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E-MTAB-5610
Arabidopsis thaliana
6 Downloadable Samples
Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
This experiment analyzes the changes in expression of twelve days old Arabidopsis roots at ten hours post inoculation upon cyst nematode H. schachtii infection.
Publication Title
Arabidopsis leucine-rich repeat receptor-like kinase NILR1 is required for induction of innate immunity to parasitic nematodes.
Sample Metadata Fields
Age, Specimen part
View Samples- Arabidopsis thaliana
- 6 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
This experiment analyzes the changes in expression of ten days old Arabidopsis roots upon NemaWater treatment.
Publication Title
Arabidopsis leucine-rich repeat receptor-like kinase NILR1 is required for induction of innate immunity to parasitic nematodes.
Sample Metadata Fields
Age, Specimen part
View Samples- Homo sapiens
- 818 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Xenograft models remain a cornerstone technology in the development of anti-cancer agents. The ability of immunocompromised rodents to support the growth of human tumors provides an invaluable transition between in vitro testing and clinical trials. Therefore, approaches to improve model selection are required. In this study, cDNA microarray data was generated for a collection of xenograft models at in vivo passages 1, 4 and 10 (P1, P4 and P10) along with originating cell lines (P0). These data can be mined to determine transcript expression 1) relative to other models 2) with successive in vivo passage and 3) during the in vitro (P0) to in vivo (P1) transition.
Publication Title
Gene expression profiling of 49 human tumor xenografts from in vitro culture through multiple in vivo passages--strategies for data mining in support of therapeutic studies.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus, Homo sapiens
- 27 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Transcriptomic studies of human tumor xenografts are complicated by the presence of murine cellular mRNA. As such, it is useful to know the extent to which mouse mRNA cross-hybridizes to any given array platform. In this study, murine cDNA samples from diverse sources were hybridized to Affymetrix Human Genome U133 Plus 2.0 Arrays. In this regard it is possible to identify specific probes that are potential targets of cross-species interference.
Publication Title
Gene expression profiling of 49 human tumor xenografts from in vitro culture through multiple in vivo passages--strategies for data mining in support of therapeutic studies.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Pseudomonas aeruginosa pao1
- 12 Downloadable Samples
- Affymetrix Pseudomonas aeruginosa Array (paeg1a)
Description
Here we examined virulence activation in Pseudomonas aeruginosa in response to the synthetic kappa opioid agonist U-50, 488 in nutrient poor media where growth conditions are limited and density dependent quorum sensing is not activated.
Publication Title
Pseudomonas aeruginosa overrides the virulence inducing effect of opioids when it senses an abundance of phosphate.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 4 Downloadable Samples
Illumina HiSeq 2500
Description
We report bulk RNAseq of in vitro cultured horizontal basal cells, and in vivo isoalted respiratory basal cells of the murine olfactory epithelium, and compared their profiles with pre-existing bulk RNAseq of in vivo isolated HBCs and single cell RNAseq of in vivo HBCs. Overall design: RNAseq of in vitro horizontal basal cells (HBCs) in triplicate under control conditions, and FACS isolated in vivo respiratory basal cells in singlet
Publication Title
Activating a Reserve Neural Stem Cell Population In Vitro Enables Engraftment and Multipotency after Transplantation.
Sample Metadata Fields
Subject
View Samples- Rattus norvegicus
- 6 Downloadable Samples
- Affymetrix Rat Gene 1.0 ST Array (ragene10st)
Description
Topoisomerase 1 (TOP1) poisons like camptothecin (CPT), which are used as chemotherapeutic agents in cancer, elicit DNA damage in quiescient neurons. In this study, we examined the effects of CPT and actinomycin D (ActD) on neuronal cells. Motor (MNs) and cortical (CNs) neurons were more susceptible to the toxic effects of CPT and ActD than fibroblasts. MNs and CNs exhibited a delayed DNA damage responseincrease in nuclear -H2AX focirelative to fibroblasts. Neuronal cells expressed higher levels of Top1 mRNA than fibroblasts which could explain their enhanced vulnerability to CPT and ActD toxicity. Microarray analysis was performed to identify differentially regulated transcripts in MNs treated with CPT for 2 hours. Many immediate-early genes including Fos and Egr-1 were upregulated in CPT-treated MNs. Fos mRNA levels were elevated in all cells types treated with CPT; Egr-1 transcript levels, however, were reduced in CPT-treated fibroblasts even though they were elevated in treated MNs and CNs. Pathway and network analysis of the differentially expressed transcripts revealed activation of ERK and JNK signaling cascades in CPT-treated MNs. In conclusion, MNs were more vulnerable than fibroblasts to the damaging effects of TOP1 poisons and they elicit a unique intracellular response to CPT treatment.
Publication Title
Identification of early gene expression changes in primary cultured neurons treated with topoisomerase I poisons.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Homo sapiens
- 9 Downloadable Samples
- Illumina Genome Analyzer IIx
Description
We have performed genome-wide DNA methylation analysis at single base resolution and gene expression analysis, resulted in hypermethylation in all autosomes in DS samples, mediated by down-regulation of all three TET family genes, and down-regulation of REST/NRSF. Genes located on chr21 were up-regulated by a median of 45% in DS compared to normal villi, while genes with promoter hypermethylation were down regulated. Overall design: Comparison of RNA expression in human placenta between 5 normal and 4 Trisomy 21 samples.
Publication Title
Global DNA hypermethylation in down syndrome placenta.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 52 Downloadable Samples
- Illumina HumanHT-12 V4.0 expression beadchip
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
ACSL1 Is Associated With Fetal Programming of Insulin Sensitivity and Cellular Lipid Content.
Sample Metadata Fields
Sex
View Samples- Homo sapiens
- 28 Downloadable Samples
- Illumina HumanHT-12 V4.0 expression beadchip
Description
We hypothesised that SGA as a proxy for intrauterine growth restriction promotes specific epigenetic marks and pathways, whose physiological implications may become apparent only in the fully differentiated state.
Publication Title
ACSL1 Is Associated With Fetal Programming of Insulin Sensitivity and Cellular Lipid Content.
Sample Metadata Fields
Sex
View Samples