Similar studies for GEO DataSets (Select 200189854) - GEO DataSets

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Items: 20

Select item 2001898541.

Ribo-Seq and RNA-seq sequencing of WT and Rpl3l-/- mouse hearts

(Submitter supplied) RPL3L is a ribosomal protein expressed exclusively in adult straited muscle tissues, and a paralogue of the ubiquitously expressed RPL3. Here, we are looking into the effects of Rpl3l knockout on translation in adult mice hearts.

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL17021
12 Samples

Download data: TAB

Series

Accession:: GSE189854

ID:: 200189854

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Select item 2001898722.

Nano-TRAP Input and IP sequencing of WT and Rpl3l-/- mouse hearts

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL24973
12 Samples

Download data: TAB

Series

Accession:: GSE189872

ID:: 200189872

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Select item 2002030723.

RPL3L-containing ribosomes determine translation elongation dynamics required for cardiac function

(Submitter supplied) Although several ribosomal protein (RP) paralogs are expressed in a tissue-specific manner, how these proteins affect translation and why they are required only in certain tissues have remained unclear. Here we show that RPL3L, a paralog of RPL3 specifically expressed in heart and skeletal muscle, influences translation elongation dynamics. Deficiency of RPL3L-containing ribosomes (RPL3L-ribosomes) in RPL3L knockout male mice resulted in impaired cardiac contractility. more...

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL24247
62 Samples

Download data: CSV, XLSX

Series

Accession:: GSE203072

ID:: 200203072

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Select item 2002161684.

Defining the effects of Rpl3L-deficiency on transcriptional profiles of mouse hearts

(Submitter supplied) The ribosomal protein L3-like (RPL3L) is a striated muscle-specific ribosomal protein, and mutations in human RPL3L are linked with childhood cardiomyopathy and age-related atrial fibrillation. However, the function served by this protein, a paralogue of the ubiquitously expressed RPL3 protein, remains poorly characterized in both heart and skeletal muscle. To address this, null mutant mice with the Rpl3L gene deleted were generated and studied. more...

Organism:: Mus musculus

Type:: Expression profiling by array

Platform:: GPL23038
4 Samples

Download data: CEL, XLSX

Series

Accession:: GSE216168

ID:: 200216168

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Select item 2002158695.

Characterizing role of striated-muscle specific ribosomal protein L3-like (Rpl3L) in mouse hearts

(Submitter supplied) Overall goal: To elucidate the function served by Rpl3L in heart. Purpose of analysis: To determine effects of Rpl3L-deficiency on translational mRNA profile in heart. Experimental structure: Polysomes and monosomes were fractionated from cardiac ventricles and associated RNA extracted for library generation and differential gene expression analyses between wild-type and Rpl3L-null samples, using standard RNAseq pipeline.

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL24247
8 Samples

Download data: XLSX

Series

Accession:: GSE215869

ID:: 200215869

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Select item 2000470986.

Expression data during plantaris muscle hypertrophy induced by synergist ablation in young adult mice

(Submitter supplied) Global gene expression patterns were determined from microarray results on day 1, 3, 5, 7, 10 and 14 during plantaris muscle hypertrophy induced by synergist ablation in young adult mice (5 months).

Organism:: Mus musculus

Type:: Expression profiling by array

Dataset:: GDS4932
Platform:: GPL6246
14 Samples

Download data: CEL

Series

Accession:: GSE47098

ID:: 200047098

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Select item 49327.

Synergist ablation effect on young adult plantaris muscle: time course

Analysis of right and left plantaris muscle from young males (5 months old) subjected to 1, 3, 5, 7, 10 and 14 days of synergist ablation surgery to induce hypertrophy. Results provide insight into the molecular response of young skeletal muscle to mechanical overload induced by synergist ablation.

Organism:: Mus musculus

Type:: Expression profiling by array, count, 2 stress, 7 time, 2 tissue sets

Platform:: GPL6246
Series:: GSE47098
14 Samples

Download data: CEL

DataSet

Accession:: GDS4932

ID:: 4932

PubMed Full text in PMC Similar studies GEO Profiles Analyze DataSet

Select item 2001449168.

Root system responses to low temperature acclimation of Arabidopsis reil ribosome biogenesis double mutants

(Submitter supplied) The REIL proteins are required for late ribosomal biogenesis and accumulation of the 60S large ribosome subunit in mature leaves of Arabidopsis thaliana upon acclimation to low temperature. To validate these functions in roots, we conducted a multi-level system analysis targeted at understanding defects and compensations responses of reil mutants before acclimation to low temperature and following temperature shift. more...

Organism:: Arabidopsis thaliana

Type:: Expression profiling by array

Platform:: GPL9020
27 Samples

Download data: TXT

Series

Accession:: GSE144916

ID:: 200144916

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Select item 2000733579.

Heterogeneous ribosomes exist and selectively translate distinct subpools of mRNAs in stem cells

(Submitter supplied) Emerging studies have linked the ribosome to more selective control of gene regulation. However, an outstanding question is whether ribosome heterogeneity at the level of core ribosomal proteins (RPs) enables ribosomes to preferentially translate specific mRNAs genome-wide. Here, we measured the absolute abundance of RPs in translating ribosomes and profiled transcripts that are enriched or depleted from select subsets of ribosomes within embryonic stem cells. more...

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing; Other

Platform:: GPL19057
20 Samples

Download data: TXT

Series

Accession:: GSE73357

ID:: 200073357

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Select item 20014636410.

Human METTL18 is a histidine-specific methyltransferase that targets RPL3 and affects ribosome biogenesis and function

(Submitter supplied) Methylation is a common post-translational modification that occurs primarily on lysine and arginine, but also on some other residues, such as histidine. METTL18 is the last uncharacterized member of a group of human methyltransferases (MTases) that mainly exert lysine methylation, and here we set out to elucidate its function. We found METTL18 to be a nuclear protein that contains a functional nuclear localization signal and accumulates in nucleoli. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL18573
5 Samples

Download data: TXT

Series

Accession:: GSE146364

ID:: 200146364

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Select item 20004515211.

Interrogating translating RNAs and cell-type specific gene expression using Cre-activated translating ribosome affinity purification

(Submitter supplied) We characterize a Cre-activated TRAP allele (Rosa26fsTRAP) to show that endothelium-specific activation of Rosa26fsTRAP identifies endothelial cell enriched transcripts, and that cardiomyocyte-restricted TRAP is a useful means to identify genes that are differentially expressed in cardiomyocytes in a disease model. We also show that TRAP is an effective means to study translational regulation, and we several nuclear-encoded mitochondrial genes are under strong translational control. more...

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing; Other

Platforms:: GPL17021 GPL13112
53 Samples

Download data: BEDGRAPH, BIGWIG, TXT

Series

Accession:: GSE45152

ID:: 200045152

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Select item 20012437112.

RNA-sequencing of RNAs found on eRpL22 paralogue-specific ribosomes in Drosophila melanogaster testis

(Submitter supplied) This study uncovers a population of eRpL22 paralogue-specific specialized ribosomes in the fly testis. Wildtype testes were used to isolate eRpL22 paralogue-specific ribosomes complexed with RNA molecules. RNA-sequencing determined the distribution of RNAs (mRNA and ncRNA) on each type of eRpL22 paralogue-specific ribosome, revealing unique translatomes for both eRpL22- and eRpL22-like- ribosomes, as well as an overlapping translatome.

Organism:: Drosophila melanogaster

Type:: Expression profiling by high throughput sequencing; Other

Platform:: GPL21306
8 Samples

Download data: XLSX

Series

Accession:: GSE124371

ID:: 200124371

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Select item 20009699813.

A Comprehensive Roadmap of the Mammalian Ribo-interactome Connects Metabolism Enzymes with Specialized ER-Ribosomes

(Submitter supplied) The ribosome has considerably increased in size during metazoan evolution in the form of an RNA shell that could serve as a platform for yet unknown protein interactions. Here, we have comprehensively identified the mammalian ‘ribo-interactome’ by establishing a ribosome affinity purification method. Our findings reveal a multitude of novel ribosome interacting factors, encompassing unanticipated functional categories including energy metabolism, cell redox homeostasis, as well as key protein and RNA modifying enzymes. more...

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing; Other

Platform:: GPL19057
6 Samples

Download data: BW, CSV

Series

Accession:: GSE96998

ID:: 200096998

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Select item 20012782714.

Selective translation by alternative bacterial ribosomes

(Submitter supplied) Mycobacteria encode several additional alternative ribosomal proteins (AltRP) and the funtion of AltRP invovling in translation is little known. In this study, we investigate the different translation landscape of AltRibo and CanRibo and found AltRibo have a relative 5' reads accumlation and preferential codon usage.

Organism:: Mycolicibacterium smegmatis

Type:: Expression profiling by high throughput sequencing; Other

Platform:: GPL26255
16 Samples

Download data: TXT

Series

Accession:: GSE127827

ID:: 200127827

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Select item 20020017215.

METTL18-mediated histidine methylation on RPL3 modulates translation elongation for proteostasis maintenance.

(Submitter supplied) Protein methylation occurs predominantly on lysine and arginine residues, but histidine also serves as a substrate for the modification. However, a limited number of enzymes responsible for this modification have been reported. Moreover, the biological role of histidine methylation has remained poorly understood. Here, we report that human METTL18 is a histidine methyltransferase for the ribosomal protein RPL3 and that the modification specifically slows ribosome traverse on tyrosine codons, allowing the proper folding of synthesized proteins. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL20795
8 Samples

Download data: TXT

Series

Accession:: GSE200172

ID:: 200200172

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Select item 20017985416.

METTL18-mediated histidine methylation on RPL3 modulates translation elongation for proteostasis maintenance

(Submitter supplied) In addition to predominant protein methylation on lysine and arginine residues, histidine also serves as a substrate for the modification. However, a limited number of enzymes responsible for this modification has been reported. Moreover, the biological mission of the histidine methylation has remained poorly understood. Here, we reported that human METTL18 is a histidine methyltransferase for ribosomal protein RPL3 and that the modification specifically slows ribosome traverse on tyrosine codons, allowing proper folding of synthesized proteins. more...

Organism:: Homo sapiens

Type:: Other

Platform:: GPL20301
8 Samples

Download data: TXT

Series

Accession:: GSE179854

ID:: 200179854

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Select item 20015168817.

RRF plays critical roles in ribosome homeostasis in E. coli but has little effect on translational coupling

(Submitter supplied) We used ribosome profiling to characterize the biological role of ribosome recycling factor (RRF) in Escherichia coli. As expected, RRF depletion leads to enrichment of post-termination 70S complexes in 3′-UTRs. We also observe that elongating ribosomes are unable to complete translation because they are blocked by non-recycled ribosomes at stop codons. Previous studies have suggested a role for recycling in translational coupling within operons; if a ribosome remains bound to an mRNA after termination, it may re-initiate downstream. more...

Organism:: Escherichia coli str. K-12 substr. MG1655

Type:: Other

Platform:: GPL18956
18 Samples

Download data: WIG

Series

Accession:: GSE151688

ID:: 200151688

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Select item 20003939918.

Ribosomal biogenesis genes play an essential and p53-independent role in pancreas development

(Submitter supplied) Analysis of transcriptional profiles in Sbds(ATG) MO-injected embryos with and without coinjection of p53(ATG) MO. We identified a large number of changes in transcript abundance associated with loss of Sbds. Among the 24,278 annotated zebrafish genes in the platform, 4,892 significantly differentially expressed genes were identified.

Organism:: Danio rerio

Type:: Expression profiling by array

Platform:: GPL14688
16 Samples

Download data: TXT

Series

Accession:: GSE39399

ID:: 200039399

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Select item 20017177419.

nRibo-Seq timecourse in mESCs

(Submitter supplied) mRNAs are generally assumed to be loaded instantly with ribosomes upon entry into the cytoplasm. To measure ribosome density on nascent mRNA, we developed nascent Ribo-Seq (nRibo-Seq) by combining Ribo-Seq with progressive 4-thiouridine labelling. In mouse macrophages, we experimentally determined, for the first time, the lag between the appearance of nascent RNA and its association with ribosomes, which was calculated to be 20 - 22 min for bulk mRNA, and approximated the time it takes for mRNAs to be fully loaded with ribosomes to be 41 - 44 min. more...