gene expression profiling dge Search Results


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  • 94
    Illumina Inc gene expression profiling dge
    <t>Microarray</t> versus <t>DGE</t> analysis . (A) Overlap of unique and named genes shared among the 3 microarray platforms and genes detected by DGE. The pool of 14645 shared genes was used for further cross-platform analysis. The total numbers of genes for each platform and for all platforms combined are indicated. (B) Overlap of significantly regulated genes considering the 3 microarray platforms at 6 h after EGF treatment and the genes found regulated after assessing significance by grouping microarray and DGE data in a RankProd analysis. Left panels show up-regulated genes and right panels show down-regulated genes.
    Gene Expression Profiling Dge, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 94/100, based on 22 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/gene expression profiling dge/product/Illumina Inc
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    86
    Illumina Inc digital gene expression profiling dge
    <t>Microarray</t> versus <t>DGE</t> analysis . (A) Overlap of unique and named genes shared among the 3 microarray platforms and genes detected by DGE. The pool of 14645 shared genes was used for further cross-platform analysis. The total numbers of genes for each platform and for all platforms combined are indicated. (B) Overlap of significantly regulated genes considering the 3 microarray platforms at 6 h after EGF treatment and the genes found regulated after assessing significance by grouping microarray and DGE data in a RankProd analysis. Left panels show up-regulated genes and right panels show down-regulated genes.
    Digital Gene Expression Profiling Dge, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 86/100, based on 38 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/digital gene expression profiling dge/product/Illumina Inc
    Average 86 stars, based on 38 article reviews
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    digital gene expression profiling dge - by Bioz Stars, 2020-04
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    86
    Solexa digital gene expression profiling dge
    <t>Microarray</t> versus <t>DGE</t> analysis . (A) Overlap of unique and named genes shared among the 3 microarray platforms and genes detected by DGE. The pool of 14645 shared genes was used for further cross-platform analysis. The total numbers of genes for each platform and for all platforms combined are indicated. (B) Overlap of significantly regulated genes considering the 3 microarray platforms at 6 h after EGF treatment and the genes found regulated after assessing significance by grouping microarray and DGE data in a RankProd analysis. Left panels show up-regulated genes and right panels show down-regulated genes.
    Digital Gene Expression Profiling Dge, supplied by Solexa, used in various techniques. Bioz Stars score: 86/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/digital gene expression profiling dge/product/Solexa
    Average 86 stars, based on 5 article reviews
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    digital gene expression profiling dge - by Bioz Stars, 2020-04
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    92
    Illumina Inc digital gene expression dge tag profile kit
    <t>Microarray</t> versus <t>DGE</t> analysis . (A) Overlap of unique and named genes shared among the 3 microarray platforms and genes detected by DGE. The pool of 14645 shared genes was used for further cross-platform analysis. The total numbers of genes for each platform and for all platforms combined are indicated. (B) Overlap of significantly regulated genes considering the 3 microarray platforms at 6 h after EGF treatment and the genes found regulated after assessing significance by grouping microarray and DGE data in a RankProd analysis. Left panels show up-regulated genes and right panels show down-regulated genes.
    Digital Gene Expression Dge Tag Profile Kit, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 92/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/digital gene expression dge tag profile kit/product/Illumina Inc
    Average 92 stars, based on 8 article reviews
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    86
    Illumina Inc digital gene expression dge profiling analysis
    <t>Microarray</t> versus <t>DGE</t> analysis . (A) Overlap of unique and named genes shared among the 3 microarray platforms and genes detected by DGE. The pool of 14645 shared genes was used for further cross-platform analysis. The total numbers of genes for each platform and for all platforms combined are indicated. (B) Overlap of significantly regulated genes considering the 3 microarray platforms at 6 h after EGF treatment and the genes found regulated after assessing significance by grouping microarray and DGE data in a RankProd analysis. Left panels show up-regulated genes and right panels show down-regulated genes.
    Digital Gene Expression Dge Profiling Analysis, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 86/100, based on 17 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/digital gene expression dge profiling analysis/product/Illumina Inc
    Average 86 stars, based on 17 article reviews
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    digital gene expression dge profiling analysis - by Bioz Stars, 2020-04
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    86
    BGI Shenzhen dge digital gene expression profiles library construction
    <t>Microarray</t> versus <t>DGE</t> analysis . (A) Overlap of unique and named genes shared among the 3 microarray platforms and genes detected by DGE. The pool of 14645 shared genes was used for further cross-platform analysis. The total numbers of genes for each platform and for all platforms combined are indicated. (B) Overlap of significantly regulated genes considering the 3 microarray platforms at 6 h after EGF treatment and the genes found regulated after assessing significance by grouping microarray and DGE data in a RankProd analysis. Left panels show up-regulated genes and right panels show down-regulated genes.
    Dge Digital Gene Expression Profiles Library Construction, supplied by BGI Shenzhen, used in various techniques. Bioz Stars score: 86/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/dge digital gene expression profiles library construction/product/BGI Shenzhen
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    dge digital gene expression profiles library construction - by Bioz Stars, 2020-04
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    86
    Solexa sequencing based digital gene expression tag profile dge technology
    <t>Microarray</t> versus <t>DGE</t> analysis . (A) Overlap of unique and named genes shared among the 3 microarray platforms and genes detected by DGE. The pool of 14645 shared genes was used for further cross-platform analysis. The total numbers of genes for each platform and for all platforms combined are indicated. (B) Overlap of significantly regulated genes considering the 3 microarray platforms at 6 h after EGF treatment and the genes found regulated after assessing significance by grouping microarray and DGE data in a RankProd analysis. Left panels show up-regulated genes and right panels show down-regulated genes.
    Sequencing Based Digital Gene Expression Tag Profile Dge Technology, supplied by Solexa, used in various techniques. Bioz Stars score: 86/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/sequencing based digital gene expression tag profile dge technology/product/Solexa
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    87
    Illumina Inc nlaiii dge protocol
    Adaptors and adaptor chimeras are a common sources of sequence artifacts . Specific outer adapter sequences, complementary to the grafting sequences on the flow cell are essentially the only requirement for sequencing a DNA library on the Genome Analyzer platform. As different sequencing primers can be used, library design is very flexible and various protocols with partially distinct adapter sequences have been established. The Illumina <t>NlaIII</t> <t>DGE</t> tag protocol illustrated here (a protocol for digital gene expression tag profiling) uses short adapters which are not compatible with paired end sequencing and are added by overhang ligation (A). For this protocol the majority of adapter dimers are removed by a gel excision step after library preparation. However, the protocol may also create adapter chimeras with a length comparable to the targeted library molecules. The resulting chimera sequences also show the sequences required for cluster generation as well as the necessary priming site, causing them to be sequenced together with the real DGE tags. A program like TagDust [ 29 ] can be used with the original adapter and primer oligonucleotide sequences to identify such artifacts (B). Shown are the twenty most frequent identified artifacts from one lane with human DGE tags, as well as the oligosequences they might be based on. One of the 20 sequences seems to be a real DGE tag that was incorrectly identified as an artifact.
    Nlaiii Dge Protocol, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 87/100, based on 14 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/nlaiii dge protocol/product/Illumina Inc
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    86
    Illumina Inc foc inoculation illumina dge
    Adaptors and adaptor chimeras are a common sources of sequence artifacts . Specific outer adapter sequences, complementary to the grafting sequences on the flow cell are essentially the only requirement for sequencing a DNA library on the Genome Analyzer platform. As different sequencing primers can be used, library design is very flexible and various protocols with partially distinct adapter sequences have been established. The Illumina <t>NlaIII</t> <t>DGE</t> tag protocol illustrated here (a protocol for digital gene expression tag profiling) uses short adapters which are not compatible with paired end sequencing and are added by overhang ligation (A). For this protocol the majority of adapter dimers are removed by a gel excision step after library preparation. However, the protocol may also create adapter chimeras with a length comparable to the targeted library molecules. The resulting chimera sequences also show the sequences required for cluster generation as well as the necessary priming site, causing them to be sequenced together with the real DGE tags. A program like TagDust [ 29 ] can be used with the original adapter and primer oligonucleotide sequences to identify such artifacts (B). Shown are the twenty most frequent identified artifacts from one lane with human DGE tags, as well as the oligosequences they might be based on. One of the 20 sequences seems to be a real DGE tag that was incorrectly identified as an artifact.
    Foc Inoculation Illumina Dge, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 86/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/foc inoculation illumina dge/product/Illumina Inc
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    87
    Illumina Inc solexa illumina s dge system
    Adaptors and adaptor chimeras are a common sources of sequence artifacts . Specific outer adapter sequences, complementary to the grafting sequences on the flow cell are essentially the only requirement for sequencing a DNA library on the Genome Analyzer platform. As different sequencing primers can be used, library design is very flexible and various protocols with partially distinct adapter sequences have been established. The Illumina <t>NlaIII</t> <t>DGE</t> tag protocol illustrated here (a protocol for digital gene expression tag profiling) uses short adapters which are not compatible with paired end sequencing and are added by overhang ligation (A). For this protocol the majority of adapter dimers are removed by a gel excision step after library preparation. However, the protocol may also create adapter chimeras with a length comparable to the targeted library molecules. The resulting chimera sequences also show the sequences required for cluster generation as well as the necessary priming site, causing them to be sequenced together with the real DGE tags. A program like TagDust [ 29 ] can be used with the original adapter and primer oligonucleotide sequences to identify such artifacts (B). Shown are the twenty most frequent identified artifacts from one lane with human DGE tags, as well as the oligosequences they might be based on. One of the 20 sequences seems to be a real DGE tag that was incorrectly identified as an artifact.
    Solexa Illumina S Dge System, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 87/100, based on 10 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/solexa illumina s dge system/product/Illumina Inc
    Average 87 stars, based on 10 article reviews
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    84
    Illumina Inc challenge solexa illumina dge analysis
    Adaptors and adaptor chimeras are a common sources of sequence artifacts . Specific outer adapter sequences, complementary to the grafting sequences on the flow cell are essentially the only requirement for sequencing a DNA library on the Genome Analyzer platform. As different sequencing primers can be used, library design is very flexible and various protocols with partially distinct adapter sequences have been established. The Illumina <t>NlaIII</t> <t>DGE</t> tag protocol illustrated here (a protocol for digital gene expression tag profiling) uses short adapters which are not compatible with paired end sequencing and are added by overhang ligation (A). For this protocol the majority of adapter dimers are removed by a gel excision step after library preparation. However, the protocol may also create adapter chimeras with a length comparable to the targeted library molecules. The resulting chimera sequences also show the sequences required for cluster generation as well as the necessary priming site, causing them to be sequenced together with the real DGE tags. A program like TagDust [ 29 ] can be used with the original adapter and primer oligonucleotide sequences to identify such artifacts (B). Shown are the twenty most frequent identified artifacts from one lane with human DGE tags, as well as the oligosequences they might be based on. One of the 20 sequences seems to be a real DGE tag that was incorrectly identified as an artifact.
    Challenge Solexa Illumina Dge Analysis, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 84/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/challenge solexa illumina dge analysis/product/Illumina Inc
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    93
    LC Sciences whole transcriptome digital rna seq dge
    Adaptors and adaptor chimeras are a common sources of sequence artifacts . Specific outer adapter sequences, complementary to the grafting sequences on the flow cell are essentially the only requirement for sequencing a DNA library on the Genome Analyzer platform. As different sequencing primers can be used, library design is very flexible and various protocols with partially distinct adapter sequences have been established. The Illumina <t>NlaIII</t> <t>DGE</t> tag protocol illustrated here (a protocol for digital gene expression tag profiling) uses short adapters which are not compatible with paired end sequencing and are added by overhang ligation (A). For this protocol the majority of adapter dimers are removed by a gel excision step after library preparation. However, the protocol may also create adapter chimeras with a length comparable to the targeted library molecules. The resulting chimera sequences also show the sequences required for cluster generation as well as the necessary priming site, causing them to be sequenced together with the real DGE tags. A program like TagDust [ 29 ] can be used with the original adapter and primer oligonucleotide sequences to identify such artifacts (B). Shown are the twenty most frequent identified artifacts from one lane with human DGE tags, as well as the oligosequences they might be based on. One of the 20 sequences seems to be a real DGE tag that was incorrectly identified as an artifact.
    Whole Transcriptome Digital Rna Seq Dge, supplied by LC Sciences, used in various techniques. Bioz Stars score: 93/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/whole transcriptome digital rna seq dge/product/LC Sciences
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    98
    Illumina Inc gene expression sample prep kit
    Adaptors and adaptor chimeras are a common sources of sequence artifacts . Specific outer adapter sequences, complementary to the grafting sequences on the flow cell are essentially the only requirement for sequencing a DNA library on the Genome Analyzer platform. As different sequencing primers can be used, library design is very flexible and various protocols with partially distinct adapter sequences have been established. The Illumina <t>NlaIII</t> <t>DGE</t> tag protocol illustrated here (a protocol for digital gene expression tag profiling) uses short adapters which are not compatible with paired end sequencing and are added by overhang ligation (A). For this protocol the majority of adapter dimers are removed by a gel excision step after library preparation. However, the protocol may also create adapter chimeras with a length comparable to the targeted library molecules. The resulting chimera sequences also show the sequences required for cluster generation as well as the necessary priming site, causing them to be sequenced together with the real DGE tags. A program like TagDust [ 29 ] can be used with the original adapter and primer oligonucleotide sequences to identify such artifacts (B). Shown are the twenty most frequent identified artifacts from one lane with human DGE tags, as well as the oligosequences they might be based on. One of the 20 sequences seems to be a real DGE tag that was incorrectly identified as an artifact.
    Gene Expression Sample Prep Kit, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 98/100, based on 592 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/gene expression sample prep kit/product/Illumina Inc
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    99
    Illumina Inc truseq rna sample preparation kit
    Adaptors and adaptor chimeras are a common sources of sequence artifacts . Specific outer adapter sequences, complementary to the grafting sequences on the flow cell are essentially the only requirement for sequencing a DNA library on the Genome Analyzer platform. As different sequencing primers can be used, library design is very flexible and various protocols with partially distinct adapter sequences have been established. The Illumina <t>NlaIII</t> <t>DGE</t> tag protocol illustrated here (a protocol for digital gene expression tag profiling) uses short adapters which are not compatible with paired end sequencing and are added by overhang ligation (A). For this protocol the majority of adapter dimers are removed by a gel excision step after library preparation. However, the protocol may also create adapter chimeras with a length comparable to the targeted library molecules. The resulting chimera sequences also show the sequences required for cluster generation as well as the necessary priming site, causing them to be sequenced together with the real DGE tags. A program like TagDust [ 29 ] can be used with the original adapter and primer oligonucleotide sequences to identify such artifacts (B). Shown are the twenty most frequent identified artifacts from one lane with human DGE tags, as well as the oligosequences they might be based on. One of the 20 sequences seems to be a real DGE tag that was incorrectly identified as an artifact.
    Truseq Rna Sample Preparation Kit, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 6339 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/truseq rna sample preparation kit/product/Illumina Inc
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    Image Search Results


    Microarray versus DGE analysis . (A) Overlap of unique and named genes shared among the 3 microarray platforms and genes detected by DGE. The pool of 14645 shared genes was used for further cross-platform analysis. The total numbers of genes for each platform and for all platforms combined are indicated. (B) Overlap of significantly regulated genes considering the 3 microarray platforms at 6 h after EGF treatment and the genes found regulated after assessing significance by grouping microarray and DGE data in a RankProd analysis. Left panels show up-regulated genes and right panels show down-regulated genes.

    Journal: BMC Genomics

    Article Title: Multiple platform assessment of the EGF dependent transcriptome by microarray and deep tag sequencing analysis

    doi: 10.1186/1471-2164-12-326

    Figure Lengend Snippet: Microarray versus DGE analysis . (A) Overlap of unique and named genes shared among the 3 microarray platforms and genes detected by DGE. The pool of 14645 shared genes was used for further cross-platform analysis. The total numbers of genes for each platform and for all platforms combined are indicated. (B) Overlap of significantly regulated genes considering the 3 microarray platforms at 6 h after EGF treatment and the genes found regulated after assessing significance by grouping microarray and DGE data in a RankProd analysis. Left panels show up-regulated genes and right panels show down-regulated genes.

    Article Snippet: Here we use a combined approach to study the EGF dependent transcriptome of HeLa cells by using multiple long oligonucleotide based microarray platforms (from Agilent, Operon, and Illumina) in combination with digital gene expression profiling (DGE) with the Illumina Genome Analyzer.

    Techniques: Microarray

    Correlation between microarrays and Illumina GA-I sequencing . (A) Comparison of estimated log2ratios from DGE ( Y -axis) and the mean of all microarray platforms ( X -axis). We consider only genes that were interrogated using all platforms and genes with a mean number of counts across lanes greater than 0. Genes with counts greater than 32 reads (colored red or green) or less than (black) 32 reads in at least one sample are shown. (Red dots) Genes called differentially expressed based on DGE data at an 10% FDR by RankProd. (Green dots) Genes not called as differentially expressed but above 32 counts. (Inset box) Correlation between technologies is higher when considering genes above the 32 count detection level (0.57) than when all genes are included (0.49). (B-C) Concordance at the top (CAT) plots of the different platforms with the 500 top genes from a reference platform, shown for Agilent in (B) and DGE in (C). See inset box for color codes identifying each platforms compared to the remaining platform used as reference. (D) Correlation plots with regression lines between log2ratios of the five high content platforms measurements (Y-axis) and quantitative real time PCR results using SYBR green assays (X-axis), based on measurements for 21 genes at the 6 h time point (see Additional file 2 , Table S1).

    Journal: BMC Genomics

    Article Title: Multiple platform assessment of the EGF dependent transcriptome by microarray and deep tag sequencing analysis

    doi: 10.1186/1471-2164-12-326

    Figure Lengend Snippet: Correlation between microarrays and Illumina GA-I sequencing . (A) Comparison of estimated log2ratios from DGE ( Y -axis) and the mean of all microarray platforms ( X -axis). We consider only genes that were interrogated using all platforms and genes with a mean number of counts across lanes greater than 0. Genes with counts greater than 32 reads (colored red or green) or less than (black) 32 reads in at least one sample are shown. (Red dots) Genes called differentially expressed based on DGE data at an 10% FDR by RankProd. (Green dots) Genes not called as differentially expressed but above 32 counts. (Inset box) Correlation between technologies is higher when considering genes above the 32 count detection level (0.57) than when all genes are included (0.49). (B-C) Concordance at the top (CAT) plots of the different platforms with the 500 top genes from a reference platform, shown for Agilent in (B) and DGE in (C). See inset box for color codes identifying each platforms compared to the remaining platform used as reference. (D) Correlation plots with regression lines between log2ratios of the five high content platforms measurements (Y-axis) and quantitative real time PCR results using SYBR green assays (X-axis), based on measurements for 21 genes at the 6 h time point (see Additional file 2 , Table S1).

    Article Snippet: Here we use a combined approach to study the EGF dependent transcriptome of HeLa cells by using multiple long oligonucleotide based microarray platforms (from Agilent, Operon, and Illumina) in combination with digital gene expression profiling (DGE) with the Illumina Genome Analyzer.

    Techniques: Sequencing, Microarray, Real-time Polymerase Chain Reaction, SYBR Green Assay

    Adaptors and adaptor chimeras are a common sources of sequence artifacts . Specific outer adapter sequences, complementary to the grafting sequences on the flow cell are essentially the only requirement for sequencing a DNA library on the Genome Analyzer platform. As different sequencing primers can be used, library design is very flexible and various protocols with partially distinct adapter sequences have been established. The Illumina NlaIII DGE tag protocol illustrated here (a protocol for digital gene expression tag profiling) uses short adapters which are not compatible with paired end sequencing and are added by overhang ligation (A). For this protocol the majority of adapter dimers are removed by a gel excision step after library preparation. However, the protocol may also create adapter chimeras with a length comparable to the targeted library molecules. The resulting chimera sequences also show the sequences required for cluster generation as well as the necessary priming site, causing them to be sequenced together with the real DGE tags. A program like TagDust [ 29 ] can be used with the original adapter and primer oligonucleotide sequences to identify such artifacts (B). Shown are the twenty most frequent identified artifacts from one lane with human DGE tags, as well as the oligosequences they might be based on. One of the 20 sequences seems to be a real DGE tag that was incorrectly identified as an artifact.

    Journal: BMC Genomics

    Article Title: Addressing challenges in the production and analysis of illumina sequencing data

    doi: 10.1186/1471-2164-12-382

    Figure Lengend Snippet: Adaptors and adaptor chimeras are a common sources of sequence artifacts . Specific outer adapter sequences, complementary to the grafting sequences on the flow cell are essentially the only requirement for sequencing a DNA library on the Genome Analyzer platform. As different sequencing primers can be used, library design is very flexible and various protocols with partially distinct adapter sequences have been established. The Illumina NlaIII DGE tag protocol illustrated here (a protocol for digital gene expression tag profiling) uses short adapters which are not compatible with paired end sequencing and are added by overhang ligation (A). For this protocol the majority of adapter dimers are removed by a gel excision step after library preparation. However, the protocol may also create adapter chimeras with a length comparable to the targeted library molecules. The resulting chimera sequences also show the sequences required for cluster generation as well as the necessary priming site, causing them to be sequenced together with the real DGE tags. A program like TagDust [ 29 ] can be used with the original adapter and primer oligonucleotide sequences to identify such artifacts (B). Shown are the twenty most frequent identified artifacts from one lane with human DGE tags, as well as the oligosequences they might be based on. One of the 20 sequences seems to be a real DGE tag that was incorrectly identified as an artifact.

    Article Snippet: Figure , exemplifies for the Illumina NlaIII DGE protocol (a protocol for digital gene expression tag profiling) that adapter chimeras might be created which are of comparable length as the targeted library molecules and thus may not be removed by selecting a specific library insert-size (e.g. by gel length selection, silica column purification or Solid Phase Reversible Immobilization (SPRI) purification [ ]).

    Techniques: Sequencing, Flow Cytometry, Expressing, Ligation