GEO DataSets

(Submitter supplied) In Alternative Expression Analysis (ALEXA)-Seq we developed a method to analyze massively parallel RNA sequence data to catalogue transcripts and assess differential and alternative expression of known and predicted messenger RNA (mRNA) isoforms in cells and tissues. As proof-of-principle, we applied the approach to a comparison of fluorouracil responsive and non-responsive human colorectal cancer cell lines. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9115

2 Samples

Download data: TXT

(Submitter supplied) In order to compare previously generated transcriptome data by second generation sequencing (Sultan et al. Science 2008), we interrogated the human Affymetrix exon chips 1.0ST using the same source of material.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL7557

2 Samples

Download data: CEL

(Submitter supplied) Transcriptome of HEK and B cells were analyzed by microarray and RNA-Seq parallely. Both platforms were then compared in terms of sensitivity. To assess whether values were a reliable indicator of gene activity, we correlated these values with hypophosphorylated RNA polymerase II (PolIIa) occupancy, used as a landmark of transcription initiation. For HEK, we identified PolIIa islands by chromatin immunoprecipitation and sequencing (ChIP-Seq).

Organism:

Homo sapiens

Type:

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

Platforms:

GPL6104 GPL9052

11 Samples

Download data: TXT

(Submitter supplied) Transcriptional profiling of head tissue of Drosophila Darkener of apricot (Doa) and found in neurons (fne) mutants was performed by RNA-SEQ in females and males. The transcriptional and post-transcriptional targets of these genes, which are involved in regulation by several processes including splicing and mRNA stability, are examined and compared to wild-type.

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL13304 GPL11203

24 Samples

Download data: BEDGRAPH

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome variation profiling by genome tiling array

Platforms:

GPL4091 GPL9052

14 Samples

Download data: TXT

(Submitter supplied) Prostate adenocarcinoma and matched adjacent normal samples were profiled by deep transcriptional sequencing to analyze transcription-induced chimeras and gene fusions. Reference samples from the MAQC and brain and universal reference libraries were also sequenced.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9052

8 Samples

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(Submitter supplied) Prostate adenocarcinoma and matched adjacent normal samples were profiled for copy number with the Agilent 244A CGH Array to support a study of deep transcriptional sequencing on these samples.

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL4091

6 Samples

Download data: TXT

(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) BACKGROUND: Breast cancer is the second most frequent type of cancer affecting women. We are increasingly aware that changes in mRNA splicing are associated with various characteristics of cancer. The most deadly aspect of cancer is metastasis, the process by which cancer spreads from the primary tumor to distant organs. However, little is known specifically about the involvement of alternative splicing in the formation of macroscopic metastases. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platforms:

GPL6193 GPL6096

24 Samples

Download data: CEL, TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by array; Expression profiling by high throughput sequencing

Platforms:

GPL17585 GPL11154

36 Samples

Download data: CEL

(Submitter supplied) Here we compared the performance of Affymetrix HTA 2.0 microarray and Illumina 2000 RNA-sequencing techniques on the clinical samples collected from patients with lung squamous cell carcinoma.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL17585

18 Samples

Download data: CEL

(Submitter supplied) Here we compared the performance of Affymetrix HTA 2.0 microarray and Illumina 2000 RNA-sequencing techniques on the clinical samples collected from patients with lung squamous cell carcinoma.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

18 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by array; Expression profiling by high throughput sequencing

Platforms:

GPL11154 GPL24082

60 Samples

Download data: CEL

(Submitter supplied) In this study, we compare the performance of RNA-seq (Illumina HiSeq) and junction arrays (Affymetrix Human Transcriptome array) for the analysis of splicing events. Three different cell lines were treated with CX-4945, a drug that severely affects splicing. To make a fair comparison, we developed EventPointer, an algorithm that detects and labels alternative splicing events in both junction arrays and RNA-seq. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

30 Samples

Download data: TXT

(Submitter supplied) In this study, we compare the performance of RNA-seq (Illumina HiSeq) and junction arrays (Affymetrix Human Transcriptome array) for the analysis of splicing events. Three different cell lines were treated with CX-4945, a drug that severely affects splicing. To make a fair comparison, we developed EventPointer, an algorithm that detects and labels alternative splicing events in both junction arrays and RNA-seq. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL24082

30 Samples

Download data: CEL

(Submitter supplied) The study of splicing has been greatly aided by the advent of RNA sequencing (RNA-seq), which can enable the genome-wide detection of discrete splice isoforms. Quantification of these splice isoforms requires analysis of splicing informative sequencing reads, those that unambiguously map to a single splice isoform, including exon-intron spanning reads corresponding to retained introns, as well as exon-exon junction spanning reads corresponding to either canonically- or alternatively-spliced isoforms. more...

Organism:

Schizosaccharomyces pombe

Type:

Other

Platform:

GPL20584

2 Samples

Download data: TXT

(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:

GPL5188 GPL5175

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) This series represents 52 tissues hybridized across 5 different chip patterns. Probes were placed at every exon-exon junction in each transcript. Keywords = junction alternate splicing oligonucleotide Keywords: parallel sample

Organism:

Homo sapiens

Type:

Expression profiling by array

Datasets:

GDS829 GDS830 GDS831 GDS832 GDS833

5 related Platforms

264 Samples

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