MRNA loading on polysomes in skeletal muscle of Eif6 heterozygous mice
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PROVIDER: PRJNA479975 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Gastrocnemius muscle from Eif6 heterozygous mice and wild-type mice was used in a polysome profiling experiment. Total RNA was extracted from the whole muscle and from monosome/polysome fractions and profiled using Agilent gene expression arrays.
2018-07-07 | GSE116715 | GEO
Project description:Skeletal muscle of Eif6 heterozygous mice
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Project description:Skeletal muscle of Eif6 heterozygous mice - soleus
| PRJNA479970 | ENA
Project description:Tibialis anterior and gastrocnemius muscle from Eif6 heterozygous mice and wild-type mice profiled using Agilent gene expression arrays
2018-07-07 | GSE116709 | GEO
Project description:Soleus muscle from Eif6 heterozygous mice and wild-type mice profiled using Agilent gene expression arrays
2018-07-07 | GSE116714 | GEO
Project description:A cohort of age-matched mice (eIF6+/+ and eIF6+/-) were fed with High-Fat Diet. All experimental mice were sacrificed after 16 weeks and the livers were recovered. RNA was isolated from liver biopsies of eIF6+/+ and eIF6+/- mice and RNAseq analysis was performed. The aim of the analysis is the investigation of the transcriptional changes driven by chronic depletion of eIF6 in the liver of mice upon High Fat Diet (HFD) feeding.
2021-06-18 | E-MTAB-9009 | biostudies-arrayexpress
Project description:RNA-seq of liver biopsies of eIF6 wild type and eIF6 heterozygous mice
| PRJEB38082 | ENA
Project description:Purpose: mRNA translation into protein is highly regulated, but the role of mRNA isoforms, noncoding RNAs (ncRNAs), and genetic variants has yet to be systematically studied. Using high-throughput sequencing (RNA-seq), we have measured cellular levels of mRNAs and ncRNAs, and their isoforms, in lymphoblast cell lines (LCL) and in polysomal fractions, the latter shown to yield strong correlations of mRNAs with expressed protein levels. Analysis of allelic RNA ratios at heterozygous SNPs served to reveal genetic factors in ribosomal loading. Methods: RNA-seq was performed on cytosolic extracts and polysomal fractions (3 ribosomes or more) from three lymphoblastoid cell lines. As each RNA fraction was amplified (NuGen kit), and relative contributions from various RNA classes differed between cytosol and polysomes, the fraction of any given RNA species loaded onto polysomes was difficult to quantitate. Therefore, we focused on relative recovery of the various RNA classes and rank order of single RNAs compared to total RNA. Results: RNA-seq of coding and non-coding RNAs (including microRNAs) in three LCLs revealed significant differences in polysomal loading of individual RNAs and isoforms, and between RNA classes. Moreover, correlated distribution between protein-coding and non-coding RNAs suggests possible interactions between them. Allele-selective RNA recruitment revealed strong genetic influence on polysomal loading for multiple RNAs. Allelic effects can be attributed to generation of different RNA isoforms before polysomal loading or to differential loading onto polysomes, the latter defining a direct genetic effect on translation. Several variants and genes identified by this approach are also associated with RNA expression and clinical phenotypes in various databases. Conclusions: These results provide a novel approach using complete transcriptome RNA-seq to study polysomal RNA recruitment and regulatory variants affecting protein translation.
2015-06-30 | GSE66135 | GEO
Project description:Despite the advanced understanding of disease mechanisms, the current therapeutic regimens fail to cure most patients with acute myeloid leukemia (AML). In the present study, we address the role of protein synthesis control in leukemia function and leukemia propagation. Using a transgenic eIF6 mouse strain that permits inducible and graded regulation of ribosomal subunit joining, we have generated a murine model of MLL-AF9 acute myeloid leukemia where the expression of transgenic eIF6 is doxycycline-inducible. Using this model system, we have performed scRNA-seq expression analysis to study the impact of eIF6 overexpression on leukemia cell function. scRNA-seq was performed using the 10x Chromium Next GEM Single Cell 3ʹ platform. BM cells were harvested from leukemia-engrafted mice that were administered doxycycline for six days and viable GFP+ leukemia cells were sorted into PBS containing 0.05 % BSA following the manusfacturer’s protocol. 5 samples: 2 control and 3 eIF6 overexpression.
2024-10-10 | E-MTAB-13567 | biostudies-arrayexpress
Project description:Purpose: mRNA translation into protein is highly regulated, but the role of mRNA isoforms, noncoding RNAs (ncRNAs), and genetic variants has yet to be systematically studied. Using high-throughput sequencing (RNA-seq), we have measured cellular levels of mRNAs and ncRNAs, and their isoforms, in lymphoblast cell lines (LCL) and in polysomal fractions, the latter shown to yield strong correlations of mRNAs with expressed protein levels. Analysis of allelic RNA ratios at heterozygous SNPs served to reveal genetic factors in ribosomal loading. Methods: RNA-seq was performed on cytosolic extracts and polysomal fractions (3 ribosomes or more) from three lymphoblastoid cell lines. As each RNA fraction was amplified (NuGen kit), and relative contributions from various RNA classes differed between cytosol and polysomes, the fraction of any given RNA species loaded onto polysomes was difficult to quantitate. Therefore, we focused on relative recovery of the various RNA classes and rank order of single RNAs compared to total RNA. Results: RNA-seq of coding and non-coding RNAs (including microRNAs) in three LCLs revealed significant differences in polysomal loading of individual RNAs and isoforms, and between RNA classes. Moreover, correlated distribution between protein-coding and non-coding RNAs suggests possible interactions between them. Allele-selective RNA recruitment revealed strong genetic influence on polysomal loading for multiple RNAs. Allelic effects can be attributed to generation of different RNA isoforms before polysomal loading or to differential loading onto polysomes, the latter defining a direct genetic effect on translation. Several variants and genes identified by this approach are also associated with RNA expression and clinical phenotypes in various databases. Conclusions: These results provide a novel approach using complete transcriptome RNA-seq to study polysomal RNA recruitment and regulatory variants affecting protein translation. cells from 3 samples were grown to 5x105 cells/mL density in T75 tissue culture flask and harvested, total RNA and polysome bound RNA was sequenced by Ion Proton
2015-06-30 | E-GEOD-66135 | biostudies-arrayexpress