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ERP000702
Mus musculus
3 Downloadable Samples
Description
Current evidence suggests that more than half of the mammalian genome is transcribed, yet how this vast transcriptome is regulated in vivo remains poorly understood. We demonstrate here an integrated, straightforward and widely applicable approach to characterize cell type-specific transcriptional programs and regulatory mechanisms by generating two genome-wide data sets. We used deep sequencing of nuclear RNA (nucRNA-Seq) to comprehensively describe the nuclear transcriptome in ex vivo murine erythroid cells. In parallel, we generated a profile of active RNA polymerase II (RNAPII) binding by chromatin-immunoprecipitation (ChIP-Seq), allowing us to explore the relationship between RNAPII occupancy and transcriptional output in erythroid cells on a genome-wide scale. Comparative analysis of both data sets enables us to not only measure primary transcriptional output and identify genes associated with more efficient polymerase usage, but also to identify putative regulatory elements such as enhancers and novel non-coding transcripts. Application of this method to different cell types allows for the characterization of important aspects of gene regulation in a cell type-specific manner. Our findings demonstrate the complex ways in which RNAPII is associated with the genome and how this affects transcription of target genes, highlighting the importance of approaching transcriptome characterization from multiple angles.
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Hordeum vulgare
- 5 Downloadable Samples
Affymetrix Barley Genome Array (barley1)
Description
Changes in gene expression during adaptation to abiotic stress conditions in the barley roots.
Publication Title
No associated publication
Sample Metadata Fields
Age, Specimen part, Time
View Samples- Drosophila melanogaster
- 6 Downloadable Samples
- Affymetrix Drosophila Genome 2.0 Array (drosophila2)
Description
Even after decades of living in the same laboratory environment two Drosophila melanogaster strains originating from North America (Canton-S) and Central Russia (D18) demonstrate a few differentially expressed genes some of which may be important for local adaptation (e.g. genes responsible for insecticide resistance). Genes with different level of expression between Canton-S and D18 strains belong to important metabolic pathways, for instance energy metabolism, carbohydrate metabolic process, locomotion, body temperature rhythm regulation and tracheal network architecture.
Publication Title
Transcriptome analysis of <i>Drosophila melanogaster</i> laboratory strains of different geographical origin after long-term laboratory maintenance.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 12 Downloadable Samples
Description
The goal of this study was to asses genome wide cross talk between Glucocorticoid Receptor (GR) and Peroxisome Proliferator Activated Receptor Alpha (PPARA) on the level of DNA binding (ChIP-seq) and gene expression (RNA-seq) in primary mouse hepatocytes.
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples