GEO DataSets

(Submitter supplied) Signal transduction pathways mediated by kinases control diverse biological outputs at the level of cells and tissues to regulate a diverse array of biological and developmental events. To gain insight into how muscle expression of the evolutionarily conserved NUAK kinase regulates the transcriptional landscape during Drosophila melanogaster development, we performed high-throughput sequencing of RNA from either whole larvae or dissected muscle fillets at the end of larval development. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21306

18 Samples

Download data: TXT

(Submitter supplied) We applied a 5'RNA-seq methodology to assess gene and differential isoform expression in striated muscle tissues extracted from adult wild-type mice.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11002

4 Samples

Download data: BEDGRAPH

(Submitter supplied) Nebulin is a giant filamentous protein that is coextensive with the actin filaments of the skeletal muscle sarcomere. Nebulin mutations are the main cause of nemaline myopathy (NEM), with typical NEM adult patients having low expression of nebulin, yet the roles of nebulin in adult muscle remain poorly understood. To establish nebulin’s functional roles in adult muscle we performed studies on a novel conditional nebulin KO (Neb cKO) mouse model in which nebulin deletion was driven by the muscle creatine kinase (MCK) promotor. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Datasets:

GDS5880 GDS5881

Platform:

GPL6246

24 Samples

Download data: CEL

Analysis of soleus muscles from 6 week old males with a conditional knockout of nebulin in their striated muscles. Nebulin is a giant filamentous protein that is coextensive with actin filaments of the skeletal muscle sarcomere. Results provide insight into the role of nebulin in adult muscles.

Organism:

Mus musculus

Type:

Expression profiling by array, count, 2 genotype/variation sets

Platform:

GPL6246

Series:

GSE70213

12 Samples

Download data: CEL

Analysis of quadriceps muscles from 6 week old males with a conditional knockout of nebulin in their striated muscles. Nebulin is a giant filamentous protein that is coextensive with actin filaments of the skeletal muscle sarcomere. Results provide insight into the role of nebulin in adult muscles.

Organism:

Mus musculus

Type:

Expression profiling by array, count, 2 genotype/variation sets

Platform:

GPL6246

Series:

GSE70213

12 Samples

Download data: CEL

(Submitter supplied) Background High-throughput RNA-Sequencing (RNA-Seq) has become the preferred technique for studying gene expression differences between biological samples and for discovering novel isoforms, though the techniques to analyze the resulting data are still immature. One pre-processing step that is widely but heterogeneously applied is trimming, in which low quality bases, identified by the probability that they are called incorrectly, are removed. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17275

4 Samples

Download data: TXT

(Submitter supplied) We present RNA-Seq data obtained from HEK293T cells and HEK293T cells with ALKBH5 and FTO demethylases double knockout (HEK293TΔALKBH5ΔFTO), showing m6A-dependent transcriptome alterations.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

6 Samples

Download data: TSV

(Submitter supplied) Both transcription and post-transcriptional processes, such as alternative splicing, play crucial roles in controlling developmental programs in metazoans. Recently emerged RNA-seq method has brought our understanding of eukaryotic transcriptomes to a new level, because it can resolve both gene expression level and alternative splicing events simultaneously. To gain a better understanding of cellular differentiation in gonads, we analyzed mRNA profiles from Drosophila testes and ovaries using RNA-seq. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9061

4 Samples

Download data: GRAPH, TXT

(Submitter supplied) Fetal life is a crucial period for sexual reproduction when bipotential gonads differentiate into either a testis or an ovary. Gaining insights into the complex molecular events underlying this process is central to a better understanding of disorders of sexual development. The present work therefore intends to improve the knowledge on molecular pathways at play during gonad development in humans using RNA-Sequencing.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

48 Samples

Download data: BED, GTF, TXT, XLSX

(Submitter supplied) We sequenced mRNA extracted from brains of (1) D. melanogaster larvae exposed to food containing 5% ethanol (v/v) for 6 conscutive days, and (2) an age-matched untreated control larvae, that grew in regular food. Differential gene expression between the two groups was calculated and reported. Each group consisted of 3 biological replicates of 30 brains each.

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19132

6 Samples

Download data: TXT

(Submitter supplied) Deep sequencing of mRNA from six different tissues

Organism:

Brassica rapa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16440

8 Samples

Download data: BEDGRAPH, TXT

(Submitter supplied) We report genome-wide binding of the highly conserved TF Sine oculis (So), which is necessary for Drosophila eye development and has few previously known direct transcriptional targets. Our data identify novel putative targets of So-mediated regulation, including genes involved in multiple aspects of development.

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11203

3 Samples

Download data: WIG

(Submitter supplied) Purpose: Transcriptome is the entire repertoire of all transcripts present in a cell at any particular time. We undertook next-generation whole transcriptome sequencing approach to gain insight of the transcriptional landscape of the developing mouse lens. Methods: We ascertained mice lenses at six developmental time points including two embryonic (E15 and E18) and four postnatal stages (P0, P3, P6, and P9). more...

Organism:

Mus musculus

Type:

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

Platform:

GPL13112

24 Samples

Download data: XLSX

(Submitter supplied) The abstract of the manuscript titled "Signalling pathways involved in adult heart formation revealed by gene expression profiling in Drosophila" is given below: "Drosophila provides a powerful system for defining the complex genetic programs that drive organogenesis. Under control of the steroid hormone ecdysone, the adult heart in Drosophila forms during metamorphosis by a remodelling of the larval cardiac organ. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by array

Platform:

GPL5112

32 Samples

Download data: TXT

(Submitter supplied) In eukaryotes, nucleosomes participate in all DNA-templated events by regulating access to the underlying DNA sequence. However, the dynamics of nucleosomes during a genome response has not been well characterized . We stimulated Drosophila S2 cells with heat-killed Gram-negative bacteria Salmonella typhimurium, and mapped genome-wide nucleosome occupancy at high temporal resolution by MNase-seq using Illumina HiSeq 2500. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17275

8 Samples

Download data: BED

(Submitter supplied) Infections with bovine viral diarrhea virus (BVDV) contribute significantly to health-related economic losses in the beef and dairy industries and are widespread throughout the world. Severe acute BVDV infection is characterized by a gastrointestinal (GI) inflammatory response. The mechanism of inflammatory lesions caused by BVDV remains unknown. The interstitial cells of Cajal (ICC) network plays a pivotal role as a pacemaker in the generation of electrical slow waves for GI motility, and it is crucial for the reception of regulatory inputs from the enteric nervous system. more...

Organism:

Ovis aries

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19778

6 Samples

Download data: TXT

(Submitter supplied) Obesity is a major risk factor for a high number of secondary diseases, including cancer. Specific insights into the role of gender differences and secondary co-morbidities, such as type 2 diabetes (T2D) and cancer risk, are yet to be fully obtained. The aim of this study is thus to find a correlation between the transcriptional deregulation present in the subcutaneous adipose tissue of obese patients and the risk of cancer, in the presence of T2D, and considering gender differences. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

20 Samples

Download data: DAT

(Submitter supplied) Background: Though Illumina has largely dominated the RNA-Seq field, the simultaneous availability of Ion Torrent has left scientists wondering which platform is most effective for differential gene expression (DGE) analysis. Previous investigations of this question have typically used reference samples derived from cell lines and brain tissue, and do not involve biological variability. While these comparisons might inform studies of tissue-specific expression, marked by large-scale transcriptional differences, this is not the common use case. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17021 GPL18635

20 Samples

Download data: TXT

(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

(Submitter supplied) Purpose: characterize the uterine transcriptome profiles of pregnant (P) versus non-pregnant (NP) cows during early pregnancy and attempted to define a potential set of marker genes that can be valuable for predicting pregnancy outcome. Methods: beef cows were synchronized and artificially inseminated at detected estrus. Six days after AI, jugular blood samples and a biopsy from the uterine horn contralateral to the ovary containing the corpus luteum were collected. more...

Organism:

Bos indicus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19671

11 Samples

Download data: TXT