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E-MEXP-3602
Arabidopsis thaliana
9 Downloadable Samples
Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Plants of Arabidopsis thaliana (ecotype Col-0, nrb4-2 and nrb4-4) were grown in phytochambers in short day conditions during three weeks. Then, samples from different pots were mixed, and the RNA extracted.
Publication Title
Non-recognition-of-BTH4, an Arabidopsis mediator subunit homolog, is necessary for development and response to salicylic acid.
Sample Metadata Fields
Age
View Samples- Rattus norvegicus
- 60 Downloadable Samples
- Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
Pyrethroids are neurotoxicants that disrupt nervous system function by interacting with a variety of membrane bound ion channels on neuronal plasma membranes. This study is designed to investigate the transcriptional events downstream of pyrethroid-induced disruption of nervous system excitability. Adult, male Long-Evans rats were orally dosed in vivo with a single dose of either permethrin (1, 10, or 100 mg/kg) or deltamethrin (0.3, 1, 3 mg/kg) at levels that produce only modest behaviroal effects in the whole animal (Wolansky et al. 2006). Transcriptional profiles were obtained from frontal cerebrocortical tissue 6 hours after acute exposure. The primary goals were 1) to identify dose-responsive biomarkers of effect for pyrethroids and 2) identify sensitive intracellular signaling or metabolic pathways sensitive to pyrethroid compounds.
Publication Title
Transcriptional response of rat frontal cortex following acute in vivo exposure to the pyrethroid insecticides permethrin and deltamethrin.
Sample Metadata Fields
Sex, Specimen part
View Samples- Mus musculus
- 15 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
In order to identify genes that are activated in differentiating WT ESCs, but are missing in Tal-1-/- and Runx1-/- ESCs, and which might be involved in the generation of definitive hematopoietic progenitors and their specification thereafter, we performed microarray analyses on purified Flk-1+ cells, differentiated from these ESCs for 4, 5, and 6 days in vitro.
Publication Title
Ectopic Runx1 expression rescues Tal-1-deficiency in the generation of primitive and definitive hematopoiesis.
Sample Metadata Fields
Specimen part, Cell line, Time
View Samples- Arabidopsis thaliana
- 18 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Arabidopsis plants were treated either with mock or MSB (0.2 mM of Menadione sodium bisulphite). <br></br>Tissue was sampled after 3, 6 and 24 hours.
Publication Title
Molecular analysis of menadione-induced resistance against biotic stress in Arabidopsis.
Sample Metadata Fields
Age, Specimen part, Compound, Time
View Samples- Mus musculus
- 53 Downloadable Samples
Illumina HiSeq 2000
Description
Two metrics, a rise in serum creatinine concentration and a decrease in urine output, are considered tantamount to the injury of the kidney tubule and the epithelial cells thereof (AKI).Yet neither criterion emphasizes the etiology or the pathogenetic heterogeneity of acute decreases in kidney excretory function. In fact, whether decreased excretory function due to contraction of the extracellular fluid volume (vAKI) or due to intrinsic kidney injury (iAKI) actually share pathogenesis and should be aggregated in the same diagnostic group remains an open question. To examine this possibility, we created mouse models of iAKI and vAKI that induced a similar increase in serum creatinine concentration. Using laser microdissection to isolate specific domains of the kidney, followed by RNA sequencing, we found that thousands of genes responded specifically to iAKI or to vAKI, but very few responded to both stimuli. In fact, the activated gene sets comprised different, functionally unrelated signal transduction pathways and were expressed in different regions of the kidney. Moreover, we identified distinctive gene expression patterns in human urine as potential biomarkers of either iAKI or vAKI, but not both. Hence, iAKI and vAKI are biologically unrelated, suggesting that molecular analysis should clarify our current definitions of acute changes in kidney excretory function. Overall design: Examining transcriptional profiles of two models of "acute kidney injury" (iAKI and pAKI), compared to controls, in different microanatomic regions of the kidney using laser capture microdissection
Publication Title
Unique Transcriptional Programs Identify Subtypes of AKI.
Sample Metadata Fields
Subject
View Samples- Homo sapiens
- 12 Downloadable Samples
- NextSeq 500
Description
Maddalena et al. showed that the limited DNA transfer capacity (~4.7kb) of adeno associated viral (AAV) vectors can be expanded up to 14kb with triple AAV vectors for the efficient expression of the therapeutic CDH23 (10.1kb) and ALMS1 (12.5kb) genes. Overall design: cells infected with triple AAV vectors carrying 2 different transgenes in 3 biological replicates; RNA extracted from WT cells was used as control .
Publication Title
Triple Vectors Expand AAV Transfer Capacity in the Retina.
Sample Metadata Fields
Cell line, Subject
View Samples- Danio rerio
- 14 Downloadable Samples
- IlluminaGenomeAnalyzerII
Description
We compared transcriptional profiles of regenerating zebrafish caudal fins following fin amputation with profiles from uninjured zebrafish caudal fins Overall design: Examination of whole fin transcriptional profiles from regenerating fins (2 pools of 10 fins) and uninjured fins (2 pools of 10 fins)
Publication Title
Modulation of tissue repair by regeneration enhancer elements.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 12 Downloadable Samples
- Affymetrix Human Transcriptome Array 2.0 (hta20)
Description
We used a microarray to examine the global gene expression profile of MCF7 cells grown in 2D and 3D culture conditions. Our goal was to identify changes in the expression of genes that regulate iron metabolism when cellular spatial organization was altered.
Publication Title
Contribution of three-dimensional architecture and tumor-associated fibroblasts to hepcidin regulation in breast cancer.
Sample Metadata Fields
Age, Specimen part, Cell line
View Samples- Danio rerio
- 4 Downloadable Samples
- IlluminaGenomeAnalyzerII
Description
We compared transcriptional and chromatin profiles of regenerating zebrafish hearts following genetic ablation with profiles from uninjured zebrafish hearts. Overall design: Examination of whole heart transcriptional profiles from ablated hearts (2 pools of 10 hearts) and uninjured hearts (2 pools of 10 hearts). Examination of differential H3K27Ac marks following genetic ablation of cardiomyocytes (regenerating hearts) and uninjured hearts.
Publication Title
Modulation of tissue repair by regeneration enhancer elements.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 18 Downloadable Samples
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Interferon-γ-stimulated genes, but not USP18, are expressed in livers of patients with acute hepatitis C.
Sample Metadata Fields
Specimen part, Disease, Disease stage, Treatment, Subject, Time
View Samples