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SRP128608
Homo sapiens
24 Downloadable Samples
NextSeq 500
Description
We report the RNAseq analysis of human dermal fibroblasts which have been treated by protocols to stimulate their differentiation towards the otic lineage. This was achieved by transfection with different transcription factors with the aim to induce an initial reprogramming of the cells and was followed by growth factor treatments known to promote otic differentiation. The results show that a partial differentiation towards the otic lineage is achieved by these protocols. Overall design: RNAseq profiles were obtained from human dermal fibroblasts with two different protocols. Prior to treatment with growth factors stimulating differentiation, the samples were either transfected with the transcription factors OCT4 or a combination of ATOH1, POU4F3 and GFI1.
Publication Title
Transcription factor induced conversion of human fibroblasts towards the hair cell lineage.
Sample Metadata Fields
Specimen part, Subject
View Samples- Drosophila melanogaster
- 140 Downloadable Samples
Affymetrix Drosophila Genome 2.0 Array (drosophila2)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Suboptimal evolutionary novel environments promote singular altered gravity responses of transcriptome during Drosophila metamorphosis.
Sample Metadata Fields
Sex, Age
View Samples- Drosophila melanogaster
- 90 Downloadable Samples
- Affymetrix Drosophila Genome 2.0 Array (drosophila2)
Description
Genome-wide transcriptional profiling showed that reducing gravity levels in the International Space Station (ISS) causes important alterations in Drosophila gene expression intimately linked to imposed spaceflight-related environmental constrains during Drosophila metamorphosis. However, simulation experiments on ground testing space-related environmental constraints, show differential responses. Curiously, although particular genes are not common in the different experiments, the same GO groups including a large multigene family related with behavior, stress response and organogenesis are over represented in them. A global and integrative analysis using the gene expression dynamics inspector (GEDI) self-organizing maps, reveals different degrees in the responses of the transcriptome when using different environmental conditions or microgravity/hypergravity simulation devices
Publication Title
Suboptimal evolutionary novel environments promote singular altered gravity responses of transcriptome during Drosophila metamorphosis.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 36 Downloadable Samples
- Illumina MouseWG-6 v2.0 expression beadchip
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Bromodomain-dependent stage-specific male genome programming by Brdt.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 36 Downloadable Samples
- Illumina MouseWG-6 v2.0 expression beadchip
Description
Male germ cell differentiation is a highly regulated multistep process initiated by the commitment of progenitor cells into meiosis and characterized by major chromatin reorganizations in haploid spermatids. We report here that a single member of the double bromodomain BET factors, Brdt, is a master regulator of both meiotic divisions and post-meiotic genome repackaging. Upon its activation at the onset of meiosis, Brdt drives and determines the developmental timing of a testis-specific gene expression program. In meiotic cells, Brdt initiates a genuine histone acetylation-guided programming of the genome by activating essential meiotic genes and repressing a progenitor cells gene expression program, while priming a post-meiotic gene group for further activation. At post-meiotic stages, a global chromatin hyperacetylation gives the signal for Brdts first bromodomain to direct the genome-wide replacement of histones by transition proteins. Brdt is therefore a unique and essential regulator of male germ cell differentiation, which, by using various domains in a developmentally controlled manner, first drives a specific spermatogenic gene expression program, and later controls the tight packaging of the male genome.
Publication Title
Bromodomain-dependent stage-specific male genome programming by Brdt.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 12 Downloadable Samples
- Illumina HiSeq 2500
Description
Granulomas are immune cell aggregates formed in response to persistent inflammatory stimuli. Granuloma macrophage subsets are diverse and carry varying copy numbers of their genomic information. The molecular programs that control the differentiation of such macrophage populations in response to a chronic stimulus, though critical for disease outcome, have not been defined. In this study, we performed scRNA-Seq experiments to gain insights into the transcriptional regulation of polyploid macrophage differentiation in response to chronically persistent inflammatory stimuli. Overall design: scRNA-Seq was performed on FACS-sorted 2c and >4c DNA content polyploid macrophages after six days of bacterial lipoprotein, FSL-1 treatment of bone marrow-derived macrophage precursors. 2c DNA content macrophages treated with M-CSF alone were used as controls. CEL-Seq2 protocol was used for single cell sequencing (Hashimshony et al. 2016).
Publication Title
DNA Damage Signaling Instructs Polyploid Macrophage Fate in Granulomas.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Mus musculus
- 26 Downloadable Samples
- Affymetrix Mouse Gene 2.0 ST Array (mogene20st)
Description
Over the last years, evidence has grown that exposure to air pollution, in addition to impairing lung function and health in individuals of all age, can be linked to negative effects in newborn when present during pregnancy. Data suggests that intrauterine exposure of fetuses (exposure of the mother to air pollution during pregnancy) in fact exerts a negative impact on lung development. However, the means by which exposure during pregnancy affects lung development, have not been studied in depth yet. In this study, we investigated alterations of the transcriptome of the developing lung in a mouse model of gestational and early-life postnatal exposure to urban PM2.5 (from Sao Paulo, Brazil).
Publication Title
Pre- and postnatal exposure of mice to concentrated urban PM<sub>2.5</sub> decreases the number of alveoli and leads to altered lung function at an early stage of life.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Dynamic gene expression in the PSM of vertebrates is critical for the spatial and temporal patterning of somites.
Publication Title
Dynamic CREB family activity drives segmentation and posterior polarity specification in mammalian somitogenesis.
Sample Metadata Fields
Specimen part
View Samples- Danio rerio
- 11 Downloadable Samples
- Affymetrix Genechip Zebrafish ST Genome Array 1.1 (zebgene11st)
Description
Public information is widely available at low cost to animals living in social groups. For instance, bystanders may eavesdrop on signaling interactions between conspecifics and use it to adapt their subsequent behavior towards the observed individuals. This social eavesdropping ability is expected to require specialized mechanisms such as social attention, which selects social information available for learning. To begin exploring the genetic basis of social eavesdropping, we used a previously established attention paradigm in the lab to study the brain gene expression profile of male zebrafish in relation to the attention they have paid towards conspecifics involved or not involved in agonistic interactions. Microarray gene chips were used to characterize their brain transcriptomes based on differential expression of single genes and gene sets. These analyses were complemented by promoter region-based techniques. Using data from both approaches, we further drafted protein interaction networks. Our results suggest that attentiveness towards conspecifics, whether interacting or not, activates pathways linked to neuronal plasticity and memory formation. The network analyses suggested that fos and jun are key players on this response, and that npas4a, nr4a1 and egr4 may also play an important role.
Publication Title
Brain Transcriptomic Response to Social Eavesdropping in Zebrafish (Danio rerio).
Sample Metadata Fields
Sex, Specimen part, Treatment
View Samples- Mus musculus
- 12 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
Histone acetylation and other modifications of the chromatin are important regulators of gene expression and, consequently, may contribute to drug-induced behaviors and neuroplasticity. Previous studies have shown that a reduction on histone deacetylase (HDAC) activity results on the enhancement of some psychostimulant-induced behaviors. In the present study, we extend those seminal findings by showing that the administration of the HDAC inhibitor sodium butyrate enhances morphine-induced locomotor sensitization and conditioned place preference. In contrast, this compound has no effects on the development of morphine tolerance and dependence. Similar effects were observed for cocaine and ethanol-induced behaviors. These behavioral changes were accompanied by a selective boosting of a component of the transcriptional program activated by chronic morphine administration that included circadian clock genes and other genes relevant in addictive behavior. Our results support an specific role for histone acetylation and the epigenetic modulation of transcription at a reduced number of biologically relevant loci on non-homeostatic, long lasting, drug-induced behavioral plasticity. To further investigate the molecular bases of sodium butyrate action on long-lasting behavioral responses to morphine, we screened for potential substrates of their interaction by performing a genome-wide comparison of the striatal transcriptome after chronic administration of morphine in the absence or presence of sodium butyrate.
Publication Title
Selective boosting of transcriptional and behavioral responses to drugs of abuse by histone deacetylase inhibition.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples