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SRP094555
Mus musculus
24 Downloadable Samples
Illumina HiSeq 2500
Description
In cell stress, mRNA in the cytoplasm is sequestered to the insoluble ribonucleoprotein (RNP) compartments containing stress granules. These RNP granules are known to be involved in the control of mRNA processing and decay, but it has been elusive whether the mRNA redistribution in cell stress is universal or specific to a subset of transcripts. Here we provide a transcriptome-wide profiles of the RNP granules in cell stress and show that mRNA accumulation in stress granule differentially affects individual transcripts. mRNA species accumulated in stress granules are largely conserved across distinct stress types, such as in endoplasmic reticulum stress, heat shock and arsenic stress. Many mRNA species involved in cell survival and proliferation are more dynamically redistributed, suggesting that mRNA sequestration can be a specific response mechanism through which cells can reshape the landscape of their transcriptome and affect the cell fate determination in stress conditions . Overall design: 24 samples are analyzed, which include 3 replicates for control (DMSO) cytoplasmic fraction, 3 replicates of control (DMSO) RNP granule fraction, 3 replicates of Thapsigargin treated cytoplasmic fraction, 3 replicates of Thapsigargin treated RNP granule fraction, 2 replicates of control (H2O) cytoplasmic fraction, 2 replicates of control (H2O) RNP granule fractions, 2 replicates of heat shock (HS) treated cytoplsmic fraction (HS), 2 replicates of heat shock (HS) treated RNP granule fraction, 2 replicates of arsenite treated cytoplasmic fraction, and 2 replicates of arsenite treated RNP granule fraction.
Publication Title
Systematic Characterization of Stress-Induced RNA Granulation.
Sample Metadata Fields
Cell line, Treatment, Subject
View Samples- Drosophila melanogaster
- 13 Downloadable Samples
- Illumina Genome Analyzer IIx, Illumina Genome Analyzer
Description
Control of RNA transcription is critical for the development and homeostasis of all organisms, and can occur at multiple steps of the transcription cycle, including RNA polymerase II (Pol II) recruitment, initiation, promoter-proximal pausing, and elongation. That Pol II accumulates on many promoters in metazoans implies that steps other than Pol II recruitment are rate-limiting and regulated 1-6. By integrating genome-wide Pol II chromatin immunoprecipition (ChIP) and Global Run-On (GRO) genomic data sets from Drosophila cells, we examined critical features of Pol II near promoters. The accumulation of promoter-proximal polymerase is widespread, occurring on 70% of active genes; and unlike elongating Pol II within the body of genes, promoter Pol II are held paused by factors like NELF, unable to transcribe unless nuclei are treated with strong detergent. Notably, we find that the vast majority of promoter-proximal Pol II detected by ChIP are paused, thereby identifying the biochemical nature of this rate-limiting step in transcription. Finally, we demonstrate that Drosophila promoters do not have the upstream divergent Pol II that is seen so broadly and prominently on mammalian promoters. We postulate this is a consequence of Drosophila's extensive use of directional core promoter sequence elements, which contrasts with mammals' lack of directional elements and prevalence of CpG island core promoters. In support of this idea, we show that the fraction of mammalian promoters containing a TATA box core element is dramatically depleted of upstream divergent transcription. Overall design: Comparison of multiple GRO-seq data sets
Publication Title
Defining the status of RNA polymerase at promoters.
Sample Metadata Fields
Cell line, Treatment, Subject
View Samples- Mus musculus
- 6 Downloadable Samples
Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
The molecular targets of SRC-2 regulation in the murine liver stimulate fatty acid degradation and glycolytic pathway while fatty acid, cholesterol, and steroid biosynthetic pathways are down-regulated.
Publication Title
The genomic analysis of the impact of steroid receptor coactivators ablation on hepatic metabolism.
Sample Metadata Fields
Sex, Specimen part
View Samples- Homo sapiens
- 54 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
Mitochondria have been implicated in insulin resistance and beta cell dysfunction, both of which comprise the core pathophysiology of type 2 diabetes mellitus (T2DM). It has also recently been found that mtDNA haplogroups are distinctively associated with susceptibility to T2DM at least in Koreans and Japanese.
Publication Title
Gene expression pattern in transmitochondrial cytoplasmic hybrid cells harboring type 2 diabetes-associated mitochondrial DNA haplogroups.
Sample Metadata Fields
Specimen part
View Samples- Drosophila melanogaster
- 6 Downloadable Samples
- Illumina HiSeq 2000
Description
Cohesin is a well-known mediator of sister chromatid cohesion, but it also influences gene expression and development. These non-canonical roles of cohesin are not well understood, but are vital: gene expression and development are altered by modest changes in cohesin function that do not disrupt chromatid cohesion. To clarify cohesin’s roles in transcription, we measured how cohesin controls RNA polymerase II (Pol II) activity by genome-wide chromatin immunoprecipitation and precision global run-on sequencing. On average, cohesin-binding genes have more transcriptionally active Pol II and promoter-proximal Pol II pausing than non-binding genes, and are more efficient, producing higher steady state levels of mRNA per transcribing Pol II complex. Cohesin depletion frequently increases pausing at cohesin-binding genes, indicating that cohesin often facilitates transition of paused Pol II to elongation. In many cases this likely reflects a role for cohesin in transcriptional enhancer function. Strikingly, more than 95% of predicted extragenic enhancers bind cohesin, and cohesin depletion can reduce their association with Pol II, indicating that cohesin facilitates enhancer-promoter contact. Cohesin directly promotes transcription of the myc gene, and cohesin depletion reduces Pol II activity at most Myc target genes. The multiple transcriptional roles of cohesin revealed by these studies likely underlie the growth and developmental deficits caused by minor changes in cohesin activity. Overall design: The PRO-seq method was used to measure transcriptionally engaged Pol II genome-wide in two replicates each of mock RNAi-treated, Nipped-B RNAi-treated, and Rad21 RNAi-treated ML-DmBG3-c2 cells.
Publication Title
Genome-wide control of RNA polymerase II activity by cohesin.
Sample Metadata Fields
Sex, Specimen part, Treatment, Subject
View Samples- Mus musculus
- 4 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
GPR15 is an orphan G-protein coupled receptor and its expression is abundant among T cells in the large intestine lamina propria.
Publication Title
GPR15-mediated homing controls immune homeostasis in the large intestine mucosa.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 29 Downloadable Samples
- Illumina HiSeq 2000
Description
Memory stabilization after learning requires transcriptional and translational regulations in the brain, yet the temporal molecular changes following learning have not been explored at the genomic scale. We here employed ribosome profiling and RNA sequencing to quantify the translational status and transcript levels in mouse hippocampus following contextual fear conditioning. We identified 104 genes that are dynamically regulated. Intriguingly, our analysis revealed novel repressive regulations in the hippocampus: translational suppression of ribosomal protein-coding genes at basal state; learning-induced early translational repression of specific genes; and late persistent suppression of a subset of genes via inhibition of ESR1/ERa signaling. Further behavioral analyses revealed that Nrsn1, one of the newly identified genes undergoing rapid translational repression, can act as a memory suppressor gene. This study unveils the yet unappreciated importance of gene repression mechanisms in memory formation. Overall design: The application of ribosome profiling and RNA-seq techniques to mouse hippocampi tissues after contextual fear conditioning and to mouse hippocampal primary cultures. Mouse ESCs were also examined.
Publication Title
Multiple repressive mechanisms in the hippocampus during memory formation.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 8 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
The genetic mechanism governing the spatial patterning of teeth still remains to be elucidated. Sonic hedgehog (Shh) is one of key signaling molecules involved in the spatial patterning of teeth. By utilizing maternal transfer of 5E1 (an IgG1 monoclonal antibody against Shh protein) through the placenta to block Shh signaling, we investigated the changes in tooth patterning and in gene expression.
Publication Title
Interactions between Shh, Sostdc1 and Wnt signaling and a new feedback loop for spatial patterning of the teeth.
Sample Metadata Fields
Specimen part, Time
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Gene 2.0 ST Array (mogene20st)
Description
Gene expression profiling of primary mouse articular chondrocyte treated with interleukin-1.
Publication Title
Estrogen-related receptor γ causes osteoarthritis by upregulating extracellular matrix-degrading enzymes.
Sample Metadata Fields
Age, Specimen part, Treatment
View Samples- Arabidopsis thaliana
- 6 Downloadable Samples
- Illumina HiSeq 2000
Description
The cell wall is a defining feature of plant cells and glues cells to each other. To overcome this physical constraint, plants must process and disconnect cell wall linkages during growth and development. However, little is known about the mechanism guiding cell-cell detachment and cell wall remodeling. Here, we identify two neighboring cell types in Arabidopsis that coordinate their activities to control cell wall processing, thereby ensuring precise abscission to discard organs. One cell type produces a honeycomb structure of lignin, which acts as a mechanical 'brace' to localize cell wall breakdown and spatially limit abscising cells. The second cell type undergoes transdifferentiation into epidermal cells, forming protective cuticle, demonstrating de novo specification of epidermal cells, previously thought to be restricted to embryogenesis. Loss of the lignin brace leads to inadequate cuticle formation, resulting in surface barrier defects and susceptible to infection. Altogether, we show how plants precisely accomplish abscission. Overall design: RECs (Residuum cells, abscission zone cells of the receptacle) and SECs (Secession cells, abscission zone cells of separated floral organs) were isolated using fluorescence-activated cell sorting of cells from transgenic plants harboring proQRT2::nlsGFP–GUS construct, and their transcriptomes were analyzed by RNA-sequencing.
Publication Title
A Lignin Molecular Brace Controls Precision Processing of Cell Walls Critical for Surface Integrity in Arabidopsis.
Sample Metadata Fields
Specimen part, Subject
View Samples