truxtrac ffpe rna kit  (Covaris)


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    Name:
    truXTRAC FFPE total NA Kit
    Description:
    Optimized to work with standard FFPE inputs 25 μm FFPE sections Kit contains reagents and consumables required for extraction and purification of DNA and RNA from 25 FFPE tissue samples
    Catalog Number:
    520220
    Price:
    None
    Applications:
    Total Nucleic Acid Extraction from FFPE
    Category:
    Reagent
    Quantity:
    25 0
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    Structured Review

    Covaris truxtrac ffpe rna kit
    truXTRAC FFPE total NA Kit
    Optimized to work with standard FFPE inputs 25 μm FFPE sections Kit contains reagents and consumables required for extraction and purification of DNA and RNA from 25 FFPE tissue samples
    https://www.bioz.com/result/truxtrac ffpe rna kit/product/Covaris
    Average 96 stars, based on 17 article reviews
    Price from $9.99 to $1999.99
    truxtrac ffpe rna kit - by Bioz Stars, 2020-08
    96/100 stars

    Images

    1) Product Images from "An optimised protocol for isolation of RNA from small sections of laser-capture microdissected FFPE tissue amenable for next-generation sequencing"

    Article Title: An optimised protocol for isolation of RNA from small sections of laser-capture microdissected FFPE tissue amenable for next-generation sequencing

    Journal: BMC Molecular Biology

    doi: 10.1186/s12867-017-0099-7

    Comparison of workflow of the ‘old’(classical) and ‘new’ protocol for RNA isolation from deparaffinised, stained and laser-capture microdissected FFPE tissue. a Workflow of the ‘old’ RNA isolation protocol, starting with proteinase K digestion of the sample. b Workflow of the ‘new’ isolation protocol, starting with a focused ultrasonication step to disrupt the tissue prior to proteinase K digestion. Values in brackets indicate the approximate timing for each step
    Figure Legend Snippet: Comparison of workflow of the ‘old’(classical) and ‘new’ protocol for RNA isolation from deparaffinised, stained and laser-capture microdissected FFPE tissue. a Workflow of the ‘old’ RNA isolation protocol, starting with proteinase K digestion of the sample. b Workflow of the ‘new’ isolation protocol, starting with a focused ultrasonication step to disrupt the tissue prior to proteinase K digestion. Values in brackets indicate the approximate timing for each step

    Techniques Used: Isolation, Staining, Formalin-fixed Paraffin-Embedded

    Direct comparison of RNA extracted from LCM samples from deparaffinised, stained FFPE tissue with the old vs the new isolation protocol. a Scatter plot with mean ± SEM of total RNA yield from the 13 clinical cases analysed obtained using the old vs the new isolation protocol. Old normal shows data obtained from using the old protocol on LCM samples of normal stroma, while old CAS shows data for the old protocol on CAS. New normal and new CAS are the equivalent for the new extraction procedure, respectively. p-values were calculated using the Student’s t test. b Bar graph displaying mean ± SEM of the increase of total RNA yield that could be achieved using a 2nd elution step with the new isolation protocol for normal and CAS samples, respectively, compared to a single elution step only. n = 8 for both types of tissue, respectively. c Scatter plot with mean ± SEM of the RIN values obtained from all 13 clinical cases isolated using the old or the new isolation procedure, respectively. RIN values could not be calculated for 3 samples of old normal and 2 samples of old CAS, and are thus omitted from this graph
    Figure Legend Snippet: Direct comparison of RNA extracted from LCM samples from deparaffinised, stained FFPE tissue with the old vs the new isolation protocol. a Scatter plot with mean ± SEM of total RNA yield from the 13 clinical cases analysed obtained using the old vs the new isolation protocol. Old normal shows data obtained from using the old protocol on LCM samples of normal stroma, while old CAS shows data for the old protocol on CAS. New normal and new CAS are the equivalent for the new extraction procedure, respectively. p-values were calculated using the Student’s t test. b Bar graph displaying mean ± SEM of the increase of total RNA yield that could be achieved using a 2nd elution step with the new isolation protocol for normal and CAS samples, respectively, compared to a single elution step only. n = 8 for both types of tissue, respectively. c Scatter plot with mean ± SEM of the RIN values obtained from all 13 clinical cases isolated using the old or the new isolation procedure, respectively. RIN values could not be calculated for 3 samples of old normal and 2 samples of old CAS, and are thus omitted from this graph

    Techniques Used: Laser Capture Microdissection, Staining, Formalin-fixed Paraffin-Embedded, Isolation

    Workflow for the isolation and analysis of RNA from normal and cancer-associated stroma from FFPE tissue by Laser-capture microdissection. ( 1 ) Canine simple mammary carcinoma cases to be analysed are chosen from the archives. ( 2 ) Sectioning and mounting of FFPE sections is followed by tissue deparaffinisation and staining to visualise structures under the microscope ( top panel on the left ). ( 3 ) Laser-capture microdissection allows excision of areas of interest, and visual validation of the excised area ( middle panel on the left ) as well as the excised tissue piece ( bottom panel on the left ). The black spots that appear on the excised tissue piece are a result of the thermoplastic film that is welded to the tissue, and not tissue damage. ( 4 ) RNA is isolated from the excised tissue of interest, and quality control is performed to measure RNA quality and quantity. ( 5 ) RT-qPCR or ( 6 ) NGS can be used to analyse the extracted RNA
    Figure Legend Snippet: Workflow for the isolation and analysis of RNA from normal and cancer-associated stroma from FFPE tissue by Laser-capture microdissection. ( 1 ) Canine simple mammary carcinoma cases to be analysed are chosen from the archives. ( 2 ) Sectioning and mounting of FFPE sections is followed by tissue deparaffinisation and staining to visualise structures under the microscope ( top panel on the left ). ( 3 ) Laser-capture microdissection allows excision of areas of interest, and visual validation of the excised area ( middle panel on the left ) as well as the excised tissue piece ( bottom panel on the left ). The black spots that appear on the excised tissue piece are a result of the thermoplastic film that is welded to the tissue, and not tissue damage. ( 4 ) RNA is isolated from the excised tissue of interest, and quality control is performed to measure RNA quality and quantity. ( 5 ) RT-qPCR or ( 6 ) NGS can be used to analyse the extracted RNA

    Techniques Used: Isolation, Formalin-fixed Paraffin-Embedded, Laser Capture Microdissection, Staining, Microscopy, Quantitative RT-PCR, Next-Generation Sequencing

    2) 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

    Variants identified in the samples extracted with different DNA extraction methods. (A-D) Venn diagram showing the distribution of variants between DNA extraction methods in four different FFPE samples, SARC1-4. Variants were detected by MuTect and Strelka, using an artificial control as normal. The data was filtered on exonic variants with allele frequency > 5% and coverage > 100x, being present at
    Figure Legend Snippet: Variants identified in the samples extracted with different DNA extraction methods. (A-D) Venn diagram showing the distribution of variants between DNA extraction methods in four different FFPE samples, SARC1-4. Variants were detected by MuTect and Strelka, using an artificial control as normal. The data was filtered on exonic variants with allele frequency > 5% and coverage > 100x, being present at

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

    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

    3) 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

    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 "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

    Variants identified in the samples extracted with different DNA extraction methods. (A-D) Venn diagram showing the distribution of variants between DNA extraction methods in four different FFPE samples, SARC1-4. Variants were detected by MuTect and Strelka, using an artificial control as normal. The data was filtered on exonic variants with allele frequency > 5% and coverage > 100x, being present at
    Figure Legend Snippet: Variants identified in the samples extracted with different DNA extraction methods. (A-D) Venn diagram showing the distribution of variants between DNA extraction methods in four different FFPE samples, SARC1-4. Variants were detected by MuTect and Strelka, using an artificial control as normal. The data was filtered on exonic variants with allele frequency > 5% and coverage > 100x, being present at

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

    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

    6) 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

    Variants identified in the samples extracted with different DNA extraction methods. (A-D) Venn diagram showing the distribution of variants between DNA extraction methods in four different FFPE samples, SARC1-4. Variants were detected by MuTect and Strelka, using an artificial control as normal. The data was filtered on exonic variants with allele frequency > 5% and coverage > 100x, being present at
    Figure Legend Snippet: Variants identified in the samples extracted with different DNA extraction methods. (A-D) Venn diagram showing the distribution of variants between DNA extraction methods in four different FFPE samples, SARC1-4. Variants were detected by MuTect and Strelka, using an artificial control as normal. The data was filtered on exonic variants with allele frequency > 5% and coverage > 100x, being present at

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

    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

    7) 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

    8) Product Images from "Robust detection of immune transcripts in FFPE samples using targeted RNA sequencing"

    Article Title: Robust detection of immune transcripts in FFPE samples using targeted RNA sequencing

    Journal: Oncotarget

    doi: 10.18632/oncotarget.13691

    Immune Advance assay performance on FFPE versus FF samples A . Samples from 14 ovarian cancer patients were halved to generate a series of matched fresh frozen (FF) and formalin-fixed paraffin embedded (FFPE) specimens, which were serially sectioned, and processed for further analysis. B . Targeted RNAseq on a panel of immunological transcripts was performed on 13 samples pairs that passed quality control upon RNA extraction, as well as on control sample NA12878 in triplicate runs. Each FFPE/FF sample pair demonstrated unique correlation distinct from all other specimens. The matrix depict inter-sample correlation based on Pearson correlation coefficient (R). R 2 are indicated for each sample pair in parentheses.
    Figure Legend Snippet: Immune Advance assay performance on FFPE versus FF samples A . Samples from 14 ovarian cancer patients were halved to generate a series of matched fresh frozen (FF) and formalin-fixed paraffin embedded (FFPE) specimens, which were serially sectioned, and processed for further analysis. B . Targeted RNAseq on a panel of immunological transcripts was performed on 13 samples pairs that passed quality control upon RNA extraction, as well as on control sample NA12878 in triplicate runs. Each FFPE/FF sample pair demonstrated unique correlation distinct from all other specimens. The matrix depict inter-sample correlation based on Pearson correlation coefficient (R). R 2 are indicated for each sample pair in parentheses.

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

    9) Product Images from "Robust detection of immune transcripts in FFPE samples using targeted RNA sequencing"

    Article Title: Robust detection of immune transcripts in FFPE samples using targeted RNA sequencing

    Journal: Oncotarget

    doi: 10.18632/oncotarget.13691

    Immune Advance assay performance on FFPE versus FF samples A . Samples from 14 ovarian cancer patients were halved to generate a series of matched fresh frozen (FF) and formalin-fixed paraffin embedded (FFPE) specimens, which were serially sectioned, and processed for further analysis. B . Targeted RNAseq on a panel of immunological transcripts was performed on 13 samples pairs that passed quality control upon RNA extraction, as well as on control sample NA12878 in triplicate runs. Each FFPE/FF sample pair demonstrated unique correlation distinct from all other specimens. The matrix depict inter-sample correlation based on Pearson correlation coefficient (R). R 2 are indicated for each sample pair in parentheses.
    Figure Legend Snippet: Immune Advance assay performance on FFPE versus FF samples A . Samples from 14 ovarian cancer patients were halved to generate a series of matched fresh frozen (FF) and formalin-fixed paraffin embedded (FFPE) specimens, which were serially sectioned, and processed for further analysis. B . Targeted RNAseq on a panel of immunological transcripts was performed on 13 samples pairs that passed quality control upon RNA extraction, as well as on control sample NA12878 in triplicate runs. Each FFPE/FF sample pair demonstrated unique correlation distinct from all other specimens. The matrix depict inter-sample correlation based on Pearson correlation coefficient (R). R 2 are indicated for each sample pair in parentheses.

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

    Related Articles

    DNA Extraction:

    Article Title: Evaluation of commercial DNA and RNA extraction methods for high-throughput sequencing of FFPE samples
    Article Snippet: .. For DNA extraction, the truXTRAC FFPE DNA kit from Covaris gave in general higher yield and more intact DNA fragments, however, no significant differences were observed in the quantity of libraries, DNA sequencing or variant calling among the different extraction methods tested. .. For detection of RNA transcripts from fusion genes, the truXTRAC FFPE RNA kit from Covaris and FormaPure kit from Beckman Coulter performed better identifying a fusion that was not detected with the kits from QIAGEN.

    Article Title: Evaluation of commercial DNA and RNA extraction methods for high-throughput sequencing of FFPE samples
    Article Snippet: .. For DNA extraction, the truXTRAC FFPE DNA kit from Covaris gave higher yields and better amplifiable DNA, but all protocols gave comparable HTS library yields using Agilent SureSelect XT and performed well in downstream variant calling. .. For RNA extraction, all protocols gave comparable yields and amplifiable RNA.

    RNA Extraction:

    Article Title: Robust detection of immune transcripts in FFPE samples using targeted RNA sequencing
    Article Snippet: .. RNA extraction RNA was extracted from FFPE tissues using the truXTRAC™ FFPE RNA Kit (Covaris), as per manufacturer's instructions with modifications. ..

    Article Title: Evaluation of commercial DNA and RNA extraction methods for high-throughput sequencing of FFPE samples
    Article Snippet: .. However, for fusion gene detection using the Archer FusionPlex Sarcoma Assay, the truXTRAC FFPE RNA kit from Covaris and Agencourt FormaPure kit from Beckman Coulter showed the highest percentage of unique read-pairs, providing higher complexity of HTS data and more frequent detection of recurrent fusion genes. truXTRAC simultaneous DNA and RNA extraction gave similar outputs as individual protocols. .. These findings show that although successful HTS libraries could be generated in most cases, the different protocols gave variable quantity and quality for FFPE nucleic acid extraction.

    Isolation:

    Article Title: An optimised protocol for isolation of RNA from small sections of laser-capture microdissected FFPE tissue amenable for next-generation sequencing
    Article Snippet: .. ‘ New’ (sonication-based) isolation protocol for RNA from FFPE tissue sections Extraction of RNA was performed immediately after microdissection using the Covaris® truXTRAC FFPE RNA kit according to the manufacturer’s protocol with following adjustments. .. A sterile blade was used to peel off the thermoplastic film from the LCM cap and transfer the tissue isolated by LCM into glass vials for sonication.

    Laser Capture Microdissection:

    Article Title: An optimised protocol for isolation of RNA from small sections of laser-capture microdissected FFPE tissue amenable for next-generation sequencing
    Article Snippet: .. ‘ New’ (sonication-based) isolation protocol for RNA from FFPE tissue sections Extraction of RNA was performed immediately after microdissection using the Covaris® truXTRAC FFPE RNA kit according to the manufacturer’s protocol with following adjustments. .. A sterile blade was used to peel off the thermoplastic film from the LCM cap and transfer the tissue isolated by LCM into glass vials for sonication.

    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: An optimised protocol for isolation of RNA from small sections of laser-capture microdissected FFPE tissue amenable for next-generation sequencing
    Article Snippet: .. ‘ New’ (sonication-based) isolation protocol for RNA from FFPE tissue sections Extraction of RNA was performed immediately after microdissection using the Covaris® truXTRAC FFPE RNA kit according to the manufacturer’s protocol with following adjustments. .. A sterile blade was used to peel off the thermoplastic film from the LCM cap and transfer the tissue isolated by LCM into glass vials for sonication.

    Article Title: Robust detection of immune transcripts in FFPE samples using targeted RNA sequencing
    Article Snippet: .. RNA extraction RNA was extracted from FFPE tissues using the truXTRAC™ FFPE RNA Kit (Covaris), as per manufacturer's instructions with modifications. ..

    Article Title: Evaluation of commercial DNA and RNA extraction methods for high-throughput sequencing of FFPE samples
    Article Snippet: .. However, for fusion gene detection using the Archer FusionPlex Sarcoma Assay, the truXTRAC FFPE RNA kit from Covaris and Agencourt FormaPure kit from Beckman Coulter showed the highest percentage of unique read-pairs, providing higher complexity of HTS data and more frequent detection of recurrent fusion genes. truXTRAC simultaneous DNA and RNA extraction gave similar outputs as individual protocols. .. These findings show that although successful HTS libraries could be generated in most cases, the different protocols gave variable quantity and quality for FFPE nucleic acid extraction.

    Article Title: Evaluation of commercial DNA and RNA extraction methods for high-throughput sequencing of FFPE samples
    Article Snippet: .. For detection of RNA transcripts from fusion genes, the truXTRAC FFPE RNA kit from Covaris and FormaPure kit from Beckman Coulter performed better identifying a fusion that was not detected with the kits from QIAGEN. ..

    Article Title: Evaluation of commercial DNA and RNA extraction methods for high-throughput sequencing of FFPE samples
    Article Snippet: .. For DNA extraction, the truXTRAC FFPE DNA kit from Covaris gave in general higher yield and more intact DNA fragments, however, no significant differences were observed in the quantity of libraries, DNA sequencing or variant calling among the different extraction methods tested. .. For detection of RNA transcripts from fusion genes, the truXTRAC FFPE RNA kit from Covaris and FormaPure kit from Beckman Coulter performed better identifying a fusion that was not detected with the kits from QIAGEN.

    Article Title: Evaluation of commercial DNA and RNA extraction methods for high-throughput sequencing of FFPE samples
    Article Snippet: .. For DNA extraction, the truXTRAC FFPE DNA kit from Covaris gave higher yields and better amplifiable DNA, but all protocols gave comparable HTS library yields using Agilent SureSelect XT and performed well in downstream variant calling. .. For RNA extraction, all protocols gave comparable yields and amplifiable RNA.

    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.

    DNA Sequencing:

    Article Title: Evaluation of commercial DNA and RNA extraction methods for high-throughput sequencing of FFPE samples
    Article Snippet: .. For DNA extraction, the truXTRAC FFPE DNA kit from Covaris gave in general higher yield and more intact DNA fragments, however, no significant differences were observed in the quantity of libraries, DNA sequencing or variant calling among the different extraction methods tested. .. For detection of RNA transcripts from fusion genes, the truXTRAC FFPE RNA kit from Covaris and FormaPure kit from Beckman Coulter performed better identifying a fusion that was not detected with the kits from QIAGEN.

    Sonication:

    Article Title: An optimised protocol for isolation of RNA from small sections of laser-capture microdissected FFPE tissue amenable for next-generation sequencing
    Article Snippet: .. ‘ New’ (sonication-based) isolation protocol for RNA from FFPE tissue sections Extraction of RNA was performed immediately after microdissection using the Covaris® truXTRAC FFPE RNA kit according to the manufacturer’s protocol with following adjustments. .. A sterile blade was used to peel off the thermoplastic film from the LCM cap and transfer the tissue isolated by LCM into glass vials for sonication.

    Variant Assay:

    Article Title: Evaluation of commercial DNA and RNA extraction methods for high-throughput sequencing of FFPE samples
    Article Snippet: .. For DNA extraction, the truXTRAC FFPE DNA kit from Covaris gave in general higher yield and more intact DNA fragments, however, no significant differences were observed in the quantity of libraries, DNA sequencing or variant calling among the different extraction methods tested. .. For detection of RNA transcripts from fusion genes, the truXTRAC FFPE RNA kit from Covaris and FormaPure kit from Beckman Coulter performed better identifying a fusion that was not detected with the kits from QIAGEN.

    Article Title: Evaluation of commercial DNA and RNA extraction methods for high-throughput sequencing of FFPE samples
    Article Snippet: .. For DNA extraction, the truXTRAC FFPE DNA kit from Covaris gave higher yields and better amplifiable DNA, but all protocols gave comparable HTS library yields using Agilent SureSelect XT and performed well in downstream variant calling. .. For RNA extraction, all protocols gave comparable yields and amplifiable RNA.

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  • 96
    Covaris truxtrac ffpe rna kit
    Comparison of workflow of the ‘old’(classical) and ‘new’ protocol for <t>RNA</t> isolation from deparaffinised, stained and laser-capture microdissected <t>FFPE</t> tissue. a Workflow of the ‘old’ RNA isolation protocol, starting with proteinase K digestion of the sample. b Workflow of the ‘new’ isolation protocol, starting with a focused ultrasonication step to disrupt the tissue prior to proteinase K digestion. Values in brackets indicate the approximate timing for each step
    Truxtrac Ffpe Rna Kit, supplied by Covaris, used in various techniques. Bioz Stars score: 96/100, based on 13 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/truxtrac ffpe rna kit/product/Covaris
    Average 96 stars, based on 13 article reviews
    Price from $9.99 to $1999.99
    truxtrac ffpe rna kit - by Bioz Stars, 2020-08
    96/100 stars
      Buy from Supplier

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    Comparison of workflow of the ‘old’(classical) and ‘new’ protocol for RNA isolation from deparaffinised, stained and laser-capture microdissected FFPE tissue. a Workflow of the ‘old’ RNA isolation protocol, starting with proteinase K digestion of the sample. b Workflow of the ‘new’ isolation protocol, starting with a focused ultrasonication step to disrupt the tissue prior to proteinase K digestion. Values in brackets indicate the approximate timing for each step

    Journal: BMC Molecular Biology

    Article Title: An optimised protocol for isolation of RNA from small sections of laser-capture microdissected FFPE tissue amenable for next-generation sequencing

    doi: 10.1186/s12867-017-0099-7

    Figure Lengend Snippet: Comparison of workflow of the ‘old’(classical) and ‘new’ protocol for RNA isolation from deparaffinised, stained and laser-capture microdissected FFPE tissue. a Workflow of the ‘old’ RNA isolation protocol, starting with proteinase K digestion of the sample. b Workflow of the ‘new’ isolation protocol, starting with a focused ultrasonication step to disrupt the tissue prior to proteinase K digestion. Values in brackets indicate the approximate timing for each step

    Article Snippet: ‘ New’ (sonication-based) isolation protocol for RNA from FFPE tissue sections Extraction of RNA was performed immediately after microdissection using the Covaris® truXTRAC FFPE RNA kit according to the manufacturer’s protocol with following adjustments.

    Techniques: Isolation, Staining, Formalin-fixed Paraffin-Embedded

    Direct comparison of RNA extracted from LCM samples from deparaffinised, stained FFPE tissue with the old vs the new isolation protocol. a Scatter plot with mean ± SEM of total RNA yield from the 13 clinical cases analysed obtained using the old vs the new isolation protocol. Old normal shows data obtained from using the old protocol on LCM samples of normal stroma, while old CAS shows data for the old protocol on CAS. New normal and new CAS are the equivalent for the new extraction procedure, respectively. p-values were calculated using the Student’s t test. b Bar graph displaying mean ± SEM of the increase of total RNA yield that could be achieved using a 2nd elution step with the new isolation protocol for normal and CAS samples, respectively, compared to a single elution step only. n = 8 for both types of tissue, respectively. c Scatter plot with mean ± SEM of the RIN values obtained from all 13 clinical cases isolated using the old or the new isolation procedure, respectively. RIN values could not be calculated for 3 samples of old normal and 2 samples of old CAS, and are thus omitted from this graph

    Journal: BMC Molecular Biology

    Article Title: An optimised protocol for isolation of RNA from small sections of laser-capture microdissected FFPE tissue amenable for next-generation sequencing

    doi: 10.1186/s12867-017-0099-7

    Figure Lengend Snippet: Direct comparison of RNA extracted from LCM samples from deparaffinised, stained FFPE tissue with the old vs the new isolation protocol. a Scatter plot with mean ± SEM of total RNA yield from the 13 clinical cases analysed obtained using the old vs the new isolation protocol. Old normal shows data obtained from using the old protocol on LCM samples of normal stroma, while old CAS shows data for the old protocol on CAS. New normal and new CAS are the equivalent for the new extraction procedure, respectively. p-values were calculated using the Student’s t test. b Bar graph displaying mean ± SEM of the increase of total RNA yield that could be achieved using a 2nd elution step with the new isolation protocol for normal and CAS samples, respectively, compared to a single elution step only. n = 8 for both types of tissue, respectively. c Scatter plot with mean ± SEM of the RIN values obtained from all 13 clinical cases isolated using the old or the new isolation procedure, respectively. RIN values could not be calculated for 3 samples of old normal and 2 samples of old CAS, and are thus omitted from this graph

    Article Snippet: ‘ New’ (sonication-based) isolation protocol for RNA from FFPE tissue sections Extraction of RNA was performed immediately after microdissection using the Covaris® truXTRAC FFPE RNA kit according to the manufacturer’s protocol with following adjustments.

    Techniques: Laser Capture Microdissection, Staining, Formalin-fixed Paraffin-Embedded, Isolation

    Workflow for the isolation and analysis of RNA from normal and cancer-associated stroma from FFPE tissue by Laser-capture microdissection. ( 1 ) Canine simple mammary carcinoma cases to be analysed are chosen from the archives. ( 2 ) Sectioning and mounting of FFPE sections is followed by tissue deparaffinisation and staining to visualise structures under the microscope ( top panel on the left ). ( 3 ) Laser-capture microdissection allows excision of areas of interest, and visual validation of the excised area ( middle panel on the left ) as well as the excised tissue piece ( bottom panel on the left ). The black spots that appear on the excised tissue piece are a result of the thermoplastic film that is welded to the tissue, and not tissue damage. ( 4 ) RNA is isolated from the excised tissue of interest, and quality control is performed to measure RNA quality and quantity. ( 5 ) RT-qPCR or ( 6 ) NGS can be used to analyse the extracted RNA

    Journal: BMC Molecular Biology

    Article Title: An optimised protocol for isolation of RNA from small sections of laser-capture microdissected FFPE tissue amenable for next-generation sequencing

    doi: 10.1186/s12867-017-0099-7

    Figure Lengend Snippet: Workflow for the isolation and analysis of RNA from normal and cancer-associated stroma from FFPE tissue by Laser-capture microdissection. ( 1 ) Canine simple mammary carcinoma cases to be analysed are chosen from the archives. ( 2 ) Sectioning and mounting of FFPE sections is followed by tissue deparaffinisation and staining to visualise structures under the microscope ( top panel on the left ). ( 3 ) Laser-capture microdissection allows excision of areas of interest, and visual validation of the excised area ( middle panel on the left ) as well as the excised tissue piece ( bottom panel on the left ). The black spots that appear on the excised tissue piece are a result of the thermoplastic film that is welded to the tissue, and not tissue damage. ( 4 ) RNA is isolated from the excised tissue of interest, and quality control is performed to measure RNA quality and quantity. ( 5 ) RT-qPCR or ( 6 ) NGS can be used to analyse the extracted RNA

    Article Snippet: ‘ New’ (sonication-based) isolation protocol for RNA from FFPE tissue sections Extraction of RNA was performed immediately after microdissection using the Covaris® truXTRAC FFPE RNA kit according to the manufacturer’s protocol with following adjustments.

    Techniques: Isolation, Formalin-fixed Paraffin-Embedded, Laser Capture Microdissection, Staining, Microscopy, Quantitative RT-PCR, Next-Generation Sequencing

    Variants identified in the samples extracted with different DNA extraction methods. (A-D) Venn diagram showing the distribution of variants between DNA extraction methods in four different FFPE samples, SARC1-4. Variants were detected by MuTect and Strelka, using an artificial control as normal. The data was filtered on exonic variants with allele frequency > 5% and coverage > 100x, being present at

    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: Variants identified in the samples extracted with different DNA extraction methods. (A-D) Venn diagram showing the distribution of variants between DNA extraction methods in four different FFPE samples, SARC1-4. Variants were detected by MuTect and Strelka, using an artificial control as normal. The data was filtered on exonic variants with allele frequency > 5% and coverage > 100x, being present at

    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.

    Techniques: DNA Extraction, Formalin-fixed Paraffin-Embedded

    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: 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.

    Techniques: Formalin-fixed Paraffin-Embedded, Standard Deviation