Similar studies for GEO DataSets (Select 200038201) - GEO DataSets

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Items: 20

Select item 2000382011.

The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts [PAR-CLIP]

(Submitter supplied) Protein-RNA interactions are fundamental to core biological processes, such as mRNA splicing, localization, degradation and translation. We developed a photoreactive nucleotide-enhanced UV crosslinking and oligo(dT) purification approach to identify the mRNA-bound proteome using quantitative proteomics and to display the protein occupancy on mRNA transcripts by next-generation sequencing. Application to a human embryonic kidney cell line identified close to 800 proteins. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL11154
5 Samples

Download data: BED

Series

Accession:: GSE38201

ID:: 200038201

PubMed Similar studies SRA Run Selector

Select item 2000383562.

The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts [RNA-seq]

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL9115
4 Samples

Download data: CSV

Series

Accession:: GSE38356

ID:: 200038356

Select item 2000383553.

The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts [protein occupancy profiling]

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL11154
2 Samples

Download data: BEDGRAPH

Series

Accession:: GSE38355

ID:: 200038355

PubMed Similar studies SRA Run Selector

Select item 2000381574.

The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts

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

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platforms:: GPL9115 GPL11154
11 Samples

Download data: BED

Series

Accession:: GSE38157

ID:: 200038157

PubMed Similar studies

Select item 2000498315.

Differential Protein Occupancy Profiling of the mRNA Transcriptome

(Submitter supplied) Protein-RNA interactions are fundamental to core biological processes, such as mRNA splicing, localization, degradation and translation. We have developed a photoreactive nucleotide-enhanced UV crosslinking and oligo(dT) purification approach to identify the mRNA-bound proteome using quantitative proteomics and to display the protein occupancy on mRNA transcripts by next-generation sequencing (Baltz and Munschauer et al. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platforms:: GPL16791 GPL11154
10 Samples

Download data: BEDGRAPH, TXT

Series

Accession:: GSE49831

ID:: 200049831

PubMed Full text in PMC Similar studies Analyze with GEO2R SRA Run Selector

Select item 2000299436.

Unstressed HeLa cells and ELAVL1/HuR knock down conditions: polyA RNA-Seq, small RNA-Seq, and PAR-CLIP

(Submitter supplied) Post-transcriptional gene regulation relies on hundreds of RNA binding proteins (RBPs) but the function of most RBPs is unknown. The human RBP HuR/ELAVL1 is a conserved mRNA stability regulator. We used PAR-CLIP, a method based on RNA-protein crosslinking, to identify transcriptome wide ~26,000 HuR binding sites. These sites were on average highly conserved, enriched for HuR binding motifs and mainly located in 3' untranslated regions. more...

Organism:: Homo sapiens

Type:: Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:: GPL11154 GPL9115
9 Samples

Download data: BED, TXT, WIG

Series

Accession:: GSE29943

ID:: 200029943

Select item 2000001047.

total RNA from yra1-1 at 37C vs. Yra1 WT at 37C (yra1-1TS_v_Yra1WT)

(Submitter supplied) Comparison of cDNA from RNA of yra1-1 temperature-sensitive mutant to RNA from Yra1 wildtype strain both at the non-permissive temperature of 37C Keywords: repeat sample

Organism:: Saccharomyces cerevisiae

Type:: Expression profiling by array

Platform:: GPL220
6 Samples

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Series

Accession:: GSE104

ID:: 200000104

Select item 2000001038.

total RNA from mex67-6 at 37C vs. Mex67 WT at 37C (mex67-5TS_v_Mex67WT)

(Submitter supplied) Comparison of cDNA from RNA of mex67-5 temperature-sensitive mutant to RNA from Mex67 wildtype strain both at the non-permissive temperature of 37C Keywords: repeat sample

Organism:: Saccharomyces cerevisiae

Type:: Expression profiling by array

Platform:: GPL220
6 Samples

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Series

Accession:: GSE103

ID:: 200000103

Select item 2000001029.

zzYra1 co-IPed RNA vs. zzMex67 co-IPed RNA (zzYra1IP_v_zzMex67IP)

(Submitter supplied) Comparison of cDNA from RNA co-IPed with zzYra1 to cDNA from RNA co-IPed with zzMex67 Keywords: repeat sample

Organism:: Saccharomyces cerevisiae

Type:: Expression profiling by array

Platforms:: GPL221 GPL220
5 Samples

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Series

Accession:: GSE102

ID:: 200000102

Select item 20000010110.

zzYra1 co-IPed RNA vs. Total RNA (zzYra1IP_v_TotalRNA)

(Submitter supplied) Comparison of cDNA from RNA IPed with zzYra1 to that from total RNA; resulting analysis gives Yra1 binding level relative to total abundance for each mRNA Keywords: repeat sample

Organism:: Saccharomyces cerevisiae

Type:: Expression profiling by array

Platforms:: GPL220 GPL221
5 Samples

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Series

Accession:: GSE101

ID:: 200000101

Select item 20000010011.

zzMex67 co-IPed RNA vs. Total RNA (zzMex67IP_v_TotalRNA)

(Submitter supplied) Comparison of cDNA from RNA IPed with zzMex67 to that from total RNA; resulting analysis gives Mex67 binding level relative to total abundance for each mRNA Keywords: repeat sample

Organism:: Saccharomyces cerevisiae

Type:: Expression profiling by array

Platform:: GPL221
4 Samples

Download data

Series

Accession:: GSE100

ID:: 200000100

Select item 20000009912.

zzYra1 co-IPed RNA vs. zz co-IPed RNA (zzYra1IP_v_zzIP)

(Submitter supplied) Comparison of cDNA from RNA IPed with zzYra1 to that from RNA co-IPed with zz tag alone (control IP) Keywords: equivalent probe

Organism:: Saccharomyces cerevisiae

Type:: Expression profiling by array

Platforms:: GPL220 GPL221
5 Samples

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Series

Accession:: GSE99

ID:: 200000099

Select item 20000009813.

zzMex67 co-IPed RNA vs. zz co-IPed RNA (zzMex67IP_v_zzIP)

(Submitter supplied) Comparison of cDNA from RNA IPed with zzMex67 to that from RNA co-IPed with zz tag alone (control IP) Keywords: repeat sample

Organism:: Saccharomyces cerevisiae

Type:: Expression profiling by array

Platforms:: GPL220 GPL221
4 Samples

Download data

Series

Accession:: GSE98

ID:: 200000098

Select item 20002195614.

Transcriptome analysis of the archaeon Thermoplasma acidophilum cultured under aerobic and anaerobic conditions

(Submitter supplied) Investigation of whole genome gene expression level changes in Thermoplasma acidophilum cultured under aerobic and anaerobic conditions. The analysis are further described in Na Sun, Cuiping Pan, Stephan Nickell, Matthias Mann, Wolfgang Baumeister, and István Nagy, Quantitative proteome and transcriptome analysis of the archaeon Thermoplasma acidophilum cultured under aerobic and anaerobic conditions (submitted).

Organism:: Thermoplasma acidophilum DSM 1728

Type:: Expression profiling by array

Platform:: GPL10453
6 Samples

Download data: TXT

Series

Accession:: GSE21956

ID:: 200021956

Select item 20011038015.

Proximity-CLIP provides a snapshot of occupied cis-acting elements on RNA in different subcellular compartments on a transcriptome-wide scale

(Submitter supplied) Many cellular RNAs localize to specific subcellular compartments. Currently, methods to systematically study subcellular RNA localization are limited and lagging behind proteomic approaches. Here, we combined APEX2-mediated proximity biotinylation of proteins with PAR-CLIP to simultaneously profile the proteome and the transcriptome bound by RNA binding proteins in any given subcellular compartment. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL21290
12 Samples

Download data: XLSX

Series

Accession:: GSE110380

ID:: 200110380

PubMed Full text in PMC Similar studies Analyze with GEO2R SRA Run Selector

Select item 20011979816.

Insight into novel RNA-binding activities via large-scale analysis of lncRNA-bound proteome and IDH1-bound transcriptome

(Submitter supplied) RNA-binding proteins (RBPs) play pivotal roles in directing RNA fate and function. Yet the current annotation of RBPs is largely limited to proteins carrying known RNA-binding domains. To systematically reveal dynamic RNA-protein interactions, we surveyed the human proteome by a protein array-based approach and identified 671 proteins with RNA-binding activity. Among these proteins, 525 lack annotated RNA-binding domains and are enriched in transcriptional and epigenetic regulators, metabolic enzymes, and small GTPases. more...

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL17021
3 Samples

Download data: BEDGRAPH

Series

Accession:: GSE119798

ID:: 200119798

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20005788117.

Transcriptome-wide ribonuclease footprinting to identify RNA-protein interaction sites

(Submitter supplied) RNA-binding proteins (RBPs) are intimately involved in all aspects of RNA processing and regulation and are linked to neurodegenerative diseases and cancer. Therefore, understanding the relationship between RBPs and their RNA targets is critical for a broader understanding of post-transcriptional regulation in normal and disease processes. The majority of approaches to study RNA-protein interactions focus on single RBPs, however there are many hundreds RBPs encoded in the human genome, and each cell type expresses a different catalog of these regulatory molecules, greatly limiting the ability of these single RBP approaches to capture the global landscape of RNA-protein interactions. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL11154
12 Samples

Download data: BED

Series

Accession:: GSE57881

ID:: 200057881

PubMed Similar studies SRA Run Selector

Select item 20015464318.

in vivo mRNA display: Large-scale Proteomics by Next Generation Sequencing

(Submitter supplied) We introduce in vivo mRNA display, a technology that converts a variety of proteomics applications into a DNA sequencing problem.

Organism:: Saccharomyces cerevisiae

Type:: Other

Platform:: GPL19756
90 Samples

Download data: XLSX

Series

Accession:: GSE154643

ID:: 200154643

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20016323019.

The type and relative distribution of the PP isolated RNAs by RNA-sequencing analysis in HeLa cells.

(Submitter supplied) Developing a psoralen probe (PP)-based method for RNA tagging and RNA-protein complex (RP-complex) enrichment, isolating of both coding and noncoding RNAs from HeLa cells was achieved by PP enrichment. Exploring the type and relative distribution of the PP isolated RNAs by RNA-sequencing analysis.