GEO DataSets

(Submitter supplied) To experimentally-validate the non-coding status of annotated lncRNAs, we performed ribosome profiling over a developmental timecourse that matched our previously-published (Pauli et al. 2012) developmental transcriptome. We find that many previously-annotated lncRNAs appear to be translated, but in a pattern more akin to 5' leaders of coding genes.

Organism:

Danio rerio

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL14875

8 Samples

Download data: BW, GTF, TXT

(Submitter supplied) Long non-coding RNAs (lncRNAs) comprise a diverse class of transcripts that structurally resemble mRNAs but do not encode proteins. Recent genome-wide studies in human and mouse have annotated lncRNAs expressed in cell lines and adult tissues, but a systematic analysis of lncRNAs expressed during vertebrate embryogenesis has been elusive. To identify lncRNAs with potential functions in vertebrate embryogenesis, we performed a time series of RNA-Seq experiments at eight stages during early zebrafish development. more...

Organism:

Danio rerio

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL9319 GPL14875

17 Samples

Download data

(Submitter supplied) Ribosome profiling with translation inhibitors reveals pervasive translation in murine ES cells.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL18061

10 Samples

Download data: TXT

(Submitter supplied) Post-transcriptional gene regulation plays a significant role in the response to Pi starvation. Here, we utilized advances in next-generation sequencing technology to examine changes in transcriptional control, RNA association with translating ribosomes in 14-day-old Arabidopsis seedlings subjected to 7 days of Pi starvation.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL13222

7 Samples

Download data: TXT

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

Organism:

Danio rerio

Type:

Non-coding RNA profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL14875 GPL9319

20 Samples

Download data

(Submitter supplied) Long non-coding RNAs (lncRNAs) comprise a diverse class of transcripts that structurally resemble mRNAs but do not encode proteins. Recent genome-wide studies in human and mouse have annotated lncRNAs expressed in cell lines and adult tissues, but a systematic analysis of lncRNAs expressed during vertebrate embryogenesis has been elusive. To identify lncRNAs with potential functions in vertebrate embryogenesis, we performed a time series of RNA-Seq experiments at eight stages during early zebrafish development. more...

Organism:

Danio rerio

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL14875

3 Samples

Download data

(Submitter supplied) A vast portion of the mammalian genome is transcribed as long non-coding RNAs (lncRNAs) acting in the cytoplasm with largely unknown functions. Surprisingly, lncRNAs have been shown to interact with ribosomes, encode uncharacterized proteins, or act as ribosome sponges. These functions still remain mostly undetected and understudied owing to the lack of efficient tools for genome-wide simultaneous identification of ribosome-associated lncRNAs and peptide-producing lncRNAs. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL17021

5 Samples

Download data: TXT

(Submitter supplied) Long noncoding RNAs (lncRNAs) are transcripts longer than 200 nucleotides but lacking canonical coding sequences. Apparently unable to produce peptides, lncRNA function seems to only involve RNA sequence and structure. Here, we exhaustively detect in-vivo translation of small open reading frames (small ORFs) within lncRNAs using Ribosomal profiling during Drosophila melanogaster embryogenesis. We show that around 30% of lncRNAs contain small ORFs engaged by ribosomes, leading to regulated translation of 100 to 300 micropeptides. more...

Organism:

Drosophila melanogaster

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL30203

9 Samples

Download data: XLSX

(Submitter supplied) Thousands of lncRNAs have been found in zebrafish embryogenesis and adult tissues, but their identification and organogenesis-related function have not elucidated. In this study, high-throughput sequencing was performed at three different organogenesis stages of zebrafish embryos, which were important for zebrafish muscle development. The three stages were 10 hpf (hours post fertilization) (T1), 24 hpf (T2) and 36 hpf (T3).

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30277

6 Samples

Download data: XLS

(Submitter supplied) Y box-binding protein 1 (Ybx1) is critical for embryogenesis and organogenesis. In zebrafish, we identify Ybx1 is predominantly expressed in the enterocytes of intestine in day5 larvae, whereas its immediately degradation driven by ubiquitination on day6. Here we show the maternal lethality with cardiac edema in ybx1-/- larvae, and postnatal larval lethality exhibited in ybx1-/- larvae within the death window from 10dpf to 20dpf. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18413

9 Samples

Download data: CSV, TAB

(Submitter supplied) We designed a custom microarray to profile the expression and used it to measure the expression of 9929 human lncRNAs manually-annotated by the GENCODE group as part of the ENCODE consortium.

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL15094

31 Samples

Download data: TXT

(Submitter supplied) This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Carrie Davis mailto:[email protected] (experimental), Alex Dobin mailto:[email protected] (computational), Felix Schlesinger mailto:[email protected] (computational), Tom Gingeras mailto:[email protected] (primary investigator), and Roderic Guigo's group mailto:[email protected] at the CRG). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:[email protected]). These tracks were generate by the ENCODE Consortium. They contain information about human RNAs > 200 nucleotides in length obtained as short reads off the Illumina GAIIx platform. Data is available from biological replicates of several cell lines. In addition to profiling Poly-A+ and Poly-A- RNA from whole cells, we have also gather data from various subcellular compartments. In many cases, there are Cap Analysis of Gene Expression (CAGE, RIKEN Institute) and Small RNA-Seq (<200 nucleotides, CSHL) and Pair-End di-TAG-RNA (PET-RNA, Genome Institute of Singapore) datasets available from the same biological replicates. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL11154 GPL9115 GPL10999

99 Samples

Download data: BAM, BEDRNAELEMENTS, BIGWIG, GFF, GTF, PDF, TXT

(Submitter supplied) This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Jonathan Preall [email protected] (Generation 0 Data from Hannon Lab), Carrie Davis [email protected] (experimental), Alex Dobin [email protected] (computational), Wei Lin [email protected] (computational), Tom Gingeras [email protected] (primary investigator)). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:[email protected]). more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL10999 GPL11154 GPL9052

87 Samples

Download data: BAM, BEDRNAELEMENTS, BIGWIG, GTF, PDF, TXT

(Submitter supplied) Recent advances in transcriptome sequencing have enabled the discovery of thousands of long non-coding RNAs (lncRNAs) across many species. Though several lncRNAs have been shown to play important roles in diverse biological processes, the functions and mechanisms of most lncRNAs remain unknown. Two significant obstacles lie between transcriptome sequencing and functional characterization of lncRNAs: identifying truly non-coding genes from de novo reconstructed transcriptomes, and prioritizing the hundreds of resulting putative lncRNAs for downstream experimental interrogation. more...

Organism:

Mus musculus castaneus; Rattus norvegicus; Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

4 related Platforms

9 Samples

Download data: TXT, WIG

(Submitter supplied) Ribosome profiling suggests that ribosomes occupy many regions of the transcriptome thought to be non-coding, including 5' UTRs and lncRNAs. Apparent ribosome footprints outside of protein-coding regions raise the possibility of artifacts unrelated to translation, particularly when they occupy multiple, overlapping open reading frames (ORFs). Here we show hallmarks of translation in these footprints: co-purification with the large ribosomal subunit, response to drugs targeting elongation, trinucleotide periodicity, and initiation at early AUGs. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL13112 GPL11154

4 Samples

Download data: TXT

(Submitter supplied) Transcriptomic data for 59 single embryos and larvae samples of the sponge Amphimedon queenslandica

Organism:

Amphimedon queenslandica

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18214

59 Samples

Download data: CSV, GTF

(Submitter supplied) The expression of long non-coding RNAs is highly enriched in the human nervous system. However, the function of neuronal lncRNAs in the cytoplasm and their potential translation remains poorly understood. Here we performed Poly-Ribo-Seq to understand the interaction of lncRNAs with the translation machinery and the functional consequences during neuronal differentiation of human SH-SH5Y cells. We discovered 237 cytoplasmic lncRNAs upregulated during early neuronal differentiation, 58-70% of which are associated with polysome translation complexes. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL18573

18 Samples

Download data: BED, XLSX

(Submitter supplied) We performed ribosome profiling to assess the translation elongation on translating RNA in HBE, A549, and H1299. We detected the new proteins in the cells.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

3 Samples

Download data: XLSX

(Submitter supplied) The ability to sequence genomes has far outstripped approaches for deciphering the information they encode. Here we present a suite of techniques, based on ribosome profiling (the deep-sequencing of ribosome-protected mRNA fragments), to provide genome-wide maps of protein synthesis as well as a pulse-chase strategy for determining rates of translation elongation. We exploit the propensity of harringtonine to cause ribosomes to accumulate at sites of translation initiation together with a machine learning algorithm to define protein products systematically. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL9250 GPL13112

18 Samples

Download data: TXT

(Submitter supplied) The EZH2 histone methyltransferase is highly expressed in germinal center (GC) B-cells and targeted by somatic mutations in B-cell lymphomas. Here we find that EZH2 deletion or pharmacologic inhibition suppresses GC formation and functions in mice. EZH2 represses proliferation checkpoint genes and helps establish bivalent chromatin domains at key regulatory loci to transiently suppress GC B-cell differentiation. more...

Organism:

Homo sapiens; Mus musculus

Type:

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

Platforms:

GPL13112 GPL10999 GPL11154

61 Samples

Download data: BED, TXT, WIG