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GSE34925
Homo sapiens
6 Downloadable Samples
Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
G9a is an H3K9m2 methyltransferase, which is critical in controlling gene suppression and DNA methylation. We used microarray analysis to identify the target genes that are regulated by G9a in MDA-MB231 cells, in which E-cadherin is silenced.
Publication Title
G9a interacts with Snail and is critical for Snail-mediated E-cadherin repression in human breast cancer.
Sample Metadata Fields
Specimen part, Cell line, Treatment
View Samples- Homo sapiens
- 16 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Besides the established selection criteria based on embryo morphology and blastomere number, new parameters for embryo viability are needed to improve the clinical outcome of in vitro fertilization (IVF) and more particular of elective single embryo transfer (eSET). The aim of the study was to analyse genome-wide whether the embryo viability was reflected by the expression of genes in the oocyte surrounding cumulus cells. Early cleavage (EC) was chosen as a parameter for embryo viability.
Publication Title
Differential gene expression in cumulus cells as a prognostic indicator of embryo viability: a microarray analysis.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 8 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
Gene expression changes in the heart of MCH3-KO mouse (HDAC3 f/f, Muscle Creatine Kinase-Cre) versus control WT mouse (HDAC3 f/f).
Publication Title
Diet-induced lethality due to deletion of the Hdac3 gene in heart and skeletal muscle.
Sample Metadata Fields
Specimen part
View Samples- Arabidopsis thaliana
- 6 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Growth in dense stands induces shade avoidance responses. Early responses to neighbors seem to be assoctaed with touch, not light signalling.
Publication Title
Plant neighbor detection through touching leaf tips precedes phytochrome signals.
Sample Metadata Fields
Specimen part
View Samples- Arabidopsis thaliana
- 24 Downloadable Samples
- Arabidopsis Gene 1.1 ST Array (aragene11st)
Description
In dense stands,the earliest neighbor response is induced by touching,leading to shade avoidance. During light competion the R:FR distribution is not homogenous, leading to local differences in light quality (R:FR) within the same leaf. Hyponasty is induced by FR-signaling in the lamina tip, which then induces local cell growth in the petiole base. Likewise, local touching of the leaf tip induces a similar phenoype.
Publication Title
Neighbor detection at the leaf tip adaptively regulates upward leaf movement through spatial auxin dynamics.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Homo sapiens
- 8 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Evidence for Alteration of Gene Regulatory Networks through MicroRNAs of the HIV-infected brain: novel analysis of retrospective cases.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Homo sapiens
- 8 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Major depressive disorder (MDD) is a clinically defined entity with little understanding as to the underlying pathological substrate. Biologically, MDD is characterized by disruption of neurotransmitters, especially serotonin and noradrenaline, which are the main targets of antidepressants. We previously demonstrated significant reduction of glial cell number in the cingulate and dorsolateral prefrontal cortical regions. Unfortunately, individuals living with HIV still have very high rates of MDD, despite the fact that mortality rates have fallen sharply with effective antiretroviral treatment. It is possible that in this treatment era, living with chronic HIV infection may result in long-term neuropathological changes that predispose to MDD. For example, it is known that HIV is associated with a range of inflammatory pathologies, neuronal loss, and dendrite-synaptic damage. In HIV, these neurodegenerative changes have been linked to neurocognitive impairments, however it is also possible that these changes potentiate MDD.
Publication Title
Evidence for Alteration of Gene Regulatory Networks through MicroRNAs of the HIV-infected brain: novel analysis of retrospective cases.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Mus musculus
- 10 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
Mammalian transcriptomes display complex circadian rhythms with multiple phases of gene expression that cannot be accounted for by current models of the molecular clock. We have determined the underlyingmechanisms by measuring nascent RNA transcription around the clock in mouse liver. Unbiased examination of eRNAs that cluster in specific circadian phasesidentified functional enhancers driven by distinct transcription factors (TFs). We further identify on a global scale the components of the TF cistromes that function to orchestrate circadian gene expression. Integrated genomicanalysesalso revealed novel mechanisms by which a single circadian factor controls opposing transcriptional phases. These findings shed new light on the diversity and specificity of TF function in the generation of multiple phases of circadian gene transcription in a mammalian organ.
Publication Title
Circadian enhancers coordinate multiple phases of rhythmic gene transcription in vivo.
Sample Metadata Fields
Sex, Time
View Samples- Mus musculus
- 98 Downloadable Samples
Illumina HiSeq 2000
Description
Acinar cells make up the majority of all cells in the pancreas, yet the source of new acinar cells during homeostasis remains unknown. Using multicolor lineage-tracing and organoid-formation assays, we identified the presence of a progenitor-like acinar cell subpopulation. These cells have long-term self-renewal capacity, albeit in a unipotent fashion. We further demonstrate that binuclear acinar cells are terminally differentiated acinar cells. Transcriptome analysis of single acinar cells revealed the existence of a minor population of cells expressing progenitor markers. Interestingly, a gain of the identified markers accompanied by a transient gain of proliferation was observed following chemically induced pancreatitis. Altogether, our study identifies a functionally and molecularly distinct acinar subpopulation and thus transforms our understanding of the acinar cell compartment as a pool of equipotent secretory cells. Overall design: The single-cell RNA-seq library preparation protocol was based on the SMART seq2 protocol (Picelli et al., 2014) with following modifications. Acinar cells were isolated as described in the section Acinar Cell Isolation and Culture and resuspended in DPBS without Ca2+ and Mg2+ (PAN-Biotech). Cells were collected in a volume of 0.5 µL and transferred to a reaction tube containing 4 µL of 6 M guanidine-HCl (Sigma-Aldrich), 0.1% (v/v) Triton X-100 (Sigma-Aldrich) and 1% (v/v) 2-mercaptoethanol (?Sigma-Aldrich). The tube was immediately transferred into liquid nitrogen and kept there for the duration of cell collection. Next, 2.2× RNA SPRI beads (Beckman Coulter) were added directly to the lysis buffer and incubated for 5 min at room temperature. The beads were washed twice with 70% ethanol. Air-dried beads were resuspended in a solution containing 2 µL of H20, 1 µL of oligo(dT) primer, and 1 µL of dNTP Mix (primer and nucleotides used as in Picelli et al., 2014). Twenty-four cells contained ERCC Spike-In RNAs (1:10,000; Mix2, Ambion) Mix in addition to primer and nucleotides. Beads were incubated for 3 min at 72°C, and reverse transcription and PCR (19 cycles) were performed as described by Picelli et al. (2014). PCR product was cleaned up using 0.8× DNA SPRI beads (Beckman Coulter), and air-dried beads were resuspended in 15 µL of H2O. The quality of cDNA library was assessed for each cell on a high-sensitivity DNA Bioanalyzer chip. Subsequent steps (tagmentation, amplification, multiplexing) were done as previously described (Llorens-Bobadilla et al., 2015). The DKFZ Genomics and Proteomics Core Facility conducted sequencing on an Illumina HiSeq2000 sequencer (paired-end 100 bp).
Publication Title
Single-Cell Analysis Uncovers Clonal Acinar Cell Heterogeneity in the Adult Pancreas.
Sample Metadata Fields
Sex, Specimen part, Cell line, Subject
View Samples- Homo sapiens
- 29 Downloadable Samples
- Affymetrix Human Exon 1.0 ST Array [transcript (gene) version (huex10st)
Description
Schizophrenia (SCZ) and bipolar disorder (BPD) are polygenic disorders with many genes contributing to their etiologies. The aim of this investigation was to search for dysregulated molecular and cellular pathways for these disorders as well as psychosis. We conducted a blood-based microarray investigation in two independent samples with SCZ and BPD from San Diego (SCZ=13, BPD=9, control=8) and Taiwan [data not included](SCZ=11, BPD=14, control=16). Diagnostic groups were compared to controls, and subjects with a history of psychosis [PSYCH(+): San Diego (n=6), Taiwan (n=14)] were compared to subjects without such history [PSYCH(-): San Diego (n=11), Taiwan (n=14)]. Analyses of covariance comparing mean expression levels on a gene-by-gene basis were conducted to generate the top 100 significantly dysregulated gene lists for both samples by each diagnostic group. Gene lists were imported into Ingenuity Pathway Analysis (IPA) software. Results showed the ubiquitin proteasome pathway (UPS) was listed in the top ten canonical pathways for BPD and psychosis diagnostic groups across both samples with a considerably low likelihood of a chance occurrence (p = .001). No overlap in dysregulated genes populating these pathways was observed between the two independent samples. Findings provide preliminary evidence of UPS dysregulation in BPD and psychosis as well as support further investigation of the UPS and other molecular and cellular pathways for potential biomarkers for SCZ, BPD, and/or psychosis.
Publication Title
Preliminary evidence of ubiquitin proteasome system dysregulation in schizophrenia and bipolar disorder: convergent pathway analysis findings from two independent samples.
Sample Metadata Fields
Sex, Age, Disease
View Samples