Data from: The splicing regulator PTBP2 controls a program of embryonic splicing required for neuronal maturation

 

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Title Li et al. Supplemental File 1: Table 1. Exons validated by RT/PCR.
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Description Table S1 for Li et al. A variety of exons showing differences in splicing between wild type and Ptbp2 nestin-KO brain at embryonic day 18 were subjected to further analysis by RT/PCR. These included exons identified by MJAY array, RNAseq, and exons previously reported to be PTBP targets. Gene names, exon coordinates, and percent spliced in values (PSI) are listed. Genome coordinates are for mm9.
Download Supplemental File 1 Table S1 RT-PCR validated E18 exons.docx (44.28Kb)
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Title Li et al. Supplemental File 2: Table 2. Splicing Changes Identified by Exon Junction Microarray.
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Description RNA from WT and Ptbp2-NestinKO E18 pups was analyzed on Affymetrix MJAY arrays (see Methods). Splicing events yielding Sepscores greater than 0.345 are listed.
Download Supplemental File 2 Table_S2_MJAY Array_top_Splicing_events_by_SepScore.xls (221.1Kb)
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Title Li et al. Supplemental File 3: Table 3. Splicing Changes Identified by RNAseq analysis in Ptbp2-NesKO mice.
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Description RNAseq reads from E18 WT and NesKO mice were subjected to Splicetrap analysis (see Methods). Events with a change in PSI of greater than 10% are shown with genome coordinates, read numbers, and coverage statistics.
Download Supplemental File 3 Table S3_nestin_nptbko_SpliceTrap_psi_over10percent_with_pvalues.xls (626.6Kb)
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Title Li et al. Supplemental File 4: Table 4. Gene Ontology Analysis of Functional or Process Enrichment for Genes Showing Splicing Changes in Ptbp2-NesKO mice.
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Description Enrichments are relative to all genes expressed in wildtype brain at E18.
Download Supplemental File 4 Table_S4_GO_analysis_nestin_splicetrap_exons.xls (188.4Kb)
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Title Li et al. Supplemental File 5: Table 5. Expression changes in Ptbp2-NesKO mice.
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Description Genes showing overall expression changes were identified by Cuffdiff analysis.
Download Supplemental File 5 Table_S5_cuffdiff_NesKOvWT_expression_change_V3.xls (4.782Mb)
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Title Li et al. Supplemental File 6: Table 6. Gene Ontology analysis of genes up-regulated in Ptbp2-NesKO mice.
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Description Genes showing a two-fold or greater increase in expression in the KO relative to WT were analyzed for functional or process enrichment relative to all genes expressed in wildtype brain.
Download Supplemental File 6 Table_S6_gene_ontology_2_fold_upregulated transcripts_v2.xls (92.67Kb)
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Title Li et al. Supplemental File 7: Table 7. Gene Ontology analysis of genes down-regulated in Ptbp2-NesKO mice.
Downloaded 13 times
Description Genes showing two-fold or greater reduced expression in the KO relative to WT were analyzed for functional or process enrichment relative to all genes expressed in wildtype brain.
Download Supplemental File 7 Table_S7_gene_ontology_2_fold_change_down_regulated_transcripts_v2.xls (51.71Kb)
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Title Li et al. Supplemental File 8: Table 8. Splicing Changes Identified by RNAseq analysis in Ptbp2-EmxKO mice.
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Description RNAseq reads from P1 WT and EmxKO mice were subjected to Splicetrap analysis (see Methods). Events with a change in PSI of greater than 10% are shown with genome coordinates, read numbers, and coverage statistics.
Download Supplemental File 8 Table_S8_Emx_P1_SpliceTrap_psi_over10percent_with_pvalues.xls (618.4Kb)
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When using this data, please cite the original publication:

Li Q, Zheng S, Han A, Lin C, Stoilov P, Fu X, Black DL (2014) The splicing regulator PTBP2 controls a program of embryonic splicing required for neuronal maturation. eLife 3: e01201. http://dx.doi.org/10.7554/eLife.01201

Additionally, please cite the Dryad data package:

Li Q, Zheng S, Han A, Lin C, Stoilov P, Fu X, Black DL (2014) Data from: The splicing regulator PTBP2 controls a program of embryonic splicing required for neuronal maturation. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.cv39v
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