Filters
Technology
Platform
GSE58063
Arabidopsis thaliana
12 Downloadable Samples
Arabidopsis Gene 1.1 ST Array (aragene11st)
Description
7-days-old Arabidopsis seedlings of wildtype (Col-0) were treated with 1 M IAA for 15 minutes or 3 hours and gene expression of whole plant was analyzed using Affymetrix Gene 1.1 ST Array strips.
Publication Title
AtCAST3.0 update: a web-based tool for analysis of transcriptome data by searching similarities in gene expression profiles.
Sample Metadata Fields
Age, Treatment, Time
View Samples- Homo sapiens
- 6 Downloadable Samples
Illumina HiSeq 2500
Description
RNA sequencing was performed to investigate ionizing radiation-dependent transcriptional change in human pluripotent cells and differentiated cells. Overall design: Examined 3 types of cells (fibroblasts, iPS cells and neural progenitor cells) and 2 types of treatments (non IR or IR), total 6 samples were analyzed.
Publication Title
Reprogramming and differentiation-dependent transcriptional alteration of DNA damage response and apoptosis genes in human induced pluripotent stem cells.
Sample Metadata Fields
Specimen part, Treatment, Subject
View Samples- Homo sapiens
- 30 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
GIST is considered to invariably arise through gain-of-function KIT or PDGFRA mutation of the interstitial cells of Cajal (ICC). However, the genetic basis of the malignant progression of GIST is poorly understood.
Publication Title
Distinct gene expression-defined classes of gastrointestinal stromal tumor.
Sample Metadata Fields
Sex, Age
View Samples- Mus musculus
- 22 Downloadable Samples
- Illumina HiSeq 2500
Description
There is a continuing need for driver strains to enable cell type-specific manipulation in the nervous system. Each cell type expresses a unique set of genes, and recapitulating expression of marker genes by BAC transgenesis or knock-in has generated useful transgenic mouse lines. However since genes are often expressed in many cell types, many of these lines have relatively broad expression patterns. We report an alternative transgenic approach capturing distal enhancers for more focused expression. We identified an enhancer trap probe often producing restricted reporter expression and developed efficient enhancer trap screening with the PiggyBac transposon. We established more than 200 lines and found many lines that label small subsets of neurons in brain substructures, including known and novel cell types. Images and other information about each line are available online (http://enhnacertrap.bio.brandeis.edu). Overall design: Examination of 6 cortical mouse neuronal cell types. 5 of which are in layer 6 in 3 different cortical regions.
Publication Title
A Mammalian enhancer trap resource for discovering and manipulating neuronal cell types.
Sample Metadata Fields
Sex, Cell line, Subject
View Samples- Mus musculus
- 2 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Perilipin A (PeriA) exclusively locates on adipocyte lipid droplets and is essential for lipid storage and lipolysis. Adipocyte specific overexpression of PeriA caused resistance to diet-induced obesity and resulted in improved insulin sensitivity. In order to better understand the biological basis for this observed phenotype we performed DNA microarray analysis on white adipose tissue (WAT) from PeriA transgenic (Tg) and control wildtype (WT) mice.
Publication Title
Perilipin overexpression in white adipose tissue induces a brown fat-like phenotype.
Sample Metadata Fields
Sex, Specimen part
View Samples- Danio rerio
- 12 Downloadable Samples
- IlluminaHiSeq2500
Description
We use the Tlr2 mutant of zebrafish embryos model to study the transcriptome response to Mycobacterium marinum infection. We injected M.marinum into the caudal vein at 28 hours post fertilization and took samples at 4 days post infection. Overall design: This deep sequence study was designed to determine the gene expression profile in the Tlr2 mutant and heterozygote by M.marinum infection. RNA was isolated at 4 days post infection. Tlr2 mutants and heterozygotes zebrafish embryos were micro-injected into the caudal vein with 150CFU M.marinum, or PBS as a control at 28 hours post fertilization. After injections embryso were transerred into fresh egg water and incubated at 28 degree. At 4 days post infection triplicateds of 10 embryos per condition were snapfrozen in liquid nitogen, and total RNA was isolated using TRIZOL reagent.
Publication Title
Infection and RNA-seq analysis of a zebrafish tlr2 mutant shows a broad function of this toll-like receptor in transcriptional and metabolic control and defense to Mycobacterium marinum infection.
Sample Metadata Fields
No sample metadata fields
View Samples- Arabidopsis thaliana
- 12 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Arabidopsis thaliana wild-type and ire1a/ire1b double mutant plants were treated with tunicamycin. RNA was extracted and subjected to microarray analysis.
Publication Title
Arabidopsis IRE1 catalyses unconventional splicing of bZIP60 mRNA to produce the active transcription factor.
Sample Metadata Fields
No sample metadata fields
View Samples- Arabidopsis thaliana
- 4 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Purine catabolism is regarded as a housekeeping function that remobilizes nitrogen for plant growth and development. However, emerging evidence suggests that certain purine metabolites might contribute to stress protection of plants. Here, we show that in Arabidopsis, the intermediary metabolite allantoin plays a role in abiotic stress tolerance via activation of abscisic acid (ABA) metabolism. The aln loss-of-function of ALN, encoding allantoinase, results in increased allantoin accumulation, genome-wide up-regulation of stress-related genes, and enhanced tolerance to drought-shock and osmotic stress in aln mutant seedlings. This phenotype is not caused by a general response to purine catabolism inhibition, but rather results from a specific effect of allantoin. Allantoin activates ABA production both through increased transcription of NCED3, encoding a key enzyme in ABA biosynthesis, and through post-translational activation via high-molecular-weight complex formation of BG1, a -glucosidase hydrolyzing glucose-conjugated ABA. Exogenous application of allantoin to wild-type plants also activates the two ABA-producing pathways that lead to ABA accumulation and stress-responsive gene expression, but this effect is abrogated in ABA-deficient and BG1-knockout mutants. We propose that purine catabolism functions not only in nitrogen metabolism, but also in stress tolerance by influencing ABA production, which is mediated by the possible regulatory action of allantoin.
Publication Title
The purine metabolite allantoin enhances abiotic stress tolerance through synergistic activation of abscisic acid metabolism.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 3 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
To determine whether enhanced self-renewal and tumorigenicity in UT2 cells (derived from the second humanmouse xenotransplantation of U2OS cell-formed osteosarcoma tissues) correlate with increased expression of stem/progenitor cell-associated genes, we measured global gene expression in MSC, U2OS and UT2 cells by microarray analysis.
Publication Title
Human osteosarcoma CD49f(-)CD133(+) cells: impaired in osteogenic fate while gain of tumorigenicity.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 78 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Coordinated regulation of hepatic and adipose tissue transcriptomes by the oral administration of an amino acid mixture simulating the larval saliva of Vespa species.
Sample Metadata Fields
Sex, Specimen part
View Samples