GEO DataSets

(Submitter supplied) We performed translatome and transcriptome sequencing of A549, H1299 and HBE cells and analyzed the translation ratio (TR) of all genes

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL11154 GPL10999

6 Samples

Download data: TXT

(Submitter supplied) This experiment performed RNA-seq of transcriptome and translatome (translating mRNA) of Caco-2 cells

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

2 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Other; Expression profiling by array

4 related Platforms

46 Samples

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(Submitter supplied) To compare total RNA levels in miR-124 and mock-transfected cells (Figure S3), 5-10 ug of total RNA from miR-124-transfected cells or mock-transfected cells or universal reference RNA (Stratagene Cat# 740000) was reverse transcribed with Superscript III (Invitrogen Cat# 18080085) in the presence of aminoallul-dUTP 5-(3-aminoallyl)-dUTP (Ambion Cat# AM8439) and natural dNTPs (GE Healthsciences Cat# US77212) with 10 ug of N9 primer (Invitrogen). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL9495 GPL9494 GPL9496

9 Samples

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(Submitter supplied) Ribosome Occupancy Experiments: for these experiments Channel 1 is amplified RNA (aRNA) from mRNA unbound to any ribosomes. Channel 2 is aRNA from mRNA associated with ribosomes. Ribosome Density Experiments: for these experiments Channel 1 is amplified RNA (aRNA) from mRNA present in the light fractions of the polysome. Channel 2 is aRNA from mRNA associated with ribosomes deep in the polysome.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL9497

10 Samples

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(Submitter supplied) HEK293T cells were either mock or miR-124 transfected. Cells were lysed 12 hours after transfection with Trizol reagent. RNA was isolated, amplified, labeled (cy5), and comparatively hybridized with a universal reference (cy3) on HEEBO arrays in biological triplicate. In addition, each biological replicate was measured twice (#2's). Data from the technical replicates was averaged before analysis. SS=steady state Compound Based Treatment: miR-124

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL9497 GPL9494

12 Samples

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(Submitter supplied) Immunoaffinity Purifications of Human Argonaute Twelve hours after transfections with mock or with miR-124, we washed each 15-cm plate once with phosphate-buffered saline (usually two plates were used per IP), then added 1 ml of 4 C lysis buffer (150 mM KCl, 25 mM Tris-HCl [pH 7.4], 5 mM Na-EDTA [pH 8.0], 0.5% Nonidet P-40, 0.5 mM DTT, 10 ul protease inhibitor cocktail [Pierce Cat# 78437], 100 U/ml SUPERaseIn [Ambion Cat# AM2694]). more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL9497

15 Samples

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(Submitter supplied) In the process of translation, ribosomes first bind to mRNAs (translation initiation) and then move along the mRNA (elongation) to synthesize proteins. Elongation pausing is deemed highly relevant to co-translational folding of nascent peptides and the functionality of protein products, which positioned the evaluation of elongation speed as one of the central questions in the field of translational control. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL11154 GPL16791

7 Samples

Download data: TXT, XLSX

(Submitter supplied) Red channel: 3 independent polysome preparations from BY4741 cells, grown in YPD to mid-log phase (OD 0.6-0.9). In each experiment 14 fractions were collected. In-vitro transcribed B.subtilis controls were added to each fraction and used for normalization. Green channel: Total RNA prepared from S288c cells. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platforms:

GPL2666 GPL3228

42 Samples

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(Submitter supplied) 7d-old WT ler seedlings were submitted to 12h of non-stress (air) or hypoxia-stress treatment under low light conditions (45 uM m-2 s-2), and Total and Large Polysome RNA from both treatments were extracted and hybridized against Affymetrix genome chips. Values were used to evaluate changes in transcript abundance and transcript association with large polysomal complexes. TABLE 1 - Comparison between transcript abundance in non-stress and hypoxia-stress conditions. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Dataset:

GDS1450

Platform:

GPL198

4 Samples

Download data: CEL, EXP

Expression profiling of 7 day old wild type Ler seedlings subjected to 12 hours of hypoxia under low light conditions. Total RNA and mRNA extracted from large polyribosomes compared. Results provide insight into the role of translational regulation in the response to hypoxia.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array, count, 2 protocol, 2 stress sets

Platform:

GPL198

Series:

GSE2218

4 Samples

Download data: CEL, EXP

(Submitter supplied) Ribsome profiling analysis of mRNA translation in mouse cells under conditions of mTOR activiation or inhibition.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9250

12 Samples

Download data: TXT

(Submitter supplied) Alternative splicing (AS) isoforms create numerous proteoforms, expanding the complexity of the genome. Highly similar sequences, incomplete reference databases and the insufficient sequence coverage of mass spectrometry limit the identification of AS proteoforms.In this work, we compared RNC-seq and Ribo-seq in the context of proteome identification, especially when identifying protein isoforms from AS. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL24106 GPL23227

3 Samples

Download data: BED, TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by array; Non-coding RNA profiling by array

Platforms:

GPL13264 GPL6480

39 Samples

Download data: TXT

(Submitter supplied) This study is complementary to the "Genome-wide analysis of host mRNA translation during hepatitis C virus infection" study (GSE44210), for which sucrose gradient ultracentrifugation followed by microarray analysis was used to identify translationally-regulated mRNAs (mRNAs associated with ribosomes) from JFH1-infected and uninfected Huh-7.5.1 cells. MicroRNA arrays have been conducted in parallel on total RNA from infected and uninfected cells, in order to determine if microRNA regulation could explain some of the mRNA translation regulations.

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL13264

7 Samples

Download data: TXT

(Submitter supplied) Sucrose gradient ultracentrifugation followed by microarray analysis was used to identify translationally-regulated mRNAs (mRNAs associated with ribosomes) from JFH1-infected and uninfected Huh-7.5.1 cells.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6480

32 Samples

Download data: TXT

(Submitter supplied) In animal oocytes and early embryos, mRNA poly(A)-tail length strongly influences translational efficiency (TE), but later in development this coupling between tail length and TE disappears. Here, we elucidate how this coupling is first established and why it disappears. Overexpressing cytoplasmic poly(A)-binding protein (PABPC) in frog oocytes specifically improved translation of short-tailed mRNAs, thereby diminishing coupling between tail length and TE. more...

Organism:

Homo sapiens; Mus musculus; Xenopus laevis

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL16791 GPL17021 GPL18936

79 Samples

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(Submitter supplied) U2AF65 is an essential splicing factor involved in the 3'splice site recognition dureing the first steps of spliceosome assembly. In addition, this protein has nucleocytoplasmic shuttling activity and the Drosophila homologue has been implicated in mRNA export. We have used microarray hybridization coupled to RNA immunoprecipitation from HeLa cell cytoplasmic extracts using anti-U2AF65 antibodies to identify mRNA molecules associated with the U2AF65 splicing factor Sample preparation methods (Gama-Carvalho et al, 2006, submitted) Suspension HeLa cells were grown in DMEM, 10% FCS, Pen/Strep and split 1:2 the day before harvesting. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

6 Samples

Download data: CEL

(Submitter supplied) PTB is multifunctional RNA binding protein reported to be involved in splicing, 3' -end processing, stability and translational regulation. Sample preparation methods (Gama-Carvalho et al, 2006, submitted) Suspension HeLa cells were grown in DMEM, 10% FCS, Pen/Strep and split 1:2 the day before harvesting. Post-nuclear cytoplasmic extracts were obtained as described (Herbert and Hecht 1999), using 5x107 cells/ml of lysis buffer. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

4 Samples

Download data: CEL

(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