GEO DataSets

(Submitter supplied) Structure probing coupled with high-throughput sequencing holds the potential to revolutionize our understanding of the role of RNA structure in regulation of gene expression. Despite major technological advances, intrinsic noise and high coverage requirements greatly limit the applicability of these techniques. Here we describe a probabilistic modeling pipeline which accounts for biological variability and biases in the data, yielding statistically interpretable scores for the probability of nucleotide modification transcriptome-wide. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL17342

4 Samples

Download data: SGR

(Submitter supplied) RNA is emerging as a key regulator of a plethora of biological processes. While its study has remained elusive for decades, the recent advent of high-throughput sequencing technologies provided the unique opportunity to develop novel techniques for the study of RNA structure and post-transcriptional modifications. Nonetheless, most of the required downstream bioinformatics analyses steps are not easily reproducible, thus making the application of these techniques a prerogative of few laboratories. more...

Organism:

Escherichia coli

Type:

Other

Platform:

GPL21222

2 Samples

Download data

(Submitter supplied) In eukaryotes, biogenesis of ribosomes requires folding and assembly of the precursor rRNA (pre-rRNA) with a large number of proteins and snoRNPs into huge RNA-protein complexes. In spite of intense genetic, biochemical and high resolution cryo-EM studies in Saccharomyces cerevisiae, information about the conformation of the earliest 35S pre-rRNA is limited. To overcome this, we performed high-throughput SHAPE chemical probing on the 35S pre-rRNA associated with 90S pre-ribosomes. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL17342

6 Samples

Download data: FA, GTF, SGR, TAB, TXT, XLSX

(Submitter supplied) Ribosome assembly in eukaryotes involves the activity of hundreds of assembly factors that direct the hierarchical assembly of ribosomal proteins and numerous ribosomal RNA folding steps. However, detailed insights into the function of assembly factors and ribosomal RNA folding events are lacking. To address this, we have developed ChemModSeq, a method that combines structure probing, high throughput sequencing and statistical modeling, to quantitatively measure RNA structural rearrangements during the assembly of macromolecular complexes. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL13821

41 Samples

Download data: TXT

(Submitter supplied) RNA molecule fold into three dimensional structures in order to fill important roles in the cell such as translation and post-transcriptional regulation. These three dimensional structures, in turn, depend on the pattern of hydrogen bonds between ribonucleotides. We employ a technique based on high throughput RNA Sequencing (RNA-Seq) to uncover this patter on a transcriptome wide scale.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL11154

4 Samples

Download data: BW

(Submitter supplied) A comparative assessment between both technologies, RNASeq and microarrays to detect differential expression in Arabidopsis transcriptome. The sequencing approach use High-throughput sequencing on different Solexa technologies (GAII,HiSeq2000 multiplex or not) Wild type samples were analyzed from 2 tissus (flower buds and leaves) which have a very contrasted transcriptomic profile (i.e very high number of genes differentially expressed).

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL13222 GPL11221

11 Samples

Download data: FA, TXT

(Submitter supplied) cat-seq - bf_vs_f - A comparative assessment of the Arabidopsis sequencing approach High-throughput sequencing cDNA GAII or HiSeq2000 sequenceur (technology Solexa) and data on CATMA array hybridation (version 6). These different characteristics will be studied through the analysis of control samples but also samples from mutants in genes coding for cytosolic or nuclear PPR proteins - The two selected samples are the flower buds and leaves of Arabidopsis. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL15719

4 Samples

Download data: PAIR

(Submitter supplied) Here we present dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq), which encodes DMS modifications as mismatches using a thermostable group II intron reverse transcriptase (TGIRT). DMS-MaPseq yields a high signal-to-noise ratio, can report multiple structural features for each molecule, and allows genome-wide studies as well as focused investigations of low abundance RNAs. We apply DMS-MaPseq to Drosophila melanogaster ovaries—the first experimental analysis of RNA structure in an animal tissue—and demonstrate its utility in the discovery of a functional RNA structure involved in the non-canonical GUG translation initiation of the human FXR2 mRNA. more...

Organism:

Drosophila melanogaster; Saccharomyces cerevisiae; Homo sapiens

Type:

Expression profiling by high throughput sequencing

10 related Platforms

29 Samples

Download data: TXT

(Submitter supplied) Proof-of-concept of a new method involving the limited digestion and subsequent ligation of intramolecular RNA structures in situ followed by deep sequencing

Organism:

Saccharomyces cerevisiae; Homo sapiens

Type:

Other

5 related Platforms

13 Samples

Download data: TXT

(Submitter supplied) New regulatory roles continue to emerge for both natural and engineered noncoding RNAs, many of which have specific secondary and tertiary structures essential to their function. Thus there is a growing need to develop technologies that enable rapid characterization of structural features within complex RNA populations. We have developed a high-throughput technique, SHAPE-Seq, that can simultaneously measure quantitative, single nucleotide-resolution secondary and tertiary structural information for hundreds of RNA molecules of arbitrary sequence. more...

Organism:

Bacillus subtilis

Type:

Other

Platform:

GPL14181

2 Samples

Download data: SAM

(Submitter supplied) To accelerate previous RNA structure probing approaches, which focus on analyzing one RNA sequence at a time, we have developed FragSeq, a high-throughput RNA structure probing method that uses high-throughput RNA sequencing to identify single-stranded RNA (ssRNA) regions from fragments generated by nuclease P1, which is specific for single-stranded nucleic acids. In the accompanying study, we show that we can accurately and simultaneously map ssRNA regions in multiple non-coding RNAs with known structure in experiments probing the entire mouse nuclear transcriptome. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL9318

10 Samples

Download data: BED, TXT

(Submitter supplied) Gene fusions and chimeric transcripts occur frequently in cancers and in some cases drive the development of the disease. An accurate detection of these events is crucial for cancer research and in a long-term perspective could be applied for personalized therapy. RNA-seq technology has been established as an efficient approach to investigate transcriptomes and search for gene fusions and chimeric transcripts on a genome-wide scale. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

4 Samples

Download data: TXT

(Submitter supplied) We describe a new method enabling the global-scale mapping of RNA-RNA duplexes cross-linked in vivo, ‘LIGation of interacting RNA followed by high-throughput Sequencing’ (LIGR-Seq). Applying this method in human cells reveals a remarkable landscape of new RNA-RNA interactions involving all major classes of ncRNA, and mRNA. LIGR-Seq data reveal unexpected interactions between small nucleolar (sno)RNAs and mRNAs, including interactions involving the orphan C/D box snoRNA, SNORD83B, that control steady-state levels of its target mRNAs. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL18573

8 Samples

Download data: TXT

(Submitter supplied) Several classes of small RNAs have been described, however to molecularly profile them require large numbers of cells. Here, we developed a method for single-cell small-RNA sequencing that we applied to naïve and primed human embryonic stem cells and to cancer cells. Single-cell profiling of microRNAs and fragments of tRNAs and snoRNAs revealed that, in particular, microRNAs have unrecognized potential to separate cell types and states.

Organism:

Homo sapiens; synthetic construct

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL11154 GPL15228

539 Samples

Download data: TXT

(Submitter supplied) We present DRUID (for Determination of Rates Using Intron Dynamics), a computational pipeline, for determining mRNA stability transcriptome-wide uses metabolic labeling and approach-to-equilibrium kinetics. Our pipeline uses endogenous introns to normalize time course data and yields more reproducible half-lives than other methods, even with datasets that were otherwise unusable. DRUID can handle datasets from a variety of organisms, spanning yeast to humans.

Organism:

Saccharomyces cerevisiae; Homo sapiens; Mus musculus; Caenorhabditis elegans; Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

4 related Platforms

66 Samples

Download data: CSV

(Submitter supplied) We applied ribosome profiling and RNA sequencing to examine gene expression regulation during oncogenic cell transformation. One model involves normal mammary epithelial cells (MCF10A) containing ER-Src. Treatment of such cells with tamoxifen rapidly induces Src, thereby making it possible to kinetically follow the transition between normal and transformed cells. The other model consists of three isogenic cell lines derived from primary fibroblasts in a serial manner (Hahn et al., 1999). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL11154

36 Samples

Download data: TXT

(Submitter supplied) In vivo probing of the Yersinia pseudotuberculosis YPIII transcriptome at 25 °C and 37 °C

Organism:

Yersinia pseudotuberculosis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27774

4 Samples

Download data: TAB

(Submitter supplied) We develop an enhanced MaP protocol based on MarathonRT and bioinformatic optimizations which enables robust DMS probing of all four RNA nucleotides within living cells. We demonstrate this on RNA from E. coli and HEK293 cell lines.

Organism:

Homo sapiens; Escherichia coli

Type:

Other

Platforms:

GPL15520 GPL16085

73 Samples

Download data: TAR

(Submitter supplied) We present a combined experimental/computational technology to reveal a catalogue of functional regulatory elements embedded in 3’UTRs of human transcripts. We used a bidirectional reporter system coupled with flow cytometry and high-throughput sequencing to measure the effect of short, non-coding vertebrate-conserved RNA sequences on transcript stability and translation. Information-theoretic motif analysis of the resulting sequence-to-gene-expression mapping revealed linear and structural RNA cis-regulatory elements that positively and negatively modulate the post-transcriptional fates of human transcripts.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL11154

14 Samples

Download data: CSV

(Submitter supplied) The measurement of RNA abundance derived from massively parallel sequencing experiments is an essential technique. Methods that reduce ribosomal RNA levels are usually required prior to sequencing library construction because ribosomal RNA typically comprises >90% of the total RNA molecules in a sample. For some experiments, ribosomal RNA depletion is favored over poly(A) selection because it offers a more inclusive representation of the transcriptome. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19132

12 Samples

Download data: CSV