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GSE93239
Mus musculus
23 Downloadable Samples
Affymetrix Mouse Gene 2.0 ST Array (mogene20st)
Description
Circadian profiling of total RNA collected from wildtype and NPY KO murine liver. Liver RNA collected every 4 hours in a 12hr light:12hr dark cycle.
Publication Title
Neural clocks and Neuropeptide F/Y regulate circadian gene expression in a peripheral metabolic tissue.
Sample Metadata Fields
No sample metadata fields
View Samples- Danio rerio
- 8 Downloadable Samples
IlluminaHiSeq2500
Description
RNA-seq analysis of zebrafish foxc1a mutant Overall design: For RNA-seq, mRNA was extracted from 38-40 hpf old embryos. We isolated wild type and foxc1a mutant samples by dissecting the entire first 6 anterior somitic segments (AS) through which the fin nerves migrate, and the adjacent posterior segments (PS; segments 7 through ~12) devoid of fin innervating nerves. Heads and yolks were excluded from all samples. Tissues were stored in RNAlater solution (Life Technologies) for up to 2 days at 4 degree before RNA was extracted using the RNAeasy kit (Qiagen) according to the manufacture’s protocol. RNA was tested for integrity using a Bioanalyzer (Agilent technologies). RNA samples showing RIN value of 8 or higher were used for generating cDNA libraries as described in the TruSeq® Stranded mRNA sample preparation guide. At the final stage, 15 cycles of PCR amplifications was performed. Barcoded libraries representing duplicates of AS and PS samples of wild type and mutants were validated using Bionalyzer (Agilent Technology) and finally sequenced in Illumina HiSeq 2500 yielding paired end reads of 100bp. The RNA-seq Unified Mapper (RUM) (Grant et al., 2011) was used to align the reads to the Zv9/danRer7 reference genome and to assign each read uniquely to a transcript. We investigated transcripts that showed the highest fold changes of expression between the different groups. For Gene Ontology annotations, genes tagged by the GO term “axon guidance” were obtained from the gene ontology database (http://www.geneontology.org/). Next we filtered this list for the “Danio rerio” taxon (resulting in 116 unique genes) and used them to annotate our RNA-seq results.
Publication Title
Zebrafish foxc1a drives appendage-specific neural circuit development.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 3 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
This is to determine in vivo kidney tissue gene expression regulated by acetate feeding in drinking water into mice for 6 weeks.
Publication Title
Chronically Elevated Levels of Short-Chain Fatty Acids Induce T Cell-Mediated Ureteritis and Hydronephrosis.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 288 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
A circadian gene expression atlas in mammals: implications for biology and medicine.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 288 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
To characterize the role of the circadian clock in mouse physiology and behavior, we used RNA-seq and DNA arrays to quantify the transcriptomes of 12 mouse organs over time. We found 43% of all protein coding genes showed circadian rhythms in transcription somewhere in the body, largely in an organ-specific manner. In most organs, we noticed the expression of many oscillating genes peaked during transcriptional rush hours preceding dawn and dusk. Looking at the genomic landscape of rhythmic genes, we saw that they clustered together, were longer, and had more spliceforms than nonoscillating genes. Systems-level analysis revealed intricate rhythmic orchestration of gene pathways throughout the body. We also found oscillations in the expression of more than 1,000 known and novel noncoding RNAs (ncRNAs). Supporting their potential role in mediating clock function, ncRNAs conserved between mouse and human showed rhythmic expression in similar proportions as protein coding genes. Importantly, we also found that the majority of best-selling drugs and World Health Organization essential medicines directly target the products of rhythmic genes. Many of these drugs have short half-lives and may benefit from timed dosage. In sum, this study highlights critical, systemic, and surprising roles of the mammalian circadian clock and provides a blueprint for advancement in chronotherapy.
Publication Title
A circadian gene expression atlas in mammals: implications for biology and medicine.
Sample Metadata Fields
Specimen part
View Samples- Rattus norvegicus
- 122 Downloadable Samples
- Affymetrix Rat Genome U34 Array (rgu34a)
Description
Large scale transcriptome analysis of Wistar and Sprague Dawley rat tissues.
Publication Title
Applications of a rat multiple tissue gene expression data set.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 48 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
High-temporal resolution profiling was performed on mouse liver to detect rhythmic transcripts
Publication Title
Harmonics of circadian gene transcription in mammals.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 47 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
High-temporal resolution profiling was performed on NIH3T3 fibroblasts to detect rhythmic transcripts
Publication Title
Harmonics of circadian gene transcription in mammals.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 9 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
Although much is known about focal adhesion signaling induced by cell adhesion, how adhesion directs changes in transcription to control cell behavior is far less understood. Here we describe a novel mechanism by which changes in adhesion switch the activities of the mitogen-activated protein kinases (MAPKs) c-Jun N-terminal kinase (JNK) and p38, resulting in the differential activation and promoter occupancy of the SRF cofactors, the ternary complex factors (TCFs) Sap-1 and Net. Adhesion-induced MAPK/TCF switching controls immediate early gene expression and proliferation. This mechanism is of physiological relevance, as proliferative regulation by the TCFs is conserved in an ex ovo model of angiogenesis. Furthermore, microarray analysis identified novel genes and adhesive functions regulated by Sap-1 and Net. Thus our data identify the TCFs as key regulators of adhesion-induced transcription and cell behavior.
Publication Title
Adhesion regulates MAP kinase/ternary complex factor exchange to control a proliferative transcriptional switch.
Sample Metadata Fields
Cell line
View Samples- Homo sapiens
- 298 Downloadable Samples
- Affymetrix Human Genome U219 Array (hgu219)
Description
Skin is the largest organ in the body and serves important barrier, regulatory, and sensory functions. Like other tissues, skin is subject to temporal fluctuations in physiological responses under both homeostatic and stressed states. To gain insight into these fluctuations, we investigated the role of the circadian clock in the transcriptional regulation of human epidermal samples collected in a time-ordered fashion. We also determined whether this circadian patterning could be applied to unordered (i.e., randomly collected) human epidermal samples. The purpose of this study was to gain insight into the evolutionarily-conserved rhythmic patterns of the circadian transcriptome in human skin and how it relates to published transcriptomes from other human tissues.
Publication Title
Population-level rhythms in human skin with implications for circadian medicine.
Sample Metadata Fields
Sex, Specimen part
View Samples