 16 LEV RNA FFPE Purification kit, n = 30. (PDF 49 kb) Investigating the relationship between elution volume, RNA concentration and yield: Geometric mean RNA yield (orange bars) and geometric mean RNA concentration (black line) across four FFPE blocks when processing 5 μm of tissue using the RNeasy FFPE kit using varied elution volumes, error bars represent the standard error of geomean. (PDF 13 kb) Validation of the in house multiplex PCR assay: Correlation between the Cq values for each housekeeping gene for samples ran in both the single and multiplex PCR assay, r2 represents the correlation coefficient (PDF 24 kb) Assessing intra assay variation of the multiplex PCR assay: Correlation between the Cq values of technical replicates for each housekeeping gene for samples ran in the multiplex PCR assay, r2 represents the correlation coefficient. (PDF 34 kb) Properties of the three primers and probes used in the in house multiplex PCR assay to asses RNA quality. .. Roche LightCycler480 PCR machine conditions: 1 pre incubation cycle at 95 °C for 10 min followed by 45 amplification cycles at 95 °C for 10 s, 60 °C for 30 s, 72 °C for 1 s before cooling to 40 °C for 30 s. (PDF 81 kb)

    Article Title: Effective DNA/RNA Co-Extraction for Analysis of MicroRNAs, mRNAs, and Genomic DNA from Formalin-Fixed Paraffin-Embedded Specimens
    Article Snippet: For analysis of the FFPE-DNA from 1 month-old archived MCF10 cells, we used bisulfite conversion and PCR reactions to assay hypo- and hyper-methylated CpG islands of FFPE genomic DNA. .. Our analyses demonstrated that the two co-extraction methods tested (optimized TRIzol method (TRI), and Qiagen AllPrep DNA/RNA FFPE kit (QDR)) provided higher yields as well as more reliable material for molecular studies than the separate extraction method (Ambion RecoverAll™ kit (AMB)).

    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.

    RNA HS Assay:

    Article Title: Organocatalytic Removal of Formaldehyde Adducts from RNA and DNA Bases
    Article Snippet: RNA recovery from FFPE specimens RNA was extracted from a FFPE Raji cell pellet using either the spin-column-based AllPrep® DNA/RNA FFPE kit (Qiagen), according to the manufacturer’s protocol, or a phenol-chloroform-isoamyl alcohol (PCI) extraction procedure. .. RNA was quantified using the Qubit® RNA HS Assay Kit (Life Technologies).

    Fluorescence:

    Article Title: Nucleic acid extraction from formalin-fixed paraffin-embedded cancer cell line samples: a trade off between quantity and quality?
    Article Snippet: .. Investigating the linearity of the multiplex PCR assay: relationship between cDNA concentration and mean Cq value for serial dilutions of a 10 ng/μl RNA sample ran in the multiplex PCR assay. (PDF 28 kb) Comparison of the Nanodrop and Qubit for RNA quantification: Correlation plot between RNA concentrations measured using the Nanodrop absorbance based assay and the Qubit fluorescence based assay, r2 represents the correlation coefficient, (a) Qiagen AllPrep DNA/RNA FFPE kit n = 30, (b) Qiagen RNeasy FFPE kit, n = 30, (c) Arcturus paradise plus FFPE RNA isolation kit, n = 25, (d) Maxwell 16 LEV RNA FFPE Purification kit, n = 30. (PDF 49 kb) Investigating the relationship between elution volume, RNA concentration and yield: Geometric mean RNA yield (orange bars) and geometric mean RNA concentration (black line) across four FFPE blocks when processing 5 μm of tissue using the RNeasy FFPE kit using varied elution volumes, error bars represent the standard error of geomean. (PDF 13 kb) Validation of the in house multiplex PCR assay: Correlation between the Cq values for each housekeeping gene for samples ran in both the single and multiplex PCR assay, r2 represents the correlation coefficient (PDF 24 kb) Assessing intra assay variation of the multiplex PCR assay: Correlation between the Cq values of technical replicates for each housekeeping gene for samples ran in the multiplex PCR assay, r2 represents the correlation coefficient. (PDF 34 kb) Properties of the three primers and probes used in the in house multiplex PCR assay to asses RNA quality. .. Roche LightCycler480 PCR machine conditions: 1 pre incubation cycle at 95 °C for 10 min followed by 45 amplification cycles at 95 °C for 10 s, 60 °C for 30 s, 72 °C for 1 s before cooling to 40 °C for 30 s. (PDF 81 kb)

    Methylation:

    Article Title: Effective DNA/RNA Co-Extraction for Analysis of MicroRNAs, mRNAs, and Genomic DNA from Formalin-Fixed Paraffin-Embedded Specimens
    Article Snippet: This heat-treatment step, which is not described in the procedure of AMB, might account for the discrepancies, between matched fresh and FFPE-DNA, observed in our methylation analysis data. .. Our analyses demonstrated that the two co-extraction methods tested (optimized TRIzol method (TRI), and Qiagen AllPrep DNA/RNA FFPE kit (QDR)) provided higher yields as well as more reliable material for molecular studies than the separate extraction method (Ambion RecoverAll™ kit (AMB)).

    Article Title: Effective DNA/RNA Co-Extraction for Analysis of MicroRNAs, mRNAs, and Genomic DNA from Formalin-Fixed Paraffin-Embedded Specimens
    Article Snippet: Electrophoretic and methylation analyses of genomic DNA recovered from older formalin-fixed paraffin-embedded benign breast disease tissue specimens. .. Analysis of 200 ng of genomic DNA recovered from 8, 13, 20, 27 and 31 year-old BBD tissue specimens using the TRIzol-based optimized method (TRI) and the Qiagen AllPrep DNA/RNA FFPE (QDR) kit.

    Article Title: Effective DNA/RNA Co-Extraction for Analysis of MicroRNAs, mRNAs, and Genomic DNA from Formalin-Fixed Paraffin-Embedded Specimens
    Article Snippet: Using a series of seven different archived specimens, we evaluated the total amounts of genomic DNA and total RNA recovered by our TRIzol-based co-extraction method and compared our results with those from two commercial kits, the Qiagen AllPrep DNA/RNA FFPE kit, for co-extraction, and the Ambion RecoverAll™ Total Nucleic Acid Isolation kit, for separate extraction of FFPE-DNA and -RNA. .. Then, to accurately assess the quality of DNA and RNA co-extracted from a single FFPE specimen, we used qRT-PCR, gene expression profiling and methylation assays to analyze microRNAs, mRNAs, and genomic DNA recovered from matched fresh and FFPE MCF10A cells.

    Isolation:

    Article Title: Nucleic acid extraction from formalin-fixed paraffin-embedded cancer cell line samples: a trade off between quantity and quality?
    Article Snippet: .. Investigating the linearity of the multiplex PCR assay: relationship between cDNA concentration and mean Cq value for serial dilutions of a 10 ng/μl RNA sample ran in the multiplex PCR assay. (PDF 28 kb) Comparison of the Nanodrop and Qubit for RNA quantification: Correlation plot between RNA concentrations measured using the Nanodrop absorbance based assay and the Qubit fluorescence based assay, r2 represents the correlation coefficient, (a) Qiagen AllPrep DNA/RNA FFPE kit n = 30, (b) Qiagen RNeasy FFPE kit, n = 30, (c) Arcturus paradise plus FFPE RNA isolation kit, n = 25, (d) Maxwell 16 LEV RNA FFPE Purification kit, n = 30. (PDF 49 kb) Investigating the relationship between elution volume, RNA concentration and yield: Geometric mean RNA yield (orange bars) and geometric mean RNA concentration (black line) across four FFPE blocks when processing 5 μm of tissue using the RNeasy FFPE kit using varied elution volumes, error bars represent the standard error of geomean. (PDF 13 kb) Validation of the in house multiplex PCR assay: Correlation between the Cq values for each housekeeping gene for samples ran in both the single and multiplex PCR assay, r2 represents the correlation coefficient (PDF 24 kb) Assessing intra assay variation of the multiplex PCR assay: Correlation between the Cq values of technical replicates for each housekeeping gene for samples ran in the multiplex PCR assay, r2 represents the correlation coefficient. (PDF 34 kb) Properties of the three primers and probes used in the in house multiplex PCR assay to asses RNA quality. .. Roche LightCycler480 PCR machine conditions: 1 pre incubation cycle at 95 °C for 10 min followed by 45 amplification cycles at 95 °C for 10 s, 60 °C for 30 s, 72 °C for 1 s before cooling to 40 °C for 30 s. (PDF 81 kb)

    Article Title: Effective DNA/RNA Co-Extraction for Analysis of MicroRNAs, mRNAs, and Genomic DNA from Formalin-Fixed Paraffin-Embedded Specimens
    Article Snippet: For co-extraction of FFPE-DNA and -RNA we used the Qiagen AllPrep DNA/RNA FFPE kit following manufacturer's instructions. .. We used the RecoverAll™ Total Nucleic Acid Isolation kit (Ambion, TX, USA) to extract FFPE-DNA or -RNA, and following manufacturers' instructions the pK digested FFPE tissue solution was separated into two halves, with one half subjected to DNase for FFPE-RNA purification, and the other half left at 55°C for 16 hours before RNase treatment and DNA purification.

    Article Title: Multiplex genomic profiling of non-small cell lung cancers from the LETS phase III trial of first-line S-1/carboplatin versus paclitaxel/carboplatin: results of a West Japan Oncology Group study
    Article Snippet: DNA and RNA were purified with the use of an Allprep DNA/RNA FFPE Kit (Qiagen, Valencia, CA). .. The isolated RNA was subjected to reverse transcription with the use of a High Capacity cDNA Reverse Transcription Kit (Applied Biosystems, Foster City, CA).

    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.

    Article Title: Effective DNA/RNA Co-Extraction for Analysis of MicroRNAs, mRNAs, and Genomic DNA from Formalin-Fixed Paraffin-Embedded Specimens
    Article Snippet: .. Using a series of seven different archived specimens, we evaluated the total amounts of genomic DNA and total RNA recovered by our TRIzol-based co-extraction method and compared our results with those from two commercial kits, the Qiagen AllPrep DNA/RNA FFPE kit, for co-extraction, and the Ambion RecoverAll™ Total Nucleic Acid Isolation kit, for separate extraction of FFPE-DNA and -RNA. .. Then, to accurately assess the quality of DNA and RNA co-extracted from a single FFPE specimen, we used qRT-PCR, gene expression profiling and methylation assays to analyze microRNAs, mRNAs, and genomic DNA recovered from matched fresh and FFPE MCF10A cells.

    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: Quantity and quality of nucleic acids extracted from archival formalin fixed paraffin embedded prostate biopsies
    Article Snippet: Paragraph title: RNA extraction comparative trials ... In the second trial of comparisons, the RNeasy® FFPE kit was compared to the RNA fraction of the samples extracted with Qiagen’s AllPrep® DNA/RNA FFPE kit.

    Purification:

    Article Title: Nucleic acid extraction from formalin-fixed paraffin-embedded cancer cell line samples: a trade off between quantity and quality?
    Article Snippet: .. Investigating the linearity of the multiplex PCR assay: relationship between cDNA concentration and mean Cq value for serial dilutions of a 10 ng/μl RNA sample ran in the multiplex PCR assay. (PDF 28 kb) Comparison of the Nanodrop and Qubit for RNA quantification: Correlation plot between RNA concentrations measured using the Nanodrop absorbance based assay and the Qubit fluorescence based assay, r2 represents the correlation coefficient, (a) Qiagen AllPrep DNA/RNA FFPE kit n = 30, (b) Qiagen RNeasy FFPE kit, n = 30, (c) Arcturus paradise plus FFPE RNA isolation kit, n = 25, (d) Maxwell 16 LEV RNA FFPE Purification kit, n = 30. (PDF 49 kb) Investigating the relationship between elution volume, RNA concentration and yield: Geometric mean RNA yield (orange bars) and geometric mean RNA concentration (black line) across four FFPE blocks when processing 5 μm of tissue using the RNeasy FFPE kit using varied elution volumes, error bars represent the standard error of geomean. (PDF 13 kb) Validation of the in house multiplex PCR assay: Correlation between the Cq values for each housekeeping gene for samples ran in both the single and multiplex PCR assay, r2 represents the correlation coefficient (PDF 24 kb) Assessing intra assay variation of the multiplex PCR assay: Correlation between the Cq values of technical replicates for each housekeeping gene for samples ran in the multiplex PCR assay, r2 represents the correlation coefficient. (PDF 34 kb) Properties of the three primers and probes used in the in house multiplex PCR assay to asses RNA quality. .. Roche LightCycler480 PCR machine conditions: 1 pre incubation cycle at 95 °C for 10 min followed by 45 amplification cycles at 95 °C for 10 s, 60 °C for 30 s, 72 °C for 1 s before cooling to 40 °C for 30 s. (PDF 81 kb)

    Article Title: Effective DNA/RNA Co-Extraction for Analysis of MicroRNAs, mRNAs, and Genomic DNA from Formalin-Fixed Paraffin-Embedded Specimens
    Article Snippet: TRI, which incorporates the use of the QD kit for FFPE-DNA purification, and QDR include a heat-treatment step at 90°c to increase FFPE-DNA quality through removal of FFPE-DNA/protein cross-links – . .. Our analyses demonstrated that the two co-extraction methods tested (optimized TRIzol method (TRI), and Qiagen AllPrep DNA/RNA FFPE kit (QDR)) provided higher yields as well as more reliable material for molecular studies than the separate extraction method (Ambion RecoverAll™ kit (AMB)).

    Article Title: Effective DNA/RNA Co-Extraction for Analysis of MicroRNAs, mRNAs, and Genomic DNA from Formalin-Fixed Paraffin-Embedded Specimens
    Article Snippet: For co-extraction of FFPE-DNA and -RNA we used the Qiagen AllPrep DNA/RNA FFPE kit following manufacturer's instructions. .. We used the RecoverAll™ Total Nucleic Acid Isolation kit (Ambion, TX, USA) to extract FFPE-DNA or -RNA, and following manufacturers' instructions the pK digested FFPE tissue solution was separated into two halves, with one half subjected to DNase for FFPE-RNA purification, and the other half left at 55°C for 16 hours before RNase treatment and DNA purification.

    Article Title: Multiplex genomic profiling of non-small cell lung cancers from the LETS phase III trial of first-line S-1/carboplatin versus paclitaxel/carboplatin: results of a West Japan Oncology Group study
    Article Snippet: .. DNA and RNA were purified with the use of an Allprep DNA/RNA FFPE Kit (Qiagen, Valencia, CA). .. The isolated RNA was subjected to reverse transcription with the use of a High Capacity cDNA Reverse Transcription Kit (Applied Biosystems, Foster City, CA).

    Reverse Transcription Polymerase Chain Reaction:

    Article Title: Organocatalytic Removal of Formaldehyde Adducts from RNA and DNA Bases
    Article Snippet: RNA recovery from FFPE specimens RNA was extracted from a FFPE Raji cell pellet using either the spin-column-based AllPrep® DNA/RNA FFPE kit (Qiagen), according to the manufacturer’s protocol, or a phenol-chloroform-isoamyl alcohol (PCI) extraction procedure. .. 200 ng RNA was used to synthesize cDNA using the Invitrogen SuperScript® III First-Strand Synthesis System for RT-PCR (Life Technologies). qPCR was performed in 384-well plates using SYBR® Green dye.

    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.

    Quantitative RT-PCR:

    Article Title: Effective DNA/RNA Co-Extraction for Analysis of MicroRNAs, mRNAs, and Genomic DNA from Formalin-Fixed Paraffin-Embedded Specimens
    Article Snippet: Using a series of seven different archived specimens, we evaluated the total amounts of genomic DNA and total RNA recovered by our TRIzol-based co-extraction method and compared our results with those from two commercial kits, the Qiagen AllPrep DNA/RNA FFPE kit, for co-extraction, and the Ambion RecoverAll™ Total Nucleic Acid Isolation kit, for separate extraction of FFPE-DNA and -RNA. .. Then, to accurately assess the quality of DNA and RNA co-extracted from a single FFPE specimen, we used qRT-PCR, gene expression profiling and methylation assays to analyze microRNAs, mRNAs, and genomic DNA recovered from matched fresh and FFPE MCF10A cells.

    Real-time Polymerase Chain Reaction:

    Article Title: Organocatalytic Removal of Formaldehyde Adducts from RNA and DNA Bases
    Article Snippet: RNA recovery from FFPE specimens RNA was extracted from a FFPE Raji cell pellet using either the spin-column-based AllPrep® DNA/RNA FFPE kit (Qiagen), according to the manufacturer’s protocol, or a phenol-chloroform-isoamyl alcohol (PCI) extraction procedure. .. 200 ng RNA was used to synthesize cDNA using the Invitrogen SuperScript® III First-Strand Synthesis System for RT-PCR (Life Technologies). qPCR was performed in 384-well plates using SYBR® Green dye.

    Multiplex Assay:

    Article Title: Nucleic acid extraction from formalin-fixed paraffin-embedded cancer cell line samples: a trade off between quantity and quality?
    Article Snippet: .. Investigating the linearity of the multiplex PCR assay: relationship between cDNA concentration and mean Cq value for serial dilutions of a 10 ng/μl RNA sample ran in the multiplex PCR assay. (PDF 28 kb) Comparison of the Nanodrop and Qubit for RNA quantification: Correlation plot between RNA concentrations measured using the Nanodrop absorbance based assay and the Qubit fluorescence based assay, r2 represents the correlation coefficient, (a) Qiagen AllPrep DNA/RNA FFPE kit n = 30, (b) Qiagen RNeasy FFPE kit, n = 30, (c) Arcturus paradise plus FFPE RNA isolation kit, n = 25, (d) Maxwell 16 LEV RNA FFPE Purification kit, n = 30. (PDF 49 kb) Investigating the relationship between elution volume, RNA concentration and yield: Geometric mean RNA yield (orange bars) and geometric mean RNA concentration (black line) across four FFPE blocks when processing 5 μm of tissue using the RNeasy FFPE kit using varied elution volumes, error bars represent the standard error of geomean. (PDF 13 kb) Validation of the in house multiplex PCR assay: Correlation between the Cq values for each housekeeping gene for samples ran in both the single and multiplex PCR assay, r2 represents the correlation coefficient (PDF 24 kb) Assessing intra assay variation of the multiplex PCR assay: Correlation between the Cq values of technical replicates for each housekeeping gene for samples ran in the multiplex PCR assay, r2 represents the correlation coefficient. (PDF 34 kb) Properties of the three primers and probes used in the in house multiplex PCR assay to asses RNA quality. .. Roche LightCycler480 PCR machine conditions: 1 pre incubation cycle at 95 °C for 10 min followed by 45 amplification cycles at 95 °C for 10 s, 60 °C for 30 s, 72 °C for 1 s before cooling to 40 °C for 30 s. (PDF 81 kb)

    Article Title: Multiplex genomic profiling of non-small cell lung cancers from the LETS phase III trial of first-line S-1/carboplatin versus paclitaxel/carboplatin: results of a West Japan Oncology Group study
    Article Snippet: DNA and RNA were purified with the use of an Allprep DNA/RNA FFPE Kit (Qiagen, Valencia, CA). .. The DNA and RNA samples were analyzed in the following order of priority: (1) multiplex analysis of somatic gene mutations (LungCarta Panel; Sequenom, San Diego, CA), (2) quantitative analysis of gene expression (results to be described elsewhere), and (3) characterization of ALK , ROS1 , and RET fusion genes (LungFusion Panel).

    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.

    Agarose Gel Electrophoresis:

    Article Title: Effective DNA/RNA Co-Extraction for Analysis of MicroRNAs, mRNAs, and Genomic DNA from Formalin-Fixed Paraffin-Embedded Specimens
    Article Snippet: Analysis of 200 ng of genomic DNA recovered from 8, 13, 20, 27 and 31 year-old BBD tissue specimens using the TRIzol-based optimized method (TRI) and the Qiagen AllPrep DNA/RNA FFPE (QDR) kit. .. For each specimen 5× 10 µm sections were used for each method and the total amounts of genomic DNA recovered are displayed below the image of the agarose gel, showing that TRI provides at least twice the amount of DNA than QDR.

    DNA Methylation Assay:

    Article Title: Effective DNA/RNA Co-Extraction for Analysis of MicroRNAs, mRNAs, and Genomic DNA from Formalin-Fixed Paraffin-Embedded Specimens
    Article Snippet: It is important to note that when using older FFPE specimens, which yield lower quality genomic DNA, methylation analyses should be performed on CpG islands spanning less than 300 bp for consistent results ( .) .. Our analyses demonstrated that the two co-extraction methods tested (optimized TRIzol method (TRI), and Qiagen AllPrep DNA/RNA FFPE kit (QDR)) provided higher yields as well as more reliable material for molecular studies than the separate extraction method (Ambion RecoverAll™ kit (AMB)).

    Produced:

    Article Title: Quantity and quality of nucleic acids extracted from archival formalin fixed paraffin embedded prostate biopsies
    Article Snippet: This observation indicates that the High Pure kit consistently produced lower yields. .. In the second trial of comparisons, the RNeasy® FFPE kit was compared to the RNA fraction of the samples extracted with Qiagen’s AllPrep® DNA/RNA FFPE kit.

    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: .. Investigating the linearity of the multiplex PCR assay: relationship between cDNA concentration and mean Cq value for serial dilutions of a 10 ng/μl RNA sample ran in the multiplex PCR assay. (PDF 28 kb) Comparison of the Nanodrop and Qubit for RNA quantification: Correlation plot between RNA concentrations measured using the Nanodrop absorbance based assay and the Qubit fluorescence based assay, r2 represents the correlation coefficient, (a) Qiagen AllPrep DNA/RNA FFPE kit n = 30, (b) Qiagen RNeasy FFPE kit, n = 30, (c) Arcturus paradise plus FFPE RNA isolation kit, n = 25, (d) Maxwell 16 LEV RNA FFPE Purification kit, n = 30. (PDF 49 kb) Investigating the relationship between elution volume, RNA concentration and yield: Geometric mean RNA yield (orange bars) and geometric mean RNA concentration (black line) across four FFPE blocks when processing 5 μm of tissue using the RNeasy FFPE kit using varied elution volumes, error bars represent the standard error of geomean. (PDF 13 kb) Validation of the in house multiplex PCR assay: Correlation between the Cq values for each housekeeping gene for samples ran in both the single and multiplex PCR assay, r2 represents the correlation coefficient (PDF 24 kb) Assessing intra assay variation of the multiplex PCR assay: Correlation between the Cq values of technical replicates for each housekeeping gene for samples ran in the multiplex PCR assay, r2 represents the correlation coefficient. (PDF 34 kb) Properties of the three primers and probes used in the in house multiplex PCR assay to asses RNA quality. .. Roche LightCycler480 PCR machine conditions: 1 pre incubation cycle at 95 °C for 10 min followed by 45 amplification cycles at 95 °C for 10 s, 60 °C for 30 s, 72 °C for 1 s before cooling to 40 °C for 30 s. (PDF 81 kb)

    Article Title: Nucleic acid extraction from formalin-fixed paraffin-embedded cancer cell line samples: a trade off between quantity and quality?
    Article Snippet: RNA quality assessment: Agilent vs RT-PCR 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: Effective DNA/RNA Co-Extraction for Analysis of MicroRNAs, mRNAs, and Genomic DNA from Formalin-Fixed Paraffin-Embedded Specimens
    Article Snippet: Our analyses demonstrated that the two co-extraction methods tested (optimized TRIzol method (TRI), and Qiagen AllPrep DNA/RNA FFPE kit (QDR)) provided higher yields as well as more reliable material for molecular studies than the separate extraction method (Ambion RecoverAll™ kit (AMB)). .. For large-scale studies, automation might be important, and thus the method described by Hennig et al. [2010], in which nucleic acids released by proteinase K digestion are magnetically purified, split, and subjected to RNAse for DNA purification and DNAse for RNA purification, might be more appropriate .

    Article Title: Effective DNA/RNA Co-Extraction for Analysis of MicroRNAs, mRNAs, and Genomic DNA from Formalin-Fixed Paraffin-Embedded Specimens
    Article Snippet: For co-extraction of FFPE-DNA and -RNA we used the Qiagen AllPrep DNA/RNA FFPE kit following manufacturer's instructions. .. We used the RecoverAll™ Total Nucleic Acid Isolation kit (Ambion, TX, USA) to extract FFPE-DNA or -RNA, and following manufacturers' instructions the pK digested FFPE tissue solution was separated into two halves, with one half subjected to DNase for FFPE-RNA purification, and the other half left at 55°C for 16 hours before RNase treatment and DNA purification.

    Staining:

    Article Title: Multiplex genomic profiling of non-small cell lung cancers from the LETS phase III trial of first-line S-1/carboplatin versus paclitaxel/carboplatin: results of a West Japan Oncology Group study
    Article Snippet: Sample processing The collected FFPE specimens underwent histological review, and only those containing sufficient tumor cells as revealed by hematoxylin-eosin staining were subjected to nucleic acid extraction. .. DNA and RNA were purified with the use of an Allprep DNA/RNA FFPE Kit (Qiagen, Valencia, CA).

    Similar Products

  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 99
    Qiagen allprep dna rna ffpe kit
    Yield and amplifiability of extracted <t>DNA</t> and <t>RNA.</t> (A) Average total amount of DNA. (B) Average total amount of RNA. (C) Amplifiable DNA quantified with the <t>FFPE</t> QC kit from Illumina. (D) Amplifiable RNA quantified with the PreSeq QC assay from ArcherDx. The average total amount and average delta Ct values for the different samples and extraction methods are shown. The standard deviation is shown as vertical bars. Methods with significant differences in yield are marked as connected with horizontal bars (p
    Allprep Dna Rna Ffpe Kit, supplied by Qiagen, used in various techniques. Bioz Stars score: 99/100, based on 98 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/allprep dna rna ffpe kit/product/Qiagen
    Average 99 stars, based on 98 article reviews
    Price from $9.99 to $1999.99
    allprep dna rna ffpe kit - by Bioz Stars, 2020-04
    99/100 stars
      Buy from Supplier

    Image Search Results


    Yield and amplifiability of extracted DNA and RNA. (A) Average total amount of DNA. (B) Average total amount of RNA. (C) Amplifiable DNA quantified with the FFPE QC kit from Illumina. (D) Amplifiable RNA quantified with the PreSeq QC assay from ArcherDx. The average total amount and average delta Ct values for the different samples and extraction methods are shown. The standard deviation is shown as vertical bars. Methods with significant differences in yield are marked as connected with horizontal bars (p

    Journal: PLoS ONE

    Article Title: Evaluation of commercial DNA and RNA extraction methods for high-throughput sequencing of FFPE samples

    doi: 10.1371/journal.pone.0197456

    Figure Lengend Snippet: Yield and amplifiability of extracted DNA and RNA. (A) Average total amount of DNA. (B) Average total amount of RNA. (C) Amplifiable DNA quantified with the FFPE QC kit from Illumina. (D) Amplifiable RNA quantified with the PreSeq QC assay from ArcherDx. The average total amount and average delta Ct values for the different samples and extraction methods are shown. The standard deviation is shown as vertical bars. Methods with significant differences in yield are marked as connected with horizontal bars (p

    Article Snippet: The QIAamp DNA FFPE Tissue Kit, miRNeasy FFPE Kit and AllPrep DNA/RNA FFPE Kit from QIAGEN have been shown to perform well in comparison with other DNA and RNA protocols in previous studies [ , , ].

    Techniques: Formalin-fixed Paraffin-Embedded, Standard Deviation

    Enhancement in recovery of RNAs from formalin-fixed, paraffin-embedded cell specimens using catalyst 3 (20 mM) as compared with different incubation and isolation conditions. Amplifiable RNA yield is plotted for eight amplicons, and quantity is determined with a standard curve. Lane 1 employs incubation conditions from a commercial kit (Qiagen AllPrep ® DNA/RNA FFPE kit), which uses an 80 °C, 0.25 h incubation step without catalyst (“no cat”) and a spin column for isolation, with the addition of catalyst to these conditions shown in lane 2 (“cat. 3”). Optimized incubation conditions (55 °C, 18 h) followed by a spin column RNA isolation are shown in lanes 3–4. A common literature procedure is shown in lane 5 (“PCI”) 28 . Addition of the catalyst to the optimized incubation conditions results in a ~2 fold increase in detectable RNA, and more substantial increases relative to the catalyst-free commercial kit protocol (see enhancements in red) or the literature protocol. The means of three independent experiments are shown, error bars indicating the standard deviation of variation in the qRT-PCR yield. SC: spin column isolation. PCI: Masuda protocol of phenol-chloroform-isoamyl alcohol extraction followed by heating in buffer. 28 A.U.: arbitrary units. Significance for pairwise comparisons shown was tested using a 1-tailed paired samples t-test. *: P

    Journal: Nature chemistry

    Article Title: Organocatalytic Removal of Formaldehyde Adducts from RNA and DNA Bases

    doi: 10.1038/nchem.2307

    Figure Lengend Snippet: Enhancement in recovery of RNAs from formalin-fixed, paraffin-embedded cell specimens using catalyst 3 (20 mM) as compared with different incubation and isolation conditions. Amplifiable RNA yield is plotted for eight amplicons, and quantity is determined with a standard curve. Lane 1 employs incubation conditions from a commercial kit (Qiagen AllPrep ® DNA/RNA FFPE kit), which uses an 80 °C, 0.25 h incubation step without catalyst (“no cat”) and a spin column for isolation, with the addition of catalyst to these conditions shown in lane 2 (“cat. 3”). Optimized incubation conditions (55 °C, 18 h) followed by a spin column RNA isolation are shown in lanes 3–4. A common literature procedure is shown in lane 5 (“PCI”) 28 . Addition of the catalyst to the optimized incubation conditions results in a ~2 fold increase in detectable RNA, and more substantial increases relative to the catalyst-free commercial kit protocol (see enhancements in red) or the literature protocol. The means of three independent experiments are shown, error bars indicating the standard deviation of variation in the qRT-PCR yield. SC: spin column isolation. PCI: Masuda protocol of phenol-chloroform-isoamyl alcohol extraction followed by heating in buffer. 28 A.U.: arbitrary units. Significance for pairwise comparisons shown was tested using a 1-tailed paired samples t-test. *: P

    Article Snippet: RNA recovery from FFPE specimens RNA was extracted from a FFPE Raji cell pellet using either the spin-column-based AllPrep® DNA/RNA FFPE kit (Qiagen), according to the manufacturer’s protocol, or a phenol-chloroform-isoamyl alcohol (PCI) extraction procedure.

    Techniques: Formalin-fixed Paraffin-Embedded, Incubation, Isolation, Standard Deviation, Quantitative RT-PCR

    Bland-Altman plots for investigation of level of agreements between DNA extraction kits. Each plot shows the differences between the two kits against the averages of the two kits. The lines represent the mean differences and upper and lower limits of agreement (LOA, mean differences ±1.96SD). a Comparison of DNA yield (ng/μl) of samples extracted with High Pure FFPET DNA Isolation kit and QIAamp® DNA FFPE Tissue kit. b Comparison of purity (A260/A280) of DNA samples extracted with High Pure FFPET DNA Isolation kit and QIAamp® DNA FFPE Tissue kit. c Comparison of DNA yield (ng/μl) of samples extracted with QIAamp® DNA FFPE Tissue kit and AllPrep® DNA/RNA FFPE kit. d Comparison of purity (A260/A280) of samples extracted with QIAamp® DNA FFPE Tissue kit and AllPrep® DNA/RNA FFPE kit

    Journal: BMC Medical Research Methodology

    Article Title: Quantity and quality of nucleic acids extracted from archival formalin fixed paraffin embedded prostate biopsies

    doi: 10.1186/s12874-018-0628-1

    Figure Lengend Snippet: Bland-Altman plots for investigation of level of agreements between DNA extraction kits. Each plot shows the differences between the two kits against the averages of the two kits. The lines represent the mean differences and upper and lower limits of agreement (LOA, mean differences ±1.96SD). a Comparison of DNA yield (ng/μl) of samples extracted with High Pure FFPET DNA Isolation kit and QIAamp® DNA FFPE Tissue kit. b Comparison of purity (A260/A280) of DNA samples extracted with High Pure FFPET DNA Isolation kit and QIAamp® DNA FFPE Tissue kit. c Comparison of DNA yield (ng/μl) of samples extracted with QIAamp® DNA FFPE Tissue kit and AllPrep® DNA/RNA FFPE kit. d Comparison of purity (A260/A280) of samples extracted with QIAamp® DNA FFPE Tissue kit and AllPrep® DNA/RNA FFPE kit

    Article Snippet: In the second trial of comparisons, the RNeasy® FFPE kit was compared to the RNA fraction of the samples extracted with Qiagen’s AllPrep® DNA/RNA FFPE kit.

    Techniques: DNA Extraction, Formalin-fixed Paraffin-Embedded

    Bland-Altman plots for investigating the level of agreement between RNA extraction kits. Each plot shows the differences between the two kits against the averages of the two kits. The lines represent the mean differences and upper and lower limits of agreement (LOA, mean differences ±1.96SD). a Comparison of RNA yield (ng/μl) of samples extracted with High Pure FFPE RNA Micro Kit and RNeasy® FFPE kit. b Comparison of purity (A260/A280) of samples extracted with High Pure FFPE RNA Micro kit and RNeasy® FFPE kit. c Comparison of RIN-values of samples extracted with High Pure FFPE RNA Micro kit and RNeasy® FFPE kit. d Comparison of RNA yield (ng/μl) of samples extracted with RNeasy® FFPE kit and AllPrep® DNA/RNA FFPE kit. e Comparison of purity (A260/A280) of samples extracted with RNeasy® FFPE kit and AllPrep® DNA/RNA FFPE kit. f Comparison of RIN-values of samples extracted with RNeasy® FFPE kit and AllPrep® DNA/RNA FFPE kit

    Journal: BMC Medical Research Methodology

    Article Title: Quantity and quality of nucleic acids extracted from archival formalin fixed paraffin embedded prostate biopsies

    doi: 10.1186/s12874-018-0628-1

    Figure Lengend Snippet: Bland-Altman plots for investigating the level of agreement between RNA extraction kits. Each plot shows the differences between the two kits against the averages of the two kits. The lines represent the mean differences and upper and lower limits of agreement (LOA, mean differences ±1.96SD). a Comparison of RNA yield (ng/μl) of samples extracted with High Pure FFPE RNA Micro Kit and RNeasy® FFPE kit. b Comparison of purity (A260/A280) of samples extracted with High Pure FFPE RNA Micro kit and RNeasy® FFPE kit. c Comparison of RIN-values of samples extracted with High Pure FFPE RNA Micro kit and RNeasy® FFPE kit. d Comparison of RNA yield (ng/μl) of samples extracted with RNeasy® FFPE kit and AllPrep® DNA/RNA FFPE kit. e Comparison of purity (A260/A280) of samples extracted with RNeasy® FFPE kit and AllPrep® DNA/RNA FFPE kit. f Comparison of RIN-values of samples extracted with RNeasy® FFPE kit and AllPrep® DNA/RNA FFPE kit

    Article Snippet: In the second trial of comparisons, the RNeasy® FFPE kit was compared to the RNA fraction of the samples extracted with Qiagen’s AllPrep® DNA/RNA FFPE kit.

    Techniques: RNA Extraction, Formalin-fixed Paraffin-Embedded