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gencode v33 gtf file  (Illumina Inc)


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    Illumina Inc gencode v33 gtf file
    Mutations in TGS1 and SMN cause global changes in RNA expression and splicing. ( A, B ) Heatmaps depicting the expression levels (TPM values estimated by Kallisto) for differentially expressed (DE) transcripts in TGS1 M1 and TGS1 M2 (A), or SMN C1 and SMN C2 (B) mutant cells, compared with parental HeLa cells (CTR). Transcripts are classified into five types: annotated transcripts per <t>GENCODE</t> (orange); novel transcripts with extended 3′ (magenta) or shortened 3′ (blue); novel transcripts with annotated identical 3′ (pink); and other (intergenic and opposite-strand) novel transcripts (purple). Transcripts within each group are ranked by unsupervised clustering. Total transcript number for each group and the DE status for each transcript (either up- or down-regulated in mutant cells) are annotated by the green/red sidebar to the right (see also ). ( C ) Venn diagram from data in (A) and (B), showing the significant number of shared DE transcript isoforms (both annotated and unannotated) between TGS1 and SMN mutant cells. See also . ( D ) Methodological approach used for quantification of intron retention (IR) levels (see also the Materials and Methods). ( E, F ) Scatter plots showing for each IR event between mutant ( TGS1 M1 and M2 or SMN C1 and C2 ) and CTR cells the differential PSI (dPSI) against the differential expression level (dTPM) of the major transcript (intron exclusion). The significant IR events are color-coded in the plots, with significantly up-regulated events colored in orange and significantly down-regulated in teal.
    Gencode V33 Gtf File, 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/gencode+v33+gtf+file/gencode+v33+gtf+file/pmc09757054-244-16-25
    Average 90 stars, based on 1 article reviews
    gencode v33 gtf file - by Bioz Stars, 2026-10
    90/100 stars

    Images

    1) Product Images from "TGS1 impacts snRNA 3′-end processing, ameliorates survival motor neuron -dependent neurological phenotypes in vivo and prevents neurodegeneration"

    Article Title: TGS1 impacts snRNA 3′-end processing, ameliorates survival motor neuron -dependent neurological phenotypes in vivo and prevents neurodegeneration

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkac659

    Mutations in TGS1 and SMN cause global changes in RNA expression and splicing. ( A, B ) Heatmaps depicting the expression levels (TPM values estimated by Kallisto) for differentially expressed (DE) transcripts in TGS1 M1 and TGS1 M2 (A), or SMN C1 and SMN C2 (B) mutant cells, compared with parental HeLa cells (CTR). Transcripts are classified into five types: annotated transcripts per GENCODE (orange); novel transcripts with extended 3′ (magenta) or shortened 3′ (blue); novel transcripts with annotated identical 3′ (pink); and other (intergenic and opposite-strand) novel transcripts (purple). Transcripts within each group are ranked by unsupervised clustering. Total transcript number for each group and the DE status for each transcript (either up- or down-regulated in mutant cells) are annotated by the green/red sidebar to the right (see also ). ( C ) Venn diagram from data in (A) and (B), showing the significant number of shared DE transcript isoforms (both annotated and unannotated) between TGS1 and SMN mutant cells. See also . ( D ) Methodological approach used for quantification of intron retention (IR) levels (see also the Materials and Methods). ( E, F ) Scatter plots showing for each IR event between mutant ( TGS1 M1 and M2 or SMN C1 and C2 ) and CTR cells the differential PSI (dPSI) against the differential expression level (dTPM) of the major transcript (intron exclusion). The significant IR events are color-coded in the plots, with significantly up-regulated events colored in orange and significantly down-regulated in teal.
    Figure Legend Snippet: Mutations in TGS1 and SMN cause global changes in RNA expression and splicing. ( A, B ) Heatmaps depicting the expression levels (TPM values estimated by Kallisto) for differentially expressed (DE) transcripts in TGS1 M1 and TGS1 M2 (A), or SMN C1 and SMN C2 (B) mutant cells, compared with parental HeLa cells (CTR). Transcripts are classified into five types: annotated transcripts per GENCODE (orange); novel transcripts with extended 3′ (magenta) or shortened 3′ (blue); novel transcripts with annotated identical 3′ (pink); and other (intergenic and opposite-strand) novel transcripts (purple). Transcripts within each group are ranked by unsupervised clustering. Total transcript number for each group and the DE status for each transcript (either up- or down-regulated in mutant cells) are annotated by the green/red sidebar to the right (see also ). ( C ) Venn diagram from data in (A) and (B), showing the significant number of shared DE transcript isoforms (both annotated and unannotated) between TGS1 and SMN mutant cells. See also . ( D ) Methodological approach used for quantification of intron retention (IR) levels (see also the Materials and Methods). ( E, F ) Scatter plots showing for each IR event between mutant ( TGS1 M1 and M2 or SMN C1 and C2 ) and CTR cells the differential PSI (dPSI) against the differential expression level (dTPM) of the major transcript (intron exclusion). The significant IR events are color-coded in the plots, with significantly up-regulated events colored in orange and significantly down-regulated in teal.

    Techniques Used: RNA Expression, Expressing, Mutagenesis, Quantitative Proteomics

    Related Articles

    RNA Expression:

    Article Title: TGS1 impacts snRNA 3′-end processing, ameliorates survival motor neuron -dependent neurological phenotypes in vivo and prevents neurodegeneration
    Article Snippet: After this, splice junctions of reads were corrected using the FLAIR correct module employing both the GENCODE v33 GTF file (gencode.v33.chr_patch_hapl_scaff.annotation.gtf) ( ) and short Illumina reads of the corresponding samples.

    Expressing:

    Article Title: TGS1 impacts snRNA 3′-end processing, ameliorates survival motor neuron -dependent neurological phenotypes in vivo and prevents neurodegeneration
    Article Snippet: After this, splice junctions of reads were corrected using the FLAIR correct module employing both the GENCODE v33 GTF file (gencode.v33.chr_patch_hapl_scaff.annotation.gtf) ( ) and short Illumina reads of the corresponding samples.

    Mutagenesis:

    Article Title: TGS1 impacts snRNA 3′-end processing, ameliorates survival motor neuron -dependent neurological phenotypes in vivo and prevents neurodegeneration
    Article Snippet: After this, splice junctions of reads were corrected using the FLAIR correct module employing both the GENCODE v33 GTF file (gencode.v33.chr_patch_hapl_scaff.annotation.gtf) ( ) and short Illumina reads of the corresponding samples.

    Quantitative Proteomics:

    Article Title: TGS1 impacts snRNA 3′-end processing, ameliorates survival motor neuron -dependent neurological phenotypes in vivo and prevents neurodegeneration
    Article Snippet: After this, splice junctions of reads were corrected using the FLAIR correct module employing both the GENCODE v33 GTF file (gencode.v33.chr_patch_hapl_scaff.annotation.gtf) ( ) and short Illumina reads of the corresponding samples.



    Similar Products

    gencode v33 gtf file  (Illumina Inc)
    90
    Illumina Inc gencode v33 gtf file
    Mutations in TGS1 and SMN cause global changes in RNA expression and splicing. ( A, B ) Heatmaps depicting the expression levels (TPM values estimated by Kallisto) for differentially expressed (DE) transcripts in TGS1 M1 and TGS1 M2 (A), or SMN C1 and SMN C2 (B) mutant cells, compared with parental HeLa cells (CTR). Transcripts are classified into five types: annotated transcripts per <t>GENCODE</t> (orange); novel transcripts with extended 3′ (magenta) or shortened 3′ (blue); novel transcripts with annotated identical 3′ (pink); and other (intergenic and opposite-strand) novel transcripts (purple). Transcripts within each group are ranked by unsupervised clustering. Total transcript number for each group and the DE status for each transcript (either up- or down-regulated in mutant cells) are annotated by the green/red sidebar to the right (see also ). ( C ) Venn diagram from data in (A) and (B), showing the significant number of shared DE transcript isoforms (both annotated and unannotated) between TGS1 and SMN mutant cells. See also . ( D ) Methodological approach used for quantification of intron retention (IR) levels (see also the Materials and Methods). ( E, F ) Scatter plots showing for each IR event between mutant ( TGS1 M1 and M2 or SMN C1 and C2 ) and CTR cells the differential PSI (dPSI) against the differential expression level (dTPM) of the major transcript (intron exclusion). The significant IR events are color-coded in the plots, with significantly up-regulated events colored in orange and significantly down-regulated in teal.
    Gencode V33 Gtf File, 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/gencode+v33+gtf+file/gencode+v33+gtf+file/pmc09757054-244-16-25
    Average 90 stars, based on 1 article reviews
    gencode v33 gtf file - by Bioz Stars, 2026-10
    90/100 stars
    		  Buy from Supplier

    Image Search Results


    Mutations in TGS1 and SMN cause global changes in RNA expression and splicing. ( A, B ) Heatmaps depicting the expression levels (TPM values estimated by Kallisto) for differentially expressed (DE) transcripts in TGS1 M1 and TGS1 M2 (A), or SMN C1 and SMN C2 (B) mutant cells, compared with parental HeLa cells (CTR). Transcripts are classified into five types: annotated transcripts per GENCODE (orange); novel transcripts with extended 3′ (magenta) or shortened 3′ (blue); novel transcripts with annotated identical 3′ (pink); and other (intergenic and opposite-strand) novel transcripts (purple). Transcripts within each group are ranked by unsupervised clustering. Total transcript number for each group and the DE status for each transcript (either up- or down-regulated in mutant cells) are annotated by the green/red sidebar to the right (see also ). ( C ) Venn diagram from data in (A) and (B), showing the significant number of shared DE transcript isoforms (both annotated and unannotated) between TGS1 and SMN mutant cells. See also . ( D ) Methodological approach used for quantification of intron retention (IR) levels (see also the Materials and Methods). ( E, F ) Scatter plots showing for each IR event between mutant ( TGS1 M1 and M2 or SMN C1 and C2 ) and CTR cells the differential PSI (dPSI) against the differential expression level (dTPM) of the major transcript (intron exclusion). The significant IR events are color-coded in the plots, with significantly up-regulated events colored in orange and significantly down-regulated in teal.

    Journal: Nucleic Acids Research

    Article Title: TGS1 impacts snRNA 3′-end processing, ameliorates survival motor neuron -dependent neurological phenotypes in vivo and prevents neurodegeneration

    doi: 10.1093/nar/gkac659

    Figure Lengend Snippet: Mutations in TGS1 and SMN cause global changes in RNA expression and splicing. ( A, B ) Heatmaps depicting the expression levels (TPM values estimated by Kallisto) for differentially expressed (DE) transcripts in TGS1 M1 and TGS1 M2 (A), or SMN C1 and SMN C2 (B) mutant cells, compared with parental HeLa cells (CTR). Transcripts are classified into five types: annotated transcripts per GENCODE (orange); novel transcripts with extended 3′ (magenta) or shortened 3′ (blue); novel transcripts with annotated identical 3′ (pink); and other (intergenic and opposite-strand) novel transcripts (purple). Transcripts within each group are ranked by unsupervised clustering. Total transcript number for each group and the DE status for each transcript (either up- or down-regulated in mutant cells) are annotated by the green/red sidebar to the right (see also ). ( C ) Venn diagram from data in (A) and (B), showing the significant number of shared DE transcript isoforms (both annotated and unannotated) between TGS1 and SMN mutant cells. See also . ( D ) Methodological approach used for quantification of intron retention (IR) levels (see also the Materials and Methods). ( E, F ) Scatter plots showing for each IR event between mutant ( TGS1 M1 and M2 or SMN C1 and C2 ) and CTR cells the differential PSI (dPSI) against the differential expression level (dTPM) of the major transcript (intron exclusion). The significant IR events are color-coded in the plots, with significantly up-regulated events colored in orange and significantly down-regulated in teal.

    Article Snippet: After this, splice junctions of reads were corrected using the FLAIR correct module employing both the GENCODE v33 GTF file (gencode.v33.chr_patch_hapl_scaff.annotation.gtf) ( ) and short Illumina reads of the corresponding samples.

    Techniques: RNA Expression, Expressing, Mutagenesis, Quantitative Proteomics