Structured Review

Illumina Inc deep sequencing
Deep Sequencing, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 97/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/deep sequencing/product/Illumina Inc
Average 97 stars, based on 5 article reviews
Price from $9.99 to $1999.99
deep sequencing - by Bioz Stars, 2020-02
97/100 stars

Images

Related Articles

Amplification:

Article Title: DNA Methylation Profiling in Inflammatory Bowel Disease Provides New Insights into Disease Pathogenesis
Article Snippet: Samples were amplified by the bisulphite–polymerase chain reaction (PCR) (HotStar Taq Polymerase, Qiagen) and sequenced using the Pyrosequencing PSQ96 HS System (Qiagen) with an assay developed by Epigendx. .. Correlation between DNA methylation levels at cg01476222 CpG sites estimated by pyrosequencing and the Illumina 450K BeadChip array was calculated using Spearman’s rank correlation coefficient.

Article Title: Massively parallel sequencing for monitoring genetic consistency and quality control of live viral vaccines
Article Snippet: Therefore, mutants at roughly 0.1% represent intrinsic errors of sequencing procedures and mutations introduced by PCR amplification. .. Various characteristics of both datasets shown in demonstrate that the average sequence length was significantly higher for pyrosequencing (195 vs. 38), but the Illumina method produced roughly 60 times more sequence information.

Functional Assay:

Article Title: A comprehensive metatranscriptome analysis pipeline and its validation using human small intestine microbiota datasets
Article Snippet: The reads were assigned to phylogenetic levels at species (Red diamond), genus (Green triangle), family (Blue circle), order (Orange asterisk), class (Pink circle), phylum (Skyblue plus), and to functional COG (Violet square). .. Click here for file Additional file 6: Figure S4 Genus phylogenetic profiling of datasets A and B. Phylogenetic profiling of detected bacterial genera in the 16S rDNA and rRNA sequences obtained from pyrosequencing (a) and for mRNA reads obtained from Illumina sequencing (b).

Article Title: Functional Assays and Metagenomic Analyses Reveals Differences between the Microbial Communities Inhabiting the Soil Horizons of a Norway Spruce Plantation
Article Snippet: The objectives were to assess whether the decreasing nutrient bioavailability and pH variations that naturally occurs between the organic and mineral horizons affects the soil microbial functional biodiversity. .. The 14 Gbp of pyrosequencing and Illumina sequences generated in this study revealed complex microbial communities dominated by bacteria.

Selection:

Article Title: In-solution hybrid capture of bisulfite-converted DNA for targeted bisulfite sequencing of 174 ADME genes
Article Snippet: Our custom SureSelect library contains a substantial proportion of AT-rich baits, as the selection of genomic regions of interest was based solely on the coordinates of ADME genes, and it was not skewed towards a certain specific CpG density. .. The validation of the DNA methylation data obtained from the NGS study with both pyrosequencing and Illumina 450K BeadChip assay shows strong correlations (see ).

Article Title: Quantitative genome re-sequencing defines multiple mutations conferring chloroquine resistance in rodent malaria
Article Snippet: .. Abbreviations AAT1: amino acid transporter 1; ABC: ATP-binding cassette; CQ: chloroquine; CQ-R: chloroquine resistant: chloroquine resistance; CQ-hiR: high level chloroquine resistance; CRT: chloroquine resistance transporter; DV: digestive vacuole; LGS: linkage group selection; LGS-pyro: LGS analysed by pyrosequencing; LGS-Illumina: LGS analysed by quantitative Illumina whole-genome sequencing; Pgh-1: P-glycoprotein homologue-1; QTL: quantitative trait loci; SNP: single nucleotide polymorphism; TM: transmembrane; WGS: whole genome (re-)sequencing; WTSI: Wellcome Trust Sanger Institute. ..

RNA Sequencing Assay:

Article Title: microRNA-181a has a critical role in ovarian cancer progression through the regulation of the epithelial-mesenchymal transition
Article Snippet: .. miR-181a is a novel modulator of the TGF-β signalling pathway To identify the cellular pathways modulated by miR-181a and define specific targets driving the observed EMT phenotype, we performed high-throughput RNA sequencing (Illumina) on A2780 pBABE and p181a cell lines with a combination of computational target prediction, global transcriptome- and pathway-based analysis. ..

Methylation:

Article Title: In-solution hybrid capture of bisulfite-converted DNA for targeted bisulfite sequencing of 174 ADME genes
Article Snippet: .. Validation of methylation data The validity of the CpG methylation levels produced by the NGS of our target-enriched samples as well as the bioinformatics analysis was confirmed with two individual techniques, both by pyrosequencing of selected DNA fragments, and by comparison with methylation values produced by the Illumina 450 K Methylation BeadChips. .. Pyrosequening, which is generally considered to be a very precise method for the quantification of DNA methylation, was used to validate the results retrieved from three genomic regions, which were randomly selected among those analysed with read depth ≥100×.

Article Title: In-solution hybrid capture of bisulfite-converted DNA for targeted bisulfite sequencing of 174 ADME genes
Article Snippet: Despite these complications, we were able to assess the methylation levels of 41 922 CpG sites in target regions with sufficient fidelity. .. The validation of the DNA methylation data obtained from the NGS study with both pyrosequencing and Illumina 450K BeadChip assay shows strong correlations (see ).

Article Title: DNA Methylation Profiling in Inflammatory Bowel Disease Provides New Insights into Disease Pathogenesis
Article Snippet: The percentage of methylation was calculated for each CpG site as methylated cytosine divided by the sum of methylated and unmethylated cytosines. .. Correlation between DNA methylation levels at cg01476222 CpG sites estimated by pyrosequencing and the Illumina 450K BeadChip array was calculated using Spearman’s rank correlation coefficient.

Article Title: Multilocus loss of DNA methylation in individuals with mutations in the histone H3 Lysine 4 Demethylase KDM5C
Article Snippet: Targeted validation by pyrosequencing We have previously shown that validation of Illumina HumanMethylation27 CpG methylation by bisulfite pyrosequencing demonstrates high correlation between the two methods and methylation determined by Illumina microarray is a good predictor of regional CpG methylation in CpG islands [ ]. .. Using pyrosequencing, we validated the direction of the differences for all 5 loci and observed high correlation DNA methylation levels between pyrosequencing and Illumina for overlapping CpG sites (R2 ranging from 0.77 to 0.98, Additional file : Figure S1).

Article Title: Silencing of GATA3 defines a novel stem cell-like subgroup of ETP-ALL
Article Snippet: .. We confirmed a high degree of concordance between pyrosequencing and the Illumina Human Methylation assay in samples analyzed in parallel on both platforms (n = 11, R 2 = .94). .. By pyrosequencing, we confirmed a higher degree of DNA methylation in GATA3low ETP-ALL (n = 19) compared to GATA3high ETP-ALL (n = 45) (mean 46 vs. 21 %, p < 0.0001).

Article Title: Distinct transcriptional control in major immunogenetic subsets of chronic lymphocytic leukemia exhibiting subset-biased global DNA methylation profiles
Article Snippet: .. Furthermore, there was a good correlation between the methylation levels as detected by the Illumina array and pyrosequencing for individual patient samples for the CD80 gene (r = 0.88). ..

Next-Generation Sequencing:

Article Title: In-solution hybrid capture of bisulfite-converted DNA for targeted bisulfite sequencing of 174 ADME genes
Article Snippet: .. Validation of methylation data The validity of the CpG methylation levels produced by the NGS of our target-enriched samples as well as the bioinformatics analysis was confirmed with two individual techniques, both by pyrosequencing of selected DNA fragments, and by comparison with methylation values produced by the Illumina 450 K Methylation BeadChips. .. Pyrosequening, which is generally considered to be a very precise method for the quantification of DNA methylation, was used to validate the results retrieved from three genomic regions, which were randomly selected among those analysed with read depth ≥100×.

Article Title: In-solution hybrid capture of bisulfite-converted DNA for targeted bisulfite sequencing of 174 ADME genes
Article Snippet: .. The validation of the DNA methylation data obtained from the NGS study with both pyrosequencing and Illumina 450K BeadChip assay shows strong correlations (see ). .. Moreover, NGS-derived DNA methylation values do not seem to manifest a systematic shift towards either hyper- or hypomethylated states of analysed DNA fragments, thus suggesting that hybrid capture of bisulfite-converted DNA is apparently not biased towards specific methylation patterns at targeted CpG sites.

Sequencing:

Article Title: A comprehensive metatranscriptome analysis pipeline and its validation using human small intestine microbiota datasets
Article Snippet: .. Click here for file Additional file 6: Figure S4 Genus phylogenetic profiling of datasets A and B. Phylogenetic profiling of detected bacterial genera in the 16S rDNA and rRNA sequences obtained from pyrosequencing (a) and for mRNA reads obtained from Illumina sequencing (b). ..

Article Title: Assessment of Metagenomic Assembly Using Simulated Next Generation Sequencing Data
Article Snippet: .. Simulated Metagenomes Metagenomic datasets were simulated for Sanger sequencing, pyrosequencing, and Illumina sequencing. .. For each sequencing technology, three metagenomes were simulated to mimic different community complexities (10, 100 and 400 genomes). ( , , , ).

Article Title: Assessing intragenomic variation of the internal transcribed spacer two: Adapting the Illumina metagenomics protocol
Article Snippet: .. Illumina sequencing vs pyrosequencing Our results demonstrated that the Illumina protocol is capable of greater depth of sequencing than 454/pyrosequencing for this unusual application of deep sequencing. ..

Article Title: microRNA-181a has a critical role in ovarian cancer progression through the regulation of the epithelial-mesenchymal transition
Article Snippet: miR-181a is a novel modulator of the TGF-β signalling pathway To identify the cellular pathways modulated by miR-181a and define specific targets driving the observed EMT phenotype, we performed high-throughput RNA sequencing (Illumina) on A2780 pBABE and p181a cell lines with a combination of computational target prediction, global transcriptome- and pathway-based analysis. .. The high-throughput mRNA sequencing data revealed alterations in the epithelial and mesenchymal markers consistent with global activation of an EMT-like genetic programme ( ).

Article Title: Massively parallel sequencing for monitoring genetic consistency and quality control of live viral vaccines
Article Snippet: .. Various characteristics of both datasets shown in demonstrate that the average sequence length was significantly higher for pyrosequencing (195 vs. 38), but the Illumina method produced roughly 60 times more sequence information. .. Therefore, the average number of times each nucleotide was sequenced was 885 for pyrosequencing and 56,650 for Illumina.

Article Title: Assessment of Metagenomic Assembly Using Simulated Next Generation Sequencing Data
Article Snippet: .. Thus, about 15 times more base pairs were generated for Illumina than for pyrosequencing, to reflect the lower cost associated with Illumina sequencing , and similarly 1.3 times more for pyrosequencing than for Sanger. .. The datasets were assembled and analyzed using SmashCommunity (pyrosequencing and Sanger) or a pipeline using freely available tools (i.e fastx toolkit , SOAPdenovo and parts of the SmashCommunity pipline) (Illumina).

Article Title: Quantitative genome re-sequencing defines multiple mutations conferring chloroquine resistance in rodent malaria
Article Snippet: .. Abbreviations AAT1: amino acid transporter 1; ABC: ATP-binding cassette; CQ: chloroquine; CQ-R: chloroquine resistant: chloroquine resistance; CQ-hiR: high level chloroquine resistance; CRT: chloroquine resistance transporter; DV: digestive vacuole; LGS: linkage group selection; LGS-pyro: LGS analysed by pyrosequencing; LGS-Illumina: LGS analysed by quantitative Illumina whole-genome sequencing; Pgh-1: P-glycoprotein homologue-1; QTL: quantitative trait loci; SNP: single nucleotide polymorphism; TM: transmembrane; WGS: whole genome (re-)sequencing; WTSI: Wellcome Trust Sanger Institute. ..

DNA Methylation Assay:

Article Title: In-solution hybrid capture of bisulfite-converted DNA for targeted bisulfite sequencing of 174 ADME genes
Article Snippet: Validation of methylation data The validity of the CpG methylation levels produced by the NGS of our target-enriched samples as well as the bioinformatics analysis was confirmed with two individual techniques, both by pyrosequencing of selected DNA fragments, and by comparison with methylation values produced by the Illumina 450 K Methylation BeadChips. .. Pyrosequening, which is generally considered to be a very precise method for the quantification of DNA methylation, was used to validate the results retrieved from three genomic regions, which were randomly selected among those analysed with read depth ≥100×.

Article Title: In-solution hybrid capture of bisulfite-converted DNA for targeted bisulfite sequencing of 174 ADME genes
Article Snippet: .. The validation of the DNA methylation data obtained from the NGS study with both pyrosequencing and Illumina 450K BeadChip assay shows strong correlations (see ). .. Moreover, NGS-derived DNA methylation values do not seem to manifest a systematic shift towards either hyper- or hypomethylated states of analysed DNA fragments, thus suggesting that hybrid capture of bisulfite-converted DNA is apparently not biased towards specific methylation patterns at targeted CpG sites.

Article Title: DNA Methylation Profiling in Inflammatory Bowel Disease Provides New Insights into Disease Pathogenesis
Article Snippet: .. Correlation between DNA methylation levels at cg01476222 CpG sites estimated by pyrosequencing and the Illumina 450K BeadChip array was calculated using Spearman’s rank correlation coefficient. .. RNA was extracted from the PBMCs of IBD patients ( n = 63) and controls ( n = 20) using an E.Z.N.A.® RNA Isolation Kit (VWR, Radnor, PA) and converted to cDNA (OmniScript, Qiagen) following the manufacturer’s instructions.

Article Title: Multilocus loss of DNA methylation in individuals with mutations in the histone H3 Lysine 4 Demethylase KDM5C
Article Snippet: .. Using pyrosequencing, we validated the direction of the differences for all 5 loci and observed high correlation DNA methylation levels between pyrosequencing and Illumina for overlapping CpG sites (R2 ranging from 0.77 to 0.98, Additional file : Figure S1). .. For FBXL5 , SCMH1, CACYBP and ZMYND2 the assays contained > 1 CpG site, and pyrosequencing data showed that DNA methylation changes affected not only the index CpG site from the array but also multiple adjacent CpGs (Figures and Additional file : Figures S6-S9).

Article Title: Silencing of GATA3 defines a novel stem cell-like subgroup of ETP-ALL
Article Snippet: Paragraph title: GATA3 silencing is mediated by aberrant DNA methylation ... We confirmed a high degree of concordance between pyrosequencing and the Illumina Human Methylation assay in samples analyzed in parallel on both platforms (n = 11, R 2 = .94).

Article Title: Distinct transcriptional control in major immunogenetic subsets of chronic lymphocytic leukemia exhibiting subset-biased global DNA methylation profiles
Article Snippet: Prompted by (1) the herein reported significant differences in methylation status of the CD80 and CD86 immune response genes and; (2) our recent immune profiling studies of subsets #1 and #4 demonstrating significantly lower CD86 expression in subset #1, we sought to evaluate further the DNA methylation levels for CD80 and CD86 by a quantitative method using pyrosequencing technology in subset #1 and #4 CLL patient samples. .. Furthermore, there was a good correlation between the methylation levels as detected by the Illumina array and pyrosequencing for individual patient samples for the CD80 gene (r = 0.88).

Produced:

Article Title: In-solution hybrid capture of bisulfite-converted DNA for targeted bisulfite sequencing of 174 ADME genes
Article Snippet: .. Validation of methylation data The validity of the CpG methylation levels produced by the NGS of our target-enriched samples as well as the bioinformatics analysis was confirmed with two individual techniques, both by pyrosequencing of selected DNA fragments, and by comparison with methylation values produced by the Illumina 450 K Methylation BeadChips. .. Pyrosequening, which is generally considered to be a very precise method for the quantification of DNA methylation, was used to validate the results retrieved from three genomic regions, which were randomly selected among those analysed with read depth ≥100×.

Article Title: Massively parallel sequencing for monitoring genetic consistency and quality control of live viral vaccines
Article Snippet: .. Various characteristics of both datasets shown in demonstrate that the average sequence length was significantly higher for pyrosequencing (195 vs. 38), but the Illumina method produced roughly 60 times more sequence information. .. Therefore, the average number of times each nucleotide was sequenced was 885 for pyrosequencing and 56,650 for Illumina.

Activation Assay:

Article Title: microRNA-181a has a critical role in ovarian cancer progression through the regulation of the epithelial-mesenchymal transition
Article Snippet: miR-181a is a novel modulator of the TGF-β signalling pathway To identify the cellular pathways modulated by miR-181a and define specific targets driving the observed EMT phenotype, we performed high-throughput RNA sequencing (Illumina) on A2780 pBABE and p181a cell lines with a combination of computational target prediction, global transcriptome- and pathway-based analysis. .. The high-throughput mRNA sequencing data revealed alterations in the epithelial and mesenchymal markers consistent with global activation of an EMT-like genetic programme ( ).

Generated:

Article Title: A comprehensive metatranscriptome analysis pipeline and its validation using human small intestine microbiota datasets
Article Snippet: Validation was performed using 10,000 random in silico reads of 100bp length generated from protein-encoding sequences of fully sequenced prokaryote genomes of NCBI. .. Click here for file Additional file 6: Figure S4 Genus phylogenetic profiling of datasets A and B. Phylogenetic profiling of detected bacterial genera in the 16S rDNA and rRNA sequences obtained from pyrosequencing (a) and for mRNA reads obtained from Illumina sequencing (b).

Article Title: Assessment of Metagenomic Assembly Using Simulated Next Generation Sequencing Data
Article Snippet: Simulated Metagenomes Metagenomic datasets were simulated for Sanger sequencing, pyrosequencing, and Illumina sequencing. .. We generated metagenomes of the three sequencing platform at different sequencing depths in order to account for the price difference between the three sequencing technologies and the usual sequencing effort for metagenomic projects using each technology.

Article Title: Functional Assays and Metagenomic Analyses Reveals Differences between the Microbial Communities Inhabiting the Soil Horizons of a Norway Spruce Plantation
Article Snippet: .. The 14 Gbp of pyrosequencing and Illumina sequences generated in this study revealed complex microbial communities dominated by bacteria. ..

Article Title: Assessment of Metagenomic Assembly Using Simulated Next Generation Sequencing Data
Article Snippet: .. Thus, about 15 times more base pairs were generated for Illumina than for pyrosequencing, to reflect the lower cost associated with Illumina sequencing , and similarly 1.3 times more for pyrosequencing than for Sanger. .. The datasets were assembled and analyzed using SmashCommunity (pyrosequencing and Sanger) or a pipeline using freely available tools (i.e fastx toolkit , SOAPdenovo and parts of the SmashCommunity pipline) (Illumina).

Polymerase Chain Reaction:

Article Title: DNA Methylation Profiling in Inflammatory Bowel Disease Provides New Insights into Disease Pathogenesis
Article Snippet: Samples were amplified by the bisulphite–polymerase chain reaction (PCR) (HotStar Taq Polymerase, Qiagen) and sequenced using the Pyrosequencing PSQ96 HS System (Qiagen) with an assay developed by Epigendx. .. Correlation between DNA methylation levels at cg01476222 CpG sites estimated by pyrosequencing and the Illumina 450K BeadChip array was calculated using Spearman’s rank correlation coefficient.

Article Title: Massively parallel sequencing for monitoring genetic consistency and quality control of live viral vaccines
Article Snippet: Therefore, mutants at roughly 0.1% represent intrinsic errors of sequencing procedures and mutations introduced by PCR amplification. .. Various characteristics of both datasets shown in demonstrate that the average sequence length was significantly higher for pyrosequencing (195 vs. 38), but the Illumina method produced roughly 60 times more sequence information.

CpG Methylation Assay:

Article Title: In-solution hybrid capture of bisulfite-converted DNA for targeted bisulfite sequencing of 174 ADME genes
Article Snippet: .. Validation of methylation data The validity of the CpG methylation levels produced by the NGS of our target-enriched samples as well as the bioinformatics analysis was confirmed with two individual techniques, both by pyrosequencing of selected DNA fragments, and by comparison with methylation values produced by the Illumina 450 K Methylation BeadChips. .. Pyrosequening, which is generally considered to be a very precise method for the quantification of DNA methylation, was used to validate the results retrieved from three genomic regions, which were randomly selected among those analysed with read depth ≥100×.

Article Title: Multilocus loss of DNA methylation in individuals with mutations in the histone H3 Lysine 4 Demethylase KDM5C
Article Snippet: Targeted validation by pyrosequencing We have previously shown that validation of Illumina HumanMethylation27 CpG methylation by bisulfite pyrosequencing demonstrates high correlation between the two methods and methylation determined by Illumina microarray is a good predictor of regional CpG methylation in CpG islands [ ]. .. Using pyrosequencing, we validated the direction of the differences for all 5 loci and observed high correlation DNA methylation levels between pyrosequencing and Illumina for overlapping CpG sites (R2 ranging from 0.77 to 0.98, Additional file : Figure S1).

In Silico:

Article Title: In-solution hybrid capture of bisulfite-converted DNA for targeted bisulfite sequencing of 174 ADME genes
Article Snippet: We found that those baits, which became extremely AT-rich (GC content ≤20%) on in silico bisulfite conversion, were unlikely to ensure sufficient read depth at the corresponding CpG sites. .. The validation of the DNA methylation data obtained from the NGS study with both pyrosequencing and Illumina 450K BeadChip assay shows strong correlations (see ).

Article Title: A comprehensive metatranscriptome analysis pipeline and its validation using human small intestine microbiota datasets
Article Snippet: Validation was performed using 10,000 random in silico reads of 100bp length generated from protein-encoding sequences of fully sequenced prokaryote genomes of NCBI. .. Click here for file Additional file 6: Figure S4 Genus phylogenetic profiling of datasets A and B. Phylogenetic profiling of detected bacterial genera in the 16S rDNA and rRNA sequences obtained from pyrosequencing (a) and for mRNA reads obtained from Illumina sequencing (b).

Expressing:

Article Title: Silencing of GATA3 defines a novel stem cell-like subgroup of ETP-ALL
Article Snippet: Capturing a segment of the GATA3 CpG island (GRCh37: chr10:8097750-8098004) (Additional file : Figure S4), we assessed 64 samples of which both GATA3 mRNA expression and GATA3 DNA methylation were available. .. We confirmed a high degree of concordance between pyrosequencing and the Illumina Human Methylation assay in samples analyzed in parallel on both platforms (n = 11, R 2 = .94).

Article Title: Distinct transcriptional control in major immunogenetic subsets of chronic lymphocytic leukemia exhibiting subset-biased global DNA methylation profiles
Article Snippet: Prompted by (1) the herein reported significant differences in methylation status of the CD80 and CD86 immune response genes and; (2) our recent immune profiling studies of subsets #1 and #4 demonstrating significantly lower CD86 expression in subset #1, we sought to evaluate further the DNA methylation levels for CD80 and CD86 by a quantitative method using pyrosequencing technology in subset #1 and #4 CLL patient samples. .. Furthermore, there was a good correlation between the methylation levels as detected by the Illumina array and pyrosequencing for individual patient samples for the CD80 gene (r = 0.88).

High Throughput Screening Assay:

Article Title: microRNA-181a has a critical role in ovarian cancer progression through the regulation of the epithelial-mesenchymal transition
Article Snippet: .. miR-181a is a novel modulator of the TGF-β signalling pathway To identify the cellular pathways modulated by miR-181a and define specific targets driving the observed EMT phenotype, we performed high-throughput RNA sequencing (Illumina) on A2780 pBABE and p181a cell lines with a combination of computational target prediction, global transcriptome- and pathway-based analysis. ..

Variant Assay:

Article Title: Multilocus loss of DNA methylation in individuals with mutations in the histone H3 Lysine 4 Demethylase KDM5C
Article Snippet: Using pyrosequencing, we validated the direction of the differences for all 5 loci and observed high correlation DNA methylation levels between pyrosequencing and Illumina for overlapping CpG sites (R2 ranging from 0.77 to 0.98, Additional file : Figure S1). .. The samples carrying the p.R1546Q variant consistently exhibited the same DNA methylation patterns as controls.

Microarray:

Article Title: Multilocus loss of DNA methylation in individuals with mutations in the histone H3 Lysine 4 Demethylase KDM5C
Article Snippet: Targeted validation by pyrosequencing We have previously shown that validation of Illumina HumanMethylation27 CpG methylation by bisulfite pyrosequencing demonstrates high correlation between the two methods and methylation determined by Illumina microarray is a good predictor of regional CpG methylation in CpG islands [ ]. .. Using pyrosequencing, we validated the direction of the differences for all 5 loci and observed high correlation DNA methylation levels between pyrosequencing and Illumina for overlapping CpG sites (R2 ranging from 0.77 to 0.98, Additional file : Figure S1).

Reverse Transcription Polymerase Chain Reaction:

Article Title: Silencing of GATA3 defines a novel stem cell-like subgroup of ETP-ALL
Article Snippet: Comparing DNMT3A -mutated (n = 6) and DNMT3A wild-type (n = 6) ETP-ALL, we found lower GATA3 methylation in DNMT3A -mutated versus DNMT3A wild-type samples (16 vs. 35 %, p < 0.0001) at the GATA3 CpG island (GRCh37: chr10:8091375-8098329), but GATA3 expression, as determined by RT-PCR, was not different between the DNMT3A mutated (n = 6) and wild-type (n = 6) ETP-ALL cases (4.4 vs. 3.8, p = 0.84). .. We confirmed a high degree of concordance between pyrosequencing and the Illumina Human Methylation assay in samples analyzed in parallel on both platforms (n = 11, R 2 = .94).

Similar Products

  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 83
    Illumina Inc small rna deep sequencing approach
    Length distribution and abundance of small RNAs sequences in chicken ovary by <t>Illumina</t> small <t>RNA</t> deep sequencing. Sequence length distribution of clean reads based on the abundance and distinct sequences; the most abundant size class was 22 nt, followed by 23 nt and 21 nt.
    Small Rna Deep Sequencing Approach, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 83/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/small rna deep sequencing approach/product/Illumina Inc
    Average 83 stars, based on 5 article reviews
    Price from $9.99 to $1999.99
    small rna deep sequencing approach - by Bioz Stars, 2020-02
    83/100 stars
      Buy from Supplier

    75
    Illumina Inc microrna targeted ap2 erf genes deep sequencing
    Distribution of reads and percentage of total <t>AP2/ERF</t> contigs in the different tissue-type libraries (latex, bark, leaf, root, embryogenic tissues) in Hevea .
    Microrna Targeted Ap2 Erf Genes Deep Sequencing, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 75/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/microrna targeted ap2 erf genes deep sequencing/product/Illumina Inc
    Average 75 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    microrna targeted ap2 erf genes deep sequencing - by Bioz Stars, 2020-02
    75/100 stars
      Buy from Supplier

    99
    Illumina Inc rna deep sequencing
    Silencing of HPV18 <t>E6/E7</t> expression by <t>RNA</t> interference. (A) qRT-PCR analysis of HPV18 E6/E7 (left panel) and p21 (right panel) mRNA expression, 72 h after transfection of HeLa cells with si18E6/E7, control siRNA siContr-1, or upon mock treatment. mRNA levels were normalized to ACTB and calculated relative to the mock control. Data represent mean ± SEM (n = 4). Asterisks above columns indicate statistically significant differences from siContr-1-treated cells (p ≤ 0.05 (*), p ≤ 0.001 (***)). (B) Immunoblot analysis of HPV18 E6, p53, and p21 protein levels, 72 h after transfection of HeLa cells with si18E6/E7 or siContr-1. α-Tubulin: loading control. (C) Immunoblot analysis of HPV18 E7, total pRb (pRb), phosphorylated pRb (pRb-P), and Cyclin A1 protein levels, 72 h after transfection of HeLa cells with si18E6/E7 or siContr-1. α-Tubulin: loading control.
    Rna Deep Sequencing, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 55 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/rna deep sequencing/product/Illumina Inc
    Average 99 stars, based on 55 article reviews
    Price from $9.99 to $1999.99
    rna deep sequencing - by Bioz Stars, 2020-02
    99/100 stars
      Buy from Supplier

    Image Search Results


    Length distribution and abundance of small RNAs sequences in chicken ovary by Illumina small RNA deep sequencing. Sequence length distribution of clean reads based on the abundance and distinct sequences; the most abundant size class was 22 nt, followed by 23 nt and 21 nt.

    Journal: BMC Genomics

    Article Title: Identification of miRNAs associated with sexual maturity in chicken ovary by Illumina small RNA deep sequencing

    doi: 10.1186/1471-2164-14-352

    Figure Lengend Snippet: Length distribution and abundance of small RNAs sequences in chicken ovary by Illumina small RNA deep sequencing. Sequence length distribution of clean reads based on the abundance and distinct sequences; the most abundant size class was 22 nt, followed by 23 nt and 21 nt.

    Article Snippet: The Illumina small RNA deep sequencing approach allows us to determine the relative abundance of various miRNA families by calculating the sequencing frequency.

    Techniques: Sequencing

    qRT-PCR validation of five differentially expressed miRNAs identified using Illumina small RNA deep sequencing. A . Fold-change of five miRNAs that were differentially expressed between 42-d and 162-d ovaries based on deep sequencing data. B . The relative expression abundance of the five miRNAs between 42-d and 162- d ovaries by real-time quantitative RT-PCR. * P

    Journal: BMC Genomics

    Article Title: Identification of miRNAs associated with sexual maturity in chicken ovary by Illumina small RNA deep sequencing

    doi: 10.1186/1471-2164-14-352

    Figure Lengend Snippet: qRT-PCR validation of five differentially expressed miRNAs identified using Illumina small RNA deep sequencing. A . Fold-change of five miRNAs that were differentially expressed between 42-d and 162-d ovaries based on deep sequencing data. B . The relative expression abundance of the five miRNAs between 42-d and 162- d ovaries by real-time quantitative RT-PCR. * P

    Article Snippet: The Illumina small RNA deep sequencing approach allows us to determine the relative abundance of various miRNA families by calculating the sequencing frequency.

    Techniques: Quantitative RT-PCR, Sequencing, Expressing

    Distribution of reads and percentage of total AP2/ERF contigs in the different tissue-type libraries (latex, bark, leaf, root, embryogenic tissues) in Hevea .

    Journal: BMC Genomics

    Article Title: Identification of the Hevea brasiliensis AP2/ERF superfamily by RNA sequencing

    doi: 10.1186/1471-2164-14-30

    Figure Lengend Snippet: Distribution of reads and percentage of total AP2/ERF contigs in the different tissue-type libraries (latex, bark, leaf, root, embryogenic tissues) in Hevea .

    Article Snippet: Prediction of microRNA-targeted AP2/ERF genes Deep sequencing of Hevea was performed with Solexa/Illumina technology and led to the identification of miRNA sequences conserved between plant species and putative novel miRNAs specific to Hevea [ ] using the LeARN pipeline [ ].

    Techniques:

    Expression profile of 10 AP2/ERF genes selected for their contrasting distribution of reads for contigs in various tissues. PC: proliferating callus grown on Maintainance Medium; EC: embryogenic callus grown on Expression Medium; SE: mature somatic embryos; Le-1 m: leaf of 1-month-old plantlets; St-1 m: stem of 1-month-old plantlets; R-1 m: root of 1-month-old plantlets; Le-1y: leaf of 1-year-old plants; B-1y: bark of 1-year-old plants; R1-1y: tap-root of 1-year-old plants; R3-1y: secondary lateral root of 1-year-old plants; B-5y: bark of 5-year-old trees; La-5y: latex of 5-year-old trees. Values are the means of the relative transcript abundance of three biological replicates. The data were analysed with XLSTAT software after log transformation. Statistical analysis was performed with an ANOVA after logarithmic transformation of raw data. The ANOVA was followed by a Student Newman-Keuls test. Values with the same letter did not differ significantly at the 0.05 probability level.

    Journal: BMC Genomics

    Article Title: Identification of the Hevea brasiliensis AP2/ERF superfamily by RNA sequencing

    doi: 10.1186/1471-2164-14-30

    Figure Lengend Snippet: Expression profile of 10 AP2/ERF genes selected for their contrasting distribution of reads for contigs in various tissues. PC: proliferating callus grown on Maintainance Medium; EC: embryogenic callus grown on Expression Medium; SE: mature somatic embryos; Le-1 m: leaf of 1-month-old plantlets; St-1 m: stem of 1-month-old plantlets; R-1 m: root of 1-month-old plantlets; Le-1y: leaf of 1-year-old plants; B-1y: bark of 1-year-old plants; R1-1y: tap-root of 1-year-old plants; R3-1y: secondary lateral root of 1-year-old plants; B-5y: bark of 5-year-old trees; La-5y: latex of 5-year-old trees. Values are the means of the relative transcript abundance of three biological replicates. The data were analysed with XLSTAT software after log transformation. Statistical analysis was performed with an ANOVA after logarithmic transformation of raw data. The ANOVA was followed by a Student Newman-Keuls test. Values with the same letter did not differ significantly at the 0.05 probability level.

    Article Snippet: Prediction of microRNA-targeted AP2/ERF genes Deep sequencing of Hevea was performed with Solexa/Illumina technology and led to the identification of miRNA sequences conserved between plant species and putative novel miRNAs specific to Hevea [ ] using the LeARN pipeline [ ].

    Techniques: Expressing, Software, Transformation Assay

    Analysis of the fusion curves after real-time RT-PCR amplification for ten AP2/ERF genes.

    Journal: BMC Genomics

    Article Title: Identification of the Hevea brasiliensis AP2/ERF superfamily by RNA sequencing

    doi: 10.1186/1471-2164-14-30

    Figure Lengend Snippet: Analysis of the fusion curves after real-time RT-PCR amplification for ten AP2/ERF genes.

    Article Snippet: Prediction of microRNA-targeted AP2/ERF genes Deep sequencing of Hevea was performed with Solexa/Illumina technology and led to the identification of miRNA sequences conserved between plant species and putative novel miRNAs specific to Hevea [ ] using the LeARN pipeline [ ].

    Techniques: Quantitative RT-PCR, Amplification

    Phylogenetic tree of Hevea AP2/ERF proteins. The amino acid sequences of the AP2 domain were aligned using Muscle (Additional file 1 ), and the phylogenetic tree was constructed using the PhyML with an LG + T model. The families and groups to which the 142 AP2/ERF proteins belong are shown.

    Journal: BMC Genomics

    Article Title: Identification of the Hevea brasiliensis AP2/ERF superfamily by RNA sequencing

    doi: 10.1186/1471-2164-14-30

    Figure Lengend Snippet: Phylogenetic tree of Hevea AP2/ERF proteins. The amino acid sequences of the AP2 domain were aligned using Muscle (Additional file 1 ), and the phylogenetic tree was constructed using the PhyML with an LG + T model. The families and groups to which the 142 AP2/ERF proteins belong are shown.

    Article Snippet: Prediction of microRNA-targeted AP2/ERF genes Deep sequencing of Hevea was performed with Solexa/Illumina technology and led to the identification of miRNA sequences conserved between plant species and putative novel miRNAs specific to Hevea [ ] using the LeARN pipeline [ ].

    Techniques: Construct

    Alignment of the AP2/ERF domains in Hevea (55 representative members). Black and light grey shading indicate identical and conserved amino acid residues, respectively. Light blue shading indicates conserved amino acid residues in group VI-L. Green indicates the V14, E19 residue conserved (Yoh Sakuma,2002); blue indicates the residue conserved in each group individually; pink indicates the supplementary residue in group IX. The black bar and block arrows represent predicted a-helix and b-sheet regions, respectively, within the AP2/ERF domain (Allen et al., 1998). Asterisks represent amino acid residues that directly make contact with DNA (Allen et al., 1998). The YRG, RAYD elements are indicated according to (Okamuro, 1997).

    Journal: BMC Genomics

    Article Title: Identification of the Hevea brasiliensis AP2/ERF superfamily by RNA sequencing

    doi: 10.1186/1471-2164-14-30

    Figure Lengend Snippet: Alignment of the AP2/ERF domains in Hevea (55 representative members). Black and light grey shading indicate identical and conserved amino acid residues, respectively. Light blue shading indicates conserved amino acid residues in group VI-L. Green indicates the V14, E19 residue conserved (Yoh Sakuma,2002); blue indicates the residue conserved in each group individually; pink indicates the supplementary residue in group IX. The black bar and block arrows represent predicted a-helix and b-sheet regions, respectively, within the AP2/ERF domain (Allen et al., 1998). Asterisks represent amino acid residues that directly make contact with DNA (Allen et al., 1998). The YRG, RAYD elements are indicated according to (Okamuro, 1997).

    Article Snippet: Prediction of microRNA-targeted AP2/ERF genes Deep sequencing of Hevea was performed with Solexa/Illumina technology and led to the identification of miRNA sequences conserved between plant species and putative novel miRNAs specific to Hevea [ ] using the LeARN pipeline [ ].

    Techniques: Blocking Assay

    Distribution of reads for each AP2/ERF contig in the different tissue-type libraries (latex, bark, leaf, root, embryogenic tissues (ET) in Hevea .

    Journal: BMC Genomics

    Article Title: Identification of the Hevea brasiliensis AP2/ERF superfamily by RNA sequencing

    doi: 10.1186/1471-2164-14-30

    Figure Lengend Snippet: Distribution of reads for each AP2/ERF contig in the different tissue-type libraries (latex, bark, leaf, root, embryogenic tissues (ET) in Hevea .

    Article Snippet: Prediction of microRNA-targeted AP2/ERF genes Deep sequencing of Hevea was performed with Solexa/Illumina technology and led to the identification of miRNA sequences conserved between plant species and putative novel miRNAs specific to Hevea [ ] using the LeARN pipeline [ ].

    Techniques:

    Silencing of HPV18 E6/E7 expression by RNA interference. (A) qRT-PCR analysis of HPV18 E6/E7 (left panel) and p21 (right panel) mRNA expression, 72 h after transfection of HeLa cells with si18E6/E7, control siRNA siContr-1, or upon mock treatment. mRNA levels were normalized to ACTB and calculated relative to the mock control. Data represent mean ± SEM (n = 4). Asterisks above columns indicate statistically significant differences from siContr-1-treated cells (p ≤ 0.05 (*), p ≤ 0.001 (***)). (B) Immunoblot analysis of HPV18 E6, p53, and p21 protein levels, 72 h after transfection of HeLa cells with si18E6/E7 or siContr-1. α-Tubulin: loading control. (C) Immunoblot analysis of HPV18 E7, total pRb (pRb), phosphorylated pRb (pRb-P), and Cyclin A1 protein levels, 72 h after transfection of HeLa cells with si18E6/E7 or siContr-1. α-Tubulin: loading control.

    Journal: PLoS Pathogens

    Article Title: Dependence of Intracellular and Exosomal microRNAs on Viral E6/E7 Oncogene Expression in HPV-positive Tumor Cells

    doi: 10.1371/journal.ppat.1004712

    Figure Lengend Snippet: Silencing of HPV18 E6/E7 expression by RNA interference. (A) qRT-PCR analysis of HPV18 E6/E7 (left panel) and p21 (right panel) mRNA expression, 72 h after transfection of HeLa cells with si18E6/E7, control siRNA siContr-1, or upon mock treatment. mRNA levels were normalized to ACTB and calculated relative to the mock control. Data represent mean ± SEM (n = 4). Asterisks above columns indicate statistically significant differences from siContr-1-treated cells (p ≤ 0.05 (*), p ≤ 0.001 (***)). (B) Immunoblot analysis of HPV18 E6, p53, and p21 protein levels, 72 h after transfection of HeLa cells with si18E6/E7 or siContr-1. α-Tubulin: loading control. (C) Immunoblot analysis of HPV18 E7, total pRb (pRb), phosphorylated pRb (pRb-P), and Cyclin A1 protein levels, 72 h after transfection of HeLa cells with si18E6/E7 or siContr-1. α-Tubulin: loading control.

    Article Snippet: Next, the effects of E6/E7 expression on exosomal miRNAs—as identified by small RNA deep sequencing—were validated by qRT-PCR analyses.

    Techniques: Expressing, Quantitative RT-PCR, Transfection

    Inhibition of endogenous HPV18 E6/E7 expression: Effects on the intracellular miRNA composition of cervical cancer cells. Small RNA deep sequencing (A—D) and qRT-PCR analyses (E) of cellular miRNAs, 72 h after transfection of HeLa cells with si18E6/E7 or control siRNA siContr-1. (A) Mean read count distribution of mature miRNA sequences in si18E6/E7- and siContr-1-transfected cells (n = 2). Only miRNAs with a mean read count > 1 were considered. (B) The 15 most frequently sequenced cellular miRNAs. Selection based on siContr-1 samples, respective values for the si18E6/E7-treatment are indicated. Data represent mean ± SEM (n = 2). Interrupted x-Axis. (C) Overview on differentially affected ( > 1.5-fold) cellular miRNAs, determined by small RNA deep sequencing. RPM values of si18E6/E7-treated samples were calculated relative to the control treatment (siContr-1). Only miRNAs with > 1,000 RPM in each sample were considered (n = 2). (D) Relative quantification of miRNAs in si18E6/E7- versus siContr-1-treated cells as assessed by small RNA deep sequencing (log 2 display). Dashed lines: 1.5-fold up- or downregulation (log 2 (1.5) = 0.585). Only miRNAs with > 1,000 RPM in each sample were considered. Data represent mean ± SEM (n = 2). (E) qRT-PCR analyses of E6/E7 -dependent cellular miRNAs identified by small RNA deep sequencing. Cellular miRNA levels were normalized to snRNA RNU6–2 and calculated relative to siContr-1 (log 2 display). Dashed lines: 1.5-fold up- or downregulation (log 2 (1.5) = 0.585). The column color shows regulation in the same (dark grey) or opposite (light grey) direction compared to the small RNA deep sequencing data of the individual miRNAs. Data represent mean ± SEM (n = 2 or 3). Asterisks indicate statistically significant differences (p ≤ 0.05 (*), p ≤ 0.01 (**) and p ≤ 0.001 (***)).

    Journal: PLoS Pathogens

    Article Title: Dependence of Intracellular and Exosomal microRNAs on Viral E6/E7 Oncogene Expression in HPV-positive Tumor Cells

    doi: 10.1371/journal.ppat.1004712

    Figure Lengend Snippet: Inhibition of endogenous HPV18 E6/E7 expression: Effects on the intracellular miRNA composition of cervical cancer cells. Small RNA deep sequencing (A—D) and qRT-PCR analyses (E) of cellular miRNAs, 72 h after transfection of HeLa cells with si18E6/E7 or control siRNA siContr-1. (A) Mean read count distribution of mature miRNA sequences in si18E6/E7- and siContr-1-transfected cells (n = 2). Only miRNAs with a mean read count > 1 were considered. (B) The 15 most frequently sequenced cellular miRNAs. Selection based on siContr-1 samples, respective values for the si18E6/E7-treatment are indicated. Data represent mean ± SEM (n = 2). Interrupted x-Axis. (C) Overview on differentially affected ( > 1.5-fold) cellular miRNAs, determined by small RNA deep sequencing. RPM values of si18E6/E7-treated samples were calculated relative to the control treatment (siContr-1). Only miRNAs with > 1,000 RPM in each sample were considered (n = 2). (D) Relative quantification of miRNAs in si18E6/E7- versus siContr-1-treated cells as assessed by small RNA deep sequencing (log 2 display). Dashed lines: 1.5-fold up- or downregulation (log 2 (1.5) = 0.585). Only miRNAs with > 1,000 RPM in each sample were considered. Data represent mean ± SEM (n = 2). (E) qRT-PCR analyses of E6/E7 -dependent cellular miRNAs identified by small RNA deep sequencing. Cellular miRNA levels were normalized to snRNA RNU6–2 and calculated relative to siContr-1 (log 2 display). Dashed lines: 1.5-fold up- or downregulation (log 2 (1.5) = 0.585). The column color shows regulation in the same (dark grey) or opposite (light grey) direction compared to the small RNA deep sequencing data of the individual miRNAs. Data represent mean ± SEM (n = 2 or 3). Asterisks indicate statistically significant differences (p ≤ 0.05 (*), p ≤ 0.01 (**) and p ≤ 0.001 (***)).

    Article Snippet: Next, the effects of E6/E7 expression on exosomal miRNAs—as identified by small RNA deep sequencing—were validated by qRT-PCR analyses.

    Techniques: Inhibition, Expressing, Sequencing, Quantitative RT-PCR, Transfection, Selection

    Characterization of exosomes secreted by HeLa cells used for small RNA deep sequencing. (A) Immunoblot analysis of total cellular extract (30, 10 and 1 μg) from exosome-producing cells, and of 1 μg protein from exosome preparations. Hsc70, CD63, Annexin-1, CD9 and β-Actin: exosomal markers; EEA1: early endosome marker; GRP78: ER marker. (B) Visualization of exosomes by electron microscopy. Bar corresponds to 100 nm. (C) Characterization of cellular and exosomal RNA. Electropherograms of total RNA isolated from HeLa cells and from RNAse A-treated exosomes. Upper panel: total RNA contents; lower panel: small RNA contents. M = marker. Shown are representative images for siContr-1-treated samples.

    Journal: PLoS Pathogens

    Article Title: Dependence of Intracellular and Exosomal microRNAs on Viral E6/E7 Oncogene Expression in HPV-positive Tumor Cells

    doi: 10.1371/journal.ppat.1004712

    Figure Lengend Snippet: Characterization of exosomes secreted by HeLa cells used for small RNA deep sequencing. (A) Immunoblot analysis of total cellular extract (30, 10 and 1 μg) from exosome-producing cells, and of 1 μg protein from exosome preparations. Hsc70, CD63, Annexin-1, CD9 and β-Actin: exosomal markers; EEA1: early endosome marker; GRP78: ER marker. (B) Visualization of exosomes by electron microscopy. Bar corresponds to 100 nm. (C) Characterization of cellular and exosomal RNA. Electropherograms of total RNA isolated from HeLa cells and from RNAse A-treated exosomes. Upper panel: total RNA contents; lower panel: small RNA contents. M = marker. Shown are representative images for siContr-1-treated samples.

    Article Snippet: Next, the effects of E6/E7 expression on exosomal miRNAs—as identified by small RNA deep sequencing—were validated by qRT-PCR analyses.

    Techniques: Sequencing, Marker, Electron Microscopy, Isolation

    Inhibition of endogenous HPV18 E6/E7 expression: Effects on the miRNA composition of exosomes secreted by cervical cancer cells. Small RNA deep sequencing (A—D) and qRT-PCR analyses (E) of exosomal miRNAs, 72 h after transfection of HeLa cells with si18E6/E7 or control siRNA (siContr-1), and subsequent exosome purification from the cell culture supernatant. (A) Mean read count distribution of mature miRNA sequences in exosomes released from si18E6/E7- and siContr-1-treated HeLa cells (n = 3). Only miRNAs with a mean read count > 1 were considered. (B) The 15 most frequently sequenced exosomal miRNAs. Selection based on siContr-1 samples, respective values for si18E6/E7-treatment are indicated. Data represent mean ± SEM (n = 3). Interrupted x-Axis. (C) Overview on differentially deregulated ( > 1.5-fold) exosomal miRNAs determined by small RNA deep sequencing. RPM values of si18E6/E7-treated samples were calculated relative to the control treatment (siContr-1). Only miRNAs with > 1,000 RPM in each sample were considered (n = 2). (D) Relative quantification of miRNAs in exosomes released from si18E6/E7- versus siContr-1-treated cells, as assessed by small RNA deep sequencing (log 2 display). Dashed lines: 1.5-fold up- or downregulation (log 2 (1.5) = 0.585). Only miRNAs with > 1,000 RPM in each sample were considered. Data represent mean ± SEM (n = 3). (E) qRT-PCR analysis of E6/E7 -dependent exosomal miRNAs identified by small RNA deep sequencing. Exosomal miRNA levels were normalized to miR-452–5p and miR-183–5p and calculated relative to siContr-1 (log 2 display). Dashed lines: 1.5-fold up- or downregulation (log 2 (1.5) = 0.585). The column color shows regulation in the same (dark grey) or opposite (light grey) direction compared to the small RNA deep sequencing data of the individual miRNAs. Ct-values > 35 were considered as not detected (n.d.). Data represent mean ± SEM (n = 2 or 3). Asterisks indicate statistically significant differences (p ≤ 0.05 (*), p ≤ 0.01 (**)).

    Journal: PLoS Pathogens

    Article Title: Dependence of Intracellular and Exosomal microRNAs on Viral E6/E7 Oncogene Expression in HPV-positive Tumor Cells

    doi: 10.1371/journal.ppat.1004712

    Figure Lengend Snippet: Inhibition of endogenous HPV18 E6/E7 expression: Effects on the miRNA composition of exosomes secreted by cervical cancer cells. Small RNA deep sequencing (A—D) and qRT-PCR analyses (E) of exosomal miRNAs, 72 h after transfection of HeLa cells with si18E6/E7 or control siRNA (siContr-1), and subsequent exosome purification from the cell culture supernatant. (A) Mean read count distribution of mature miRNA sequences in exosomes released from si18E6/E7- and siContr-1-treated HeLa cells (n = 3). Only miRNAs with a mean read count > 1 were considered. (B) The 15 most frequently sequenced exosomal miRNAs. Selection based on siContr-1 samples, respective values for si18E6/E7-treatment are indicated. Data represent mean ± SEM (n = 3). Interrupted x-Axis. (C) Overview on differentially deregulated ( > 1.5-fold) exosomal miRNAs determined by small RNA deep sequencing. RPM values of si18E6/E7-treated samples were calculated relative to the control treatment (siContr-1). Only miRNAs with > 1,000 RPM in each sample were considered (n = 2). (D) Relative quantification of miRNAs in exosomes released from si18E6/E7- versus siContr-1-treated cells, as assessed by small RNA deep sequencing (log 2 display). Dashed lines: 1.5-fold up- or downregulation (log 2 (1.5) = 0.585). Only miRNAs with > 1,000 RPM in each sample were considered. Data represent mean ± SEM (n = 3). (E) qRT-PCR analysis of E6/E7 -dependent exosomal miRNAs identified by small RNA deep sequencing. Exosomal miRNA levels were normalized to miR-452–5p and miR-183–5p and calculated relative to siContr-1 (log 2 display). Dashed lines: 1.5-fold up- or downregulation (log 2 (1.5) = 0.585). The column color shows regulation in the same (dark grey) or opposite (light grey) direction compared to the small RNA deep sequencing data of the individual miRNAs. Ct-values > 35 were considered as not detected (n.d.). Data represent mean ± SEM (n = 2 or 3). Asterisks indicate statistically significant differences (p ≤ 0.05 (*), p ≤ 0.01 (**)).

    Article Snippet: Next, the effects of E6/E7 expression on exosomal miRNAs—as identified by small RNA deep sequencing—were validated by qRT-PCR analyses.

    Techniques: Inhibition, Expressing, Sequencing, Quantitative RT-PCR, Transfection, Purification, Cell Culture, Selection

    Northern blot detection of the sRNAs in Ea1189 and Ea1189Δ hfq at 6 and 12 hrs post-inoculation in Hrp-inducing minimal medium. 5S rRNA was used as the loading control. A biotin-labeled RNA marker was used to estimate the sizes of the sRNAs. sRNA Hrs5, Hrs6, Hrs8, Hrs10, Hrs12, Hrs13, Hrs19, Hrs27 have only one major band whereas sRNA Hrs1, Hrs9, Hrs21, and Hrs31 have two major bands.

    Journal: BMC Genomics

    Article Title: Genome-wide identification of Hfq-regulated small RNAs in the fire blight pathogen Erwinia amylovora discovered small RNAs with virulence regulatory function

    doi: 10.1186/1471-2164-15-414

    Figure Lengend Snippet: Northern blot detection of the sRNAs in Ea1189 and Ea1189Δ hfq at 6 and 12 hrs post-inoculation in Hrp-inducing minimal medium. 5S rRNA was used as the loading control. A biotin-labeled RNA marker was used to estimate the sizes of the sRNAs. sRNA Hrs5, Hrs6, Hrs8, Hrs10, Hrs12, Hrs13, Hrs19, Hrs27 have only one major band whereas sRNA Hrs1, Hrs9, Hrs21, and Hrs31 have two major bands.

    Article Snippet: Identification of Hfq-dependent sRNAs by RNA-seq To identify Hfq-dependent sRNAs, Illumina deep sequencing (RNA-seq) was performed to identify small intergenic RNA transcripts whose expression was reduced in the absence of hfq .

    Techniques: Northern Blot, Labeling, Marker

    Identification of sRNAs using RNA-seq transcriptomics. (A) Illustration of examples of sRNAs identified by RNA-seq. (B) sRNA length distribution. The box and whisker plot diagram represents the minimum and maximum size, the median as well as the average sizes of the sRNA identified. (C) Comparison of the GcvB RNA amount detected by Northern blot and by RNA-seq.

    Journal: BMC Genomics

    Article Title: Genome-wide identification of Hfq-regulated small RNAs in the fire blight pathogen Erwinia amylovora discovered small RNAs with virulence regulatory function

    doi: 10.1186/1471-2164-15-414

    Figure Lengend Snippet: Identification of sRNAs using RNA-seq transcriptomics. (A) Illustration of examples of sRNAs identified by RNA-seq. (B) sRNA length distribution. The box and whisker plot diagram represents the minimum and maximum size, the median as well as the average sizes of the sRNA identified. (C) Comparison of the GcvB RNA amount detected by Northern blot and by RNA-seq.

    Article Snippet: Identification of Hfq-dependent sRNAs by RNA-seq To identify Hfq-dependent sRNAs, Illumina deep sequencing (RNA-seq) was performed to identify small intergenic RNA transcripts whose expression was reduced in the absence of hfq .

    Techniques: RNA Sequencing Assay, Whisker Assay, Northern Blot