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GSE69512
Mus musculus
12 Downloadable Samples
Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Msi2 is a critical regulatior of myeoid leukemia, and these data identify genes that are changed following Msi2 deletion in bcCML and de novo AML stem cells.
Publication Title
Tetraspanin 3 Is Required for the Development and Propagation of Acute Myelogenous Leukemia.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 12 Downloadable Samples
Illumina HiSeq 2500
Description
miRNA-Sequencing was performed on human aortic valve interestitial cells (AVICs) exposed to 14% stretch at 1 hz or static conditions for 24h. Overall design: Six static control and six samples exposed to cyclic stretch 14% for 24h
Publication Title
The stretch responsive microRNA miR-148a-3p is a novel repressor of IKBKB, NF-κB signaling, and inflammatory gene expression in human aortic valve cells.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 6 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
AVICs were exposed to cyclic stretch to examine the role of mechanical stimuli on gene expression
Publication Title
The stretch responsive microRNA miR-148a-3p is a novel repressor of IKBKB, NF-κB signaling, and inflammatory gene expression in human aortic valve cells.
Sample Metadata Fields
Specimen part
View Samples- Arabidopsis thaliana
- 52 Downloadable Samples
- Arabidopsis Gene 1.1 ST Array (aragene11st)
Description
Plants have evolved shoot elongation mechanisms to escape from diverse environmental stresses such as flooding and vegetative shade. The apparent similarity in growth responses suggests possible convergence of the signalling pathways. Shoot elongation is mediated by passive ethylene accumulating in flooded plant organs and by changes in light quality and quantity under vegetation shade. Here we study hypocotyl elongation as a proxy for shoot elongation and delineated Arabidopsis hypocotyl length kinetics in response to ethylene and shade. Based on these kinetics, we further investigated ethylene and shade-induced genome-wide gene expression changes in hypocotyls and cotyledons separately. Both treatments induced a more extensive transcriptome reconfiguration in the hypocotyls compared to the cotyledons. Bioinformatics analyses suggested contrasting regulation of growth promotion- and photosynthesis-related genes. These analyses also suggested an induction of auxin, brassinosteroid and gibberellin signatures and the involvement of several candidate regulators in the elongating hypocotyls. Pharmacological and mutant analyses confirmed the functional involvement of several of these candidate genes and physiological control points in regulating stress-escape responses to different environmental stimuli. We discuss how these signaling networks might be integrated and conclude that plants, when facing different stresses, utilise a conserved set of transcriptionally regulated genes to modulate and fine tune growth.
Publication Title
Ethylene- and Shade-Induced Hypocotyl Elongation Share Transcriptome Patterns and Functional Regulators.
Sample Metadata Fields
Specimen part, Treatment, Time
View Samples- Homo sapiens
- 9 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Esophageal cancer is one of the deadliest cancers as patients present at late stages of disease. Frequent gene alterations include the loss of E-cadherin and TGFb receptor type II. The goal of this study was to establish a model of esophageal cancer by introducing dominant-negative mutants of E-cadherin and TGFb receptor II.
Publication Title
Imbalance of desmoplastic stromal cell numbers drives aggressive cancer processes.
Sample Metadata Fields
Cell line
View Samples- Homo sapiens
- 4 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
SCC12 cells were seeded ontop of organotypic gels with HN-CAF (head and neck carcinoma associated fibroblasts). Differential gene expression was analysed between cancer cells not exposed to CAFs or non-invading cancer cells exposed to CAFs.
Publication Title
Imbalance of desmoplastic stromal cell numbers drives aggressive cancer processes.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Homo sapiens
- 9 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Studies of adult human hematopoiesis have until now relied on the expression of CD10 to define lymphoid commitment. We report a novel lymphoid-primed population in human bone marrow that is generated from hematopoietic stem cells (HSC) prior to the onset of CD10 expression and B cell commitment, and is identified by high levels of the homing molecule L-selectin (CD62L). CD10-CD62Lhi progenitors have full lymphoid (B/T/NK) potential, and show reduced myeloid and absent erythroid potential. Genome-wide gene expression analysis demonstrates that the CD10-CD62Lhi population represents an intermediate stage of differentiation between CD34+CD38- HSC and CD34+lin-CD10+ progenitors marked by down-regulation of TAL1 and MPL, upregulation of E2A, CD3E and IL2RG expression, and absent B cell commitment or RAG1/2 expression. Immature CD34+CD1a- thymocytes are also CD62Lhi and L-selectin ligands are expressed at the cortico-medullary junction, suggesting a possible role for L-selectin in human thymic homing. These studies identify the earliest stage of lymphoid priming in human bone marrow.
Publication Title
Lymphoid priming in human bone marrow begins before expression of CD10 with upregulation of L-selectin.
Sample Metadata Fields
Specimen part
View Samples- Arabidopsis thaliana
- 20 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
This study profiles transcriptomic changes of Arabidopsis thaliana Col-0 in response to submergence. This dataset includes CEL files, RMA signal values and MAS5 P/M/A calls from total mRNA populations of plants at 9 to 10 leaf rosette stage. Biological replicates of root and shoot tissues were harvested after 7 h and 24 h of submergence in darkness along with corresponding non-submerged dark controls. To characterize the dark response, non-submerged light controls plants were harvested at the 0 h time point. Quantitative profiling of cellular mRNAs was accomplished with the Affymetrix ATH1 platform. Changes in the transcriptome in response to submergence and early darkness were evaluated, and the data led to identification of genes co-regulated at the conditional and organ-specific level.
Publication Title
Molecular characterization of the submergence response of the Arabidopsis thaliana ecotype Columbia.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Mus musculus
- 20 Downloadable Samples
- Illumina HiSeq 2000
Description
Purpose: The goals of this study were to identify quantitative gene expression differences between whole tumor and tumor-associated macrophages (TAMs) derived from Lewis lung carcinoma (LLC) tumors grown in wild type and PI3Kinase-gamma-null mice. Methods: mRNA profiles of whole tumor or tumor-associated macrophages (CD11b+Gr1- cells) from wild type (WT) or PI3Kinase-gamma-knockout (p110g-/-) mice were generated by single deep read sequencing, in triplicate or quadruplicate, using Illumina HiSeq 2000. The sequence reads that passed quality filters were aligned to mouse transcriptome using the bowtie2 aligner. Gene-level summaries were normalized and analyzed for differential expression using DESeq. Overall design: mRNA profiles of whole tumor and tumor-associated macrophages from WT and p110g-/- mice were generated by deep sequencing in triplicate or quadruplicate using Illumina HiSeq 2000.
Publication Title
PI3Kγ is a molecular switch that controls immune suppression.
Sample Metadata Fields
Specimen part, Subject, Time
View Samples- Mus musculus
- 18 Downloadable Samples
- Illumina HiSeq 2000
Description
Purpose: The goals of this study were to identify quantitative gene expression differences between macrophages derived from wild type and PI3Kgamma null macrophages Methods: mRNA profiles of MCSF, IL4 and IFNg/LPS stimulated macrophage wild-type (WT) and PI3Kinase gamma knockout (p110g-/-) mice were generated by single read deep sequencing, in triplicate, using Illumina HiSeq2000. The sequence reads that passed quality filters were aligned to mouse transcriptome using the bowtie2 aligner. Gene-level summaries were normalized and analyzed for differential expression using DESeq. qRT–PCR validation was performed using SYBR Green assays. Conclusions: Our study represents the first detailed analysis of the role of p110g in the control of the macrophage immune response, with biological replicates, generated by RNA-seq technology. Overall design: mRNA profiles of wild type (WT) and p110g-/- macrophages were generated by deep sequencing, in triplicate, using Illumina HiSeq2000.
Publication Title
PI3Kγ is a molecular switch that controls immune suppression.
Sample Metadata Fields
No sample metadata fields
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