GEO DataSets

(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

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(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

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(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

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(Submitter supplied) Pancreatic ductal adenocarcinoma (PDAC) is known by its aggressiveness and lack of effective therapeutic options. Thus, improvement in current knowledge of molecular changes associated with pancreatic cancer is urgently needed to explore novel venues of diagnostics and treatment of this dismal disease. While there is mounting evidence that long noncoding RNAs (ncRNAs) transcribed from intronic and intergenic regions of the human genome may play different roles in the regulation of gene expression in normal and cancer cells, their expression pattern and biological relevance in pancreatic cancer is currently unknown. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL3985

38 Samples

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(Submitter supplied) We sequenced mRNA from embryonic heart of zebrafish larvae 4 days post fertilization, adult heart of 6-month-old WIK fish, and adult muscle of adult fish consisting of both fast-twitch and slow-twitch fibers.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14875

9 Samples

Download data: DIFF, TXT

(Submitter supplied) Thousands of large intervening non-coding RNAs (lincRNAs) have been identified in mammals. To better understand the evolution and functions of these enigmatic RNAs, we used chromatin marks, poly(A)-site mapping and RNA-Seq data, to identify more than 550 distinct lincRNAs in zebrafish. Although these shared many characteristics with mammalian lincRNAs, only 29 had detectable sequence similarity with putative mammalian orthologs, typically restricted to a single short region of high conservation. more...

Organism:

Danio rerio

Type:

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

Platform:

GPL9319

16 Samples

Download data: BAM, BED, BW

(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) 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) LncRNA and mRNA expression profiles in five mouse tissues like brain, heart, kidney, liver and testis and three germ cell-related cell lines such as F9, GC-1 and GC-2

Organism:

Mus musculus

Type:

Non-coding RNA profiling by array

Platform:

GPL24126

24 Samples

Download data: TXT

(Submitter supplied) We used this array as described in Babak, Blencowe, anf Hughes (2005), to screen novel ncRNA predictions. See author supplementary data for more detailed probe information. Keywords: parallel sample

Organism:

Mus musculus

Type:

Non-coding RNA profiling by array

Platform:

GPL1896

16 Samples

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(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) DNA methylation is a dynamic process through which specific chromatin modifications can be stably transmitted from parent to daughter cells. A large body of work has suggested that DNA methylation influences gene expression by silencing gene promoters. However, these conclusions were drawn from data focused mostly on promoter regions. With regards to the entire genome, it is unclear how methylation and gene transcription patterns are related during vertebrate development. more...

Organism:

Danio rerio

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL14875

11 Samples

Download data: BED

(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) Methods: RNA profiles of 12 tissues were generated by deep sequencing using Illumina HiSeq 2000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. Results: This work has focused on identification of non-coding RNAs expressed in human tissues. We have identified a set of non-coding RNAs that are both expressed and conserved, as described in the manuscript accompagnying this work.

Organism:

Homo sapiens

Type:

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

Platform:

GPL11154

12 Samples

Download data: GTF

(Submitter supplied) Thousands of novel non-coding RNAs (ncRNA) has been identified in recent years. Only few have been functionally characterized and it is thus unclear which and how many are functional. Here, we characterize expression of ncRNAs in twelve human tissues using a costum designed microarray. The study serve as a first analysis to gain further insight into expression behavior of a broad and comprehensive collection of ncRNAs and pinpoint a set of ncRNAs we believe are functional.

Organism:

Homo sapiens

Type:

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

Platform:

GPL16228

36 Samples

Download data: XYS

(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) We compared the gene expression profiles of prostate carcinoma cells, LNCaP, treated or not with an inhibitor of RNA Polymerase II (RNAP II), alpha-amanitin. These experiments pointed to a fraction of intronic messages that seems to be insensitive to alpha-amanitin or up-regulated in cells with blocked RNAP II transcription. Keywords: RNA-polymerase II inhibition experiments

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL4051

8 Samples

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(Submitter supplied) The experiments described here aim to generate a set of gene expression profiles from prostate, liver and kidney tissues using a custom-designed oligo-array platform enriched in messages that map to intronic regions of known human genes. Expression profiles of these tissues were combined in order to find a tissue-specific signature of intronic transcripts. Keywords: Tissue-specific, Intronic transcripts

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL4051

12 Samples

Download data