high pure ffpe rna micro kit  (Roche)


Bioz Verified Symbol Roche is a verified supplier
Bioz Manufacturer Symbol Roche manufactures this product  
  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 86

    Structured Review

    Roche high pure ffpe rna micro kit
    Development of a high-throughput microfluidic gene expression assay for analysis of <t>FFPE</t> breast tumor samples. (A) Schematic of the gene expression assay protocol. (B) Representative five-point standard curves of FFPE tumor <t>RNA</t> (red and black lines) and universal RNA (blue line) run on the breast cancer gene expression assay (slope of line indicated). (C) Intra-chip reproducibility of FFPE tumor samples run on the same 96.96 Dynamic Array. (D) Inter-chip reproducibility of the breast cancer gene expression assay assessed by comparing Ct values of universal RNA across seven independent assay runs. R-squared values are indicated in boxes.
    High Pure Ffpe Rna Micro Kit, supplied by Roche, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/high pure ffpe rna micro kit/product/Roche
    Average 86 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    high pure ffpe rna micro kit - by Bioz Stars, 2021-09
    86/100 stars

    Images

    1) Product Images from "Targeted Biomarker Profiling of Matched Primary and Metastatic Estrogen Receptor Positive Breast Cancers"

    Article Title: Targeted Biomarker Profiling of Matched Primary and Metastatic Estrogen Receptor Positive Breast Cancers

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0088401

    Development of a high-throughput microfluidic gene expression assay for analysis of FFPE breast tumor samples. (A) Schematic of the gene expression assay protocol. (B) Representative five-point standard curves of FFPE tumor RNA (red and black lines) and universal RNA (blue line) run on the breast cancer gene expression assay (slope of line indicated). (C) Intra-chip reproducibility of FFPE tumor samples run on the same 96.96 Dynamic Array. (D) Inter-chip reproducibility of the breast cancer gene expression assay assessed by comparing Ct values of universal RNA across seven independent assay runs. R-squared values are indicated in boxes.
    Figure Legend Snippet: Development of a high-throughput microfluidic gene expression assay for analysis of FFPE breast tumor samples. (A) Schematic of the gene expression assay protocol. (B) Representative five-point standard curves of FFPE tumor RNA (red and black lines) and universal RNA (blue line) run on the breast cancer gene expression assay (slope of line indicated). (C) Intra-chip reproducibility of FFPE tumor samples run on the same 96.96 Dynamic Array. (D) Inter-chip reproducibility of the breast cancer gene expression assay assessed by comparing Ct values of universal RNA across seven independent assay runs. R-squared values are indicated in boxes.

    Techniques Used: High Throughput Screening Assay, Expressing, Formalin-fixed Paraffin-Embedded, Chromatin Immunoprecipitation

    2) Product Images from "The impact of RNA extraction method on accurate RNA sequencing from formalin-fixed paraffin-embedded tissues"

    Article Title: The impact of RNA extraction method on accurate RNA sequencing from formalin-fixed paraffin-embedded tissues

    Journal: BMC Cancer

    doi: 10.1186/s12885-019-6363-0

    Concordance of gene expression between FFPE and FF samples for wtRNAseq data. a Distribution of concordance correlation coefficient (CCC) for all genes within each RNA extraction kit used. b Association between gene expression and CCC value. c High expression (normalized expression higher than − 7.5) and high concordant (CCC > 0.5) genes between different kits. d Concordance of molecular signatures scores for 3 FFPE kits in comparison to FF
    Figure Legend Snippet: Concordance of gene expression between FFPE and FF samples for wtRNAseq data. a Distribution of concordance correlation coefficient (CCC) for all genes within each RNA extraction kit used. b Association between gene expression and CCC value. c High expression (normalized expression higher than − 7.5) and high concordant (CCC > 0.5) genes between different kits. d Concordance of molecular signatures scores for 3 FFPE kits in comparison to FF

    Techniques Used: Expressing, Formalin-fixed Paraffin-Embedded, Countercurrent Chromatography, RNA Extraction

    3) Product Images from "Development and Application of a Microfluidics-Based Panel in the Basal/Luminal Transcriptional Characterization of Archival Bladder Cancers"

    Article Title: Development and Application of a Microfluidics-Based Panel in the Basal/Luminal Transcriptional Characterization of Archival Bladder Cancers

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0165856

    Technical validation of the bladder cancer panel. (A) Bar chart reflecting the failure counts for each of the assays on the bladder cancer panel, as determined by the number of times an assay failed to produce a measurable signal above background in 664 attempted measurements. (B) CV calculations from triplicate experimental measurements using standard deviation over the mean expression values for each of the assays on the panel. (C) Chip-to-chip data reproducibility for high quality control uRNA samples from different runs. (D) Run to run data reproducibility for archival tissues, as seen for two representative FFPE-derived RNA samples run on different days.
    Figure Legend Snippet: Technical validation of the bladder cancer panel. (A) Bar chart reflecting the failure counts for each of the assays on the bladder cancer panel, as determined by the number of times an assay failed to produce a measurable signal above background in 664 attempted measurements. (B) CV calculations from triplicate experimental measurements using standard deviation over the mean expression values for each of the assays on the panel. (C) Chip-to-chip data reproducibility for high quality control uRNA samples from different runs. (D) Run to run data reproducibility for archival tissues, as seen for two representative FFPE-derived RNA samples run on different days.

    Techniques Used: Standard Deviation, Expressing, Chromatin Immunoprecipitation, Formalin-fixed Paraffin-Embedded, Derivative Assay

    4) Product Images from "New miRNA Profiles Accurately Distinguish Renal Cell Carcinomas and Upper Tract Urothelial Carcinomas from the Normal Kidney"

    Article Title: New miRNA Profiles Accurately Distinguish Renal Cell Carcinomas and Upper Tract Urothelial Carcinomas from the Normal Kidney

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0091646

    Haematoxylin and eosin (H E) staining and immunohistochemistry (IHC). Upper pannel: Representative H E staining from ccRCC, papRCC, chRCC and normal kidney tissue. About 5–10 serial tissue sections of 10 μm were cut from each FFPE block, deparaffinized with xylene, hydrated and stained with H E before microscopic examination. When the proportion of tumour cells was > 70% the FFPE block was subjected to total RNA extraction. Lower pannel: IHC of FFPE tissue sections using anti-vimentin as primary antibody. Vimentin was predominantly seen in ccRCC and papRCC (∼70% and ∼50%, respectively), but only rarely in chRCC (4%) and absent in the normal kidney. Vimentin was also down-regulated in the majority of UT-UC cases.
    Figure Legend Snippet: Haematoxylin and eosin (H E) staining and immunohistochemistry (IHC). Upper pannel: Representative H E staining from ccRCC, papRCC, chRCC and normal kidney tissue. About 5–10 serial tissue sections of 10 μm were cut from each FFPE block, deparaffinized with xylene, hydrated and stained with H E before microscopic examination. When the proportion of tumour cells was > 70% the FFPE block was subjected to total RNA extraction. Lower pannel: IHC of FFPE tissue sections using anti-vimentin as primary antibody. Vimentin was predominantly seen in ccRCC and papRCC (∼70% and ∼50%, respectively), but only rarely in chRCC (4%) and absent in the normal kidney. Vimentin was also down-regulated in the majority of UT-UC cases.

    Techniques Used: Staining, Immunohistochemistry, Formalin-fixed Paraffin-Embedded, Blocking Assay, RNA Extraction

    5) 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

    6) Product Images from "A multiplex endpoint RT-PCR assay for quality assessment of RNA extracted from formalin-fixed paraffin-embedded tissues"

    Article Title: A multiplex endpoint RT-PCR assay for quality assessment of RNA extracted from formalin-fixed paraffin-embedded tissues

    Journal: BMC Biotechnology

    doi: 10.1186/1472-6750-10-89

    Assessment of RNA degradation and RNA performance in RT-PCR by the multiplex endpoint RT-PCR assay . The sizes of the molecular weight markers (MW) are given on the left, whereas the sizes of the TBP amplicons are indicated on the right. Sizes are given in base pairs. Lane 1 and 10 were loaded with the no template control (NTC). Lane 2 and 9 were loaded with the PCR reaction obtained from a cDNA mixture synthesised from RNA extracted from different cell lines and serves as positive control, showing all four PCR amplification products of the expected size. Lane 8 was loaded with the PCR reaction obtained from genomic DNA and served as negative control. Lanes 3 to 7 were loaded with RT-PCR reactions obtained from cDNAs synthesised from total RNA derived from needle microdissected FFPE breast tumour tissues (Lane 3: P1-98-05, replicate 1; Lane 4: P1-98-06, replicate 1; Lane 5: P1-98-07, replicate 1; Lane 6: P1-98-08, replicate 1; Lane 7: P1-98-09, replicate 1).
    Figure Legend Snippet: Assessment of RNA degradation and RNA performance in RT-PCR by the multiplex endpoint RT-PCR assay . The sizes of the molecular weight markers (MW) are given on the left, whereas the sizes of the TBP amplicons are indicated on the right. Sizes are given in base pairs. Lane 1 and 10 were loaded with the no template control (NTC). Lane 2 and 9 were loaded with the PCR reaction obtained from a cDNA mixture synthesised from RNA extracted from different cell lines and serves as positive control, showing all four PCR amplification products of the expected size. Lane 8 was loaded with the PCR reaction obtained from genomic DNA and served as negative control. Lanes 3 to 7 were loaded with RT-PCR reactions obtained from cDNAs synthesised from total RNA derived from needle microdissected FFPE breast tumour tissues (Lane 3: P1-98-05, replicate 1; Lane 4: P1-98-06, replicate 1; Lane 5: P1-98-07, replicate 1; Lane 6: P1-98-08, replicate 1; Lane 7: P1-98-09, replicate 1).

    Techniques Used: Reverse Transcription Polymerase Chain Reaction, Multiplex Assay, Molecular Weight, Polymerase Chain Reaction, Positive Control, Amplification, Negative Control, Derivative 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 "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

    9) Product Images from "New miRNA Profiles Accurately Distinguish Renal Cell Carcinomas and Upper Tract Urothelial Carcinomas from the Normal Kidney"

    Article Title: New miRNA Profiles Accurately Distinguish Renal Cell Carcinomas and Upper Tract Urothelial Carcinomas from the Normal Kidney

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0091646

    Haematoxylin and eosin (H E) staining and immunohistochemistry (IHC). Upper pannel: Representative H E staining from ccRCC, papRCC, chRCC and normal kidney tissue. About 5–10 serial tissue sections of 10 μm were cut from each FFPE block, deparaffinized with xylene, hydrated and stained with H E before microscopic examination. When the proportion of tumour cells was > 70% the FFPE block was subjected to total RNA extraction. Lower pannel: IHC of FFPE tissue sections using anti-vimentin as primary antibody. Vimentin was predominantly seen in ccRCC and papRCC (∼70% and ∼50%, respectively), but only rarely in chRCC (4%) and absent in the normal kidney. Vimentin was also down-regulated in the majority of UT-UC cases.
    Figure Legend Snippet: Haematoxylin and eosin (H E) staining and immunohistochemistry (IHC). Upper pannel: Representative H E staining from ccRCC, papRCC, chRCC and normal kidney tissue. About 5–10 serial tissue sections of 10 μm were cut from each FFPE block, deparaffinized with xylene, hydrated and stained with H E before microscopic examination. When the proportion of tumour cells was > 70% the FFPE block was subjected to total RNA extraction. Lower pannel: IHC of FFPE tissue sections using anti-vimentin as primary antibody. Vimentin was predominantly seen in ccRCC and papRCC (∼70% and ∼50%, respectively), but only rarely in chRCC (4%) and absent in the normal kidney. Vimentin was also down-regulated in the majority of UT-UC cases.

    Techniques Used: Staining, Immunohistochemistry, Formalin-fixed Paraffin-Embedded, Blocking Assay, RNA Extraction

    10) Product Images from "Evaluation and Validation of Total RNA Extraction Methods for MicroRNA Expression Analyses in Formalin-Fixed, Paraffin-Embedded Tissues"

    Article Title: Evaluation and Validation of Total RNA Extraction Methods for MicroRNA Expression Analyses in Formalin-Fixed, Paraffin-Embedded Tissues

    Journal:

    doi: 10.2353/jmoldx.2008.070153

    Armored RNA Quant as a process control. RNA isolation was performed using 16 20-μm slices from 15 pairs of matched FFPE lung tumor and NAT specimens with 10 10 copies of ARQ spiked at the proteinase K digestion step. qRT-PCR were performed in duplicate
    Figure Legend Snippet: Armored RNA Quant as a process control. RNA isolation was performed using 16 20-μm slices from 15 pairs of matched FFPE lung tumor and NAT specimens with 10 10 copies of ARQ spiked at the proteinase K digestion step. qRT-PCR were performed in duplicate

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

    Comparison between FFPE and matching frozen samples. A: Average expression levels for miR-24, -103, and -191 in RNA samples isolated from FFPE and matched frozen breast (three specimens), cervix (three specimens), and gall bladder (two specimens) tissues.
    Figure Legend Snippet: Comparison between FFPE and matching frozen samples. A: Average expression levels for miR-24, -103, and -191 in RNA samples isolated from FFPE and matched frozen breast (three specimens), cervix (three specimens), and gall bladder (two specimens) tissues.

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

    Method Comparison for RNA Extraction from FFPE Tissues
    Figure Legend Snippet: Method Comparison for RNA Extraction from FFPE Tissues

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

    Scale-up of the RecoverAll procedure. RNA isolation was performed with four, eight, 12, or 16 FFPE tissue slices (20-μm) from two prostate cancer FFPE blocks that differed in tissue cross-sectional area. For the block with a tissue area > 150
    Figure Legend Snippet: Scale-up of the RecoverAll procedure. RNA isolation was performed with four, eight, 12, or 16 FFPE tissue slices (20-μm) from two prostate cancer FFPE blocks that differed in tissue cross-sectional area. For the block with a tissue area > 150

    Techniques Used: Isolation, Formalin-fixed Paraffin-Embedded, Blocking Assay

    qRT-PCR analysis of RNA samples isolated with the RecoverAll or RNeasy kit. Total RNA was extracted in triplicate from five different FFPE tissue blocks using the indicated method. Each RNA sample was analyzed in duplicate using qRT-PCR assays specific
    Figure Legend Snippet: qRT-PCR analysis of RNA samples isolated with the RecoverAll or RNeasy kit. Total RNA was extracted in triplicate from five different FFPE tissue blocks using the indicated method. Each RNA sample was analyzed in duplicate using qRT-PCR assays specific

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

    11) Product Images from "Evaluation and Validation of Total RNA Extraction Methods for MicroRNA Expression Analyses in Formalin-Fixed, Paraffin-Embedded Tissues"

    Article Title: Evaluation and Validation of Total RNA Extraction Methods for MicroRNA Expression Analyses in Formalin-Fixed, Paraffin-Embedded Tissues

    Journal:

    doi: 10.2353/jmoldx.2008.070153

    Armored RNA Quant as a process control. RNA isolation was performed using 16 20-μm slices from 15 pairs of matched FFPE lung tumor and NAT specimens with 10 10 copies of ARQ spiked at the proteinase K digestion step. qRT-PCR were performed in duplicate
    Figure Legend Snippet: Armored RNA Quant as a process control. RNA isolation was performed using 16 20-μm slices from 15 pairs of matched FFPE lung tumor and NAT specimens with 10 10 copies of ARQ spiked at the proteinase K digestion step. qRT-PCR were performed in duplicate

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

    Comparison between FFPE and matching frozen samples. A: Average expression levels for miR-24, -103, and -191 in RNA samples isolated from FFPE and matched frozen breast (three specimens), cervix (three specimens), and gall bladder (two specimens) tissues.
    Figure Legend Snippet: Comparison between FFPE and matching frozen samples. A: Average expression levels for miR-24, -103, and -191 in RNA samples isolated from FFPE and matched frozen breast (three specimens), cervix (three specimens), and gall bladder (two specimens) tissues.

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

    Method Comparison for RNA Extraction from FFPE Tissues
    Figure Legend Snippet: Method Comparison for RNA Extraction from FFPE Tissues

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

    Scale-up of the RecoverAll procedure. RNA isolation was performed with four, eight, 12, or 16 FFPE tissue slices (20-μm) from two prostate cancer FFPE blocks that differed in tissue cross-sectional area. For the block with a tissue area > 150
    Figure Legend Snippet: Scale-up of the RecoverAll procedure. RNA isolation was performed with four, eight, 12, or 16 FFPE tissue slices (20-μm) from two prostate cancer FFPE blocks that differed in tissue cross-sectional area. For the block with a tissue area > 150

    Techniques Used: Isolation, Formalin-fixed Paraffin-Embedded, Blocking Assay

    qRT-PCR analysis of RNA samples isolated with the RecoverAll or RNeasy kit. Total RNA was extracted in triplicate from five different FFPE tissue blocks using the indicated method. Each RNA sample was analyzed in duplicate using qRT-PCR assays specific
    Figure Legend Snippet: qRT-PCR analysis of RNA samples isolated with the RecoverAll or RNeasy kit. Total RNA was extracted in triplicate from five different FFPE tissue blocks using the indicated method. Each RNA sample was analyzed in duplicate using qRT-PCR assays specific

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

    12) Product Images from "Integrated digital pathology and transcriptome analysis identifies molecular mediators of T-cell exclusion in ovarian cancer"

    Article Title: Integrated digital pathology and transcriptome analysis identifies molecular mediators of T-cell exclusion in ovarian cancer

    Journal: Nature Communications

    doi: 10.1038/s41467-020-19408-2

    In situ validation of key features of T-cell excluded tumours. The tumour-immune phenotypes for a vendor-procured collection (including both primary tumours and recurrent tumours, n = 84 samples) were predicted based on gene expression. The pattern of CD8 + T-cell infiltration and molecular features associated with excluded tumours were validated using immunohistochemistry and in situ hybridization (ISH) on FFPE tumour tissues. a Representative images of CD8 IHC (top), MHC-I-IHC (middle) and FAP ISH (bottom) are shown for the three tumour-immune phenotypes. b Percentage of CD8 staining over tumour/stroma area ( n = 72 samples), H scores for MHC-I ( n = 77 samples) and FAP expression in the tumour or the stroma ( n = 77 samples) were presented by the three-class tumour-immune phenotypes. c RNA-seq gene expression level, represented as Log 2 (RPKM+1) for CD8A , HLA-A and FAP , is presented across the three-class tumour-immune phenotypes. b , c Whiskers ranging from minima to maxima, median and 25–75% IQR shown by boxplots; each dot is a tumour sample (primary tumours and recurrent tumours are pooled). The statistical significance is displayed with the exact P values on the graphs and calculated with a Kruskal–Wallis test corrected for multiple comparisons (Dunn’s test). Source data are provided as a Source Data file.
    Figure Legend Snippet: In situ validation of key features of T-cell excluded tumours. The tumour-immune phenotypes for a vendor-procured collection (including both primary tumours and recurrent tumours, n = 84 samples) were predicted based on gene expression. The pattern of CD8 + T-cell infiltration and molecular features associated with excluded tumours were validated using immunohistochemistry and in situ hybridization (ISH) on FFPE tumour tissues. a Representative images of CD8 IHC (top), MHC-I-IHC (middle) and FAP ISH (bottom) are shown for the three tumour-immune phenotypes. b Percentage of CD8 staining over tumour/stroma area ( n = 72 samples), H scores for MHC-I ( n = 77 samples) and FAP expression in the tumour or the stroma ( n = 77 samples) were presented by the three-class tumour-immune phenotypes. c RNA-seq gene expression level, represented as Log 2 (RPKM+1) for CD8A , HLA-A and FAP , is presented across the three-class tumour-immune phenotypes. b , c Whiskers ranging from minima to maxima, median and 25–75% IQR shown by boxplots; each dot is a tumour sample (primary tumours and recurrent tumours are pooled). The statistical significance is displayed with the exact P values on the graphs and calculated with a Kruskal–Wallis test corrected for multiple comparisons (Dunn’s test). Source data are provided as a Source Data file.

    Techniques Used: In Situ, Expressing, Immunohistochemistry, In Situ Hybridization, Formalin-fixed Paraffin-Embedded, Staining, RNA Sequencing Assay

    Related Articles

    Expressing:

    Article Title: Development and Application of a Microfluidics-Based Panel in the Basal/Luminal Transcriptional Characterization of Archival Bladder Cancers
    Article Snippet: .. Expression analysis of FFPE tissues Gene expression analysis was carried out on RNA extracted from macro-dissected FFPE tissues using the High Pure FFPE RNA Micro Kit (Roche Diagnostics, Indianapolis, IN) after de-paraffinization with Envirene, as described previously [ ]. ..

    Formalin-fixed Paraffin-Embedded:

    Article Title: Development and Application of a Microfluidics-Based Panel in the Basal/Luminal Transcriptional Characterization of Archival Bladder Cancers
    Article Snippet: .. Expression analysis of FFPE tissues Gene expression analysis was carried out on RNA extracted from macro-dissected FFPE tissues using the High Pure FFPE RNA Micro Kit (Roche Diagnostics, Indianapolis, IN) after de-paraffinization with Envirene, as described previously [ ]. ..

    Article Title: New miRNA Profiles Accurately Distinguish Renal Cell Carcinomas and Upper Tract Urothelial Carcinomas from the Normal Kidney
    Article Snippet: .. RNA extraction and microRNA microarray analysis Total RNA containing small RNAs was isolated from 18 ccRCC, 5 papRCC, 3 chRCC, 4 UT-UC and 20 normal tissue samples using the High Pure FFPE RNA Micro Kit (Roche Applied Science, IN). ..

    Article Title: The impact of RNA extraction method on accurate RNA sequencing from formalin-fixed paraffin-embedded tissues
    Article Snippet: .. For FFPE samples, RNA was extracted from adjacent tissue sections for each of three commonly-used commercial kits: N – Norgen (FFPE RNA purification Kit, Norgen, Thorold, Canada), Q – Qiagen (AllPrep DNA/RNA FFPE kit, Qiagen, Valencia, CA) and R – Roche (High Pure FFPE RNA Micro Kit, Roche, Indianapolis, IN). ..

    Article Title: Targeted Biomarker Profiling of Matched Primary and Metastatic Estrogen Receptor Positive Breast Cancers
    Article Snippet: .. RNA was isolated using the High Pure FFPE RNA Micro Kit (Roche Applied Sciences, Indianapolis, IN) according to the manufacturer’s protocol. ..

    Article Title: Clinical-pathological study on β-APP, IL-1β, GFAP, NFL, Spectrin II, 8OHdG, TUNEL, miR-21, miR-16, miR-92 expressions to verify DAI-diagnosis, grade and prognosis
    Article Snippet: .. RNA Extraction Total RNA, including miRNAs, was extracted from FFPE tissues using the High Pure miRNA isolation kit (Roche Basilea, Switzerland) according to the manufacturer’s instructions. ..

    Article Title: Interrogation of transcriptomic changes associated with drug-induced hepatic sinusoidal dilatation in colorectal cancer
    Article Snippet: .. Alternatively, five FFPE whole liver sections with SD present or absent derived from anti-DLL4 or vehicle-treated NHPs had RNA extracted using the High Pure FFPE RNA Micro Kit (Roche Applied Sciences, Indianapolis, IN) according to the manufacturer’s protocol. ..

    Article Title: MicroRNA-494 is a master epigenetic regulator of multiple invasion-suppressor microRNAs by targeting ten eleven translocation 1 in invasive human hepatocellular carcinoma tumors
    Article Snippet: .. MiRNA Isolation and Microarray Analysis MiRNA was isolated from FFPE HCC tumors using the Roche High Pure miRNA isolation kit (Roche Diagnostics, Mannheim, Germany). miRNA extraction was carried out from individual tissue blocks using seven sections of 10 microns each. ..

    RNA Extraction:

    Article Title: New miRNA Profiles Accurately Distinguish Renal Cell Carcinomas and Upper Tract Urothelial Carcinomas from the Normal Kidney
    Article Snippet: .. RNA extraction and microRNA microarray analysis Total RNA containing small RNAs was isolated from 18 ccRCC, 5 papRCC, 3 chRCC, 4 UT-UC and 20 normal tissue samples using the High Pure FFPE RNA Micro Kit (Roche Applied Science, IN). ..

    Article Title: Clinical-pathological study on β-APP, IL-1β, GFAP, NFL, Spectrin II, 8OHdG, TUNEL, miR-21, miR-16, miR-92 expressions to verify DAI-diagnosis, grade and prognosis
    Article Snippet: .. RNA Extraction Total RNA, including miRNAs, was extracted from FFPE tissues using the High Pure miRNA isolation kit (Roche Basilea, Switzerland) according to the manufacturer’s instructions. ..

    Microarray:

    Article Title: New miRNA Profiles Accurately Distinguish Renal Cell Carcinomas and Upper Tract Urothelial Carcinomas from the Normal Kidney
    Article Snippet: .. RNA extraction and microRNA microarray analysis Total RNA containing small RNAs was isolated from 18 ccRCC, 5 papRCC, 3 chRCC, 4 UT-UC and 20 normal tissue samples using the High Pure FFPE RNA Micro Kit (Roche Applied Science, IN). ..

    Article Title: MicroRNA-494 is a master epigenetic regulator of multiple invasion-suppressor microRNAs by targeting ten eleven translocation 1 in invasive human hepatocellular carcinoma tumors
    Article Snippet: .. MiRNA Isolation and Microarray Analysis MiRNA was isolated from FFPE HCC tumors using the Roche High Pure miRNA isolation kit (Roche Diagnostics, Mannheim, Germany). miRNA extraction was carried out from individual tissue blocks using seven sections of 10 microns each. ..

    Isolation:

    Article Title: New miRNA Profiles Accurately Distinguish Renal Cell Carcinomas and Upper Tract Urothelial Carcinomas from the Normal Kidney
    Article Snippet: .. RNA extraction and microRNA microarray analysis Total RNA containing small RNAs was isolated from 18 ccRCC, 5 papRCC, 3 chRCC, 4 UT-UC and 20 normal tissue samples using the High Pure FFPE RNA Micro Kit (Roche Applied Science, IN). ..

    Article Title: Targeted Biomarker Profiling of Matched Primary and Metastatic Estrogen Receptor Positive Breast Cancers
    Article Snippet: .. RNA was isolated using the High Pure FFPE RNA Micro Kit (Roche Applied Sciences, Indianapolis, IN) according to the manufacturer’s protocol. ..

    Article Title: Clinical-pathological study on β-APP, IL-1β, GFAP, NFL, Spectrin II, 8OHdG, TUNEL, miR-21, miR-16, miR-92 expressions to verify DAI-diagnosis, grade and prognosis
    Article Snippet: .. RNA Extraction Total RNA, including miRNAs, was extracted from FFPE tissues using the High Pure miRNA isolation kit (Roche Basilea, Switzerland) according to the manufacturer’s instructions. ..

    Article Title: MicroRNA-494 is a master epigenetic regulator of multiple invasion-suppressor microRNAs by targeting ten eleven translocation 1 in invasive human hepatocellular carcinoma tumors
    Article Snippet: .. MiRNA Isolation and Microarray Analysis MiRNA was isolated from FFPE HCC tumors using the Roche High Pure miRNA isolation kit (Roche Diagnostics, Mannheim, Germany). miRNA extraction was carried out from individual tissue blocks using seven sections of 10 microns each. ..

    Purification:

    Article Title: The impact of RNA extraction method on accurate RNA sequencing from formalin-fixed paraffin-embedded tissues
    Article Snippet: .. For FFPE samples, RNA was extracted from adjacent tissue sections for each of three commonly-used commercial kits: N – Norgen (FFPE RNA purification Kit, Norgen, Thorold, Canada), Q – Qiagen (AllPrep DNA/RNA FFPE kit, Qiagen, Valencia, CA) and R – Roche (High Pure FFPE RNA Micro Kit, Roche, Indianapolis, IN). ..

    Derivative Assay:

    Article Title: Interrogation of transcriptomic changes associated with drug-induced hepatic sinusoidal dilatation in colorectal cancer
    Article Snippet: .. Alternatively, five FFPE whole liver sections with SD present or absent derived from anti-DLL4 or vehicle-treated NHPs had RNA extracted using the High Pure FFPE RNA Micro Kit (Roche Applied Sciences, Indianapolis, IN) according to the manufacturer’s protocol. ..

    Similar Products

  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 86
    Roche high pure ffpe rna micro kit
    Development of a high-throughput microfluidic gene expression assay for analysis of <t>FFPE</t> breast tumor samples. (A) Schematic of the gene expression assay protocol. (B) Representative five-point standard curves of FFPE tumor <t>RNA</t> (red and black lines) and universal RNA (blue line) run on the breast cancer gene expression assay (slope of line indicated). (C) Intra-chip reproducibility of FFPE tumor samples run on the same 96.96 Dynamic Array. (D) Inter-chip reproducibility of the breast cancer gene expression assay assessed by comparing Ct values of universal RNA across seven independent assay runs. R-squared values are indicated in boxes.
    High Pure Ffpe Rna Micro Kit, supplied by Roche, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/high pure ffpe rna micro kit/product/Roche
    Average 86 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    high pure ffpe rna micro kit - by Bioz Stars, 2021-09
    86/100 stars
      Buy from Supplier

    86
    Roche high pure mirna isolation kit
    miR-494 is associated with <t>HCC</t> EMT and vascular invasion in human HCC tumors. (A) Analysis of miR-494 expression of 91 VI − and 81 VI + HCC tumors by qRT-PCR. (B) Vascular invasion is associated with higher miR-494 levels in human HCC tumors. Human HCC tumor samples were classified into two groups according to low and high miR-494 expression levels by median division of qRT-PCR results. (C) Representative Images of immunohistochemical staining for vimentin, E-cadherin, 5hmC, and TET1 in HCC tumors with low (miR-494 low ) and high miR-494 (miR-494 high ) expression levels. Scale bars, 100 μm. (D) Bioluminescent images showed a suppression of tumor formation in nude mice implanted with miR-494 knockdown SNU449-Luc cells (n = 5 for each group). (E) Suppression of lung metastasis in nude mice implanted with miR-494 knockdown SNU449-Luc cells was monitored by ex vivo bioluminescent imaging. Luciferase activity of lung metastasis was quantified for anti-miR-494 or anti-miR control group (n = 7 for each group). (F) Schematic presentation of miR-494 action in HCC EMT and vascular invasion. miR-494 suppresses multiple invasion-suppressor <t>miRNAs</t> though epigenetic repression by targeting TET methylcytosine dioxygenase in invasive human hepatocarcinoma tumors.
    High Pure Mirna Isolation Kit, supplied by Roche, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/high pure mirna isolation kit/product/Roche
    Average 86 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    high pure mirna isolation kit - by Bioz Stars, 2021-09
    86/100 stars
      Buy from Supplier

    Image Search Results


    Development of a high-throughput microfluidic gene expression assay for analysis of FFPE breast tumor samples. (A) Schematic of the gene expression assay protocol. (B) Representative five-point standard curves of FFPE tumor RNA (red and black lines) and universal RNA (blue line) run on the breast cancer gene expression assay (slope of line indicated). (C) Intra-chip reproducibility of FFPE tumor samples run on the same 96.96 Dynamic Array. (D) Inter-chip reproducibility of the breast cancer gene expression assay assessed by comparing Ct values of universal RNA across seven independent assay runs. R-squared values are indicated in boxes.

    Journal: PLoS ONE

    Article Title: Targeted Biomarker Profiling of Matched Primary and Metastatic Estrogen Receptor Positive Breast Cancers

    doi: 10.1371/journal.pone.0088401

    Figure Lengend Snippet: Development of a high-throughput microfluidic gene expression assay for analysis of FFPE breast tumor samples. (A) Schematic of the gene expression assay protocol. (B) Representative five-point standard curves of FFPE tumor RNA (red and black lines) and universal RNA (blue line) run on the breast cancer gene expression assay (slope of line indicated). (C) Intra-chip reproducibility of FFPE tumor samples run on the same 96.96 Dynamic Array. (D) Inter-chip reproducibility of the breast cancer gene expression assay assessed by comparing Ct values of universal RNA across seven independent assay runs. R-squared values are indicated in boxes.

    Article Snippet: RNA was isolated using the High Pure FFPE RNA Micro Kit (Roche Applied Sciences, Indianapolis, IN) according to the manufacturer’s protocol.

    Techniques: High Throughput Screening Assay, Expressing, Formalin-fixed Paraffin-Embedded, Chromatin Immunoprecipitation

    Concordance of gene expression between FFPE and FF samples for wtRNAseq data. a Distribution of concordance correlation coefficient (CCC) for all genes within each RNA extraction kit used. b Association between gene expression and CCC value. c High expression (normalized expression higher than − 7.5) and high concordant (CCC > 0.5) genes between different kits. d Concordance of molecular signatures scores for 3 FFPE kits in comparison to FF

    Journal: BMC Cancer

    Article Title: The impact of RNA extraction method on accurate RNA sequencing from formalin-fixed paraffin-embedded tissues

    doi: 10.1186/s12885-019-6363-0

    Figure Lengend Snippet: Concordance of gene expression between FFPE and FF samples for wtRNAseq data. a Distribution of concordance correlation coefficient (CCC) for all genes within each RNA extraction kit used. b Association between gene expression and CCC value. c High expression (normalized expression higher than − 7.5) and high concordant (CCC > 0.5) genes between different kits. d Concordance of molecular signatures scores for 3 FFPE kits in comparison to FF

    Article Snippet: For FFPE samples, RNA was extracted from adjacent tissue sections for each of three commonly-used commercial kits: N – Norgen (FFPE RNA purification Kit, Norgen, Thorold, Canada), Q – Qiagen (AllPrep DNA/RNA FFPE kit, Qiagen, Valencia, CA) and R – Roche (High Pure FFPE RNA Micro Kit, Roche, Indianapolis, IN).

    Techniques: Expressing, Formalin-fixed Paraffin-Embedded, Countercurrent Chromatography, RNA Extraction

    Technical validation of the bladder cancer panel. (A) Bar chart reflecting the failure counts for each of the assays on the bladder cancer panel, as determined by the number of times an assay failed to produce a measurable signal above background in 664 attempted measurements. (B) CV calculations from triplicate experimental measurements using standard deviation over the mean expression values for each of the assays on the panel. (C) Chip-to-chip data reproducibility for high quality control uRNA samples from different runs. (D) Run to run data reproducibility for archival tissues, as seen for two representative FFPE-derived RNA samples run on different days.

    Journal: PLoS ONE

    Article Title: Development and Application of a Microfluidics-Based Panel in the Basal/Luminal Transcriptional Characterization of Archival Bladder Cancers

    doi: 10.1371/journal.pone.0165856

    Figure Lengend Snippet: Technical validation of the bladder cancer panel. (A) Bar chart reflecting the failure counts for each of the assays on the bladder cancer panel, as determined by the number of times an assay failed to produce a measurable signal above background in 664 attempted measurements. (B) CV calculations from triplicate experimental measurements using standard deviation over the mean expression values for each of the assays on the panel. (C) Chip-to-chip data reproducibility for high quality control uRNA samples from different runs. (D) Run to run data reproducibility for archival tissues, as seen for two representative FFPE-derived RNA samples run on different days.

    Article Snippet: Expression analysis of FFPE tissues Gene expression analysis was carried out on RNA extracted from macro-dissected FFPE tissues using the High Pure FFPE RNA Micro Kit (Roche Diagnostics, Indianapolis, IN) after de-paraffinization with Envirene, as described previously [ ].

    Techniques: Standard Deviation, Expressing, Chromatin Immunoprecipitation, Formalin-fixed Paraffin-Embedded, Derivative Assay

    miR-494 is associated with HCC EMT and vascular invasion in human HCC tumors. (A) Analysis of miR-494 expression of 91 VI − and 81 VI + HCC tumors by qRT-PCR. (B) Vascular invasion is associated with higher miR-494 levels in human HCC tumors. Human HCC tumor samples were classified into two groups according to low and high miR-494 expression levels by median division of qRT-PCR results. (C) Representative Images of immunohistochemical staining for vimentin, E-cadherin, 5hmC, and TET1 in HCC tumors with low (miR-494 low ) and high miR-494 (miR-494 high ) expression levels. Scale bars, 100 μm. (D) Bioluminescent images showed a suppression of tumor formation in nude mice implanted with miR-494 knockdown SNU449-Luc cells (n = 5 for each group). (E) Suppression of lung metastasis in nude mice implanted with miR-494 knockdown SNU449-Luc cells was monitored by ex vivo bioluminescent imaging. Luciferase activity of lung metastasis was quantified for anti-miR-494 or anti-miR control group (n = 7 for each group). (F) Schematic presentation of miR-494 action in HCC EMT and vascular invasion. miR-494 suppresses multiple invasion-suppressor miRNAs though epigenetic repression by targeting TET methylcytosine dioxygenase in invasive human hepatocarcinoma tumors.

    Journal: Hepatology (Baltimore, Md.)

    Article Title: MicroRNA-494 is a master epigenetic regulator of multiple invasion-suppressor microRNAs by targeting ten eleven translocation 1 in invasive human hepatocellular carcinoma tumors

    doi: 10.1002/hep.27816

    Figure Lengend Snippet: miR-494 is associated with HCC EMT and vascular invasion in human HCC tumors. (A) Analysis of miR-494 expression of 91 VI − and 81 VI + HCC tumors by qRT-PCR. (B) Vascular invasion is associated with higher miR-494 levels in human HCC tumors. Human HCC tumor samples were classified into two groups according to low and high miR-494 expression levels by median division of qRT-PCR results. (C) Representative Images of immunohistochemical staining for vimentin, E-cadherin, 5hmC, and TET1 in HCC tumors with low (miR-494 low ) and high miR-494 (miR-494 high ) expression levels. Scale bars, 100 μm. (D) Bioluminescent images showed a suppression of tumor formation in nude mice implanted with miR-494 knockdown SNU449-Luc cells (n = 5 for each group). (E) Suppression of lung metastasis in nude mice implanted with miR-494 knockdown SNU449-Luc cells was monitored by ex vivo bioluminescent imaging. Luciferase activity of lung metastasis was quantified for anti-miR-494 or anti-miR control group (n = 7 for each group). (F) Schematic presentation of miR-494 action in HCC EMT and vascular invasion. miR-494 suppresses multiple invasion-suppressor miRNAs though epigenetic repression by targeting TET methylcytosine dioxygenase in invasive human hepatocarcinoma tumors.

    Article Snippet: MiRNA Isolation and Microarray Analysis MiRNA was isolated from FFPE HCC tumors using the Roche High Pure miRNA isolation kit (Roche Diagnostics, Mannheim, Germany). miRNA extraction was carried out from individual tissue blocks using seven sections of 10 microns each.

    Techniques: Expressing, Quantitative RT-PCR, Immunohistochemistry, Staining, Mouse Assay, Ex Vivo, Imaging, Luciferase, Activity Assay

    miR-494, associated with poor clinical outcome, is the most up-regulated miRNA in invasive human HCC tumors and cell lines. (A) Representative photomicrographs of human HCC without and with vascular invasion. Left panel, HCC tumor capsule without vascular invasion. Right panel, HCC tumor with vascular invasion. (B) Kaplan-Meier’s plot shows recurrence-free survival of patients who carried at least 1 tumor with vascular invasion, and that of those patients who only carried tumor(s) without vascular invasion. Total HCC patient numbers are 86. (C, D, and E) Hierarchical clustering of differentially expressed miRNAs. miR-494 is indicated by an arrowhead. (C) Data set 1 includes 23 human HCC tumors with vascular invasion (yellow bars) and 34 tumors without vascular invasion (blue bars). (D) Data set 2 includes 58 human HCC tumors with vascular invasion (yellow bars) and 57 tumors without vascular invasion (blue bars). (E) Data set 3 includes two high-invasive human HCC cell lines (SNU423 and SNU449) and three low-invasive cell lines (HepG2, Hep3B, and SNU398). (F) Venn diagram identifies overlapped differentially expressed miRNAs among data sets 1, 2, and 3. (G) Kaplan-Meier’s plot represents recurrence-free survival of HCC patients who carried at least 1 tumor with high expression of miR-494 and that of those patients who only carried tumor(s) with low miR-494 expression. Total HCC patient numbers are 86.

    Journal: Hepatology (Baltimore, Md.)

    Article Title: MicroRNA-494 is a master epigenetic regulator of multiple invasion-suppressor microRNAs by targeting ten eleven translocation 1 in invasive human hepatocellular carcinoma tumors

    doi: 10.1002/hep.27816

    Figure Lengend Snippet: miR-494, associated with poor clinical outcome, is the most up-regulated miRNA in invasive human HCC tumors and cell lines. (A) Representative photomicrographs of human HCC without and with vascular invasion. Left panel, HCC tumor capsule without vascular invasion. Right panel, HCC tumor with vascular invasion. (B) Kaplan-Meier’s plot shows recurrence-free survival of patients who carried at least 1 tumor with vascular invasion, and that of those patients who only carried tumor(s) without vascular invasion. Total HCC patient numbers are 86. (C, D, and E) Hierarchical clustering of differentially expressed miRNAs. miR-494 is indicated by an arrowhead. (C) Data set 1 includes 23 human HCC tumors with vascular invasion (yellow bars) and 34 tumors without vascular invasion (blue bars). (D) Data set 2 includes 58 human HCC tumors with vascular invasion (yellow bars) and 57 tumors without vascular invasion (blue bars). (E) Data set 3 includes two high-invasive human HCC cell lines (SNU423 and SNU449) and three low-invasive cell lines (HepG2, Hep3B, and SNU398). (F) Venn diagram identifies overlapped differentially expressed miRNAs among data sets 1, 2, and 3. (G) Kaplan-Meier’s plot represents recurrence-free survival of HCC patients who carried at least 1 tumor with high expression of miR-494 and that of those patients who only carried tumor(s) with low miR-494 expression. Total HCC patient numbers are 86.

    Article Snippet: MiRNA Isolation and Microarray Analysis MiRNA was isolated from FFPE HCC tumors using the Roche High Pure miRNA isolation kit (Roche Diagnostics, Mannheim, Germany). miRNA extraction was carried out from individual tissue blocks using seven sections of 10 microns each.

    Techniques: Expressing

    TET methylcytosine dioxygenase is essential for inhibition of miR-494-mediated HCC invasion/EMT and suppression of multiple invasion-suppressor miRNAs. (A) SNU449 cells transduced with the combination of anti-miR-494, TET1 (wild-type), or negative controls (anti-miR control and catalytic-dead TET1m mutant) and (B) HepG2 cells transduced with the combination of miR-494, TET1, or negative controls (anti-miR control and catalytic-dead TET1m mutant) were subjected to cell invasion assay. Migrated cells in fields were quantified and representative photographs are shown. Data are represented as mean ± standard deviation (SD) from four independent experiments. (C) Cell lysates from HepG2 cells infected with the combination of the miR-494 with TET1 or the control vector were subjected to western blotting for the indicated proteins. (D) qRT-PCR analysis of invasion-suppressor miRNAs with total RNAs isolated from HepG2 cells transduced with the combination of miR-494 with TET1 or the empty vector. Data are represented as mean ± SD from five independent experiments. (E) gDNA isolated from HepG2 cells transduced with the combination of miR-494 with TET1 or TET3 expression vector was denatured and neutralized. 5hmC levels were determined by the dot blot assay using anti-5hmC antibody. (F and G) SNU449 cells expressing a combination of the control and anti-miR-494 and the TET1 short hairpin RNA (shRNA) expression vector were subjected to either (F) western blotting analysis of TET1 or (G) cell invasion assay. Data are represented as mean ± SD from five independent experiments. * P

    Journal: Hepatology (Baltimore, Md.)

    Article Title: MicroRNA-494 is a master epigenetic regulator of multiple invasion-suppressor microRNAs by targeting ten eleven translocation 1 in invasive human hepatocellular carcinoma tumors

    doi: 10.1002/hep.27816

    Figure Lengend Snippet: TET methylcytosine dioxygenase is essential for inhibition of miR-494-mediated HCC invasion/EMT and suppression of multiple invasion-suppressor miRNAs. (A) SNU449 cells transduced with the combination of anti-miR-494, TET1 (wild-type), or negative controls (anti-miR control and catalytic-dead TET1m mutant) and (B) HepG2 cells transduced with the combination of miR-494, TET1, or negative controls (anti-miR control and catalytic-dead TET1m mutant) were subjected to cell invasion assay. Migrated cells in fields were quantified and representative photographs are shown. Data are represented as mean ± standard deviation (SD) from four independent experiments. (C) Cell lysates from HepG2 cells infected with the combination of the miR-494 with TET1 or the control vector were subjected to western blotting for the indicated proteins. (D) qRT-PCR analysis of invasion-suppressor miRNAs with total RNAs isolated from HepG2 cells transduced with the combination of miR-494 with TET1 or the empty vector. Data are represented as mean ± SD from five independent experiments. (E) gDNA isolated from HepG2 cells transduced with the combination of miR-494 with TET1 or TET3 expression vector was denatured and neutralized. 5hmC levels were determined by the dot blot assay using anti-5hmC antibody. (F and G) SNU449 cells expressing a combination of the control and anti-miR-494 and the TET1 short hairpin RNA (shRNA) expression vector were subjected to either (F) western blotting analysis of TET1 or (G) cell invasion assay. Data are represented as mean ± SD from five independent experiments. * P

    Article Snippet: MiRNA Isolation and Microarray Analysis MiRNA was isolated from FFPE HCC tumors using the Roche High Pure miRNA isolation kit (Roche Diagnostics, Mannheim, Germany). miRNA extraction was carried out from individual tissue blocks using seven sections of 10 microns each.

    Techniques: Inhibition, Transduction, Mutagenesis, Invasion Assay, Standard Deviation, Infection, Plasmid Preparation, Western Blot, Quantitative RT-PCR, Isolation, Expressing, Dot Blot, shRNA

    Knockdown of miR-494 or TET1 impacts on HCC cell invasion ability and expression of multiple invasion-suppressor miRNAs. (A and B) (A) SNU449 cells or (B) SNU423 cells, stably transduced with anti-miR-494 or anti-miR control vector, were subjected to cell migration and invasion assays. Migrated/invaded cells in fields were quantified and representative photographs are shown. Data are represented as mean ± standard deviation (SD) from four independent experiments. (C) Cell lysates from SNU449 cells, stably transduced with anti-miR-494 expressing vector or anti-miR control vector, were subjected to western blotting analysis for the indicated proteins. (D) qRT-PCR analysis of the indicated miRNAs with total RNAs from SNU449 cells transduced with anti-miR-494 or anti-miR control. Data are represented as mean ± SD from five independent experiments. (E) HepG2 cells transduced with the combination of miR-494, TET1 short hairpin RNA (shRNA) or the control vectors were subjected to the cell migration assay and then migrated cells were quantified. Data are represented as mean ± SD from four independent experiments. (F) Cell lysates from HepG2 cells transduced with TET1 shRNA or the scrambled control vector were subjected to western blotting analysis for the indicated proteins. (G) qRT-PCR analysis of invasion-suppressor miRNAs with total RNAs isolated from HepG2 transduced with TET1 short hairpin RNA (shRNA) and the scrambled control. Data are represented as mean ± SD from five independent experiments. * P

    Journal: Hepatology (Baltimore, Md.)

    Article Title: MicroRNA-494 is a master epigenetic regulator of multiple invasion-suppressor microRNAs by targeting ten eleven translocation 1 in invasive human hepatocellular carcinoma tumors

    doi: 10.1002/hep.27816

    Figure Lengend Snippet: Knockdown of miR-494 or TET1 impacts on HCC cell invasion ability and expression of multiple invasion-suppressor miRNAs. (A and B) (A) SNU449 cells or (B) SNU423 cells, stably transduced with anti-miR-494 or anti-miR control vector, were subjected to cell migration and invasion assays. Migrated/invaded cells in fields were quantified and representative photographs are shown. Data are represented as mean ± standard deviation (SD) from four independent experiments. (C) Cell lysates from SNU449 cells, stably transduced with anti-miR-494 expressing vector or anti-miR control vector, were subjected to western blotting analysis for the indicated proteins. (D) qRT-PCR analysis of the indicated miRNAs with total RNAs from SNU449 cells transduced with anti-miR-494 or anti-miR control. Data are represented as mean ± SD from five independent experiments. (E) HepG2 cells transduced with the combination of miR-494, TET1 short hairpin RNA (shRNA) or the control vectors were subjected to the cell migration assay and then migrated cells were quantified. Data are represented as mean ± SD from four independent experiments. (F) Cell lysates from HepG2 cells transduced with TET1 shRNA or the scrambled control vector were subjected to western blotting analysis for the indicated proteins. (G) qRT-PCR analysis of invasion-suppressor miRNAs with total RNAs isolated from HepG2 transduced with TET1 short hairpin RNA (shRNA) and the scrambled control. Data are represented as mean ± SD from five independent experiments. * P

    Article Snippet: MiRNA Isolation and Microarray Analysis MiRNA was isolated from FFPE HCC tumors using the Roche High Pure miRNA isolation kit (Roche Diagnostics, Mannheim, Germany). miRNA extraction was carried out from individual tissue blocks using seven sections of 10 microns each.

    Techniques: Expressing, Stable Transfection, Transduction, Plasmid Preparation, Migration, Standard Deviation, Western Blot, Quantitative RT-PCR, shRNA, Cell Migration Assay, Isolation

    miR-494 triggers gene inactivation of multiple invasion-suppressor microRNAs by targeting TET methylcytosine dioxygenase. (A) A list of selected high-scoring predicted miR-494 targets was produced by various programs using different algorithms. (B) Cell lysates isolated from five HCC cell lines were subjected to western blotting analysis for TET1, TET2, and TET3 proteins. (C and D) Total RNAs or cell lysates isolated from HepG2 cells transfected with miR-494 mimic or (C) SNU449 cells transfected with miR-494 inhibitor (D) were subjected to qRT-PCR or western blotting analysis for TET1, TET2, and TET3 mRNA. Data are represented as mean ± standard deviation (SD) from five independent experiments. (E) Putative binding sites of miR-494 in TET1 3′ UTR. Predicted 8- or 7-mer binding seeds of miR-494 to TET1 3′ UTR are indicated with vertical lines. (F) Luciferase assay of the TET1 3′ UTR luciferase plasmid. CV-1 cells were transiently cotransfected with the wild-type or miR-494-binding mutant of human TET1 3′ UTR luciferase plasmid with Renilla luciferase reporter for normalization. Data are represented as mean ± SD from four independent experiments. Putative miR-494-binding site on the 242-248 base-pair region of TET1 3′ UTR was mutated as indicated. (G) gDNA purified from HepG2 cells transfected with miR-494 or TET1 short hairpin RNA-expressing vector or the negative control was denatured and neutralized. Global 5hmC levels were then determined using a dot blot assay with anti-5hmC antibody. * P

    Journal: Hepatology (Baltimore, Md.)

    Article Title: MicroRNA-494 is a master epigenetic regulator of multiple invasion-suppressor microRNAs by targeting ten eleven translocation 1 in invasive human hepatocellular carcinoma tumors

    doi: 10.1002/hep.27816

    Figure Lengend Snippet: miR-494 triggers gene inactivation of multiple invasion-suppressor microRNAs by targeting TET methylcytosine dioxygenase. (A) A list of selected high-scoring predicted miR-494 targets was produced by various programs using different algorithms. (B) Cell lysates isolated from five HCC cell lines were subjected to western blotting analysis for TET1, TET2, and TET3 proteins. (C and D) Total RNAs or cell lysates isolated from HepG2 cells transfected with miR-494 mimic or (C) SNU449 cells transfected with miR-494 inhibitor (D) were subjected to qRT-PCR or western blotting analysis for TET1, TET2, and TET3 mRNA. Data are represented as mean ± standard deviation (SD) from five independent experiments. (E) Putative binding sites of miR-494 in TET1 3′ UTR. Predicted 8- or 7-mer binding seeds of miR-494 to TET1 3′ UTR are indicated with vertical lines. (F) Luciferase assay of the TET1 3′ UTR luciferase plasmid. CV-1 cells were transiently cotransfected with the wild-type or miR-494-binding mutant of human TET1 3′ UTR luciferase plasmid with Renilla luciferase reporter for normalization. Data are represented as mean ± SD from four independent experiments. Putative miR-494-binding site on the 242-248 base-pair region of TET1 3′ UTR was mutated as indicated. (G) gDNA purified from HepG2 cells transfected with miR-494 or TET1 short hairpin RNA-expressing vector or the negative control was denatured and neutralized. Global 5hmC levels were then determined using a dot blot assay with anti-5hmC antibody. * P

    Article Snippet: MiRNA Isolation and Microarray Analysis MiRNA was isolated from FFPE HCC tumors using the Roche High Pure miRNA isolation kit (Roche Diagnostics, Mannheim, Germany). miRNA extraction was carried out from individual tissue blocks using seven sections of 10 microns each.

    Techniques: Produced, Isolation, Western Blot, Transfection, Quantitative RT-PCR, Standard Deviation, Binding Assay, Luciferase, Plasmid Preparation, Mutagenesis, Purification, shRNA, Expressing, Negative Control, Dot Blot

    miR-494 promotes HCC cell migration/invasion and suppresses multiple invasion-suppressor microRNAs by inhibiting DNA demethylation of their proximal CpG islands. (A, B, and C) (A) HepG2 cells, (B) Hep3B cells, or (C) SNU398 cells, transduced with miR-494 or the nontarget control vector, were subjected to cell migration and invasion assays. Migrated/invaded cells in fields were quantified and representative photographs are shown. Data are represented as mean ± standard deviation (SD) from four independent experiments. (D and E) qRT-PCR analysis of RNAs from HepG2 cells transduced with miR-494-expressing vector or the nontarget control vector for (D) indicated biomarkers of EMT and (E) indicated microRNAs. (F) Methylation-specific PCR analysis of the proximal CpG island regions of the indicated miRNA genes with gDNAs purified from HepG2 cells transduced with the miR-494 expression vector. PBGD served as the control. (G) DNA methylation status of the proximal CpG regions of the indicated miRNA genes in HepG2 cells transduced with either miR-494-expressing vector or the nontarget control vector. DNA methylation status was determined using methylation-sensitive/dependent restriction digestion followed by qRT-PCR analysis. Data are represented as mean ± SD from three independent experiments. (H) Restored expression of miR-200c upon adding DNA demethylating agent 5′-Aza in HepG2 cells transduced with the miR-494-expressing vector. Data are represented as mean ± SD from five independent experiments. (I) GlucMS-qPCR analysis of proximal CpG islands within the indicated miRNA gene’s upstream regions enriched for 5hmC in HepG2 cells transduced with the miR-494-expressing vector. Data are represented as mean ± SD from five independent experiments. ** P

    Journal: Hepatology (Baltimore, Md.)

    Article Title: MicroRNA-494 is a master epigenetic regulator of multiple invasion-suppressor microRNAs by targeting ten eleven translocation 1 in invasive human hepatocellular carcinoma tumors

    doi: 10.1002/hep.27816

    Figure Lengend Snippet: miR-494 promotes HCC cell migration/invasion and suppresses multiple invasion-suppressor microRNAs by inhibiting DNA demethylation of their proximal CpG islands. (A, B, and C) (A) HepG2 cells, (B) Hep3B cells, or (C) SNU398 cells, transduced with miR-494 or the nontarget control vector, were subjected to cell migration and invasion assays. Migrated/invaded cells in fields were quantified and representative photographs are shown. Data are represented as mean ± standard deviation (SD) from four independent experiments. (D and E) qRT-PCR analysis of RNAs from HepG2 cells transduced with miR-494-expressing vector or the nontarget control vector for (D) indicated biomarkers of EMT and (E) indicated microRNAs. (F) Methylation-specific PCR analysis of the proximal CpG island regions of the indicated miRNA genes with gDNAs purified from HepG2 cells transduced with the miR-494 expression vector. PBGD served as the control. (G) DNA methylation status of the proximal CpG regions of the indicated miRNA genes in HepG2 cells transduced with either miR-494-expressing vector or the nontarget control vector. DNA methylation status was determined using methylation-sensitive/dependent restriction digestion followed by qRT-PCR analysis. Data are represented as mean ± SD from three independent experiments. (H) Restored expression of miR-200c upon adding DNA demethylating agent 5′-Aza in HepG2 cells transduced with the miR-494-expressing vector. Data are represented as mean ± SD from five independent experiments. (I) GlucMS-qPCR analysis of proximal CpG islands within the indicated miRNA gene’s upstream regions enriched for 5hmC in HepG2 cells transduced with the miR-494-expressing vector. Data are represented as mean ± SD from five independent experiments. ** P

    Article Snippet: MiRNA Isolation and Microarray Analysis MiRNA was isolated from FFPE HCC tumors using the Roche High Pure miRNA isolation kit (Roche Diagnostics, Mannheim, Germany). miRNA extraction was carried out from individual tissue blocks using seven sections of 10 microns each.

    Techniques: Migration, Transduction, Plasmid Preparation, Standard Deviation, Quantitative RT-PCR, Expressing, Methylation, Polymerase Chain Reaction, Purification, DNA Methylation Assay, Real-time Polymerase Chain Reaction