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rna-seq protocol  (Illumina Inc)


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    Illumina Inc rna-seq protocol
    Rna Seq Protocol, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/rna-seq+protocols/rna+seq+protocol/pmc12256325-280-12-9
    Average 90 stars, based on 1 article reviews
    rna-seq protocol - by Bioz Stars, 2026-11
    90/100 stars

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    Related Articles

    Amplification:

    Article Title: A novel role of miR-223-3p in reducing NLRP3-mediated inflammation and deep vein thrombosis in a mouse model.
    Article Snippet: An RNA library was generated according to Illumina’s RNA-seq protocol.

    Article Title: Paracrine regulation of pancreatic cancer cell response to chemotherapy by GLI2–collagen I signaling
    Article Snippet: PANC-1 or MIA Paca-2 cells were incubated 3 h with a solution of 5 mg/ml of MTT reagent (M5655-1G; Sigma).

    Article Title: Th1 cells contribute to retinal ganglion cell loss in glaucoma in a VCAM-1-dependent manner
    Article Snippet: The standard Illumina RNA-seq protocol was followed for library preparation.

    Article Title: Population-wide DNA methylation polymorphisms at single-nucleotide resolution in 207 cotton accessions reveal epigenomic contributions to complex traits.
    Article Snippet: Transcriptome libraries were constructed according to the standard Illumina RNA-seq protocol (Illumina, Inc., San Diego, CA, USA, Cat# RS-100-0801).

    Article Title: Hedgehog signalling is involved in acquired resistance to KRAS G12C inhibitors in lung cancer cells.
    Article Snippet: Amplification of cDNA was carried out according to the RNA-seq protocol provided by Illumina and sequenced using an Illumina HiSeq 2500 system to obtain 150-bp paired-end reads.

    Article Title: A novel role of miR-223-3p in reducing NLRP3-mediated inflammation and deep vein thrombosis in a mouse model
    Article Snippet: An RNA library was generated according to Illumina's RNA-seq protocol.

    Article Title: Synergy of genetics and lipid metabolism driving feed utilization efficiency in chickens
    Article Snippet: Transcriptome sequencing libraries were prepared from high-quality RNA samples with RIN numbers > 7.0, according to the standard Illumina RNAseq protocol.

    Article Title: A systematic benchmark of Nanopore long-read RNA sequencing for transcript-level analysis in human cell lines
    Article Snippet: 36 Figure R3.3 Boxplots of transcript expression correlation generated using different RNA-seq protocols (direct cDNA, cDNA, direct RNA, Illumina) for all pairwise matched replicates from 7 cell lines Note t-test is performed to test the significance between different transcript groups. non-significance (p > 0.05) is indicated with ns, and significance of p <0.0001 is indicated with *** (3) Simulated read fragmentation recapitulates short read-specific transcript expression To further investigate the source for the discrepancy in replicability within technologies (higher for short read) and across technologies (higher for long read), we followed the suggestion from Reviewer #3 (point [10]) to simulate short read fragmentation, thereby generating simulated, matched short read RNA-Seq samples for each long read RNA-Seq sample in the SG-NEx resource (please refer to our response below for additional details and analyses).

    Polymerase Chain Reaction:

    Article Title: A novel role of miR-223-3p in reducing NLRP3-mediated inflammation and deep vein thrombosis in a mouse model.
    Article Snippet: An RNA library was generated according to Illumina’s RNA-seq protocol.

    Article Title: Paracrine regulation of pancreatic cancer cell response to chemotherapy by GLI2–collagen I signaling
    Article Snippet: PANC-1 or MIA Paca-2 cells were incubated 3 h with a solution of 5 mg/ml of MTT reagent (M5655-1G; Sigma).

    Article Title: Th1 cells contribute to retinal ganglion cell loss in glaucoma in a VCAM-1-dependent manner
    Article Snippet: The standard Illumina RNA-seq protocol was followed for library preparation.

    Article Title: Population-wide DNA methylation polymorphisms at single-nucleotide resolution in 207 cotton accessions reveal epigenomic contributions to complex traits.
    Article Snippet: Transcriptome libraries were constructed according to the standard Illumina RNA-seq protocol (Illumina, Inc., San Diego, CA, USA, Cat# RS-100-0801).

    Article Title: Hedgehog signalling is involved in acquired resistance to KRAS G12C inhibitors in lung cancer cells.
    Article Snippet: Amplification of cDNA was carried out according to the RNA-seq protocol provided by Illumina and sequenced using an Illumina HiSeq 2500 system to obtain 150-bp paired-end reads.

    Article Title: A novel role of miR-223-3p in reducing NLRP3-mediated inflammation and deep vein thrombosis in a mouse model
    Article Snippet: An RNA library was generated according to Illumina's RNA-seq protocol.

    Article Title: Synergy of genetics and lipid metabolism driving feed utilization efficiency in chickens
    Article Snippet: Transcriptome sequencing libraries were prepared from high-quality RNA samples with RIN numbers > 7.0, according to the standard Illumina RNAseq protocol.

    Article Title: A systematic benchmark of Nanopore long-read RNA sequencing for transcript-level analysis in human cell lines
    Article Snippet: 36 Figure R3.3 Boxplots of transcript expression correlation generated using different RNA-seq protocols (direct cDNA, cDNA, direct RNA, Illumina) for all pairwise matched replicates from 7 cell lines Note t-test is performed to test the significance between different transcript groups. non-significance (p > 0.05) is indicated with ns, and significance of p <0.0001 is indicated with *** (3) Simulated read fragmentation recapitulates short read-specific transcript expression To further investigate the source for the discrepancy in replicability within technologies (higher for short read) and across technologies (higher for long read), we followed the suggestion from Reviewer #3 (point [10]) to simulate short read fragmentation, thereby generating simulated, matched short read RNA-Seq samples for each long read RNA-Seq sample in the SG-NEx resource (please refer to our response below for additional details and analyses).

    Generated:

    Article Title: A novel role of miR-223-3p in reducing NLRP3-mediated inflammation and deep vein thrombosis in a mouse model.
    Article Snippet: An RNA library was generated according to Illumina’s RNA-seq protocol.

    Article Title: Paracrine regulation of pancreatic cancer cell response to chemotherapy by GLI2–collagen I signaling
    Article Snippet: PANC-1 or MIA Paca-2 cells were incubated 3 h with a solution of 5 mg/ml of MTT reagent (M5655-1G; Sigma).

    Article Title: Th1 cells contribute to retinal ganglion cell loss in glaucoma in a VCAM-1-dependent manner
    Article Snippet: The standard Illumina RNA-seq protocol was followed for library preparation.

    Article Title: Population-wide DNA methylation polymorphisms at single-nucleotide resolution in 207 cotton accessions reveal epigenomic contributions to complex traits.
    Article Snippet: Transcriptome libraries were constructed according to the standard Illumina RNA-seq protocol (Illumina, Inc., San Diego, CA, USA, Cat# RS-100-0801).

    Article Title: Hedgehog signalling is involved in acquired resistance to KRAS G12C inhibitors in lung cancer cells.
    Article Snippet: Amplification of cDNA was carried out according to the RNA-seq protocol provided by Illumina and sequenced using an Illumina HiSeq 2500 system to obtain 150-bp paired-end reads.

    Article Title: A novel role of miR-223-3p in reducing NLRP3-mediated inflammation and deep vein thrombosis in a mouse model
    Article Snippet: An RNA library was generated according to Illumina's RNA-seq protocol.

    Article Title: Synergy of genetics and lipid metabolism driving feed utilization efficiency in chickens
    Article Snippet: Transcriptome sequencing libraries were prepared from high-quality RNA samples with RIN numbers > 7.0, according to the standard Illumina RNAseq protocol.

    Article Title: A systematic benchmark of Nanopore long-read RNA sequencing for transcript-level analysis in human cell lines
    Article Snippet: 36 Figure R3.3 Boxplots of transcript expression correlation generated using different RNA-seq protocols (direct cDNA, cDNA, direct RNA, Illumina) for all pairwise matched replicates from 7 cell lines Note t-test is performed to test the significance between different transcript groups. non-significance (p > 0.05) is indicated with ns, and significance of p <0.0001 is indicated with *** (3) Simulated read fragmentation recapitulates short read-specific transcript expression To further investigate the source for the discrepancy in replicability within technologies (higher for short read) and across technologies (higher for long read), we followed the suggestion from Reviewer #3 (point [10]) to simulate short read fragmentation, thereby generating simulated, matched short read RNA-Seq samples for each long read RNA-Seq sample in the SG-NEx resource (please refer to our response below for additional details and analyses).

    RNA Sequencing:

    Article Title: A novel role of miR-223-3p in reducing NLRP3-mediated inflammation and deep vein thrombosis in a mouse model.
    Article Snippet: An RNA library was generated according to Illumina’s RNA-seq protocol.

    Article Title: Paracrine regulation of pancreatic cancer cell response to chemotherapy by GLI2–collagen I signaling
    Article Snippet: PANC-1 or MIA Paca-2 cells were incubated 3 h with a solution of 5 mg/ml of MTT reagent (M5655-1G; Sigma).

    Article Title: Th1 cells contribute to retinal ganglion cell loss in glaucoma in a VCAM-1-dependent manner
    Article Snippet: The standard Illumina RNA-seq protocol was followed for library preparation.

    Article Title: Population-wide DNA methylation polymorphisms at single-nucleotide resolution in 207 cotton accessions reveal epigenomic contributions to complex traits.
    Article Snippet: Transcriptome libraries were constructed according to the standard Illumina RNA-seq protocol (Illumina, Inc., San Diego, CA, USA, Cat# RS-100-0801).

    Article Title: Hedgehog signalling is involved in acquired resistance to KRAS G12C inhibitors in lung cancer cells.
    Article Snippet: Amplification of cDNA was carried out according to the RNA-seq protocol provided by Illumina and sequenced using an Illumina HiSeq 2500 system to obtain 150-bp paired-end reads.

    Article Title: A novel role of miR-223-3p in reducing NLRP3-mediated inflammation and deep vein thrombosis in a mouse model
    Article Snippet: An RNA library was generated according to Illumina's RNA-seq protocol.

    Article Title: Synergy of genetics and lipid metabolism driving feed utilization efficiency in chickens
    Article Snippet: Transcriptome sequencing libraries were prepared from high-quality RNA samples with RIN numbers > 7.0, according to the standard Illumina RNAseq protocol.

    Article Title: A systematic benchmark of Nanopore long-read RNA sequencing for transcript-level analysis in human cell lines
    Article Snippet: 36 Figure R3.3 Boxplots of transcript expression correlation generated using different RNA-seq protocols (direct cDNA, cDNA, direct RNA, Illumina) for all pairwise matched replicates from 7 cell lines Note t-test is performed to test the significance between different transcript groups. non-significance (p > 0.05) is indicated with ns, and significance of p <0.0001 is indicated with *** (3) Simulated read fragmentation recapitulates short read-specific transcript expression To further investigate the source for the discrepancy in replicability within technologies (higher for short read) and across technologies (higher for long read), we followed the suggestion from Reviewer #3 (point [10]) to simulate short read fragmentation, thereby generating simulated, matched short read RNA-Seq samples for each long read RNA-Seq sample in the SG-NEx resource (please refer to our response below for additional details and analyses).

    Expressing:

    Article Title: A novel role of miR-223-3p in reducing NLRP3-mediated inflammation and deep vein thrombosis in a mouse model.
    Article Snippet: An RNA library was generated according to Illumina’s RNA-seq protocol.

    Article Title: Paracrine regulation of pancreatic cancer cell response to chemotherapy by GLI2–collagen I signaling
    Article Snippet: PANC-1 or MIA Paca-2 cells were incubated 3 h with a solution of 5 mg/ml of MTT reagent (M5655-1G; Sigma).

    Article Title: Th1 cells contribute to retinal ganglion cell loss in glaucoma in a VCAM-1-dependent manner
    Article Snippet: The standard Illumina RNA-seq protocol was followed for library preparation.

    Article Title: Population-wide DNA methylation polymorphisms at single-nucleotide resolution in 207 cotton accessions reveal epigenomic contributions to complex traits.
    Article Snippet: Transcriptome libraries were constructed according to the standard Illumina RNA-seq protocol (Illumina, Inc., San Diego, CA, USA, Cat# RS-100-0801).

    Article Title: Hedgehog signalling is involved in acquired resistance to KRAS G12C inhibitors in lung cancer cells.
    Article Snippet: Amplification of cDNA was carried out according to the RNA-seq protocol provided by Illumina and sequenced using an Illumina HiSeq 2500 system to obtain 150-bp paired-end reads.

    Article Title: A novel role of miR-223-3p in reducing NLRP3-mediated inflammation and deep vein thrombosis in a mouse model
    Article Snippet: An RNA library was generated according to Illumina's RNA-seq protocol.

    Article Title: Synergy of genetics and lipid metabolism driving feed utilization efficiency in chickens
    Article Snippet: Transcriptome sequencing libraries were prepared from high-quality RNA samples with RIN numbers > 7.0, according to the standard Illumina RNAseq protocol.

    Article Title: A systematic benchmark of Nanopore long-read RNA sequencing for transcript-level analysis in human cell lines
    Article Snippet: 36 Figure R3.3 Boxplots of transcript expression correlation generated using different RNA-seq protocols (direct cDNA, cDNA, direct RNA, Illumina) for all pairwise matched replicates from 7 cell lines Note t-test is performed to test the significance between different transcript groups. non-significance (p > 0.05) is indicated with ns, and significance of p <0.0001 is indicated with *** (3) Simulated read fragmentation recapitulates short read-specific transcript expression To further investigate the source for the discrepancy in replicability within technologies (higher for short read) and across technologies (higher for long read), we followed the suggestion from Reviewer #3 (point [10]) to simulate short read fragmentation, thereby generating simulated, matched short read RNA-Seq samples for each long read RNA-Seq sample in the SG-NEx resource (please refer to our response below for additional details and analyses).

    Comparison:

    Article Title: A novel role of miR-223-3p in reducing NLRP3-mediated inflammation and deep vein thrombosis in a mouse model.
    Article Snippet: An RNA library was generated according to Illumina’s RNA-seq protocol.

    Article Title: Paracrine regulation of pancreatic cancer cell response to chemotherapy by GLI2–collagen I signaling
    Article Snippet: PANC-1 or MIA Paca-2 cells were incubated 3 h with a solution of 5 mg/ml of MTT reagent (M5655-1G; Sigma).

    Article Title: Th1 cells contribute to retinal ganglion cell loss in glaucoma in a VCAM-1-dependent manner
    Article Snippet: The standard Illumina RNA-seq protocol was followed for library preparation.

    Article Title: Population-wide DNA methylation polymorphisms at single-nucleotide resolution in 207 cotton accessions reveal epigenomic contributions to complex traits.
    Article Snippet: Transcriptome libraries were constructed according to the standard Illumina RNA-seq protocol (Illumina, Inc., San Diego, CA, USA, Cat# RS-100-0801).

    Article Title: Hedgehog signalling is involved in acquired resistance to KRAS G12C inhibitors in lung cancer cells.
    Article Snippet: Amplification of cDNA was carried out according to the RNA-seq protocol provided by Illumina and sequenced using an Illumina HiSeq 2500 system to obtain 150-bp paired-end reads.

    Article Title: A novel role of miR-223-3p in reducing NLRP3-mediated inflammation and deep vein thrombosis in a mouse model
    Article Snippet: An RNA library was generated according to Illumina's RNA-seq protocol.

    Article Title: Synergy of genetics and lipid metabolism driving feed utilization efficiency in chickens
    Article Snippet: Transcriptome sequencing libraries were prepared from high-quality RNA samples with RIN numbers > 7.0, according to the standard Illumina RNAseq protocol.

    Article Title: A systematic benchmark of Nanopore long-read RNA sequencing for transcript-level analysis in human cell lines
    Article Snippet: 36 Figure R3.3 Boxplots of transcript expression correlation generated using different RNA-seq protocols (direct cDNA, cDNA, direct RNA, Illumina) for all pairwise matched replicates from 7 cell lines Note t-test is performed to test the significance between different transcript groups. non-significance (p > 0.05) is indicated with ns, and significance of p <0.0001 is indicated with *** (3) Simulated read fragmentation recapitulates short read-specific transcript expression To further investigate the source for the discrepancy in replicability within technologies (higher for short read) and across technologies (higher for long read), we followed the suggestion from Reviewer #3 (point [10]) to simulate short read fragmentation, thereby generating simulated, matched short read RNA-Seq samples for each long read RNA-Seq sample in the SG-NEx resource (please refer to our response below for additional details and analyses).

    Sequencing:

    Article Title: A novel role of miR-223-3p in reducing NLRP3-mediated inflammation and deep vein thrombosis in a mouse model.
    Article Snippet: An RNA library was generated according to Illumina’s RNA-seq protocol.

    Article Title: Paracrine regulation of pancreatic cancer cell response to chemotherapy by GLI2–collagen I signaling
    Article Snippet: PANC-1 or MIA Paca-2 cells were incubated 3 h with a solution of 5 mg/ml of MTT reagent (M5655-1G; Sigma).

    Article Title: Th1 cells contribute to retinal ganglion cell loss in glaucoma in a VCAM-1-dependent manner
    Article Snippet: The standard Illumina RNA-seq protocol was followed for library preparation.

    Article Title: Population-wide DNA methylation polymorphisms at single-nucleotide resolution in 207 cotton accessions reveal epigenomic contributions to complex traits.
    Article Snippet: Transcriptome libraries were constructed according to the standard Illumina RNA-seq protocol (Illumina, Inc., San Diego, CA, USA, Cat# RS-100-0801).

    Article Title: Hedgehog signalling is involved in acquired resistance to KRAS G12C inhibitors in lung cancer cells.
    Article Snippet: Amplification of cDNA was carried out according to the RNA-seq protocol provided by Illumina and sequenced using an Illumina HiSeq 2500 system to obtain 150-bp paired-end reads.

    Article Title: A novel role of miR-223-3p in reducing NLRP3-mediated inflammation and deep vein thrombosis in a mouse model
    Article Snippet: An RNA library was generated according to Illumina's RNA-seq protocol.

    Article Title: Synergy of genetics and lipid metabolism driving feed utilization efficiency in chickens
    Article Snippet: Transcriptome sequencing libraries were prepared from high-quality RNA samples with RIN numbers > 7.0, according to the standard Illumina RNAseq protocol.

    Article Title: A systematic benchmark of Nanopore long-read RNA sequencing for transcript-level analysis in human cell lines
    Article Snippet: 36 Figure R3.3 Boxplots of transcript expression correlation generated using different RNA-seq protocols (direct cDNA, cDNA, direct RNA, Illumina) for all pairwise matched replicates from 7 cell lines Note t-test is performed to test the significance between different transcript groups. non-significance (p > 0.05) is indicated with ns, and significance of p <0.0001 is indicated with *** (3) Simulated read fragmentation recapitulates short read-specific transcript expression To further investigate the source for the discrepancy in replicability within technologies (higher for short read) and across technologies (higher for long read), we followed the suggestion from Reviewer #3 (point [10]) to simulate short read fragmentation, thereby generating simulated, matched short read RNA-Seq samples for each long read RNA-Seq sample in the SG-NEx resource (please refer to our response below for additional details and analyses).

    Construct:

    Article Title: A novel role of miR-223-3p in reducing NLRP3-mediated inflammation and deep vein thrombosis in a mouse model.
    Article Snippet: An RNA library was generated according to Illumina’s RNA-seq protocol.

    Article Title: Paracrine regulation of pancreatic cancer cell response to chemotherapy by GLI2–collagen I signaling
    Article Snippet: PANC-1 or MIA Paca-2 cells were incubated 3 h with a solution of 5 mg/ml of MTT reagent (M5655-1G; Sigma).

    Article Title: Th1 cells contribute to retinal ganglion cell loss in glaucoma in a VCAM-1-dependent manner
    Article Snippet: The standard Illumina RNA-seq protocol was followed for library preparation.

    Article Title: Population-wide DNA methylation polymorphisms at single-nucleotide resolution in 207 cotton accessions reveal epigenomic contributions to complex traits.
    Article Snippet: Transcriptome libraries were constructed according to the standard Illumina RNA-seq protocol (Illumina, Inc., San Diego, CA, USA, Cat# RS-100-0801).

    Article Title: Hedgehog signalling is involved in acquired resistance to KRAS G12C inhibitors in lung cancer cells.
    Article Snippet: Amplification of cDNA was carried out according to the RNA-seq protocol provided by Illumina and sequenced using an Illumina HiSeq 2500 system to obtain 150-bp paired-end reads.

    Article Title: A novel role of miR-223-3p in reducing NLRP3-mediated inflammation and deep vein thrombosis in a mouse model
    Article Snippet: An RNA library was generated according to Illumina's RNA-seq protocol.

    Article Title: Synergy of genetics and lipid metabolism driving feed utilization efficiency in chickens
    Article Snippet: Transcriptome sequencing libraries were prepared from high-quality RNA samples with RIN numbers > 7.0, according to the standard Illumina RNAseq protocol.

    Article Title: A systematic benchmark of Nanopore long-read RNA sequencing for transcript-level analysis in human cell lines
    Article Snippet: 36 Figure R3.3 Boxplots of transcript expression correlation generated using different RNA-seq protocols (direct cDNA, cDNA, direct RNA, Illumina) for all pairwise matched replicates from 7 cell lines Note t-test is performed to test the significance between different transcript groups. non-significance (p > 0.05) is indicated with ns, and significance of p <0.0001 is indicated with *** (3) Simulated read fragmentation recapitulates short read-specific transcript expression To further investigate the source for the discrepancy in replicability within technologies (higher for short read) and across technologies (higher for long read), we followed the suggestion from Reviewer #3 (point [10]) to simulate short read fragmentation, thereby generating simulated, matched short read RNA-Seq samples for each long read RNA-Seq sample in the SG-NEx resource (please refer to our response below for additional details and analyses).



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    Differential MsMYBs expression in anther development stages. ( A ) Venn diagram displaying the intersection of significantly up-regulated and down-regulated DEGs between stages S9, S10, and S11. ( B ) Heatmaps and principal component analysis (PCA) reveal the relationships between <t>transcriptomes.</t> ( C ) GO enrichment bubble chart of upregulated DEGs during stages S9, S10, and S11. ( D ) Expression patterns of MsMYBs during anther development. Color scales with Z scores beside the heatmap indicate gene expression levels, with low and high transcript abundance indicated by blue and red, respectively. Error bars represent standard deviation, and asterisks denote significant differences between control and treatments, with * P < 0.05, ** P < 0.01, *** P < 0.001, **** P < 0.0001
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    Image Search Results


    Differential MsMYBs expression in anther development stages. ( A ) Venn diagram displaying the intersection of significantly up-regulated and down-regulated DEGs between stages S9, S10, and S11. ( B ) Heatmaps and principal component analysis (PCA) reveal the relationships between transcriptomes. ( C ) GO enrichment bubble chart of upregulated DEGs during stages S9, S10, and S11. ( D ) Expression patterns of MsMYBs during anther development. Color scales with Z scores beside the heatmap indicate gene expression levels, with low and high transcript abundance indicated by blue and red, respectively. Error bars represent standard deviation, and asterisks denote significant differences between control and treatments, with * P < 0.05, ** P < 0.01, *** P < 0.001, **** P < 0.0001

    Journal: BMC Plant Biology

    Article Title: Genome-wide identification of the Medicago sativa L. MYB family and its transcriptional dynamics during pollen development

    doi: 10.1186/s12870-025-06542-6

    Figure Lengend Snippet: Differential MsMYBs expression in anther development stages. ( A ) Venn diagram displaying the intersection of significantly up-regulated and down-regulated DEGs between stages S9, S10, and S11. ( B ) Heatmaps and principal component analysis (PCA) reveal the relationships between transcriptomes. ( C ) GO enrichment bubble chart of upregulated DEGs during stages S9, S10, and S11. ( D ) Expression patterns of MsMYBs during anther development. Color scales with Z scores beside the heatmap indicate gene expression levels, with low and high transcript abundance indicated by blue and red, respectively. Error bars represent standard deviation, and asterisks denote significant differences between control and treatments, with * P < 0.05, ** P < 0.01, *** P < 0.001, **** P < 0.0001

    Article Snippet: Construction of transcriptome libraries adhered to the Illumina RNA-seq protocol (Illumina, Inc., San Diego, CA, catalog no. RS-100-0801).

    Techniques: Expressing, Gene Expression, Standard Deviation, Control