Regulation of alternative splicing by the circadian clock and food related cues

Additional file 1:

Supplemental Data. Supplemental Figures 1 to 10 and associated legends, supplemental experimental procedures and supplemental references.

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Table S1. Information regarding the positive probesets identified by the FIRMA analysis, compiled using the exonmap and xmapcore bioconductor packages [1-3]. probeset refers to the exon-probeset of interest. Fields: sotaCluster refers to the self-organizing tree algorithm (sota) cluster the probeset is part of (Figure 1b); adj.P.Val.Limma refers to the multiple-testing corrected P-value associated with the one-way ANOVA for an effect of time executed in limma [68,81] (see Materials and methods); ensExonID refers to the Ensembl [82] identifier for the exon within which the probeset is located; probeLoc refers to the mm9 genomic co-ordinates for the probeset of interest; exonSequence refers to the sequence of the exon identified by ensExonID; divisableBy3 indicates whether the exon's length is a multiple of three or not; ensGeneID refers to the Ensembl [82] identifier for the gene within which the exon identified by ensExonID is located; geneLoc refers to the mm9 genomic co-ordinates for the gene of interest; validation refers to validation status of the exon of interest (nd, not determined); description refers to official long name of the gene of interest.

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Table S2. Summary of the functional annotation data obtained for the positive genes from the FIRMA analysis, using DAVID [76]. Fields: Category refers to the source of the functional annotation term; Term refers to the particular enriched annotation term; PValue refers to the raw P-value associated with the enrichment of the term; Genes refers to the gene symbols of those genes from the list that contribute to the enrichment of this term; Fold Enrichment refers to the level of enrichment of this term over the background distribution; Benjamini refers to the P-value for enrichment after correction for multiple testing according to the method of Benjamini and Hochberg [83]; ofInterest refers to whether this term was considered pertinent to our analysis.

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Table S3. Results of the Gene Ontology term [29] enrichment analysis performed using WebGestalt [77].

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Table S4. Results of the KEGG pathway [28,84,85] enrichment analysis performed using WebGestalt [77].

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Table S5. Output of MotifScanner from the analysis of predicted clock transcription factor binding sites in the proximal promoter region of circadian splicing factors/RBPs. refseq refers to the Refseq mRNA relative to which the examined sequence was extracted. location refers to the genomic co-ordinates of the sequence examined.

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Additional file 7:

Table S6. Correlations between microarray data from Hughes et al. [41] and QPCR measurements from this study for circadian splicing factors/RBPs identified from Hughes et al. [41]. Quality refers to a manual assessment of the robustness of the circadian expression profile for that probeset, 1 being best and 3 being worst.

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Table S7. Details of all the oligonucleotides used in this study.

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