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SRP067490
Mus musculus
12 Downloadable Samples
Illumina HiSeq 2000
Description
The ability to generate defined null mutations in mice revolutionized the analysis of gene function in mammals. However, gene-deficient mice generated by using 129-derived embryonic stem (ES) cells may carry large segments of 129 DNA, even when extensively backcrossed to reference strains, such as C57BL/6J, and this may confound interpretation of experiments performed in these mice. Tissue plasminogen activator (tPA), encoded by the PLAT gene, is a fibrinolytic serine protease that is widely expressed in the brain. A large number of neurological abnormalities have been reported in tPA-deficient mice. The studies here compare genes differentially expressed in the brains of Plat-/- mice from two independent Plat-/- mouse derivations to wild-type C57BL/6J mice. One strain denoted “Old” was constructed in ES cells from a 129 mouse and backcrossed extensively to C57BL/6J, and one denoted “New” Plat-/- mouse was constructed using zinc finger nucleases directly in the C57BL/6J-Plat-/- mouse strain. We identify a significant set of genes that are differentially expressed in the brains of Old Plat-/- mice that preferentially cluster in the vicinity of Plat on chromosome 8, apparently linked to more than 20 Mbp of DNA flanking Plat being of 129 origin. No such clustering is seen in the New Plat-/- mice. Overall design: Whole-transcriptome profiling of the cerebral cortex of wild-type control C57BL/6J mice and two independent Plat-/- mice strains on the C57BL/6J background.
Publication Title
Passenger mutations and aberrant gene expression in congenic tissue plasminogen activator-deficient mouse strains.
Sample Metadata Fields
Age, Specimen part, Cell line, Subject
View Samples- Saccharomyces cerevisiae
- 18 Downloadable Samples
Affymetrix Yeast Genome S98 Array (ygs98)
Description
We are investigating the transcriptional response of yeast to treatment with enediynes or gamma radiation, which generate different extents of double or single strand breaks in DNA.
Publication Title
The DNA-damage signature in Saccharomyces cerevisiae is associated with single-strand breaks in DNA.
Sample Metadata Fields
No sample metadata fields
View Samples- Saccharomyces cerevisiae
- 12 Downloadable Samples
- Affymetrix Yeast Genome S98 Array (ygs98)
Description
We are investigating the transcriptional response of Anc1 deficient yeast under basal and MMS exposed conditions
Publication Title
Anc1, a protein associated with multiple transcription complexes, is involved in postreplication repair pathway in S. cerevisiae.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 98 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
We have investigated whether gene expression signatures can be used to predict inter-individual responses to DNA damaging agents
Publication Title
Genomic predictors of interindividual differences in response to DNA damaging agents.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 6 Downloadable Samples
- Illumina HiSeq 2000
Description
We report genome-wide expression changes that occur in adipose-derived mesenchymal stem cells upon treatment with CytoD cytoskeletal drug. mRNA-Seq analysis shows that CytoD-treated samples cluster together. In addition, we also see that cells treated with CytoD show upregulation of osteogenic markers, epiregulators, and a number of key molecular function pathways including extracellular matrix, cell membrane gene expression. Overall design: Adipose MSCs were cultured in Advanced-MEM base (Life Technologies), 5% platelet lysate, and 1% non-essential amino acids (Life Technologies), and 2U/ml heparin. Cells used for experiments were of passage 6. Adipose MSCs were seeded at 3,000 cells per cm2 in maintenance medium in 6-well plates and incubated under standard culture conditions for 24 hours before being changed to osteogenic medium containing vehicle (DMSO) or 0.1 µg/ml cytochalasin D (Sigma). Osteogenic medium maintenance media supplemented with 10 nM dexamethasone, 25 µg/ml ascorbic acid, and 10 mM ß-glycerophosphate. Cells in culture were prepared for RNA isolation by lysing with Qiazol. Purified RNA was then submitted for RNA-sequencing.
Publication Title
Osteogenic Stimulation of Human Adipose-Derived Mesenchymal Stem Cells Using a Fungal Metabolite That Suppresses the Polycomb Group Protein EZH2.
Sample Metadata Fields
Specimen part, Subject
View Samples- Mus musculus
- 5 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
We are investigating the transcriptional response of mice infected with Helicobacter hepaticus and links to liver cancer
Publication Title
Genetic susceptibility to chronic hepatitis is inherited codominantly in Helicobacter hepaticus-infected AB6F1 and B6AF1 hybrid male mice, and progression to hepatocellular carcinoma is linked to hepatic expression of lipogenic genes and immune function-associated networks.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 12 Downloadable Samples
- Illumina HiSeq 2000
Description
We report genome-wide expression changes that occur in mouse bone marrow-derived mesenchymal stem cells treated in triplicate for 24 hours with or without Cytochalasin D and/or CK666. mRNA-Seq analysis shows that both cell surface and the nucleus undergo phenotypic changes. Cytochalasin D enhanced expression of genes involved in pathways known to regulate osteoblast differentiation, including genes involved in development and cell signaling, including calcium ion binding, WNT and PI3K/AKT pathway. In summary, RNA-seq data reveal that the CytoD activates genes linked to osteogenesis, while CK666stimulates adipogenic genes. Overall design: Bone marrow-derived MSCs were maintained in MEM containing 10% fetal bovine serum, 100 µg/ml penicillin/streptomycin. For experiments, the cells were plated at a density of 10,000 cells/cm2 in 6-well culture plates and cultured for 1 day prior to application of treatments. Cells were treated with CytochalasinD and/or CK666 for 24h followed by preparation for RNA isolation. Purified RNA was then submitted for RNA-sequencing.
Publication Title
Intranuclear Actin Structure Modulates Mesenchymal Stem Cell Differentiation.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 8 Downloadable Samples
- Illumina HiSeq 2000
Description
We report genome-wide expression changes that occur in H9-iMSCs frozen with different freezing methods that include DMSO and non-DMSO experimental solutions such as SGC (sucrose-glycerol-creatinine, SMC (sucrose-mannitol-creatinine), and SGI (sucrose-mannitol-isoleucine). mRNA-Seq analysis shows that DMSO samples cluster with fresh samples in the same clade, while all samples using the experimental solutions cluster together. In addition, we also see that cells frozen using experimental solutions have upregulation of a number of key molecular function pathways including extracellular matrix structural genes, receptor binding, and growth factor expression. Overall design: H9 MSCs were cultured in alpha-MEM base (Life Technologies), 10% FBS (qualified), and 1% non-essential amino acids (Life Technologies). Culture flasks were coated with 0.01% porcine gelatin (Fisher) for a minimum of 2 hours before H9 MSC seeding. H9 MSCs were seeded in gelatin-coated flasks at a density of approximately 2500 cells/cm2. Cells were split when they reached 70% confluence and were used for experiments only from passages 8 to 12. Control cells in media were similarly combined stepwise with DMSO at a 1:1 final volume ratio. Each of these vials was incubated at room temperature for 0, 1, or 2 hours. Experimental solutions were frozen using a 3°C/min cooling rate while DMSO solutions were frozen using a 1°C/min cooling rate. Samples were submerged in a 37ºC bath to just under cap level, and agitated until only a small ice crystal was present. The cells were combined with acridine orange/propidium iodide (AO/PI) and enumerated using a hemocytometer. Samples were diluted, centrifuged and supernatant was aspirated, followed by preparation for RNA isolation. Purified RNA was then submitted for RNA-sequencing.
Publication Title
Improved Post-Thaw Function and Epigenetic Changes in Mesenchymal Stromal Cells Cryopreserved Using Multicomponent Osmolyte Solutions.
Sample Metadata Fields
Cell line, Subject
View Samples- Homo sapiens
- 75 Downloadable Samples
- Illumina HumanHT-12 V4.0 expression beadchip
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Promiscuous targeting of bromodomains by bromosporine identifies BET proteins as master regulators of primary transcription response in leukemia.
Sample Metadata Fields
Cell line, Treatment
View Samples- Homo sapiens
- 40 Downloadable Samples
- Illumina HumanHT-12 V4.0 expression beadchip
Description
Bromodomains (BRDs) have emerged as compelling targets for cancer therapy. The development of selective and potent BET inhibitors and their significant activity in diverse tumor models has rapidly translated into clinical studies and has motivated drug development efforts targeting non-BET BRDs. However, the complex multidomain/subunit architecture of bromodomain protein complexes complicates predictions of consequences of their pharmacological targeting. To address this issue we developed a promiscuous bromodomain inhibitor (bromosporine, BSP) that broadly targets BRDs (including BETs) with nanomolar affinity, creating a tool for the identification of cellular processes and diseases where BRDs have a regulatory function. As a proof of principle we studied the effect of BSP in leukemic cell-lines known to be sensitive to BET inhibition and found as expected strong anti-proliferative activity. Comparison of the modulation of transcriptional profiles by BSP at short inhibitor exposure resulted in a BET inhibitor signature but no significant additional changes in transcription that could account for inhibition of other BRDs. Thus, non-selective targeting of BRDs identified BETs, but not other BRDs, as master regulators of a context dependent primary transcription response.
Publication Title
Promiscuous targeting of bromodomains by bromosporine identifies BET proteins as master regulators of primary transcription response in leukemia.
Sample Metadata Fields
Cell line, Treatment
View Samples