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  • 99
    Illumina Inc amplicon sequencing
    Dilution of variant allele frequency when primers are not clipped after mapping. NGS read alignments in BRCA1 c.4372C > T region from primer handling approaches 2 and 3 are shown in conjunction with the <t>amplicon</t> design and reference genome sequence. The c.4372C > T mutation is located in the region of interest of one amplicon and gene-specific primer site of another amplicon. Since primer sequences retained in approach 2 contributed to wild-type allele frequency, VAF of c.4372C > T was in turn underestimated by 82% (9% in approach 2 and 51% in approach 3).
    Amplicon Sequencing, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 1976 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/amplicon sequencing/product/Illumina Inc
    Average 99 stars, based on 1976 article reviews
    Price from $9.99 to $1999.99
    amplicon sequencing - by Bioz Stars, 2020-02
    99/100 stars
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    91
    Illumina Inc sequencing platform
    Length distribution of transcripts obtained by different sequencing platforms. <t>Illumina_1</t> and Illumina_2 represent the transcripts assembled by Zhang [ 20 ] and Zhou [ 21 ], respectively, using the Illumina sequencing platform
    Sequencing Platform, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 91/100, based on 81 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/sequencing platform/product/Illumina Inc
    Average 91 stars, based on 81 article reviews
    Price from $9.99 to $1999.99
    sequencing platform - by Bioz Stars, 2020-02
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    98
    Illumina Inc nextgen sequencing
    Length distribution of transcripts obtained by different sequencing platforms. <t>Illumina_1</t> and Illumina_2 represent the transcripts assembled by Zhang [ 20 ] and Zhou [ 21 ], respectively, using the Illumina sequencing platform
    Nextgen Sequencing, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 98/100, based on 107 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/nextgen sequencing/product/Illumina Inc
    Average 98 stars, based on 107 article reviews
    Price from $9.99 to $1999.99
    nextgen sequencing - by Bioz Stars, 2020-02
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    99
    Illumina Inc miseq sequencing platform
    Sampling overview. Swab samples were taken from ovaries dissected out of pipefish ( Syngnathus typhle ) females (Gonads-GO); from the brood pouch tissue of non-pregnant pipefish males (Non-Pregnant-NP); on the surface of eggs and embryos inside the brood pouch of pregnant males in increasing developmental stages: early pregnancy (EP) circa (1–2 weeks); mid pregnant (MP) (2–4 weeks); late pregnant (LP) (4–6 weeks). In total 20 females, 20 males per pregnancy stage (3*20), and 40 non-pregnant males were used for the study (120 fish). For each group half of the individuals were intraperitoneally injected with heat-killed bacteria suspension ( Vibrio spp. and Tenacibaculum maritimum ) to trigger a parental immune transfer (injected with bacteria solution vs. non-injected). Microbiota samples were taken with sterile swabs by scratching the mucus from the surface of ovaries, brood pouch tissue and embryos inside the paternal brood pouch. Microbiota analysis was performed by <t>Illumina</t> <t>Miseq</t> Sequencing.
    Miseq Sequencing Platform, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 2582 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/miseq sequencing platform/product/Illumina Inc
    Average 99 stars, based on 2582 article reviews
    Price from $9.99 to $1999.99
    miseq sequencing platform - by Bioz Stars, 2020-02
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    99
    Illumina Inc hiseq2500 sequencing platform
    Sampling overview. Swab samples were taken from ovaries dissected out of pipefish ( Syngnathus typhle ) females (Gonads-GO); from the brood pouch tissue of non-pregnant pipefish males (Non-Pregnant-NP); on the surface of eggs and embryos inside the brood pouch of pregnant males in increasing developmental stages: early pregnancy (EP) circa (1–2 weeks); mid pregnant (MP) (2–4 weeks); late pregnant (LP) (4–6 weeks). In total 20 females, 20 males per pregnancy stage (3*20), and 40 non-pregnant males were used for the study (120 fish). For each group half of the individuals were intraperitoneally injected with heat-killed bacteria suspension ( Vibrio spp. and Tenacibaculum maritimum ) to trigger a parental immune transfer (injected with bacteria solution vs. non-injected). Microbiota samples were taken with sterile swabs by scratching the mucus from the surface of ovaries, brood pouch tissue and embryos inside the paternal brood pouch. Microbiota analysis was performed by <t>Illumina</t> <t>Miseq</t> Sequencing.
    Hiseq2500 Sequencing Platform, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 453 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/hiseq2500 sequencing platform/product/Illumina Inc
    Average 99 stars, based on 453 article reviews
    Price from $9.99 to $1999.99
    hiseq2500 sequencing platform - by Bioz Stars, 2020-02
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    99
    Illumina Inc hiseq2000 sequencing platform
    Effect of the integration procedures on TCGA LUSC datasets. Two datasets comprising of Illumina <t>HiSeq-2000</t> and Affymetrix HG-U133A data were employed to evaluate the effect of the integration on two different platforms. After applying the integration procedure, DEGs were computed varying the p-value threshold. Receiver-Operating Characteristic (ROC) curves were computed using known DEGs, and the performances were assessed by means of Area Under the ROC Curve (AUC)
    Hiseq2000 Sequencing Platform, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 1114 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/hiseq2000 sequencing platform/product/Illumina Inc
    Average 99 stars, based on 1114 article reviews
    Price from $9.99 to $1999.99
    hiseq2000 sequencing platform - by Bioz Stars, 2020-02
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    82
    Illumina Inc sequencing platform gaii
    Effect of the integration procedures on TCGA LUSC datasets. Two datasets comprising of Illumina <t>HiSeq-2000</t> and Affymetrix HG-U133A data were employed to evaluate the effect of the integration on two different platforms. After applying the integration procedure, DEGs were computed varying the p-value threshold. Receiver-Operating Characteristic (ROC) curves were computed using known DEGs, and the performances were assessed by means of Area Under the ROC Curve (AUC)
    Sequencing Platform Gaii, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 82/100, based on 42 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 82 stars, based on 42 article reviews
    Price from $9.99 to $1999.99
    sequencing platform gaii - by Bioz Stars, 2020-02
    82/100 stars
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    99
    Illumina Inc hiseq sequencing platform
    The scheme for constructing improved degradome library. For sequencing purposes, the degradome library generated by this method can be treated as small RNA library and the resulting reads are ~ 27 nt long. The procedure includes: (1) poly(A) RNA isolation; (2) 5′RNA adapter ligation to uncapped poly(A) RNA with 5′ monophosphate; (3) reverse transcription to generate 1st strand cDNA using an oligo(dT)-tailed adapter (RT-primer); (4) second strand synthesis (1st PCR amplification); (5) <t>EcoP15I</t> digestion to generate ~ 27 nt long reads; (6) ligation of EcoP15I digestion products with a 3′ds-DNA adapter; (7) purification of ligation products on a PAGE gel; (8) degradome library enrichment (2nd PCR amplification); (9) purification of the final product on a PAGE gel; (10) library pooling and sequencing using Illumina <t>HiSeq</t> platform
    Hiseq Sequencing Platform, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 887 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/hiseq sequencing platform/product/Illumina Inc
    Average 99 stars, based on 887 article reviews
    Price from $9.99 to $1999.99
    hiseq sequencing platform - by Bioz Stars, 2020-02
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    86
    Illumina Inc miseq300 platform sequencing
    The scheme for constructing improved degradome library. For sequencing purposes, the degradome library generated by this method can be treated as small RNA library and the resulting reads are ~ 27 nt long. The procedure includes: (1) poly(A) RNA isolation; (2) 5′RNA adapter ligation to uncapped poly(A) RNA with 5′ monophosphate; (3) reverse transcription to generate 1st strand cDNA using an oligo(dT)-tailed adapter (RT-primer); (4) second strand synthesis (1st PCR amplification); (5) <t>EcoP15I</t> digestion to generate ~ 27 nt long reads; (6) ligation of EcoP15I digestion products with a 3′ds-DNA adapter; (7) purification of ligation products on a PAGE gel; (8) degradome library enrichment (2nd PCR amplification); (9) purification of the final product on a PAGE gel; (10) library pooling and sequencing using Illumina <t>HiSeq</t> platform
    Miseq300 Platform Sequencing, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 86/100, based on 21 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/miseq300 platform sequencing/product/Illumina Inc
    Average 86 stars, based on 21 article reviews
    Price from $9.99 to $1999.99
    miseq300 platform sequencing - by Bioz Stars, 2020-02
    86/100 stars
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    79
    Illumina Inc 2000 sequencing platform
    The scheme for constructing improved degradome library. For sequencing purposes, the degradome library generated by this method can be treated as small RNA library and the resulting reads are ~ 27 nt long. The procedure includes: (1) poly(A) RNA isolation; (2) 5′RNA adapter ligation to uncapped poly(A) RNA with 5′ monophosphate; (3) reverse transcription to generate 1st strand cDNA using an oligo(dT)-tailed adapter (RT-primer); (4) second strand synthesis (1st PCR amplification); (5) <t>EcoP15I</t> digestion to generate ~ 27 nt long reads; (6) ligation of EcoP15I digestion products with a 3′ds-DNA adapter; (7) purification of ligation products on a PAGE gel; (8) degradome library enrichment (2nd PCR amplification); (9) purification of the final product on a PAGE gel; (10) library pooling and sequencing using Illumina <t>HiSeq</t> platform
    2000 Sequencing Platform, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 79/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/2000 sequencing platform/product/Illumina Inc
    Average 79 stars, based on 7 article reviews
    Price from $9.99 to $1999.99
    2000 sequencing platform - by Bioz Stars, 2020-02
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    82
    Illumina Inc 550 sequencing platform
    The scheme for constructing improved degradome library. For sequencing purposes, the degradome library generated by this method can be treated as small RNA library and the resulting reads are ~ 27 nt long. The procedure includes: (1) poly(A) RNA isolation; (2) 5′RNA adapter ligation to uncapped poly(A) RNA with 5′ monophosphate; (3) reverse transcription to generate 1st strand cDNA using an oligo(dT)-tailed adapter (RT-primer); (4) second strand synthesis (1st PCR amplification); (5) <t>EcoP15I</t> digestion to generate ~ 27 nt long reads; (6) ligation of EcoP15I digestion products with a 3′ds-DNA adapter; (7) purification of ligation products on a PAGE gel; (8) degradome library enrichment (2nd PCR amplification); (9) purification of the final product on a PAGE gel; (10) library pooling and sequencing using Illumina <t>HiSeq</t> platform
    550 Sequencing Platform, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 82/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/550 sequencing platform/product/Illumina Inc
    Average 82 stars, based on 6 article reviews
    Price from $9.99 to $1999.99
    550 sequencing platform - by Bioz Stars, 2020-02
    82/100 stars
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    75
    Illumina Inc nextseq500 sequencing instrument
    The scheme for constructing improved degradome library. For sequencing purposes, the degradome library generated by this method can be treated as small RNA library and the resulting reads are ~ 27 nt long. The procedure includes: (1) poly(A) RNA isolation; (2) 5′RNA adapter ligation to uncapped poly(A) RNA with 5′ monophosphate; (3) reverse transcription to generate 1st strand cDNA using an oligo(dT)-tailed adapter (RT-primer); (4) second strand synthesis (1st PCR amplification); (5) <t>EcoP15I</t> digestion to generate ~ 27 nt long reads; (6) ligation of EcoP15I digestion products with a 3′ds-DNA adapter; (7) purification of ligation products on a PAGE gel; (8) degradome library enrichment (2nd PCR amplification); (9) purification of the final product on a PAGE gel; (10) library pooling and sequencing using Illumina <t>HiSeq</t> platform
    Nextseq500 Sequencing Instrument, 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/nextseq500 sequencing instrument/product/Illumina Inc
    Average 75 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    nextseq500 sequencing instrument - by Bioz Stars, 2020-02
    75/100 stars
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    82
    Illumina Inc highseq2000 sequencing platform
    The scheme for constructing improved degradome library. For sequencing purposes, the degradome library generated by this method can be treated as small RNA library and the resulting reads are ~ 27 nt long. The procedure includes: (1) poly(A) RNA isolation; (2) 5′RNA adapter ligation to uncapped poly(A) RNA with 5′ monophosphate; (3) reverse transcription to generate 1st strand cDNA using an oligo(dT)-tailed adapter (RT-primer); (4) second strand synthesis (1st PCR amplification); (5) <t>EcoP15I</t> digestion to generate ~ 27 nt long reads; (6) ligation of EcoP15I digestion products with a 3′ds-DNA adapter; (7) purification of ligation products on a PAGE gel; (8) degradome library enrichment (2nd PCR amplification); (9) purification of the final product on a PAGE gel; (10) library pooling and sequencing using Illumina <t>HiSeq</t> platform
    Highseq2000 Sequencing Platform, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 82/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/highseq2000 sequencing platform/product/Illumina Inc
    Average 82 stars, based on 8 article reviews
    Price from $9.99 to $1999.99
    highseq2000 sequencing platform - by Bioz Stars, 2020-02
    82/100 stars
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    95
    Illumina Inc nextseq500 sequencing platform
    The scheme for constructing improved degradome library. For sequencing purposes, the degradome library generated by this method can be treated as small RNA library and the resulting reads are ~ 27 nt long. The procedure includes: (1) poly(A) RNA isolation; (2) 5′RNA adapter ligation to uncapped poly(A) RNA with 5′ monophosphate; (3) reverse transcription to generate 1st strand cDNA using an oligo(dT)-tailed adapter (RT-primer); (4) second strand synthesis (1st PCR amplification); (5) <t>EcoP15I</t> digestion to generate ~ 27 nt long reads; (6) ligation of EcoP15I digestion products with a 3′ds-DNA adapter; (7) purification of ligation products on a PAGE gel; (8) degradome library enrichment (2nd PCR amplification); (9) purification of the final product on a PAGE gel; (10) library pooling and sequencing using Illumina <t>HiSeq</t> platform
    Nextseq500 Sequencing Platform, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 95/100, based on 120 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/nextseq500 sequencing platform/product/Illumina Inc
    Average 95 stars, based on 120 article reviews
    Price from $9.99 to $1999.99
    nextseq500 sequencing platform - by Bioz Stars, 2020-02
    95/100 stars
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    89
    Illumina Inc multiplexed sequencing platform
    The scheme for constructing improved degradome library. For sequencing purposes, the degradome library generated by this method can be treated as small RNA library and the resulting reads are ~ 27 nt long. The procedure includes: (1) poly(A) RNA isolation; (2) 5′RNA adapter ligation to uncapped poly(A) RNA with 5′ monophosphate; (3) reverse transcription to generate 1st strand cDNA using an oligo(dT)-tailed adapter (RT-primer); (4) second strand synthesis (1st PCR amplification); (5) <t>EcoP15I</t> digestion to generate ~ 27 nt long reads; (6) ligation of EcoP15I digestion products with a 3′ds-DNA adapter; (7) purification of ligation products on a PAGE gel; (8) degradome library enrichment (2nd PCR amplification); (9) purification of the final product on a PAGE gel; (10) library pooling and sequencing using Illumina <t>HiSeq</t> platform
    Multiplexed Sequencing Platform, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 89/100, based on 10 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/multiplexed sequencing platform/product/Illumina Inc
    Average 89 stars, based on 10 article reviews
    Price from $9.99 to $1999.99
    multiplexed sequencing platform - by Bioz Stars, 2020-02
    89/100 stars
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    91
    Illumina Inc hiseq sequencing platforms
    The scheme for constructing improved degradome library. For sequencing purposes, the degradome library generated by this method can be treated as small RNA library and the resulting reads are ~ 27 nt long. The procedure includes: (1) poly(A) RNA isolation; (2) 5′RNA adapter ligation to uncapped poly(A) RNA with 5′ monophosphate; (3) reverse transcription to generate 1st strand cDNA using an oligo(dT)-tailed adapter (RT-primer); (4) second strand synthesis (1st PCR amplification); (5) <t>EcoP15I</t> digestion to generate ~ 27 nt long reads; (6) ligation of EcoP15I digestion products with a 3′ds-DNA adapter; (7) purification of ligation products on a PAGE gel; (8) degradome library enrichment (2nd PCR amplification); (9) purification of the final product on a PAGE gel; (10) library pooling and sequencing using Illumina <t>HiSeq</t> platform
    Hiseq Sequencing Platforms, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 91/100, based on 61 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/hiseq sequencing platforms/product/Illumina Inc
    Average 91 stars, based on 61 article reviews
    Price from $9.99 to $1999.99
    hiseq sequencing platforms - by Bioz Stars, 2020-02
    91/100 stars
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    90
    Illumina Inc nextseq sequencing platform
    The scheme for constructing improved degradome library. For sequencing purposes, the degradome library generated by this method can be treated as small RNA library and the resulting reads are ~ 27 nt long. The procedure includes: (1) poly(A) RNA isolation; (2) 5′RNA adapter ligation to uncapped poly(A) RNA with 5′ monophosphate; (3) reverse transcription to generate 1st strand cDNA using an oligo(dT)-tailed adapter (RT-primer); (4) second strand synthesis (1st PCR amplification); (5) <t>EcoP15I</t> digestion to generate ~ 27 nt long reads; (6) ligation of EcoP15I digestion products with a 3′ds-DNA adapter; (7) purification of ligation products on a PAGE gel; (8) degradome library enrichment (2nd PCR amplification); (9) purification of the final product on a PAGE gel; (10) library pooling and sequencing using Illumina <t>HiSeq</t> platform
    Nextseq Sequencing Platform, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 21 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/nextseq sequencing platform/product/Illumina Inc
    Average 90 stars, based on 21 article reviews
    Price from $9.99 to $1999.99
    nextseq sequencing platform - by Bioz Stars, 2020-02
    90/100 stars
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    80
    Illumina Inc hiseqxten sequencing platform
    The scheme for constructing improved degradome library. For sequencing purposes, the degradome library generated by this method can be treated as small RNA library and the resulting reads are ~ 27 nt long. The procedure includes: (1) poly(A) RNA isolation; (2) 5′RNA adapter ligation to uncapped poly(A) RNA with 5′ monophosphate; (3) reverse transcription to generate 1st strand cDNA using an oligo(dT)-tailed adapter (RT-primer); (4) second strand synthesis (1st PCR amplification); (5) <t>EcoP15I</t> digestion to generate ~ 27 nt long reads; (6) ligation of EcoP15I digestion products with a 3′ds-DNA adapter; (7) purification of ligation products on a PAGE gel; (8) degradome library enrichment (2nd PCR amplification); (9) purification of the final product on a PAGE gel; (10) library pooling and sequencing using Illumina <t>HiSeq</t> platform
    Hiseqxten Sequencing Platform, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 80/100, based on 11 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/hiseqxten sequencing platform/product/Illumina Inc
    Average 80 stars, based on 11 article reviews
    Price from $9.99 to $1999.99
    hiseqxten sequencing platform - by Bioz Stars, 2020-02
    80/100 stars
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    99
    Illumina Inc hiseq4000 sequencing platform
    The scheme for constructing improved degradome library. For sequencing purposes, the degradome library generated by this method can be treated as small RNA library and the resulting reads are ~ 27 nt long. The procedure includes: (1) poly(A) RNA isolation; (2) 5′RNA adapter ligation to uncapped poly(A) RNA with 5′ monophosphate; (3) reverse transcription to generate 1st strand cDNA using an oligo(dT)-tailed adapter (RT-primer); (4) second strand synthesis (1st PCR amplification); (5) <t>EcoP15I</t> digestion to generate ~ 27 nt long reads; (6) ligation of EcoP15I digestion products with a 3′ds-DNA adapter; (7) purification of ligation products on a PAGE gel; (8) degradome library enrichment (2nd PCR amplification); (9) purification of the final product on a PAGE gel; (10) library pooling and sequencing using Illumina <t>HiSeq</t> platform
    Hiseq4000 Sequencing Platform, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 119 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/hiseq4000 sequencing platform/product/Illumina Inc
    Average 99 stars, based on 119 article reviews
    Price from $9.99 to $1999.99
    hiseq4000 sequencing platform - by Bioz Stars, 2020-02
    99/100 stars
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    75
    Illumina Inc pe150 sequencing platform
    The scheme for constructing improved degradome library. For sequencing purposes, the degradome library generated by this method can be treated as small RNA library and the resulting reads are ~ 27 nt long. The procedure includes: (1) poly(A) RNA isolation; (2) 5′RNA adapter ligation to uncapped poly(A) RNA with 5′ monophosphate; (3) reverse transcription to generate 1st strand cDNA using an oligo(dT)-tailed adapter (RT-primer); (4) second strand synthesis (1st PCR amplification); (5) <t>EcoP15I</t> digestion to generate ~ 27 nt long reads; (6) ligation of EcoP15I digestion products with a 3′ds-DNA adapter; (7) purification of ligation products on a PAGE gel; (8) degradome library enrichment (2nd PCR amplification); (9) purification of the final product on a PAGE gel; (10) library pooling and sequencing using Illumina <t>HiSeq</t> platform
    Pe150 Sequencing Platform, 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/pe150 sequencing platform/product/Illumina Inc
    Average 75 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    pe150 sequencing platform - by Bioz Stars, 2020-02
    75/100 stars
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    79
    Illumina Inc 2500 sequencing platform
    The scheme for constructing improved degradome library. For sequencing purposes, the degradome library generated by this method can be treated as small RNA library and the resulting reads are ~ 27 nt long. The procedure includes: (1) poly(A) RNA isolation; (2) 5′RNA adapter ligation to uncapped poly(A) RNA with 5′ monophosphate; (3) reverse transcription to generate 1st strand cDNA using an oligo(dT)-tailed adapter (RT-primer); (4) second strand synthesis (1st PCR amplification); (5) <t>EcoP15I</t> digestion to generate ~ 27 nt long reads; (6) ligation of EcoP15I digestion products with a 3′ds-DNA adapter; (7) purification of ligation products on a PAGE gel; (8) degradome library enrichment (2nd PCR amplification); (9) purification of the final product on a PAGE gel; (10) library pooling and sequencing using Illumina <t>HiSeq</t> platform
    2500 Sequencing Platform, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 79/100, based on 14 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/2500 sequencing platform/product/Illumina Inc
    Average 79 stars, based on 14 article reviews
    Price from $9.99 to $1999.99
    2500 sequencing platform - by Bioz Stars, 2020-02
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    85
    Illumina Inc sequencing sgs platforms
    The scheme for constructing improved degradome library. For sequencing purposes, the degradome library generated by this method can be treated as small RNA library and the resulting reads are ~ 27 nt long. The procedure includes: (1) poly(A) RNA isolation; (2) 5′RNA adapter ligation to uncapped poly(A) RNA with 5′ monophosphate; (3) reverse transcription to generate 1st strand cDNA using an oligo(dT)-tailed adapter (RT-primer); (4) second strand synthesis (1st PCR amplification); (5) <t>EcoP15I</t> digestion to generate ~ 27 nt long reads; (6) ligation of EcoP15I digestion products with a 3′ds-DNA adapter; (7) purification of ligation products on a PAGE gel; (8) degradome library enrichment (2nd PCR amplification); (9) purification of the final product on a PAGE gel; (10) library pooling and sequencing using Illumina <t>HiSeq</t> platform
    Sequencing Sgs Platforms, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 85/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/sequencing sgs platforms/product/Illumina Inc
    Average 85 stars, based on 6 article reviews
    Price from $9.99 to $1999.99
    sequencing sgs platforms - by Bioz Stars, 2020-02
    85/100 stars
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    77
    Illumina Inc sequencing by synthesis platform
    The scheme for constructing improved degradome library. For sequencing purposes, the degradome library generated by this method can be treated as small RNA library and the resulting reads are ~ 27 nt long. The procedure includes: (1) poly(A) RNA isolation; (2) 5′RNA adapter ligation to uncapped poly(A) RNA with 5′ monophosphate; (3) reverse transcription to generate 1st strand cDNA using an oligo(dT)-tailed adapter (RT-primer); (4) second strand synthesis (1st PCR amplification); (5) <t>EcoP15I</t> digestion to generate ~ 27 nt long reads; (6) ligation of EcoP15I digestion products with a 3′ds-DNA adapter; (7) purification of ligation products on a PAGE gel; (8) degradome library enrichment (2nd PCR amplification); (9) purification of the final product on a PAGE gel; (10) library pooling and sequencing using Illumina <t>HiSeq</t> platform
    Sequencing By Synthesis Platform, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 77/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/sequencing by synthesis platform/product/Illumina Inc
    Average 77 stars, based on 4 article reviews
    Price from $9.99 to $1999.99
    sequencing by synthesis platform - by Bioz Stars, 2020-02
    77/100 stars
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    75
    Illumina Inc solexa sequencing platform
    The scheme for constructing improved degradome library. For sequencing purposes, the degradome library generated by this method can be treated as small RNA library and the resulting reads are ~ 27 nt long. The procedure includes: (1) poly(A) RNA isolation; (2) 5′RNA adapter ligation to uncapped poly(A) RNA with 5′ monophosphate; (3) reverse transcription to generate 1st strand cDNA using an oligo(dT)-tailed adapter (RT-primer); (4) second strand synthesis (1st PCR amplification); (5) <t>EcoP15I</t> digestion to generate ~ 27 nt long reads; (6) ligation of EcoP15I digestion products with a 3′ds-DNA adapter; (7) purification of ligation products on a PAGE gel; (8) degradome library enrichment (2nd PCR amplification); (9) purification of the final product on a PAGE gel; (10) library pooling and sequencing using Illumina <t>HiSeq</t> platform
    Solexa Sequencing Platform, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 75/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/solexa sequencing platform/product/Illumina Inc
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    The scheme for constructing improved degradome library. For sequencing purposes, the degradome library generated by this method can be treated as small RNA library and the resulting reads are ~ 27 nt long. The procedure includes: (1) poly(A) RNA isolation; (2) 5′RNA adapter ligation to uncapped poly(A) RNA with 5′ monophosphate; (3) reverse transcription to generate 1st strand cDNA using an oligo(dT)-tailed adapter (RT-primer); (4) second strand synthesis (1st PCR amplification); (5) <t>EcoP15I</t> digestion to generate ~ 27 nt long reads; (6) ligation of EcoP15I digestion products with a 3′ds-DNA adapter; (7) purification of ligation products on a PAGE gel; (8) degradome library enrichment (2nd PCR amplification); (9) purification of the final product on a PAGE gel; (10) library pooling and sequencing using Illumina <t>HiSeq</t> platform
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    Illumina Inc illuminahiseq2000 sequencing platform
    The scheme for constructing improved degradome library. For sequencing purposes, the degradome library generated by this method can be treated as small RNA library and the resulting reads are ~ 27 nt long. The procedure includes: (1) poly(A) RNA isolation; (2) 5′RNA adapter ligation to uncapped poly(A) RNA with 5′ monophosphate; (3) reverse transcription to generate 1st strand cDNA using an oligo(dT)-tailed adapter (RT-primer); (4) second strand synthesis (1st PCR amplification); (5) <t>EcoP15I</t> digestion to generate ~ 27 nt long reads; (6) ligation of EcoP15I digestion products with a 3′ds-DNA adapter; (7) purification of ligation products on a PAGE gel; (8) degradome library enrichment (2nd PCR amplification); (9) purification of the final product on a PAGE gel; (10) library pooling and sequencing using Illumina <t>HiSeq</t> platform
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    The scheme for constructing improved degradome library. For sequencing purposes, the degradome library generated by this method can be treated as small RNA library and the resulting reads are ~ 27 nt long. The procedure includes: (1) poly(A) RNA isolation; (2) 5′RNA adapter ligation to uncapped poly(A) RNA with 5′ monophosphate; (3) reverse transcription to generate 1st strand cDNA using an oligo(dT)-tailed adapter (RT-primer); (4) second strand synthesis (1st PCR amplification); (5) <t>EcoP15I</t> digestion to generate ~ 27 nt long reads; (6) ligation of EcoP15I digestion products with a 3′ds-DNA adapter; (7) purification of ligation products on a PAGE gel; (8) degradome library enrichment (2nd PCR amplification); (9) purification of the final product on a PAGE gel; (10) library pooling and sequencing using Illumina <t>HiSeq</t> platform
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    The scheme for constructing improved degradome library. For sequencing purposes, the degradome library generated by this method can be treated as small RNA library and the resulting reads are ~ 27 nt long. The procedure includes: (1) poly(A) RNA isolation; (2) 5′RNA adapter ligation to uncapped poly(A) RNA with 5′ monophosphate; (3) reverse transcription to generate 1st strand cDNA using an oligo(dT)-tailed adapter (RT-primer); (4) second strand synthesis (1st PCR amplification); (5) <t>EcoP15I</t> digestion to generate ~ 27 nt long reads; (6) ligation of EcoP15I digestion products with a 3′ds-DNA adapter; (7) purification of ligation products on a PAGE gel; (8) degradome library enrichment (2nd PCR amplification); (9) purification of the final product on a PAGE gel; (10) library pooling and sequencing using Illumina <t>HiSeq</t> platform
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    Illumina Inc hiseqtm 2500 sequencing platform
    The scheme for constructing improved degradome library. For sequencing purposes, the degradome library generated by this method can be treated as small RNA library and the resulting reads are ~ 27 nt long. The procedure includes: (1) poly(A) RNA isolation; (2) 5′RNA adapter ligation to uncapped poly(A) RNA with 5′ monophosphate; (3) reverse transcription to generate 1st strand cDNA using an oligo(dT)-tailed adapter (RT-primer); (4) second strand synthesis (1st PCR amplification); (5) <t>EcoP15I</t> digestion to generate ~ 27 nt long reads; (6) ligation of EcoP15I digestion products with a 3′ds-DNA adapter; (7) purification of ligation products on a PAGE gel; (8) degradome library enrichment (2nd PCR amplification); (9) purification of the final product on a PAGE gel; (10) library pooling and sequencing using Illumina <t>HiSeq</t> platform
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    Illumina Inc smrt sequencing platforms
    The scheme for constructing improved degradome library. For sequencing purposes, the degradome library generated by this method can be treated as small RNA library and the resulting reads are ~ 27 nt long. The procedure includes: (1) poly(A) RNA isolation; (2) 5′RNA adapter ligation to uncapped poly(A) RNA with 5′ monophosphate; (3) reverse transcription to generate 1st strand cDNA using an oligo(dT)-tailed adapter (RT-primer); (4) second strand synthesis (1st PCR amplification); (5) <t>EcoP15I</t> digestion to generate ~ 27 nt long reads; (6) ligation of EcoP15I digestion products with a 3′ds-DNA adapter; (7) purification of ligation products on a PAGE gel; (8) degradome library enrichment (2nd PCR amplification); (9) purification of the final product on a PAGE gel; (10) library pooling and sequencing using Illumina <t>HiSeq</t> platform
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    Illumina Inc miseq fgx sequencing platforms
    The scheme for constructing improved degradome library. For sequencing purposes, the degradome library generated by this method can be treated as small RNA library and the resulting reads are ~ 27 nt long. The procedure includes: (1) poly(A) RNA isolation; (2) 5′RNA adapter ligation to uncapped poly(A) RNA with 5′ monophosphate; (3) reverse transcription to generate 1st strand cDNA using an oligo(dT)-tailed adapter (RT-primer); (4) second strand synthesis (1st PCR amplification); (5) <t>EcoP15I</t> digestion to generate ~ 27 nt long reads; (6) ligation of EcoP15I digestion products with a 3′ds-DNA adapter; (7) purification of ligation products on a PAGE gel; (8) degradome library enrichment (2nd PCR amplification); (9) purification of the final product on a PAGE gel; (10) library pooling and sequencing using Illumina <t>HiSeq</t> platform
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    Illumina Inc next generation sequencing platforms
    The scheme for constructing improved degradome library. For sequencing purposes, the degradome library generated by this method can be treated as small RNA library and the resulting reads are ~ 27 nt long. The procedure includes: (1) poly(A) RNA isolation; (2) 5′RNA adapter ligation to uncapped poly(A) RNA with 5′ monophosphate; (3) reverse transcription to generate 1st strand cDNA using an oligo(dT)-tailed adapter (RT-primer); (4) second strand synthesis (1st PCR amplification); (5) <t>EcoP15I</t> digestion to generate ~ 27 nt long reads; (6) ligation of EcoP15I digestion products with a 3′ds-DNA adapter; (7) purification of ligation products on a PAGE gel; (8) degradome library enrichment (2nd PCR amplification); (9) purification of the final product on a PAGE gel; (10) library pooling and sequencing using Illumina <t>HiSeq</t> platform
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    Image Search Results


    Dilution of variant allele frequency when primers are not clipped after mapping. NGS read alignments in BRCA1 c.4372C > T region from primer handling approaches 2 and 3 are shown in conjunction with the amplicon design and reference genome sequence. The c.4372C > T mutation is located in the region of interest of one amplicon and gene-specific primer site of another amplicon. Since primer sequences retained in approach 2 contributed to wild-type allele frequency, VAF of c.4372C > T was in turn underestimated by 82% (9% in approach 2 and 51% in approach 3).

    Journal: Scientific Reports

    Article Title: BAMClipper: removing primers from alignments to minimize false-negative mutations in amplicon next-generation sequencing

    doi: 10.1038/s41598-017-01703-6

    Figure Lengend Snippet: Dilution of variant allele frequency when primers are not clipped after mapping. NGS read alignments in BRCA1 c.4372C > T region from primer handling approaches 2 and 3 are shown in conjunction with the amplicon design and reference genome sequence. The c.4372C > T mutation is located in the region of interest of one amplicon and gene-specific primer site of another amplicon. Since primer sequences retained in approach 2 contributed to wild-type allele frequency, VAF of c.4372C > T was in turn underestimated by 82% (9% in approach 2 and 51% in approach 3).

    Article Snippet: BAMClipper was tested to be sequencing platform-independent by clipping primers from amplicon sequencing reads from both Illumina MiSeq and Ion Torrent PGM platforms.

    Techniques: Variant Assay, Next-Generation Sequencing, Amplification, Sequencing, Mutagenesis

    Amplicon library design and bioinformatics approaches of handling gene-specific primers. ( A ) Gene-specific primer sequences are present as part of NGS reads. The observed primer sequences are usually identical to reference genome sequence but may be slightly different due to errors in primer synthesis and/or sequencing. Common read mapping tools are not aware of the amplicon library design and thus map the primers as if they are part of region of interest that lies in between. Although sequencing adapters may exist as part of NGS reads (depending of amplicon length and sequencing read length), they will become soft-clipped after mapping due to the lack of similarity to reference genome by design. Soft-clipped part of alignments is usually ignored by downstream processing. ( B ) In primer handling approach 1, primer sequence was trimmed from sequencing reads (in FASTQ format) and the shorter trimmed reads are mapped to give BAM alignments for downstream variant calling and quality control such as sequencing depth statistics. In approach 2, original reads are directly mapped that primers are present in BAM alignments as if they are part of region of interest. In approach 3 represented by BAMClipper, reads are also directly mapped but BAM alignments are further processed to soft-clip primer sequences as if they were sequencing adapters.

    Journal: Scientific Reports

    Article Title: BAMClipper: removing primers from alignments to minimize false-negative mutations in amplicon next-generation sequencing

    doi: 10.1038/s41598-017-01703-6

    Figure Lengend Snippet: Amplicon library design and bioinformatics approaches of handling gene-specific primers. ( A ) Gene-specific primer sequences are present as part of NGS reads. The observed primer sequences are usually identical to reference genome sequence but may be slightly different due to errors in primer synthesis and/or sequencing. Common read mapping tools are not aware of the amplicon library design and thus map the primers as if they are part of region of interest that lies in between. Although sequencing adapters may exist as part of NGS reads (depending of amplicon length and sequencing read length), they will become soft-clipped after mapping due to the lack of similarity to reference genome by design. Soft-clipped part of alignments is usually ignored by downstream processing. ( B ) In primer handling approach 1, primer sequence was trimmed from sequencing reads (in FASTQ format) and the shorter trimmed reads are mapped to give BAM alignments for downstream variant calling and quality control such as sequencing depth statistics. In approach 2, original reads are directly mapped that primers are present in BAM alignments as if they are part of region of interest. In approach 3 represented by BAMClipper, reads are also directly mapped but BAM alignments are further processed to soft-clip primer sequences as if they were sequencing adapters.

    Article Snippet: BAMClipper was tested to be sequencing platform-independent by clipping primers from amplicon sequencing reads from both Illumina MiSeq and Ion Torrent PGM platforms.

    Techniques: Amplification, Next-Generation Sequencing, Sequencing, Variant Assay, Cross-linking Immunoprecipitation

    A BRCA1 deletion escaped from variant calling when primers were trimmed before mapping. NGS read alignments of BRCA1 c.1620_1636del allele from three primer handling approaches are shown in conjunction with the amplicon design and reference genome sequence. Individual forward and reverse sequencing reads after any soft-clipping were represented by red and purple horizontal lines, respectively. The expected deletion event (black box) was present in the alignments from approaches 2 and 3 only.

    Journal: Scientific Reports

    Article Title: BAMClipper: removing primers from alignments to minimize false-negative mutations in amplicon next-generation sequencing

    doi: 10.1038/s41598-017-01703-6

    Figure Lengend Snippet: A BRCA1 deletion escaped from variant calling when primers were trimmed before mapping. NGS read alignments of BRCA1 c.1620_1636del allele from three primer handling approaches are shown in conjunction with the amplicon design and reference genome sequence. Individual forward and reverse sequencing reads after any soft-clipping were represented by red and purple horizontal lines, respectively. The expected deletion event (black box) was present in the alignments from approaches 2 and 3 only.

    Article Snippet: BAMClipper was tested to be sequencing platform-independent by clipping primers from amplicon sequencing reads from both Illumina MiSeq and Ion Torrent PGM platforms.

    Techniques: Variant Assay, Next-Generation Sequencing, Amplification, Sequencing

    Length distribution of transcripts obtained by different sequencing platforms. Illumina_1 and Illumina_2 represent the transcripts assembled by Zhang [ 20 ] and Zhou [ 21 ], respectively, using the Illumina sequencing platform

    Journal: BMC Genomics

    Article Title: Full-length transcriptome sequences of Agropyron cristatum facilitate the prediction of putative genes for thousand-grain weight in a wheat-A. cristatum translocation line

    doi: 10.1186/s12864-019-6416-4

    Figure Lengend Snippet: Length distribution of transcripts obtained by different sequencing platforms. Illumina_1 and Illumina_2 represent the transcripts assembled by Zhang [ 20 ] and Zhou [ 21 ], respectively, using the Illumina sequencing platform

    Article Snippet: Analysis of tissue-enriched transcripts All raw sequence reads from the Illumina sequencing platform were cleaned by removing the RNA adapters and trimming the low-quality bases (Q < 20) with a minimum read length of 36 bases using Trimmomatic (version 0.39) [ ].

    Techniques: Sequencing

    Sampling overview. Swab samples were taken from ovaries dissected out of pipefish ( Syngnathus typhle ) females (Gonads-GO); from the brood pouch tissue of non-pregnant pipefish males (Non-Pregnant-NP); on the surface of eggs and embryos inside the brood pouch of pregnant males in increasing developmental stages: early pregnancy (EP) circa (1–2 weeks); mid pregnant (MP) (2–4 weeks); late pregnant (LP) (4–6 weeks). In total 20 females, 20 males per pregnancy stage (3*20), and 40 non-pregnant males were used for the study (120 fish). For each group half of the individuals were intraperitoneally injected with heat-killed bacteria suspension ( Vibrio spp. and Tenacibaculum maritimum ) to trigger a parental immune transfer (injected with bacteria solution vs. non-injected). Microbiota samples were taken with sterile swabs by scratching the mucus from the surface of ovaries, brood pouch tissue and embryos inside the paternal brood pouch. Microbiota analysis was performed by Illumina Miseq Sequencing.

    Journal: Scientific Reports

    Article Title: Microbial embryonal colonization during pipefish male pregnancy

    doi: 10.1038/s41598-018-37026-3

    Figure Lengend Snippet: Sampling overview. Swab samples were taken from ovaries dissected out of pipefish ( Syngnathus typhle ) females (Gonads-GO); from the brood pouch tissue of non-pregnant pipefish males (Non-Pregnant-NP); on the surface of eggs and embryos inside the brood pouch of pregnant males in increasing developmental stages: early pregnancy (EP) circa (1–2 weeks); mid pregnant (MP) (2–4 weeks); late pregnant (LP) (4–6 weeks). In total 20 females, 20 males per pregnancy stage (3*20), and 40 non-pregnant males were used for the study (120 fish). For each group half of the individuals were intraperitoneally injected with heat-killed bacteria suspension ( Vibrio spp. and Tenacibaculum maritimum ) to trigger a parental immune transfer (injected with bacteria solution vs. non-injected). Microbiota samples were taken with sterile swabs by scratching the mucus from the surface of ovaries, brood pouch tissue and embryos inside the paternal brood pouch. Microbiota analysis was performed by Illumina Miseq Sequencing.

    Article Snippet: Distinct microbiomes in developmental stages, depending on parental immunological status In total, 994,755 16S rRNA sequences were retained from Illumina Miseq sequencing platform after merging and quality control.

    Techniques: Sampling, Fluorescence In Situ Hybridization, Injection, Sequencing

    Effect of the integration procedures on TCGA LUSC datasets. Two datasets comprising of Illumina HiSeq-2000 and Affymetrix HG-U133A data were employed to evaluate the effect of the integration on two different platforms. After applying the integration procedure, DEGs were computed varying the p-value threshold. Receiver-Operating Characteristic (ROC) curves were computed using known DEGs, and the performances were assessed by means of Area Under the ROC Curve (AUC)

    Journal: BMC Bioinformatics

    Article Title: TACITuS: transcriptomic data collector, integrator, and selector on big data platform

    doi: 10.1186/s12859-019-2912-4

    Figure Lengend Snippet: Effect of the integration procedures on TCGA LUSC datasets. Two datasets comprising of Illumina HiSeq-2000 and Affymetrix HG-U133A data were employed to evaluate the effect of the integration on two different platforms. After applying the integration procedure, DEGs were computed varying the p-value threshold. Receiver-Operating Characteristic (ROC) curves were computed using known DEGs, and the performances were assessed by means of Area Under the ROC Curve (AUC)

    Article Snippet: The dataset comprises of 552 RNA-seq samples (501 cases and 51 controls) obtained using the Illumina HiSeq-2000 sequencing platform.

    Techniques:

    28S gene sequence analysis. (A) 28S sequence for  Lepas anatifera  from Illumina Hi-Seq 2000 platform; (B) The AU rich stretch of rRNA where the UAAU sequence at position 1,781 nt is likely responsible for splitting the rRNA into ∼1,780 nt and ∼2,000 nt fragments which migrate together on a heat-denaturing gel. The CGAAAGGG sequence at the 3′ end of the AU rich region (highlighted in red) is highly conserved in all 28S rRNAs; (C) Sequence alignment for 28S rDNA of centipede and barnacles upstream of the TAAT (UAAU) cleavage site (yellow highlight). The 28S rDNA sequence for spider  Grammostola porteri  is not available.

    Journal: PeerJ

    Article Title: ‘Degraded’ RNA profiles in Arthropoda and beyond

    doi: 10.7717/peerj.1436

    Figure Lengend Snippet: 28S gene sequence analysis. (A) 28S sequence for Lepas anatifera from Illumina Hi-Seq 2000 platform; (B) The AU rich stretch of rRNA where the UAAU sequence at position 1,781 nt is likely responsible for splitting the rRNA into ∼1,780 nt and ∼2,000 nt fragments which migrate together on a heat-denaturing gel. The CGAAAGGG sequence at the 3′ end of the AU rich region (highlighted in red) is highly conserved in all 28S rRNAs; (C) Sequence alignment for 28S rDNA of centipede and barnacles upstream of the TAAT (UAAU) cleavage site (yellow highlight). The 28S rDNA sequence for spider Grammostola porteri is not available.

    Article Snippet: Transcriptome analysis for this species was carried out on an Illumina Hi-Seq 2000 sequencing platform by Source BioScience LifeSciences, UK.

    Techniques: Sequencing

    The scheme for constructing improved degradome library. For sequencing purposes, the degradome library generated by this method can be treated as small RNA library and the resulting reads are ~ 27 nt long. The procedure includes: (1) poly(A) RNA isolation; (2) 5′RNA adapter ligation to uncapped poly(A) RNA with 5′ monophosphate; (3) reverse transcription to generate 1st strand cDNA using an oligo(dT)-tailed adapter (RT-primer); (4) second strand synthesis (1st PCR amplification); (5) EcoP15I digestion to generate ~ 27 nt long reads; (6) ligation of EcoP15I digestion products with a 3′ds-DNA adapter; (7) purification of ligation products on a PAGE gel; (8) degradome library enrichment (2nd PCR amplification); (9) purification of the final product on a PAGE gel; (10) library pooling and sequencing using Illumina HiSeq platform

    Journal: Plant Methods

    Article Title: An improved method of constructing degradome library suitable for sequencing using Illumina platform

    doi: 10.1186/s13007-019-0524-7

    Figure Lengend Snippet: The scheme for constructing improved degradome library. For sequencing purposes, the degradome library generated by this method can be treated as small RNA library and the resulting reads are ~ 27 nt long. The procedure includes: (1) poly(A) RNA isolation; (2) 5′RNA adapter ligation to uncapped poly(A) RNA with 5′ monophosphate; (3) reverse transcription to generate 1st strand cDNA using an oligo(dT)-tailed adapter (RT-primer); (4) second strand synthesis (1st PCR amplification); (5) EcoP15I digestion to generate ~ 27 nt long reads; (6) ligation of EcoP15I digestion products with a 3′ds-DNA adapter; (7) purification of ligation products on a PAGE gel; (8) degradome library enrichment (2nd PCR amplification); (9) purification of the final product on a PAGE gel; (10) library pooling and sequencing using Illumina HiSeq platform

    Article Snippet: Given the advantages of Illumina sequencing, a detailed methodology that combines the use of EcoP15I and Illumina HiSeq sequencing platform is ideal.

    Techniques: Sequencing, Generated, Isolation, Ligation, Polymerase Chain Reaction, Amplification, Purification, Polyacrylamide Gel Electrophoresis