GEO DataSets

(Submitter supplied) To identificate long noncoding RNAs in maize, we profiled transcriptome of shoots and roots using non-directional paired-end RNA-seq based on poly(A) selection.

Organism:

Zea mays subsp. mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17914

2 Samples

Download data: TXT

(Submitter supplied) To identificate long noncoding RNAs in rice, we profiled transcriptome of various organs at different developmental stages using stranded single-end RNA-seq based on poly(A) selection.

Organism:

Oryza sativa Japonica Group

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18525

8 Samples

Download data: TXT

(Submitter supplied) To identificate long noncoding RNAs in rice, we profiled transcriptome of various organs at different developmental stages using nondirectional paired-end RNA-seq based on poly(A) selection.

Organism:

Oryza sativa Japonica Group

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13834

8 Samples

Download data: TXT

(Submitter supplied) To identificate long noncoding RNAs in maize, we profiled transcriptome of shoots and roots using stranded single-end RNA-seq based on poly(A) selection.

Organism:

Zea mays subsp. mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18523

2 Samples

Download data: TXT

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

Organism:

Arabidopsis thaliana; Oryza sativa Japonica Group; Zea mays subsp. mays

Type:

Expression profiling by array

Platforms:

GPL18525 GPL18523 GPL17639

8 Samples

Download data: GTF

(Submitter supplied) Long intergenic noncoding RNAs (lincRNAs) are widespread in cellular organisms, however, the origins and functions of many lincRNAs remain to be explored. Transposable elements (TEs) are widely distributed in many eukaryotic genomes, and often account for large fractions of plant and animal genomes. By using strand-specific RNA sequencing, we profiled the expression patterns of lincRNAs in Arabidopsis, rice and maize, and identified TE-associated lincRNAs (TE-lincRNAs). more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17639

4 Samples

Download data: TXT

(Submitter supplied) Long intergenic noncoding RNAs (lincRNAs) are widespread in cellular organisms, however, the origins and functions of many lincRNAs remain to be explored. Transposable elements (TEs) are widely distributed in many eukaryotic genomes, and often account for large fractions of plant and animal genomes. By using strand-specific RNA sequencing, we profiled the expression patterns of lincRNAs in Arabidopsis, rice and maize, and identified TE-associated lincRNAs (TE-lincRNAs). more...

Organism:

Zea mays subsp. mays; Arabidopsis thaliana; Oryza sativa Japonica Group

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL17639 GPL18523 GPL18525

4 Samples

Download data: GTF

(Submitter supplied) The Polycomb Repressive Complex 2 (PRC2) represses the transcriptional activity of target genes through trimethylation of Lysine 27 of Histone H3. The functions of the plant PRC2 have been chiefly described in Arabidopsis but specific PRC2 functions in other plant species, especially the cereals, are still largely unknown. Here we utilize ChIP-seq data in the analysis of protein coding and non-coding RNAs in early WT panicles of rice.

Organism:

Oryza sativa

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13160

6 Samples

Download data: WIG

(Submitter supplied) We performed poly(A)+, poly(A)-, nuclear, small RNA-seq analysis on Oryza sativa japonica WT plants.

Organism:

Oryza sativa Japonica Group

Type:

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

Platforms:

GPL18525 GPL13834

38 Samples

Download data: XLSX

(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; Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing

4 related Platforms

9 Samples

Download data: TXT, WIG

(Submitter supplied) We present the NEUTRA database, a catalogue of the Neurospora transcriptome, based on RNA-Seq, RNAPII ChIP-Seq and ribosome fractionation studies. The database also includes genome-wide binding sites of transcription factors involved in regulation of circadian gene expression. In a comprehensive analysis of the transcriptome we identified and characterized 1478 long intergenic non-coding RNAs (lincRNAs) and 1056 natural antisense transcripts. more...

Organism:

Neurospora crassa

Type:

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

Platforms:

GPL16164 GPL20705 GPL17918

8 Samples

Download data: BIGWIG, 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) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

16 Samples

Download data

(Submitter supplied) Osteoarthritis (OA) is the most prevalent joint disease with the typifying feature being the progressive degradation of articular cartilage during disease progression. In this study we used whole transcriptome RNA-seq as a tool to compare gene expression changes between age-matched osteoarthritic human hip OA cartilage (n=10) compared to control (neck of femur fracture) cartilage (n=6) [GSE107308]. All cartilage was from patients undergoing acetabulofemoral joint replacement. Cartilage RNA was isolated from cartilage within 2 hr of joint replacement surgery, mRNA was polyA purified and transcript expression was analysed using 78-base paired-end sequencing generating on average 28 million reads/sample sequencing. The data shows excellent correlation with our previous microarray data but identifies significantly more differentially expressed transcripts plus novel transcript variants, several of which have been validated by real-time qPCR. Our work sheds further light on chondrocyte transcriptome expression and highlights gene expression changes and novel transcripts potentially important in osteoarthritis progression

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

10 Samples

Download data: CSV

(Submitter supplied) Long non-coding RNAs (lncRNAs) are expressed in a highly tissue-specific manner where they function in various aspects of cell biology, often as key regulators of gene expression. In this study we established a role for lncRNAs in chondrocyte differentiation. Using RNA sequencing we identified a human articular chondrocyte repertoire of lncRNAs from normal hip cartilage donated by neck of femur fracture patients. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL16791

6 Samples

Download data: XLSX

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

Organism:

Sus scrofa

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platform:

GPL11429

2 Samples

Download data: WIG, XLS

(Submitter supplied) Somatic cell nuclear transfer has brought considerable chances to breed excellent breeds and protect endanger animals, while also produced numerous fail embryos and abnormal individuals due to inefficient epigenetic modification at the same time. To understand some mechanisms of abnormal piglets with phenotypes such as macroglossia, standing and walking disabilities in our study and find some differences between abnormal piglets and conventionally bred normal piglets, DNA methylation profile and genome-wide gene expression were conducted in two groups, using methylated DNA immunoprecipitation binding highthroughput sequencing (MeDIP-Seq) and RNA sequencing(RNA-Seq). more...

Organism:

Sus scrofa

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL11429

1 Sample

Download data: WIG

(Submitter supplied) Somatic cell nuclear transfer has brought considerable chances to breed excellent breeds and protect endanger animals, while also produced numerous fail embryos and abnormal individuals due to inefficient epigenetic modification at the same time. To understand some mechanisms of abnormal piglets with phenotypes such as macroglossia, standing and walking disabilities in our study and find some differences between abnormal piglets and conventionally bred normal piglets, DNA methylation profile and genome-wide gene expression were conducted in two groups, using methylated DNA immunoprecipitation binding highthroughput sequencing (MeDIP-Seq) and RNA sequencing(RNA-Seq). more...

Organism:

Sus scrofa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11429

1 Sample

Download data: XLS

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

Organism:

Sus scrofa

Type:

Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platform:

GPL11429

4 Samples

Download data: TXT, WIG

(Submitter supplied) Backgroud:Epigenetic modifications (especially altered DNA methylation) resulting in altered gene expression may be one reason for development failure or the abnormality of the cloned animals, but the underlying mechanism of the abnormal phenotype in the cloned piglets remains unrevealed. Some cloned piglets in our study showed abnormal phenotypes such as big tongue (longer and thicker), limp, and exomphalos, which is similar to the human BWS syndrome. more...

Organism:

Sus scrofa

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL11429

2 Samples

Download data: WIG