Numbers of nuclear and cytoplasmic mRNAs per cell in MIN6 cells and liver cells

Range Excel Table - link mRNAs/cell
Organism Mouse Mus musculus
Reference Bahar Halpern K et al., Nuclear Retention of mRNA in Mammalian Tissues. Cell Rep. 2015 Dec 29 13(12):2653-62. doi: 10.1016/j.celrep.2015.11.036. Supplemental Information table S2PubMed ID26711333
Method Abstract:"Here, to explore the extent of mRNA retention in metabolic tissues, [investigators] combine deep sequencing of nuclear and cytoplasmic RNA fractions with single-molecule transcript imaging in mouse beta cells, liver, and gut."
Comments P.2653 right column bottom paragraph:"To obtain a genome-wide catalog of genes in mammalian metabolic tissues that are potentially nuclearly retained, [investigators] extracted nuclear and cytoplasmic fractions from MIN6 pancreatic beta cell line (Miyazaki et al., 1990) and mouse liver and performed whole-transcriptome RNA sequencing (RNA-seq). [They] used single-molecule fluorescence in situ hybridization (smFISH) (Bahar Halpern et al., 2015, Itzkovitz et al., 2011 and Lyubimova et al., 2013) of representative genes to convert the number of reads to estimates of cytoplasmic and nuclear mRNA numbers per cell (Tables S1 and S2). [Their] analysis revealed that most genes had more transcripts in the cytoplasm compared to the nucleus in MIN6 cells (mean cytoplasm/nucleus = 3.8 ± 0.05, Figure 1A). Examples include the insulin genes Ins1 (cytoplasm/nucleus = 13.2 ± 4.6) and Ins2 (cytoplasm/nucleus = 10.2 ± 0.45), as well as housekeeping genes such as beta-actin (Actb, cytoplasm/nucleus = 10.6 ± 1.1)." Supplemental Information p.9:"Table S2 (related to Figure 1) – Numbers of nuclear and cytoplasmic mRNAs per cell in MIN6 cells and liver cells. Reads were normalized to estimated numbers per cell based on the calibration factors of Table S1."
Entered by Uri M
ID 112415