GEO DataSets

(Submitter supplied) Background: RNA-seq based on short reads generated by next generation sequencing technologies has become the main approach to study differential gene expression. Until now the main applications of this technique have been to study the variation of gene expression in a whole organism, tissue or cell type under different conditions or at different developmental stages. However, RNA-seq also has a great potential to be used in evolutionary studies to investigate gene expression divergence in closely related species. more...

Organism:

Drosophila melanogaster; Drosophila mauritiana; Drosophila simulans

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21269 GPL13306 GPL13304

12 Samples

Download data: FA, GFF, TXT

(Submitter supplied) oligo-dT and random primed RNA-seq libraries were used to test an improved annotation of the zebrafish transcriptome

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14875

12 Samples

Download data: CSV

(Submitter supplied) We performed CAGE-Seq on dissected ovaries and testes as well as female and male carcasses of two species of Drosophila (D. melanogaster and D. pseudoobscura). These data are used to map transcription start sites. 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:

Drosophila melanogaster; Drosophila pseudoobscura

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17883 GPL11203

8 Samples

Download data: BED

(Submitter supplied) The model organism Encyclopedia of DNA Elements project (modENCODE) has produced a comprehensive annotation of D. melanogaster transcript models based on an enormous amount of high-throughput experimental data. However, some transcribed elements may not be functional, and technical artifacts may lead to erroneous inference of transcription. Inter-species comparison provides confidence to predicted annotation, since transcriptional activity that has been evolutionarily conserved is likely to have an advantageous function. more...

Organism:

Drosophila ananassae; Drosophila simulans; Drosophila virilis; Drosophila elegans; Drosophila biarmipes; Drosophila melanogaster; Drosophila pseudoobscura; Drosophila mojavensis; Drosophila yakuba; Drosophila eugracilis; Drosophila takahashii; Drosophila ficusphila; Drosophila kikkawai; Drosophila bipectinata; Drosophila rhopaloa

Type:

Expression profiling by high throughput sequencing

34 related Platforms

93 Samples

Download data: BAM, BED, RPKM, TXT

(Submitter supplied) We performed transcriptional profiling of sexed whole adults and mixed sex embryos of eight Drosophila species. These data were used in a comparative transcriptomics analysis of multiple Drosophila species to define functional elements conserved throughout the Drosophila genus.

Organism:

Drosophila ficusphila; Drosophila bipectinata; Drosophila biarmipes; Drosophila eugracilis; Drosophila takahashii; Drosophila kikkawai; Drosophila rhopaloa; Drosophila elegans

Type:

Expression profiling by high throughput sequencing

16 related Platforms

26 Samples

Download data: RPKM, TXT

(Submitter supplied) We sequenced mRNA from head tissue of females and male of Drosophila mojavensis to identify genes differentially expressed between the sexes and sex-specific alternative splicing events. 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:

Drosophila mojavensis

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL10181 GPL10180

4 Samples

Download data: TXT

(Submitter supplied) We sequenced mRNA from head tissue of females and male of Drosophila melanogaster to identify genes differentially expressed between the sexes and sex-specific alternative splicing events. 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:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9061

4 Samples

Download data: TXT

(Submitter supplied) We sequenced mRNA from head tissue of females and male of Drosophila pseudobscura to identify genes differentially expressed between the sexes and sex-specific alternative splicing events. 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:

Drosophila pseudoobscura

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9395

2 Samples

Download data: TXT

(Submitter supplied) Background: Whole transcriptome sequencing (RNA-seq) represents a powerful approach for whole transcriptome gene expression analysis. However, RNA-seq carries a few limitations, e.g., the requirement of a significant amount of input RNA and complications led by non-specific mapping of short reads. The Ion AmpliSeqTM Transcriptome Human Gene Expression Kit (AmpliSeq) was recently introduced by Life Technologies as a whole-transcriptome, targeted gene quantification kit to overcome these limitations of RNA-seq.To assess the performance of this new methodology, we performed a comprehensive comparison of AmpliSeq with RNA-seq using two well-established next-generation sequencing platforms (Illumina HiSeq and Ion Torrent Proton). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17303

6 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) Transcription profiling by high throughput sequencing of polyA+ RNAs from eight different human tissues to test a set of de novo transcript models (GENCODE PCR-Seq Batch IX) As part of the ENCODE consortium the GENCODE project is producing a reference gene set through manual and automated gene prediction. Selected transcript models are verified experimentally by RT-PCR amplification followed by sequencing. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

8 Samples

Download data

(Submitter supplied) Transcription profiling by high throughput sequencing of polyA+ RNAs from eight different human tissues (GENCODE PCR-Seq Batch X) As part of the ENCODE consortium the GENCODE project is producing a reference gene set through manual and automated gene prediction. Selected transcript models are verified experimentally by RT-PCR amplification of at least one of their unique splice junctions followed by sequencing. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

8 Samples

Download data

(Submitter supplied) Transcription profiling by high throughput sequencing of polyA+ RNAs from eight different human tissues to test a set of de novo transcript models (GENCODE PCR-Seq Batch IX) As part of the ENCODE consortium the GENCODE project is producing a reference gene set through manual and automated gene prediction. Selected transcript models are verified experimentally by RT-PCR amplification followed by sequencing. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

8 Samples

Download data

(Submitter supplied) Transcriptional profiling by high throughput sequencing of RACE-PCR-amplified human brain and testis samples to determine lncRNA transcript 5' and 3'-ends (GENCODE Batch VIII b) As part of the ENCODE consortium the GENCODE project is producing a reference gene set through manual and automated gene prediction. In the current phase of ENCODE we have found strong evidence that many lncRNAs transcript termini are still unknown. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9186

2 Samples

Download data

(Submitter supplied) Transcriptional profiling by high throughput sequencing of RACE-PCR-amplified human brain and testis samples to determine lncRNA transcript 5' and 3'-ends (GENCODE Batch VIII a) As part of the ENCODE consortium the GENCODE project is producing a reference gene set through manual and automated gene prediction. In the current phase of ENCODE we have found strong evidence that many lncRNAs transcript termini are still unknown. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9186

2 Samples

Download data

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

Organism:

Harpegnathos saltator

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL30014 GPL22089

28 Samples

Download data: FASTA, GTF

(Submitter supplied) RNA from brain and fat body/ovary (combined) was sequenced to use in Harpegnathos annotation improvement.

Organism:

Harpegnathos saltator

Type:

Other

Platform:

GPL30014

2 Samples

Download data

(Submitter supplied) This RNA-seq was done separate from any annotation and used to calculate the % of reads mapping to features.

Organism:

Harpegnathos saltator

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22089

26 Samples

Download data: TXT

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

Organism:

Drosophila melanogaster; Harpegnathos saltator

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL22089 GPL19132

49 Samples

Download data

(Submitter supplied) We used 10x Genomics and Drop-seq single-cell RNA-seq to identify the cell type composition of the Harpegnathos brain and study how it changes during the process of adult caste transition (from worker to pseudo-queen), aging, and brain injury.

Organism:

Harpegnathos saltator

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22089

42 Samples

Download data: TXT