GEO DataSets

(Submitter supplied) Deep sequencing of transcriptomes allows quantitative and qualitative analysis of many RNA species in a sample, with parallel comparison of expression levels, splicing variants, natural antisense transcripts, RNA editing and transcriptional start and stop sites the ideal goal. By computational modeling, we show how libraries of multiple insert sizes combined with strand-specific, paired-end (SS-PE) sequencing can increase the information gained on alternative splicing, especially in higher eukaryotes. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13776

4 Samples

Download data: BED

(Submitter supplied) Background:Alternative splicing and isoform level expression profiling is an emerging field of interest within genomics. Splicing sensitive microarrays, with probes targeted to individual exons or exon-junctions, are becoming increasingly popular as a tool capable of both expression profiling and finer scale isoform detection. Despite their intuitive appeal, relatively little is known about the performance of such tools, particularly in comparison with more traditional 3’ targeted microarrays. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL5175 GPL5188

40 Samples

Download data: CEL

(Submitter supplied) Background:Alternative splicing and isoform level expression profiling is an emerging field of interest within genomics. Splicing sensitive microarrays, with probes targeted to individual exons or exon-junctions, are becoming increasingly popular as a tool capable of both expression profiling and finer scale isoform detection. Despite their intuitive appeal, relatively little is known about the performance of such tools, particularly in comparison with more traditional 3’ targeted microarrays. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5188

20 Samples

Download data: CEL

(Submitter supplied) Background:Alternative splicing and isoform level expression profiling is an emerging field of interest within genomics. Splicing sensitive microarrays, with probes targeted to individual exons or exon-junctions, are becoming increasingly popular as a tool capable of both expression profiling and finer scale isoform detection. Despite their intuitive appeal, relatively little is known about the performance of such tools, particularly in comparison with more traditional 3’ targeted microarrays. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5175

20 Samples

Download data: CEL

(Submitter supplied) We carried out the first analysis of alternative splicing complexity in human tissues using mRNA-Seq data. New splice junctions were detected in 20% of multiexon genes, many of which are tissue specific. By combining mRNA-Seq and EST-cDNA sequence data, we estimate that transcripts from 95% of multiexon genes undergo alternative splicing and that there are 100,000 intermediate- to high-abundance alternative splicing events in major human tissues. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9052

6 Samples

Download data: TXT

(Submitter supplied) Neuromodulatory cells transduce environmental information into long lasting behavioral responses. However, the mechanisms governing how defined neuronal cell types influence behavioral plasticity are difficult to characterize. Here we adapted the Translating Ribosome Affinity Purification (TRAP) approach in C. elegans to profile ribosome-associated mRNAs from three major tissues and the neuromodulatory dopaminergic and serotonergic cells. more...

Organism:

Caenorhabditis elegans

Type:

Other

Platform:

GPL13657

20 Samples

Download data: XLSX

(Submitter supplied) Direct pairwise comparison of Mouse ES and Mouse Embryonic Day 4 cells Keywords: Direct pairwise comparison

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6481

2 Samples

Download data: TXT

(Submitter supplied) The number of annotated protein coding genes in the genome of Caenorhabditis elegans is similar to that of other animals, but the extent of its non-protein coding transcriptome remains unknown. Expression profiling on whole genome tiling microarrays applied to a mixed stage C. elegans population verified the expression of 71% of all annotated exons. Only a small fraction (11 %) of the polyadenylated transcription is non-annotated, and appears to consist of approximately 3200 missed or alternative exons and 7800 small transcripts of unknown function (TUFs). more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by genome tiling array

Platform:

GPL5634

3 Samples

Download data: BAR, CEL, TXT

(Submitter supplied) RNA-sequencing was conducted to profile the transcriptome of the post-ischemic mouse cortex at multiple reperfusion time-points. RNA was isolated from sham and middle cerebral artery occlusion (MCAO)-operated mice at different reperfusion time points (6 h, 12 h or 24 h; three independent biological replicates per group), converted into cDNA libraries, and used for Illumina deep sequencing on a NexSeq500 instrument. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

12 Samples

Download data: GTF

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

Organism:

Sus scrofa

Type:

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

Platforms:

GPL10945 GPL11429

12 Samples

Download data: TXT

(Submitter supplied) Pig is an important animal model for human obesity and diseases. However, the complexity of the porcine transcriptome is not yet fully elucidated. Here we have used massively parallel high-throughput sequencing of cDNA (RNA-Seq) to generate a high-resolution map of the porcine transcriptome and miRNA in liver (LI), longissimus dorsi (LD) and abdominal fat (AF) from an F2 female full-sib pair with extreme phenotypes in growth and fat deposit. more...

Organism:

Sus scrofa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11429

6 Samples

Download data: TXT, XML

(Submitter supplied) Pig is the important animal model for human obesity and diseases. However, the complexity of the porcine transcriptome is not yet fully elucidated. Here we have used massively parallel high-throughput sequencing of cDNA (RNA-seq) to generate a high-resolution map of the porcine miRNA in liver (LI), longissimus dorsi (LD) and abdominal fat (AF) from a F2 female full-sib pair with extreme phenotypes on growth and fat deposit. more...

Organism:

Sus scrofa

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL10945

6 Samples

Download data: TXT

(Submitter supplied) Alternative splicing (AS) plays a crucial role in the diversification of gene function and regulation. Consequently, the systematic identification and characterization of temporally regulated splice variants is of critical importance to understanding animal development. We have used high-throughput RNA sequencing and microarray profiling to analyze AS in C. elegans across various stages of development. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by array

Platform:

GPL11296

5 Samples

Download data: TXT

(Submitter supplied) The comparative advantages of RNA-Seq and microarrays in transcriptome profiling were evaluated in the context of a comprehensive study design. Gene expression data from Illumina RNA-Seq and Affymetrix microarrays were obtained from livers of rats exposed to 27 agents that comprised of seven modes of action (MOAs); they were split into training and test sets and verified with real time PCR.

Organism:

Rattus norvegicus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17116 GPL14844

116 Samples

Download data: PDF, TXT

(Submitter supplied) The comparative advantages of RNA-Seq and microarrays in transcriptome profiling were evaluated in the context of a comprehensive study design. Gene expression data from Illumina RNA-Seq and Affymetrix microarrays were obtained from livers of rats exposed to 27 agents that comprised of seven modes of action (MOAs); they were split into training and test sets and verified with real time PCR. contributor: DrugMatrix, National Toxicology program (NTP)

Organism:

Rattus norvegicus

Type:

Expression profiling by array

Platform:

GPL1355

105 Samples

Download data: CEL

(Submitter supplied) To explore the methylome differences of swine breeds with different traits of commercial interest, we sampled liver tissues from a Chinese well-known elite native breed of Enshi black pig, a Large White pig, and a Chinese wild boar living within the same environment at the same daya-old (90d).

Organism:

Sus scrofa

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL10945

3 Samples

Download data: TXT

(Submitter supplied) We developed a new method of preparing libraries for strand-specific RNA sequencing (ssRNA-Seq). It employs Direct Ligation of Adaptors to First-strand cDNA (DLAF). We compared ssRNA-Seq libraries prepared using either the DLAF and dUTP methods from mouse embryonic stem cells (mES) and libraries were sequenced from one end or both ends. We also conducted a comparison of ssRNA-Seq libraries prepared using DLAF and ScriptSeq v2 kit (Epicenter) from mouse embryonic cortex (mECx).

Organism:

Mus musculus

Type:

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

Platform:

GPL13112

32 Samples

Download data

(Submitter supplied) We have developed a single-worm RNA-seq method to effectively profile gene expression in individual C. elegans and applied this method to study C. elegans responses to pathogen infection.

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18245

20 Samples

Download data: CSV

(Submitter supplied) Caenorhabditis elegans is a major eukaryotic experimental system employed to unravel a broad range of cellular and biological processes. Despite the many advantages of C. elegans, biochemical approaches to study tissue-specific gene expression in postembryonic stages are challenging. Here we report a novel experimental approach that enables the efficient determination of tissue-enriched transcriptomes by rapidly releasing nuclei from major tissues of postembryonic animals followed by fluorescence-activated nuclei sorting (FANS). more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13776

2 Samples

Download data: BED

(Submitter supplied) RNA-seq was used to generate an extensive map of the Drosophila melanogaster transcriptome by broad sampling of 10 developmental stages. In total, 142.2 million uniquely mapped 64-100bp paired-end reads were generated on the Illumina GA II yielding 356x sequencing coverage. More than 95% of FlyBase genes and 90% of splicing junctions were observed. Modifications to 30% of FlyBase gene models were made by extension of untranslated regions, inclusion of novel exons, and identification of novel splicing events. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9061

12 Samples

Download data: PSLX, WIG