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TranscriptomicsIdentification of allele-specific alternative mRNA processing via transcriptome sequencing
Establishing the functional roles of genetic variants remains a significant challenge in the post-genomic era. Here, we present a method, allele-specific alternative mRNA processing (ASARP), to identify genetically influenced mRNA processing events using transcriptome sequencing (RNA-Seq) data. The ...
ORGANISM(S): Homo sapiens 
2012-03-29 | E-GEOD-29738 | biostudies-arrayexpress
ProteomicsPolysomal profiling coupled to allele-specific proteomics reveals an EIF4H tranSNP allele possessing higher mRNA translation potential
To search for genetic sources of allele-specific mRNA translation, we leveraged heterozygous polymorphisms and variants present in the exome of HCT116-derived cell lines, computing allelic fractions in total and polysome-associated RNA from RNA-seq data. Allelic imbalance in polysomal RNA led us to ...
ORGANISM(S): Homo Sapiens 
2026-06-17 | PXD073180 | panorama
GenomicsExtensive allele-specific translational regulation
Extensive allele-specific translational regulation in hybrid mice
PRJEB8233 | ENA
TranscriptomicsDynamics of gene silencing during X inactivation using allele-specific RNA-Seq
Background: During early embryonic development, one of the two X chromosomes in mammalian female cells is inactivated to compensate for a potential imbalance in transcript levels with male cells containing a single X chromosome. We use mouse female Embryonic Stem Cells (ESCs) with nonrandom XCI and ...
ORGANISM(S): Mus musculus 
2015-06-15 | E-GEOD-60738 | biostudies-arrayexpress
TranscriptomicsAllele specific expression in Arabidopsis thaliana Col-0 x Van-0 F1 hybrids
This SuperSeries is composed of the following subset Series: GSE16503: Genomic DNA concentration series in Allele Specific Expression study GSE16504: Genomic DNA mixture series in Allele Specific Expression study GSE16505: Genomic DNA 1:1 mixtures in Allele Specific Expression study GSE16506: mRNA s...
ORGANISM(S): Arabidopsis thaliana 
2009-08-15 | E-GEOD-16520 | biostudies-arrayexpress
TranscriptomicsmRNA samples in Allele Specific Expression study
Col-0 and Van-0 total RNA were mixed at 1:1. Total RNA also extracted from F1 hybrid samples from Col x Van and Van x Col. PolyA RNA were purified and double-strand cDNA were synthesized, followed by bioprime random labeling. A total of 16ug labelled products were hybridized to AtSNPtile1. cis regul...
ORGANISM(S): Arabidopsis thaliana 
2010-05-06 | E-GEOD-16506 | biostudies-arrayexpress
GenomicsAllele-specific mRNA expression experiment in lactis-wickerhamii and lactis-marxianus interespecies hybrids
Allele-specific mRNA expression experiment in lactis-wickerhamii and lactis-marxianus interespecies hybrids
PRJNA427120 | ENA
TranscriptomicsNatural selection on cis and trans regulation in yeasts
Gene expression is regulated both by cis elements, which are DNA segments closely linked to the genes they regulate, and by trans activating factors, which are usually proteins capable of diffusing to unlinked genes. Understanding the patterns and sources of regulatory variation is crucial for under...
ORGANISM(S): Saccharomyces cerevisiae 
2010-04-02 | E-GEOD-20749 | biostudies-arrayexpress
TranscriptomicsDevelopment of a versatile, target-oriented tiling microarray assay for measuring allele-specific gene expression
In the study of gene expression regulation in plants, it is often desirable to distinguish transcript pools derived from different alleles present in the same organism. We report here an oligonucleotide tiling microarray designed to specifically target 518 single nucleotide polymorphisms (SNPs) betw...
ORGANISM(S): Oryza sativa 
2010-07-01 | E-GEOD-20678 | biostudies-arrayexpress
UnknownIdentification of allele-specific alternative mRNA processing via transcriptome sequencing.
Not available
S-EPMC3401465 | biostudies-literature
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