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SRP055413
Homo sapiens
6 Downloadable Samples
IonTorrentProton
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. Overall design: 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
Publication Title
Allele-Selective Transcriptome Recruitment to Polysomes Primed for Translation: Protein-Coding and Noncoding RNAs, and RNA Isoforms.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 20 Downloadable Samples
Affymetrix Mouse Genome 430A 2.0 Array (mouse430a2)
Description
We have used primary MEFs derived from wild type and E2F4 null mice growing asynchrounously in serum to generate a signature for E2F4 pathway activation. 10 wild type and 10 E2F4 null samples were each assayed using the Affymetrics Mouse Genome 430A 2.0 array.
Publication Title
Patterns of cell signaling pathway activation that characterize mammary development.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 12 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
EDI3 was shown to be relevant in cell migration, adhesion and spreading. Gene expression analysis was performed to determine the effect of EDI3 silencing in MCF7 cells in order to gain insight into potential underlying mechanisms.
Publication Title
EDI3 links choline metabolism to integrin expression, cell adhesion and spreading.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Rattus norvegicus
- 6 Downloadable Samples
- Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
Placentation differs in the BN rat strain when compared to HSD and DSS rat strains. Intrauterine trophoblast invasion is shallow and the junctional zone is underdeveloped in the BN rat. These structural differences are striking but their quantification is not conducive to high throughput analyses. In the rat, the junctional zone can be readily dissected and is more homogenous than other components of the placentation site. HSD and BN rat gestation day 18.5 junctional zone gene expression profiles were determined using DNA microarray analysis to identity placenta-associate quantitate traits.
Publication Title
Chromosome-substituted rat strains provide insights into the genetics of placentation.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 57 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
We have made use of the E-myc transgenic mouse, a model for the study of B-cell lymphoma development that is initiated through a defined genetic alteration, to explore the contributions of additional somatic alterations that contribute to the heterogeneity of the resulting tumors. As one example of such heterogeneity, we have focused on the observation that lymphomas develop in E-myc mice with a variable time of onset. Twenty-five early-onset, 25 late-onset lymphomas and 10 normal samples were each assayed on an Affymetrix Mouse Genome 430 2.0 array.
Publication Title
Utilization of pathway signatures to reveal distinct types of B lymphoma in the Emicro-myc model and human diffuse large B-cell lymphoma.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 115 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Utilization of the Eμ-Myc mouse to model heterogeneity of therapeutic response.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 44 Downloadable Samples
Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
We used gene expression data from E-myc mouse lymphomas to test various genomic signatures and select lymphomas for further study
Publication Title
Utilization of the Eμ-Myc mouse to model heterogeneity of therapeutic response.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 39 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
We used gene expression data from E-myc mouse lymphomas to perform unsupervised analyses that identified two lymphoma subgroups.
Publication Title
Utilization of the Eμ-Myc mouse to model heterogeneity of therapeutic response.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 32 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
We used gene expression data from E-myc mouse lymphomas to test various genomic signatures and select lymphomas for further study
Publication Title
Utilization of the Eμ-Myc mouse to model heterogeneity of therapeutic response.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 33 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Molecular pathways activated in MALT lymphoma are not well defined.
Publication Title
Gene expression profiling of pulmonary mucosa-associated lymphoid tissue lymphoma identifies new biologic insights with potential diagnostic and therapeutic applications.
Sample Metadata Fields
Sex
View Samples