GEO DataSets

(Submitter supplied) We mapped and quantified poly(A) sites in BJ and MCF10A cells under proliferative, arrested and transformed states

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL9115 GPL11154

10 Samples

Download data: WIG

(Submitter supplied) Much of posttranscriptional mRNA regulation occurs through cis-acting sequences in mRNA 3´ untranslated regions (UTRs), which interact with specific proteins and ribonucleoprotein complexes that modulate translation, mRNA stability and subcellular localization. Studies in Caenorhabditis elegans have revealed indispensable roles for 3´UTR-mediated gene regulation, yet most C. elegans genes have lacked annotated 3´UTRs. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9269

10 Samples

Download data: BED, TXT

(Submitter supplied) Messenger RNA stability, localization, and translation are largely determined by sequences in their 3′ untranslated regions (3’UTRs), which recruit regulatory proteins and RNAs. More than half of the mammalian genes generate multiple mRNA isoforms differing in their 3′UTRs and therefore in their regulatory elements. The Cytoplasmic Polyadenylation Element Binding protein 1 (CPEB1) binds to cognate sites in 3’ UTRs and regulates translation. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10635

6 Samples

Download data: GPR

(Submitter supplied) In eukaryotes, the 3' ends of RNA polymerase II-generated transcripts are made in the majority of cases by site-specific endonucleolytic cleavage, followed by the addition of a poly(A) tail. By alternative polyadenylation, a gene can give rise to multiple mRNA isoforms that differ in the length of their 3' UTRs and hence in their susceptibility to post-transcriptional regulatory factors such as microRNAs. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

6 Samples

Download data: BED

(Submitter supplied) Purpose: To identify all of the APA targets of CFIm25 on a global scale and develop an algorithm that can idenitify APA events from standard RNA-seq data Methods: RNA from HeLa cells treated with control siRNA and CFIm25 siRNA were subject to RNA-Seq. Using a custom-designed algorithm to mine RNA-seq data for novel APA events regulated by CFIm25. Results: We identified over 1,400 genes with shortened 3’UTRs after CFIm25 knockdown. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

4 Samples

Download data: BEDGRAPH

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL11154 GPL16791 GPL18573

30 Samples

Download data: BED, BIGWIG

(Submitter supplied) About 70% of human genes carry multiple polyadenylation signals, and mRNA 3’end formation is dynamically regulated under different physiological conditions. Global 3’end shortening through alternative polyadenylation (APA) correlates with enhanced cellular proliferation, and 3’ untranslated region (UTR) shortening is a widespread phenomenon in tumour cells, where it appears to enhance tumorigenic properties. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

4 Samples

Download data: TAB, TXT

(Submitter supplied) About 70% of human genes carry multiple polyadenylation signals, and mRNA 3’end formation is dynamically regulated under different physiological conditions. Global 3’end shortening through alternative polyadenylation (APA) correlates with enhanced cellular proliferation, and 3’ untranslated region (UTR) shortening is a widespread phenomenon in tumour cells, where it appears to enhance tumorigenic properties. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL16791 GPL18573

22 Samples

Download data: BED, BIGWIG

(Submitter supplied) About 70% of human genes carry multiple polyadenylation signals, and mRNA 3’end formation is dynamically regulated under different physiological conditions. Global 3’end shortening through alternative polyadenylation (APA) correlates with enhanced cellular proliferation, and 3’ untranslated region (UTR) shortening is a widespread phenomenon in tumour cells, where it appears to enhance tumorigenic properties. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

4 Samples

Download data: BED

(Submitter supplied) Cleavage and polyadenylation is essential for 3’ end processing of almost all eukaryotic mRNAs. Recent studies have shown widespread alternative cleavage and polyadenylation (APA) events leading to mRNA isoforms with different 3’UTRs and/or coding sequences. Here we present a compendium of conserved cleavage and polyadenylation sites (PASs) in mammalian genes, based on ~1.2 billion 3’ end sequencing reads from over 360 human, mouse and rat samples. more...

Organism:

Rattus norvegicus; Mus musculus; Homo sapiens

Type:

Other

5 related Platforms

128 Samples

Download data: TXT

(Submitter supplied) Poly(A)-ClickSeq is a new methodology for the sequencing of the 3'UTR/poly(A) tail junction of RNA. We analysed both wild-type and CF25Im knock-down HeLa cells in culture using Poly(A)-ClickSeq to find the distribution of poly(A) sites in these samples and determine the role of CF25Im in poly(A) site selection (alternative poly-adenylation, APA).

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18460 GPL15520

11 Samples

Download data: BEDGRAPH

(Submitter supplied) Alternative polyadenylation (APA) of mRNAs has emerged as an important mechanism for post-transcriptional gene regulation in higher eukaryotes. Although microarrays have recently been used to characterize APA globally, they have a number of serious limitations that prevents comprehensive and highly quantitative analysis. To better characterize APA and its regulation, we have developed a deep sequencing-based method called Poly(A) Site Sequencing (PAS-Seq) for quantitatively profiling RNA polyadenylation at the transcriptome level. more...

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL9052 GPL9185

4 Samples

Download data: PDF, TXT

(Submitter supplied) Here, using genome wide analysis, we demonstrate that canonical mRNA is processed post-transcriptionally through an alternative cleavage and polyadenylation mechanism. As a result of this process, the downstream cleavage fragment of the 3′UTR remains uncapped and stable This finding indicates that different parts of gene mRNA are separate and independent, by re-annotating the human transcriptome using this model, we provide a new overview of the function and impact of microRNA (miRNA) Our results shed new light on the mammalian transcriptome and show that what were considered as 3′UTRs are in fact autonomous RNA fragments.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL18573

36 Samples

Download data: BIGWIG, TSV

(Submitter supplied) Genes containing multiple polyadenylation (polyA) sites express mRNA isoforms with variable 3’ untranslated regions (3’UTRs). We found that short and long 3’UTR isoforms were relatively more abundant when genes were highly and lowly expressed, respectively, in human and mouse cells. Consistently, upregulated and downregulated genes were more likely to have shortened and lengthened 3’UTRs, respectively, when genes changed expression under different cell conditions or in response to extracellular stimuli. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9250

1 Sample

Download data: BED

(Submitter supplied) we generated developmental and tissue-specific 3'-seq libraries from D. yakuba and D. virilis to study the role of alternative polyadenylation across Drosophila species

Organism:

Drosophila melanogaster; Drosophila yakuba; Drosophila virilis

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL23800 GPL15334 GPL23801

44 Samples

Download data: BW, TAB

(Submitter supplied) Alternative polyadenylation is an important cellular mechanism that enables generation of mRNA isoforms that differ in their 3' untranslated regions (3' UTRs) and consequently in their susceptibility to miRNA and RNA binding protein mediated regulation. A dramatic change in polyadenylation site usage, leading to the systematic expression of short 3’ UTR isoforms is known to occur upon induction of proliferation in resting cells. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL13112 GPL11154

6 Samples

Download data: BED

(Submitter supplied) Alternative cleavage and polyadenylation (APA) results in mRNA isoforms containing different 3’ untranslated regions (3’UTRs) and/or coding sequences. How core cleavage and polyadenylation (C/P) factors regulate APA is not well understood. Using siRNA knockdown coupled with deep sequencing, we found that several C/P factors can play significant roles in 3’UTR-APA. Whereas Pcf11 and Fip1 enhance usage of proximal poly(A) sites (pAs), CFI-25/68, PABPN1, and PABPC1 promote usage of distal pAs. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL13112 GPL9250 GPL17021

54 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL11154 GPL9052

22 Samples

Download data: BED, WIG

(Submitter supplied) Through alternative polyadenylation, human mRNAs acquire longer or shorter 3' untranslated regions, the latter typically associated with higher transcript stability and increased protein production. To understand the dynamics of polyadenylation site usage, we mapped transcriptome‐wide both binding sites of 3' end processing factors CPSF‐160, CPSF‐100, CPSF‐73, CPSF‐30, Fip1, CstF‐64, CstF-64tau, CF Im25, CF Im59, and CF Im68 and 3' end processing sites in HEK293 cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9052

18 Samples

Download data: WIG

(Submitter supplied) Through alternative polyadenylation, human mRNAs acquire longer or shorter 3' untranslated regions, the latter typically associated with higher transcript stability and increased protein production. To understand the dynamics of polyadenylation site usage, we mapped transcriptome‐wide both binding sites of 3' end processing factors CPSF‐160, CPSF‐100, CPSF‐73, CPSF‐30, Fip1, CstF‐64, CstF-64tau, CF Im25, CF Im59, and CF Im68 and 3' end processing sites in HEK293 cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL11154

4 Samples

Download data: BED