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Homo sapiens
7 Downloadable Samples
IlluminaHiSeq2500
Description
Human transcripts can typically be processed at multiple polyadenylation sites to yield mRNA isoforms with distinct 3 ends. A multitude of factors contributes to the choice of individual polyadenylation sites in different cell types and tissues. In this study we have found that the heterogenous ribonucleoprotein C (hnRNP C), an RNA binding protein that was previously linked to splicing and polyadenylation at Alu repeat elements, is a general regulator of pre-mRNA cleavage and polyadenylation. By sequencing mRNA 3 ends from cells expressing normal and reduced levels of hnRNP C we found that transcripts that contain poly(U) tracts around their poly(A) sites respond in a manner indicative of hnRNP C repressing cleavage and polyadenylation. The 3 UTR isoforms whose abundance is modulated by hnRNP C contain U-rich elements and can thereby interact with A/U-rich element binding proteins that have been shown to alter transcript stability, sub-cellular localization and even the localization of the translated proteins.
Publication Title
A comprehensive analysis of 3' end sequencing data sets reveals novel polyadenylation signals and the repressive role of heterogeneous ribonucleoprotein C on cleavage and polyadenylation.
Sample Metadata Fields
No sample metadata fields
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SRP011480- Zea mays
- 92 Downloadable Samples
- Illumina HiSeq 2000, Illumina Genome Analyzer IIx
Description
Maize exhibits levels of structural variation (SV) of non-repeat sequences that are unprecedented among higher eukaryotes. This SV includes hundreds of copy number variants (CNVs) and thousands of presence/absence variants (PAVs). Many of the PAVs contain intact, expressed, single-copy genes that are present in one haplotype but absent from another. The goal of this project is to test the hypothesis that differences in gene copy number (both gains and losses) contribute to the extraordinary phenotypic diversity and plasticity of maize. Maize is a good model for these studies because it exhibits a rapid decay of linkage disequilibrium (LD) and because a draft genome sequence of the B73 inbred and mapping populations are available. As a first step, the "Zeanome", a near-complete set of genes present in B73, other maize lines and the wild ancestor of maize (teosinte), is being defined using transcriptomic data.
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Saccharomyces cerevisiae
- 83 Downloadable Samples
- Illumina HiSeq 2000
Description
No description.
Publication Title
No associated publication
Sample Metadata Fields
Cell line
View Samples- Mus musculus
- 74 Downloadable Samples
- Illumina HiSeq 2500
Description
RNA-seq transcriptome profiles of genetically fate-mapped serotonin neurons, manually sorted from multiple anatomic domains, at both population and single cell resolution.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part, Cell line
View Samples- Zea mays
- 64 Downloadable Samples
- Illumina HiSeq 2000
Description
Heterosis which is the improved vigor of F1-hybrids compared to their parents is widely exploited in maize (Zea mays L.) breeding to produce elite hybrids of superior yield. The transcriptomes of the maize inbred lines B73 and Mo17 and their reciprocal hybrid offspring were surveyed in the meristematic zone, the elongation zone, cortex and stele tissues of primary roots, prior to the developmental manifestation of heterosis. Single parent expression (SPE) is consistent with the dominance model for heterosis in that it denotes genes that are expressed in only one parent but in both reciprocal hybrids. In primary root tissues, between 1,027 (elongation zone) and 1,206 (stele) SPE patterns were observed. As a consequence, hybrids displayed in each tissue >400 active genes more than either parent. Analysis of tissue-specific SPE dynamics revealed that 1,233 of 2,233 SPE genes displayed SPE in all tissues in which they were expressed while 1,000 SPE genes displayed in at least one tissue a non-SPE pattern. In addition, 64% (17,351/ 27,164) of all expressed genes were assigned to the two subgenomes which are the result of an ancient genome duplication. By contrast, only between 18 and 25% of the SPE genes were assigned to a subgenome suggesting that a disproportionate number of SPE genes are evolutionary young and emerged after genome duplication. We hypothesize that this phenomenon is associated with human selection of favorable maize genotypes which might primarily affect younger genes rather than genes whose functions have been conserved for millions of years.
Publication Title
Nonsyntenic genes drive highly dynamic complementation of gene expression in maize hybrids.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 52 Downloadable Samples
- Illumina HiSeq 2000
Description
RNA-Seq of reciprocally crossed Black6 x CAST hybrid mouse tissues.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Cell line
View Samples- Zea mays
- 49 Downloadable Samples
- Illumina Genome Analyzer IIx
Description
The genomic distribution of trait-associated SNPs (TASs) discovered in genome-wide association studies (GWAS) can provide insight into the genetic architecture of complex traits and the design of future studies. Here we report on a maize GWAS that identified TASs underlying five quantitative traits measured across a large panel of samples and examine the characteristics of these TASs. A set of SNPs obtained via RNA sequencing (RNA-seq), most of which are located within annotated genes (~87%) were complemented with additional SNPs from the maize HapMap Project that contains approximately equal proportions of intragenic and intergenic SNPs. TASs were identified via a genome scan while controlling for polygenic background effects. The diverse functions of TAS-containing candidate genes indicate that complex genetic networks shape these traits. The vast majority of the TAS-containing candidate genes have dynamic expression levels among developmental stages. Overall, TASs explain 44~54% of the total phenotypic variation for these traits, with equal contributions from intra- and inter-genic TASs. Association of ligueless2 with upper leaf angle was implicated by two intragenic TASs; rough sheath1 was associated with leaf width by an upstream intergenic TAS; and Zea agamous5 was associated with days to silking by both intra- and inter-genic TASs. A large proportion (82%) of these TASs comes from noncoding regions, similar to findings from human diseases and traits. However, TASs were enriched in both intergenic (53%) and promoter 5kb (24%) regions, but under-represented in a set of nonsynonymous SNPs.
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Anopheles gambiae
- 42 Downloadable Samples
- Illumina Genome Analyzer II
Description
Study on sex biased gene expression during multiple life stages and different strains in malaria vector Anopheles gambiae
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part, Cell line, Treatment
View Samples- Homo sapiens
- 48 Downloadable Samples
- IlluminaGenomeAnalyzerII, IlluminaHiSeq2000
Description
Circulating cell-free RNA in the blood provides a potential window into the health, phenotype, and developmental programs of a variety of human organs. We used high-throughput methods of RNA analysis such as microarrays and next-generation sequencing to characterize the global landscape of circulating RNA in human subjects. By focusing on tissue-specific genes, we were able to identify the relative contributions of these tissues to circulating RNA and monitor changes during tissue development and neurodegenerative disease states.
Publication Title
Noninvasive in vivo monitoring of tissue-specific global gene expression in humans.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 36 Downloadable Samples
- Illumina HiSeq 2500
Description
RNA-seq raw reads of sorted immune cell populations (Epcam+ cells, T cells) from two models of genetically engineered mice (1: EGFR TL790M and L858R and 2: KRAS G12D) comparing untreated and PD1-treated tumors in these mice.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part, Cell line
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