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SRP071232
Homo sapiens
24 Downloadable Samples
IlluminaHiSeq2500
Description
Tuberous sclerosis complex (TSC) is a rare genetic disease characterized by mTOR hyperfunction induced benign tumor growths in multiple organs and neurological symptoms. Because the molecular pathology is highly complex and the etiology poorly understood we employed a defined human neuronal model with a single mTOR activating mutation to dissect the disease-relevant molecular responses driving the neuropathology. TSC2 deficient neural stem cells showed severely reduced neuronal functional maturation and characteristics of astrogliosis instead. Accordingly, transcriptome analysis uncovered an inflammatory response and increased metabolic activity, while ribosome profiling revealed excessive translation of ribosomal transcripts and higher synthesis rates of angiogenic growth factors. Treatment with mTOR inhibitors corrected translational alterations but not transcriptional dysfunction. These results extend our understanding of the molecular pathophysiology of TSC brain lesions, and suggest phenotype-tailored pharmacological treatment strategies. Overall design: Two TSC+/- cell lines and two TSC-/- cell lines were independently generated from wild-type human embryonic stem cells by genome editting with zinc finger nucleases. Two cell lines were handled in the same way but without any known human gene editted and they are used as negative controls. Two independent biological replicates of each of the six cell lines are profiled with ribosome profiling technique.
Publication Title
Genomic analysis of the molecular neuropathology of tuberous sclerosis using a human stem cell model.
Sample Metadata Fields
No sample metadata fields
View Samples- Drosophila melanogaster
- 20 Downloadable Samples
- Illumina HiSeq 2000
Description
In Drosophila, fibrillar flight muscles (IFMs) enable flight, while tubular muscles mediate other body movements. Here, we use RNA-sequencing and isoform-specific reporters to show that spalt major (salm) determines fibrillar muscle physiology by regulating transcription and alternative splicing of a large set of sarcomeric proteins. We identify the RNA binding protein Arrest (Aret, Bruno) as downstream of salm. Aret shuttles between cytoplasm and nuclei, and is essential for myofibril maturation and sarcomere growth of IFMs. Molecularly, Aret regulates IFM-specific transcription and splicing of various sarcomeric targets, including Stretchin and wupA (TnI), and thus maintains muscle fiber integrity. As Aret and its sarcomeric targets are evolutionarily conserved, similar principles may regulate mammalian muscle morphogenesis. Overall design: 9 samples from Drosophila melanogaster were analyzed in duplicate: control dissected wildtype flight muscle at 30h APF, 72h APF and 0 day adult, jump muscle and whole leg from 1d adult and RNAi/mutant conditions for salm (1d flight muscle) and aret (30h, 72h and 1d flight muscle)
Publication Title
The RNA-binding protein Arrest (Bruno) regulates alternative splicing to enable myofibril maturation in Drosophila flight muscle.
Sample Metadata Fields
Subject
View Samples- Drosophila melanogaster
- 28 Downloadable Samples
- Illumina HiSeq 2000, Illumina HiSeq 2500
Description
Muscles organise a pseudo-crystalline array of actin, myosin and titin filaments to build force-producing sarcomeres. To study how sarcomeres are built, we performed mRNA-sequencing of developing Drosophila flight muscles and identified 40 distinct expression profile clusters. Strikingly, two clusters are strongly enriched for sarcomeric components. Temporal gene expression together with detailed morphological analysis enabled us to define two distinct phases of sarcomere development, both of which require the transcriptional regulator Spalt major. During the first sarcomere formation phase, 2.0 µm long immature sarcomeres assemble myofibrils that spontaneously contract. In the second sarcomere maturation phase, sarcomeres grow to their final 3.2 µm length and 1.5 µm diameter and acquire stretch-sensitivity. Interestingly, the final number of myofibrils per flight muscle fiber is determined at the onset of the first phase and remains constant. Together, this defines a biphasic mode of sarcomere and myofibril morphogenesis – a new concept which may also apply to vertebrate muscle or heart development. Overall design: Part I: An 8-point timecourse of wild-type flight muscle development in Drosophila melanogaster was analyzed with duplicates/triplicates for each timepoint Part II: A Mef2-Gal4 x salmIR timecourse in duplicate at 4 timepoints was compared to wild-type flight muscle
Publication Title
A transcriptomics resource reveals a transcriptional transition during ordered sarcomere morphogenesis in flight muscle.
Sample Metadata Fields
Specimen part, Subject
View Samples- Mus musculus
- 5 Downloadable Samples
Affymetrix Murine Genome U74A Array (mgu74a)
Description
Identification of host responses at the gene transcription level provides a molecular profile of the events that occur following infection. Brucella abortus is a facultative intracellular pathogen of macrophages that induces chronic infection in humans and domestic animals. Using microarray technology, the response of macrophages 4 hours following B. abortus infection was analyzed to identify early intracellular infection events that occur in macrophages. Of the more than 6,000 genes, we identified over 140 genes that were reproducibly differentially transcribed. First, an increase in the transcription of a number of pro-inflammatory cytokines and chemokines, such as TNF-, IL-1, IL-1, and members of the SCY family of proteins, was evident that may constitute a general host recruitment of antibacterial defenses. Alternatively, Brucella may subvert newly arriving macrophages for additional intracellular infection. Second, transcription of receptors and cytokines associated with antigen presentation, e.g., MHC class II and IL-12p40, were not evident at this 4 hour period of infection. Third, Brucella inhibited transcription of various host genes involved in apoptosis, cell cycling, and intracellular vesicular trafficking. Identification of macrophage genes whose transcription was inhibited suggests that Brucella utilizes specific mechanisms to target certain cell pathways. In conclusion, these data suggest that B. abortus can alter macrophage pathways to recruit additional macrophages for future infection while simultaneously inhibiting apoptosis and innate immune mechanisms within the macrophage permitting intracellular survival of the bacterium. These results provide insights into the pathogenic strategies used by Brucella to survive long-term within a hostile environment.
Publication Title
Microarray analysis of mRNA levels from RAW264.7 macrophages infected with Brucella abortus.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 16 Downloadable Samples
Affymetrix Murine Genome U74A Array (mgu74a)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Brucella melitensis, B. neotomae and B. ovis elicit common and distinctive macrophage defense transcriptional responses.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 11 Downloadable Samples
- Affymetrix Murine Genome U74A Array (mgu74a)
Description
Brucella dynamically engage macrophages while trafficking to an intracellular replicative niche as macrophages, the first line of innate host defense, attempt to eliminate organisms. Brucella melitensis, B. neotomae, and B. ovis are highly homologous, yet exhibit a range of host pathogenicity and specificity. RAW 264.7 macrophages infected with B. melitensis, and B. ovis exhibit divergent patterns of bacterial persistence and clearance; conversely, B. melitensis and B. neotomae exhibit similar patterns of infection. Evaluating early macrophage interaction with Brucella spp. allows discovery of host entry and intracellular translocation mechanisms, rather than bacterial replication. Microarray analysis of macrophage transcript levels following a 4 hr Brucella spp. infection revealed 130 probe sets altered compared to uninfected macrophages; specifically, 72 probe sets were increased and 58 probe sets were decreased with any Brucella spp. Interestingly, much of the inflammatory response was not regulated by the number of Brucella gaining intracellular entry, as macrophage transcript levels were often equivalent among B. melitensis, B. ovis, and B. neotomae infections. An additional 33 probe sets were identified with altered macrophage transcript levels among Brucella spp. infections that may correlate with species specific host defenses and intracellular survival. Gene ontological categorization unveiled genes altered among species are involved in cell growth and maintenance, response to external stimuli, transcription regulation, transporter activity, endopeptidase inhibitor activity and G-protein mediated signaling. Host transcript profiles provide a foundation to understand variations in Brucella spp. infections, while structure of the macrophage response and intracellular niche of Brucella spp. will be revealed through piecewise consideration of host signaling pathways.
Publication Title
Brucella melitensis, B. neotomae and B. ovis elicit common and distinctive macrophage defense transcriptional responses.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
The spatial and temporal control of Hox gene transcription is essential for patterning the vertebrate body axis. Although this process involves changes in histone posttranslational modifications, the existence of particular three-dimensional (3D) architectures remained to be assessed in vivo. Using high-resolution chromatin conformation capture methodology, we examined the spatial configuration of Hox clusters in embryonic mouse tissues where different Hox genes are active. When the cluster is transcriptionally inactive, Hox genes associate into a single 3D structure delimited from flanking regions. Once transcription starts, Hox clusters switch to a bimodal 3D organization where newly activated genes progressively cluster into a transcriptionally active compartment. This transition in spatial configurations coincides with the dynamics of chromatin marks, which label the progression of the gene clusters from a negative to a positive transcription status. This spatial compartmentalization may be key to process the collinear activation of these compact gene clusters.
Publication Title
The dynamic architecture of Hox gene clusters.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
The spatial organization of DNA in the cell nucleus is an emerging key contributor to genomic function. We have developed 4C technology, or 3C-on-chip, which allows for an unbiased genome-wide search for DNA loci that contact a given locus in the nuclear space. We demonstrate here that active and inactive genes are engaged in many long-range intrachromosomal interactions and can also form interchromosomal contacts. The active b-globin locus in fetal liver contacts mostly transcribed, but not necessarily tissue-specific, loci elsewhere on chromosome 7, while the inactive locus in fetal brain contacts different, transcriptionally silent, loci. A housekeeping gene in a gene dense region on chromosome 8 forms long-range contacts predominantly with other active gene clusters, both in cis and in trans, and many of these intra- and interchromosomal interactions are conserved between the tissues analyzed. Our data demonstrate that chromosomes fold into areas of active chromatin and areas of inactive chromatin and establish 4C technology as a powerful tool to study nuclear architecture.
Publication Title
Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C).
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 60 Downloadable Samples
- Illumina HiSeq 2000
Description
Xist is indispensable for X chromosome inactivation (XCI) in female mammalian cells. However, how Xist RNA directs chromosome-wide transcriptional inactivation of the X chromosome is largely unknown. Here, to study chromosome inactivation by Xist, we generated a system where ectopic Xist expression can be induced from several genomic contexts in aneuploid mouse ES cells. We found that ectopic Xist expression from any location on the X chromosome faithfully recapitulated endogenous XCI, showing the potency of Xist to initiate XCI. Genes that escape XCI remain consistently transcriptionally active upon ectopic XCI, regardless of their position relative to Xist transgenes, and the enrichment of CTCF at their promoters is implicated in directing XCI escape. Xist expression from autosomes facilitates their transcriptional silencing to different degrees, and gene density in proximity of the Xist transcription locus plays a central role in determining the efficiency of gene inactivation. We also show that the enrichment of LINE elements together with a specific chromatin environment facilitates Xist-mediated silencing of both X-linked and autosomal genes. These findings provide new insights into the epigenetic mechanisms that mediate XCI and identify genomic features that promote Xist-mediated chromosome-wide gene inactivation Overall design: 60 RNA-seq from mouse embryonic stem cells and fully differentiated neurons in which ectopic Xist epression is either triggered (plus samples) or not (minus samples) upon doxycycline treatment.
Publication Title
Genetic and epigenetic features direct differential efficiency of Xist-mediated silencing at X-chromosomal and autosomal locations.
Sample Metadata Fields
Sex, Specimen part, Cell line, Subject
View Samples- Mus musculus
- 12 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Allelic exclusion of the immunoglobulin heavy chain locus is independent of its nuclear localization in mature B cells.
Sample Metadata Fields
Specimen part
View Samples