Open Access Research article

Comparison of total and cytoplasmic mRNA reveals global regulation by nuclear retention and miRNAs

Beata Werne Solnestam1, Henrik Stranneheim1, Jimmie Hällman1, Max Käller1, Emma Lundberg2, Joakim Lundeberg1* and Pelin Akan1

Author Affiliations

1 KTH Royal Institute of Technology, Science for Life Laboratory (SciLifeLab Stockholm), School of Biotechnology, Division of Gene Technology, SE-171 65, Solna, Sweden

2 KTH Royal Institute of Technology, Science for Life Laboratory (SciLifeLab Stockholm), School of Biotechnology, Division of Proteomics, SE-171 65, Solna, Sweden

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BMC Genomics 2012, 13:574  doi:10.1186/1471-2164-13-574

Published: 30 October 2012

Additional files

Additional file 1:

Figure S1. Overlays of electrophoresis diagrams of purified RNA. Total RNA and cytoplasmic RNA, showing the two ribosomal peaks (18S and 28S). In addition, the total RNA contains a nucleus-specific peak at roughly 4000 nucleotides (~52 s), marked with an arrow in the upper diagram, which is missing in the cytoplasmic RNA fraction.

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Additional file 2:

Figure S2. Scatter plots of gene expression levels between total and cytoplasmic RNA. The median of the gene expression values of total and cytoplasmic RNA. The Pearson correlation coefficient R2 is displayed in each scatter plot. A: U-2 OS, B: U-251 MG, C: A-431.

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Additional file 3:

Figure S3. Boxplot showing the length and coding sequence for all three cell lines. Genes detected at a significantly higher level in total RNA than in cytoplasmic RNA (Tot>Cyt), lower level (Tot<Cyt), and genes with no significant differential detection (No Diff). A: Length of 5’ UTRs. B: Length of 3’ UTRs. C: Coding sequence length.

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Additional file 4:

Figure S4. Boxplot showing the fold energies of UTRs for all three cell lines. Genes detected at a significantly higher level in total RNA than in cytoplasmic RNA (Tot>Cyt), lower level (Tot<Cyt), and genes with no significant differential detection (No Diff). A: Fold energy of 5’ UTRs. B: Fold energy of 3’ UTRs.

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Additional file 5:

Table S1. Spearman correlation for differentially and not differentially detected genes in all three cell lines.

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Additional file 6:

Table S2. Summary of information from the sequencing run.

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Additional file 7:

Table S3. Reads assigned to features using HTSeq.

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Additional file 8:

Table S4. Estimation of intergenic expressions levels within replicates based on RPKM.

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