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Links from GEO DataSets

Items: 20

1.

The PARN deadenylase targets a discrete set of mRNAs for decay and regulates cell motility in mouse myoblasts

(Submitter supplied) Almost all cellular mRNAs terminate in a 3’ poly(A) tail, the removal of which can induce both translational silencing and mRNA decay. Mammalian cells encode many poly(A)-specific exoribonucleases but their individual roles are poorly understood. Here, we undertook an analysis of the role of PARN deadenylase in mouse myoblasts using global measurements of mRNA decay rates. Our results reveal that a discrete set of mRNAs exhibit altered mRNA decay as a result of PARN depletion and that stabilization is associated with increased poly(A) tail length and translation. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL6246
30 Samples
Download data: CEL
Series
Accession:
GSE35944
ID:
200035944
2.

Poly(A)-Specifc Ribonuclease 1 (PARN-1) Overexpression in Procyclic T. brucei

(Submitter supplied) We sought to determine the effect of TbPARN-1 overexpression on global mRNA steady-state levels in T. brucei. The mRNA expression profile of tet-induced TbPARN-1 OvEx procyclic cells was compared to the mRNA profile of control cells (expressing tet-induced TAP tag alone) by microarray analysis. Since overexpression of TbPARN-1 showed increased deadenylation activity in cytoplasmic extracts, overexpressing PARN-1 in vivo should result in more rapid deadenylation and decay of mRNAs targeted by PARN-1. more...
Organism:
Trypanosoma brucei
Type:
Expression profiling by array
Platform:
GPL10075
6 Samples
Download data: TXT
Series
Accession:
GSE20593
ID:
200020593
3.

Systematic analysis of cis-elements in unstable mRNAs demonstrates that CUGBP1 is a key regulator of mRNA decay in muscle cells

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL6246
19 Samples
Download data: CEL
Series
Accession:
GSE21236
ID:
200021236
4.

mRNA immunoprecipitated with CUGBP1 in C2C12

(Submitter supplied) Dramatic changes in gene expression occur in response to extracellular stimuli and during differentiation. Although transcriptional effects are important, alterations in mRNA decay also play a major role in achieving rapid and massive changes in mRNA abundance. Moreover, just as transcription factor activity varies between different cell types, the factors influencing mRNA decay are also cell-type specific.GREs are recognized by CUGBP1, an RNA-binding protein and instability factor whose function is affected in several neuromuscular diseases. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL6246
4 Samples
Download data: CEL
Series
Accession:
GSE21235
ID:
200021235
5.

Expression data from C2C12 mouse myoblast with treatment actinomycin D

(Submitter supplied) Dramatic changes in gene expression occur in response to extracellular stimuli and during differentiation. Although transcriptional effects are important, alterations in mRNA decay also play a major role in achieving rapid and massive changes in mRNA abundance. Moreover, just as transcription factor activity varies between different cell types, the factors influencing mRNA decay are also cell-type specific. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL6246
15 Samples
Download data: CEL
Series
Accession:
GSE21233
ID:
200021233
6.

A specialized mechanism of translation mediated by FXR1a-associated microRNP in cellular quiescence

(Submitter supplied) MicroRNAs predominantly decrease gene expression; however, specific mRNAs are translationally upregulated in quiescent (G0) mammalian cells and immature Xenopus laevis oocytes by an FXR1a-associated microRNP (microRNA-protein complex) that lacks the microRNP repressor, GW182. We conducted global proteomic analysis in THP1 cells depleted of FXR1 to globally identify activation targets of more than one microRNA, since FXR1 is required for microRNAmediated translation activation in THP1 G0 cells by FXR1-microRNPs.Since proteomic data changes could also be due to changes at the RNA level, total RNA levels in FXR1knockdown compared to control shRNA cells were examined in parallel by microarray analysis using Affymetrix Human GeneChip 2.0 ST. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL16686
2 Samples
Download data: CEL
Series
Accession:
GSE77512
ID:
200077512
7.

Analysis of gene expression regulated by Drosophila melanogaster Tis11

(Submitter supplied) In mammalian cells, AU-rich elements (AREs) are well known regulatory sequences located in the 3' untranslated region (UTR) of many short-lived mRNAs that suppress gene expression at the posttranscriptional level. Tis11, a zinc finger RNA-binding protein homologous to mammalian tristetraprolin, targets ARE-containing reporter mRNAs for rapid degradation in SL2 cells. To identify Drosophila mRNA targets of Tis11, we performed genome-wide expression profiling after dsRNA-mediated depletion of endogenous Tis11 in SL2 cells. more...
Organism:
Drosophila melanogaster
Type:
Expression profiling by array
Platform:
GPL1322
12 Samples
Download data: CEL
Series
Accession:
GSE28147
ID:
200028147
8.

Genomewide measurements of neural-specific mRNA decay in Drosophila embryos

(Submitter supplied) Neural-specific mRNA decay measurements by TU-Decay technique in control and Pumilio knockdown embryos
Organism:
Drosophila melanogaster
Type:
Expression profiling by array
Platform:
GPL17080
15 Samples
Download data: TXT
Series
Accession:
GSE67512
ID:
200067512
9.

Genomewide measurements of whole embryo mRNA decay in Drosophila

(Submitter supplied) whole embryo (all tissues) measurement of mRNA decay by 4-thiouridine pulse-chase
Organism:
Drosophila melanogaster
Type:
Expression profiling by array
Platform:
GPL6385
6 Samples
Download data: TXT
Series
Accession:
GSE67435
ID:
200067435
10.

Changes in gene expression and RNA editing in Adar2-WT and Adar2-KO Mouse embryonic Fibroblasts (MEFs)

(Submitter supplied) Purpose: Measure gene expression and RNA editing changes in Adar-WT and Adar2-KO MEFs Methods: Performed PolyA+ RNA-seq (single end, one sample each) of Adar2-WT and Adar2-KO MEFs Results: Observed changes in editing and gene expression of several genes Conclusion: Adar2 influences gene expression and editing of transcripts
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17021
2 Samples
Download data: TXT
Series
Accession:
GSE74746
ID:
200074746
11.

TTP mRNA targets identified by global analysis of stabilized transcripts in TTP-deficient fibroblasts

(Submitter supplied) Tristetraprolin (TTP) is a tandem CCCH zinc finger protein that was identified through its rapid induction by mitogens in fibroblasts. Studies of TTP-deficient mice, and cells derived from them, showed that TTP could bind to certain AU-rich elements in mRNAs, leading to increases in the rates of mRNA deadenylation and destruction. Known physiological target mRNAs for TTP include tumor necrosis factor alpha (TNF), granulocyte macrophage colony stimulating factor (GM-CSF) and interleukin 2 beta (IL2 beta). more...
Organism:
Mus musculus
Type:
Expression profiling by array
Dataset:
GDS2456
Platform:
GPL1261
48 Samples
Download data: CEL
Series
Accession:
GSE5324
ID:
200005324
12.
Full record GDS2456

Tristetrapolin-deficiency and mRNA decay in fibroblasts: time course

Analysis of tristetrapolin (TTP)-deficient fibroblasts after serum activation and subsequent actinomycin D treatment for up to 120 minutes. TTP is a tandem CCCH zinc finger protein that binds to AU-rich elements in mRNA, leading to increases in the rates of mRNA deadenylation and destruction.
Organism:
Mus musculus
Type:
Expression profiling by array, transformed count, 2 agent, 2 genotype/variation, 5 time sets
Platform:
GPL1261
Series:
GSE5324
48 Samples
Download data: CEL
13.

Determination of global decay rates of yeast transcriptome and identification of factors impact mRNA stability

(Submitter supplied) In this work, we determine total mRNA decay rates in rpb1-1 and rpb1-1/caf1∆ cells, calculate half-lives in rpb1-1/caf1∆ cells relative to rpb1-1 cells and correlate them with codon optimality.
Organism:
Saccharomyces cerevisiae
Type:
Expression profiling by high throughput sequencing
Platform:
GPL13821
10 Samples
Download data: TXT
Series
Accession:
GSE114560
ID:
200114560
14.

PARN and TOE1 constitute a 3′ end maturation module for nuclear non-coding RNAs

(Submitter supplied) Poly(A)-specific ribonuclease (PARN) and target of EGR1 protein 1 (TOE1) are nuclear granule-associated deadenylases, whose mutations are linked to multiple human diseases. Here, we applied mTAIL-seq and RNA sequencing (RNA-seq) to systematically identify the substrates of PARN and TOE1 and elucidate their molecular functions. We found that PARN and TOE1 do not modulate the length of mRNA poly(A) tails. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18573
4 Samples
Download data: CSV
Series
Accession:
GSE111511
ID:
200111511
15.

Gene Expression Analysis in NCI-H520 human cancer cells upon deadenylase silencing

(Submitter supplied) The first and rate-limiting step in eukaryotic mRNA decay is the shortening of the poly(A) tail catalyzed by a family of enzymes known as deadenylases. In humans, several deadenylases have been recognized so far, yet it is not clear what the advantage is to have many enzymes catalyzing the same reaction. It is hypothesized that specific deadenylases may target unique subsets of mRNAs, or multiple deadenylases can act on the same mRNA, with discrete but overlapping functions. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL14550
7 Samples
Download data: TXT
Series
Accession:
GSE67598
ID:
200067598
16.

Gene Expression Analysis in Hep2 human cancer cells upon deadenylase silencing

(Submitter supplied) The first and rate-limiting step in eukaryotic mRNA decay is the shortening of the poly(A) tail catalyzed by a family of enzymes known as deadenylases. In humans, several deadenylases have been recognized so far, yet it is not clear what the advantage is to have many enzymes catalyzing the same reaction. It is hypothesized that specific deadenylases may target unique subsets of mRNAs, or multiple deadenylases can act on the same mRNA, with discrete but overlapping functions. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL4133
8 Samples
Download data: TXT
Series
Accession:
GSE67536
ID:
200067536
17.

Genome-wide mapping of decay factor-mRNA interactions in yeast identifies nutrient responsive transcripts as targets of the deadenylase Ccr4

(Submitter supplied) The Ccr4-Not complex is a major regulator of stress responses that controls gene expression at multiple levels, from transcription to mRNA decay. Ccr4, a core subunit of the complex, is the main cytoplasmic deadenylase in Saccharomyces cerevisiae, however its mRNA targets have not been mapped on a genome-wide scale. Here we describe a genome-wide approach, RNA immunoprecipitation-high throughput sequencing (RIP-seq), to identify the RNAs bound to Ccr4, and two proteins that associate with it, Dhh1 and Puf5. more...
Organism:
Saccharomyces cerevisiae
Type:
Other
Platform:
GPL15263
14 Samples
Download data: TXT
Series
Accession:
GSE72366
ID:
200072366
18.

Poly(A)-specific ribonuclease (PARN) mediates 3' end maturation of the telomerase RNA component

(Submitter supplied) Mutations in the poly(A) ribonuclease (PARN) gene cause telomere diseases including familial idiopathic pulmonary fibrosis (IPF) and dyskeratosis congenita (DC)1,2, but how PARN deficiency impacts telomere maintenance is unclear. Here, using somatic cells and induced pluripotent stem (iPS) cells from DC patients with PARN mutations, we show that PARN is required for the 3′ end maturation of the telomerase RNA component (TERC). more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL16791
9 Samples
Download data: XLS
19.

Database for mRNA Half-Life of 19,977 Genes Obtained by DNA Microarray Analysis of Pluripotent and Differentiating Mouse

(Submitter supplied) Degradation of mRNA is one of the key processes that control the steady-state level of gene expression. However, the rate of mRNA decay for the majority of genes is not known. We successfully obtained the rate of mRNA decay for 19 977 non-redundant genes by microarray analysis of RNA samples obtained from mouse embryonic stem (ES) cells. Median estimated half-life was 7.1 h and only <100 genes, including Prdm1, Myc, Gadd45 g, Foxa2, Hes5 and Trib1, showed half-life less than 1 h. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL6867
40 Samples
Download data: TXT
Series
Accession:
GSE13609
ID:
200013609
20.

mRNA expression in Zfp36L2 knockout E14.5 fetal liver

(Submitter supplied) ZFP36L2, zinc finger protein 36, C3H type-like 2 (also known as Brf2, Erf2, Tis11D) is a member of the tristetraprolin (TTP; Zfp36) family of tandem CCCH zinc finger proteins that can bind to AU-rich elements (AREs) in the 3'-untranslated region of mRNAs, leading to their deadenylation and subsequent degradation. We have generated Zfp36l2 knockout mice. Knockout mice were born at the expected Mendelian frequency, but within several weeks of birth they died rather suddenly with pallor and frequent intestinal hemorrhage. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Dataset:
GDS3574
Platform:
GPL1261
10 Samples
Download data: CEL
Series
Accession:
GSE15146
ID:
200015146
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