GEO DataSets

(Submitter supplied) Eukaryotic genes generate multiple mRNA transcript isoforms though alternative transcription, splicing, and polyadenylation. However, the relationship between human transcript diversity and protein production is complex as each isoform can be translated differently. We fractionated a polysome profile and reconstructed transcript isoforms from each fraction, which we term Transcript Isoforms in Polysomes sequencing (TrIP-seq). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

18 Samples

Download data: CSV

(Submitter supplied) Transcriptional and translational control are key determinants of gene expression, however, to what extent these two processes can be collectively coordinated is still poorly understood. Here, we use Nanopore long-read sequencing and cap analysis of gene expression (CAGE-seq) to document the landscape of 5′ and 3′ untranslated region (UTR) isoforms and transcription start sites of epidermal stem cells, wild-type keratinocytes and squamous cell carcinomas. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

11 Samples

Download data: BIGWIG

(Submitter supplied) Transcriptional and translational control are key determinants of gene expression, however, to what extent these two processes can be collectively coordinated is still poorly understood. Here, we use Nanopore long-read sequencing and cap analysis of gene expression (CAGE-seq) to document the landscape of 5′ and 3′ untranslated region (UTR) isoforms and transcription start sites of epidermal stem cells, wild-type keratinocytes and squamous cell carcinomas. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL13112 GPL26624

6 Samples

Download data: TXT

(Submitter supplied) The goal of this study was to test the hypothesis that minor alternative mRNA isoforms can be preferentially translated.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

4 Samples

Download data: TXT

(Submitter supplied) Purpose: mRNA translation into protein is highly regulated, but the role of mRNA isoforms, noncoding RNAs (ncRNAs), and genetic variants has yet to be systematically studied. Using high-throughput sequencing (RNA-seq), we have measured cellular levels of mRNAs and ncRNAs, and their isoforms, in lymphoblast cell lines (LCL) and in polysomal fractions, the latter shown to yield strong correlations of mRNAs with expressed protein levels. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing; Genome variation profiling by high throughput sequencing

Platform:

GPL17303

6 Samples

Download data: TXT

(Submitter supplied) Microarray experiment with polysomal and non-polysomal RNAs extracted under non-stress and mild-dehydration stress. Keywords = translation Keywords = ribosome loading Keywords = polysome Keywords = dehyrdation Keywords: other

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Dataset:

GDS1382

Platform:

GPL198

4 Samples

Download data: CEL, EXP

Evaluation of proportion of individual mRNAs in polysomal complexes in leaves under control and mild dehydration stress (DS) conditions. DS reduces level of mRNA in polysomes (ribosome loading) for most genes. Results suggest transcript sequence features that regulate differential mRNA translation.

Organism:

Arabidopsis thaliana

Type:

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

Platform:

GPL198

Series:

GSE2268

4 Samples

Download data: CEL, EXP

(Submitter supplied) It has been shown that in mammalian cells alternative transcription initiation is extensively regulated during development and across cell-types, which confers dynamic transcript 5’UTR repertoire. However it is underexplored how the heterogeneity of 5’UTR isoforms would affect the downstream steps for protein expression, such as translation. To this end, we globally compared the translational profile of distinct mRNA TSS isoforms in mouse fibroblast cells, by combining deep-sequencing based mRNA 5’ends profiling and polysome fractionation. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

14 Samples

Download data: TXT

(Submitter supplied) Intrinsic molecular pathways in the central nervous system dictate neuronal cell fate during development. However, interplay of RNA binding proteins (RBPs) dictating mRNA translation, and their spatiotemporal extracellular regulators in neocortical neural stem cells during neurogenesis are poorly understood. Using an unbiased RNAseq screen of polysomes between early and mid-neurogenesis, we identified functionally related mRNA groups and their isoforms are regulated translationally in prenatal neocortices, including mRNAs encoding RBPs. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

18 Samples

Download data: CSV

(Submitter supplied) Faithful cellular differentiation requires precise coordination of changes in gene expression. However, the relative contributions of transcriptional and translational regulation during human cellular differentiation are unclear. Here, we induced forebrain neuronal differentiation of human embryonic stem cells (hESCs) and characterized genome-wide RNA and translation levels during neurogenesis. We find that thousands of genes change at the translation level across differentiation without a corresponding change in RNA level. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL20301

52 Samples

Download data: TSV

(Submitter supplied) During the peri-partum period, the lung must respond to many factors with potential to impact protein synthesis via regulation of translation initiation. Microarray analysis of polysomal versus total RNA from fetal day (FD) 19, FD22 and postnatal day 1 (P1) rat lungs was used to identify genes whose association with large polysomes changed either pre- or postnatally. Keywords: development

Organism:

Rattus norvegicus

Type:

Expression profiling by array

Platform:

GPL1355

18 Samples

Download data: CEL

(Submitter supplied) Sequencing of total RNA and polysomal RNA of two cell lines, MCF7 (tumoral) and MCF10A (non-tumoral)

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9115

12 Samples

Download data

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

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL9020

16 Samples

Download data: TXT

(Submitter supplied) Translational control is a key regulatory step in the expression of genes as proteins. In plant cells, translational efficiency of mRNAs differs on different mRNA species, and the efficiency dynamically changes in various conditions. To gain a global view of translational control throughout growth and development, we performed genome-wide analysis of polysome association of mRNA over growth and leaf development in Arabidopsis thaliana by applying the mRNAs in polysome to DNA microarray. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL9020

8 Samples

Download data: TXT

(Submitter supplied) Translational control is a key regulatory step in the expression of genes as proteins. In plant cells, translational efficiency of mRNAs differs on different mRNA species, and the efficiency dynamically changes in various conditions. To gain a global view of translational control throughout growth and development, we performed genome-wide analysis of polysome association of mRNA over growth and leaf development in Arabidopsis thaliana by applying the mRNAs in polysome to DNA microarray. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL9020

8 Samples

Download data: TXT

(Submitter supplied) Deep sequencing methods have matured to comprehensively detect the full set of transcribed loci, but there is a gap to determine the function of the resulting highly complex transcriptomes. To this end, we have developed a new approach named ORFquant to annotate and quantify translation at the single open reading frame (ORF) level using Ribo-seq data.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

4 Samples

Download data: BW, TSV

(Submitter supplied) The goal was to measure the expression and polysome association of genes with polysomes in human embryonic stem cells

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6244

3 Samples

Download data: CEL

(Submitter supplied) To date, the search for expression quantitative trait loci (eQTL) has centered entirely on transcription; variants with effects on mRNA translation have not been systematically studied. We tested the use of ribosomal association as proxy for translational efficiency of polymorphic mRNAs to develop a novel high throughput approach for translational cis-regulation in the human genome.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL16807

126 Samples

Download data: TXT

(Submitter supplied) Long Undecoded Transcript Isoforms (LUTIs) represent a class of non-canonical mRNAs that downregulate gene expression through the combined act of transcriptional and translational repression. While single gene studies revealed some important aspects of LUTI-based repression, how these features impact gene regulation at a global scale is unknown. By using transcript leader and direct RNA sequencing, here we identify 74 LUTI candidates that are expressed specifically during meiotic prophase. more...

Organism:

Saccharomyces cerevisiae

Type:

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

Platforms:

GPL27812 GPL25739 GPL21656

72 Samples

Download data: BW, CSV, FA, GFF, NARROWPEAK, SF, TXT

(Submitter supplied) Translation canonically begins at a single AUG and terminates at the stop codon, generating one protein species per transcript. However, some transcripts may use alternative initiation sites or sustain translation past their stop codon, generating multiple protein isoforms. Through other mechanisms such as alternative splicing, both neurons and glia exhibit remarkable transcriptional diversity, and these other forms of post-transcriptional regulation are impacted by neural activity and disease. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL13112

4 Samples

Download data: TXT