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SF3B1 mutation effect is independent of the biological background, but its manifestation depends on the transcriptomic profile. ( A ) The number of alternative splicing events (ASEs) identified with Iso-Seq <t>separated</t> by splicing event type in all groups investigated, differentiated by the novelty class. ( B ) Overlap between significantly altered ASEs in samples with the SF3B1 mutation identified in the three data sets used (cell lines, CLL patients, or MDS patients). ( C ) Correlation of isoform usage measured by the difference in PSI from all events listed in B ; namely, events called significant in at least one of the three data sets are shown. The colors of the dots correspond to significance reached only in one set: blue indicates x -axis only; red, y -axis only; light blue, both; and gray, none (i.e., called significant in a data set absent from the graph). Pearson correlation coefficient ( R ) and associated P -value ( P ) are given. ( D ) Violin plots with boxplots show the distribution of expression values of the genes with data set–specific ASEs from C . Significant differences are marked with as follows: (***) paired, two-tailed Student's t -test P -value < 0.001, (**) P -value < 0.01, (*) P -value < 0.05, (N.S.) not significant with P -value ≥ 0.05.
Rosettesep Immunodensity Based Cell Separation, supplied by STEMCELL Technologies Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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rosettesep immunodensity cell separation  (STEMCELL Technologies Inc)
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SF3B1 mutation effect is independent of the biological background, but its manifestation depends on the transcriptomic profile. ( A ) The number of alternative splicing events (ASEs) identified with Iso-Seq <t>separated</t> by splicing event type in all groups investigated, differentiated by the novelty class. ( B ) Overlap between significantly altered ASEs in samples with the SF3B1 mutation identified in the three data sets used (cell lines, CLL patients, or MDS patients). ( C ) Correlation of isoform usage measured by the difference in PSI from all events listed in B ; namely, events called significant in at least one of the three data sets are shown. The colors of the dots correspond to significance reached only in one set: blue indicates x -axis only; red, y -axis only; light blue, both; and gray, none (i.e., called significant in a data set absent from the graph). Pearson correlation coefficient ( R ) and associated P -value ( P ) are given. ( D ) Violin plots with boxplots show the distribution of expression values of the genes with data set–specific ASEs from C . Significant differences are marked with as follows: (***) paired, two-tailed Student's t -test P -value < 0.001, (**) P -value < 0.01, (*) P -value < 0.05, (N.S.) not significant with P -value ≥ 0.05.
Rosettesep Immunodensity Cell Separation, supplied by STEMCELL Technologies Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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t cell separation reagent rosettesep human t cell enrichment cocktail  (STEMCELL Technologies Inc)
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SF3B1 mutation effect is independent of the biological background, but its manifestation depends on the transcriptomic profile. ( A ) The number of alternative splicing events (ASEs) identified with Iso-Seq <t>separated</t> by splicing event type in all groups investigated, differentiated by the novelty class. ( B ) Overlap between significantly altered ASEs in samples with the SF3B1 mutation identified in the three data sets used (cell lines, CLL patients, or MDS patients). ( C ) Correlation of isoform usage measured by the difference in PSI from all events listed in B ; namely, events called significant in at least one of the three data sets are shown. The colors of the dots correspond to significance reached only in one set: blue indicates x -axis only; red, y -axis only; light blue, both; and gray, none (i.e., called significant in a data set absent from the graph). Pearson correlation coefficient ( R ) and associated P -value ( P ) are given. ( D ) Violin plots with boxplots show the distribution of expression values of the genes with data set–specific ASEs from C . Significant differences are marked with as follows: (***) paired, two-tailed Student's t -test P -value < 0.001, (**) P -value < 0.01, (*) P -value < 0.05, (N.S.) not significant with P -value ≥ 0.05.
T Cell Separation Reagent Rosettesep Human T Cell Enrichment Cocktail, supplied by STEMCELL Technologies Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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negative separation rosettesep  (StemCells Inc)
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SF3B1 mutation effect is independent of the biological background, but its manifestation depends on the transcriptomic profile. ( A ) The number of alternative splicing events (ASEs) identified with Iso-Seq <t>separated</t> by splicing event type in all groups investigated, differentiated by the novelty class. ( B ) Overlap between significantly altered ASEs in samples with the SF3B1 mutation identified in the three data sets used (cell lines, CLL patients, or MDS patients). ( C ) Correlation of isoform usage measured by the difference in PSI from all events listed in B ; namely, events called significant in at least one of the three data sets are shown. The colors of the dots correspond to significance reached only in one set: blue indicates x -axis only; red, y -axis only; light blue, both; and gray, none (i.e., called significant in a data set absent from the graph). Pearson correlation coefficient ( R ) and associated P -value ( P ) are given. ( D ) Violin plots with boxplots show the distribution of expression values of the genes with data set–specific ASEs from C . Significant differences are marked with as follows: (***) paired, two-tailed Student's t -test P -value < 0.001, (**) P -value < 0.01, (*) P -value < 0.05, (N.S.) not significant with P -value ≥ 0.05.
Negative Separation Rosettesep, supplied by StemCells Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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rosettesep immunodensity separation  (STEMCELL Technologies Inc)
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SF3B1 mutation effect is independent of the biological background, but its manifestation depends on the transcriptomic profile. ( A ) The number of alternative splicing events (ASEs) identified with Iso-Seq <t>separated</t> by splicing event type in all groups investigated, differentiated by the novelty class. ( B ) Overlap between significantly altered ASEs in samples with the SF3B1 mutation identified in the three data sets used (cell lines, CLL patients, or MDS patients). ( C ) Correlation of isoform usage measured by the difference in PSI from all events listed in B ; namely, events called significant in at least one of the three data sets are shown. The colors of the dots correspond to significance reached only in one set: blue indicates x -axis only; red, y -axis only; light blue, both; and gray, none (i.e., called significant in a data set absent from the graph). Pearson correlation coefficient ( R ) and associated P -value ( P ) are given. ( D ) Violin plots with boxplots show the distribution of expression values of the genes with data set–specific ASEs from C . Significant differences are marked with as follows: (***) paired, two-tailed Student's t -test P -value < 0.001, (**) P -value < 0.01, (*) P -value < 0.05, (N.S.) not significant with P -value ≥ 0.05.
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SF3B1 mutation effect is independent of the biological background, but its manifestation depends on the transcriptomic profile. ( A ) The number of alternative splicing events (ASEs) identified with Iso-Seq <t>separated</t> by splicing event type in all groups investigated, differentiated by the novelty class. ( B ) Overlap between significantly altered ASEs in samples with the SF3B1 mutation identified in the three data sets used (cell lines, CLL patients, or MDS patients). ( C ) Correlation of isoform usage measured by the difference in PSI from all events listed in B ; namely, events called significant in at least one of the three data sets are shown. The colors of the dots correspond to significance reached only in one set: blue indicates x -axis only; red, y -axis only; light blue, both; and gray, none (i.e., called significant in a data set absent from the graph). Pearson correlation coefficient ( R ) and associated P -value ( P ) are given. ( D ) Violin plots with boxplots show the distribution of expression values of the genes with data set–specific ASEs from C . Significant differences are marked with as follows: (***) paired, two-tailed Student's t -test P -value < 0.001, (**) P -value < 0.01, (*) P -value < 0.05, (N.S.) not significant with P -value ≥ 0.05.
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rosettesep cell separation procedure  (STEMCELL Technologies Inc)
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SF3B1 mutation effect is independent of the biological background, but its manifestation depends on the transcriptomic profile. ( A ) The number of alternative splicing events (ASEs) identified with Iso-Seq <t>separated</t> by splicing event type in all groups investigated, differentiated by the novelty class. ( B ) Overlap between significantly altered ASEs in samples with the SF3B1 mutation identified in the three data sets used (cell lines, CLL patients, or MDS patients). ( C ) Correlation of isoform usage measured by the difference in PSI from all events listed in B ; namely, events called significant in at least one of the three data sets are shown. The colors of the dots correspond to significance reached only in one set: blue indicates x -axis only; red, y -axis only; light blue, both; and gray, none (i.e., called significant in a data set absent from the graph). Pearson correlation coefficient ( R ) and associated P -value ( P ) are given. ( D ) Violin plots with boxplots show the distribution of expression values of the genes with data set–specific ASEs from C . Significant differences are marked with as follows: (***) paired, two-tailed Student's t -test P -value < 0.001, (**) P -value < 0.01, (*) P -value < 0.05, (N.S.) not significant with P -value ≥ 0.05.
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SF3B1 mutation effect is independent of the biological background, but its manifestation depends on the transcriptomic profile. ( A ) The number of alternative splicing events (ASEs) identified with Iso-Seq separated by splicing event type in all groups investigated, differentiated by the novelty class. ( B ) Overlap between significantly altered ASEs in samples with the SF3B1 mutation identified in the three data sets used (cell lines, CLL patients, or MDS patients). ( C ) Correlation of isoform usage measured by the difference in PSI from all events listed in B ; namely, events called significant in at least one of the three data sets are shown. The colors of the dots correspond to significance reached only in one set: blue indicates x -axis only; red, y -axis only; light blue, both; and gray, none (i.e., called significant in a data set absent from the graph). Pearson correlation coefficient ( R ) and associated P -value ( P ) are given. ( D ) Violin plots with boxplots show the distribution of expression values of the genes with data set–specific ASEs from C . Significant differences are marked with as follows: (***) paired, two-tailed Student's t -test P -value < 0.001, (**) P -value < 0.01, (*) P -value < 0.05, (N.S.) not significant with P -value ≥ 0.05.

Journal: Genome Research

Article Title: Long-read transcriptome sequencing of CLL and MDS patients uncovers molecular effects of SF3B1 mutations

doi: 10.1101/gr.279327.124

Figure Lengend Snippet: SF3B1 mutation effect is independent of the biological background, but its manifestation depends on the transcriptomic profile. ( A ) The number of alternative splicing events (ASEs) identified with Iso-Seq separated by splicing event type in all groups investigated, differentiated by the novelty class. ( B ) Overlap between significantly altered ASEs in samples with the SF3B1 mutation identified in the three data sets used (cell lines, CLL patients, or MDS patients). ( C ) Correlation of isoform usage measured by the difference in PSI from all events listed in B ; namely, events called significant in at least one of the three data sets are shown. The colors of the dots correspond to significance reached only in one set: blue indicates x -axis only; red, y -axis only; light blue, both; and gray, none (i.e., called significant in a data set absent from the graph). Pearson correlation coefficient ( R ) and associated P -value ( P ) are given. ( D ) Violin plots with boxplots show the distribution of expression values of the genes with data set–specific ASEs from C . Significant differences are marked with as follows: (***) paired, two-tailed Student's t -test P -value < 0.001, (**) P -value < 0.01, (*) P -value < 0.05, (N.S.) not significant with P -value ≥ 0.05.

Article Snippet: Peripheral blood B cells were isolated via negative selection using RosetteSep immunodensity-based cell separation (Stemcell Technologies).

Techniques: Mutagenesis, Alternative Splicing, Expressing, Two Tailed Test