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SRP095338
Danio rerio
6 Downloadable Samples
IlluminaHiSeq2500
Description
To understand the basic biological property of hair cells (HCs) from lower vertebrates, we examined transcriptomes of adult zebrafish HCs. GFP-labeled HCs were isolated from the utricle, saccule, and lagena, the three inner-ear sensory epithelia of a pou4f3 promoter-driven GAP-GFP line of transgenic zebrafish. 2,000 HCs and 2,000 non-sensory cells from the inner ear were individually collected by suction pipet technique. RNA sequencing was performed and the resulting sequences were mapped, analyzed, and compared. Comparisons allow us to identify enriched genes in HCs, which may underlie HC specialization. Overall design: Examination of transcriptomes of adult zebrafish inner ear hair cells and surrounding cells individually collected and sorted using pou4f3 promoter-driven GFP marking hair cells.
Publication Title
RNA-seq transcriptomic analysis of adult zebrafish inner ear hair cells.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 203 Downloadable Samples
Affymetrix Human Genome U133A Array (hgu133a)
Description
Esophageal squamous cell carcinoma (ESCC) is an aggressive tumor with poor prognosis. Understanding molecular changes in ESCC should improve identification of risk factors in molecular subtypes and provide potential targets for early detection and therapy. To better characterize molecular changes in ESCC, we followed up a previous cDNA array study with additional discovery and confirmatory studies in new ESCC cases using alternative methods. We profiled global gene expression (Affymetrix U133A/B chip) for discovery and confirmation, and validated selected dysregulated genes with additional RNA (qRT-PCR, N=51) or protein studies (immunohistochemistry [IHC] of tumor tissue microarray [TMA], N=275).We also found genes associated with survival.
Publication Title
Global gene expression profiling and validation in esophageal squamous cell carcinoma and its association with clinical phenotypes.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 224 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
We identified different and common dysregulated genes in cardia and non-cardia gastric cancer in the two type of gastric cancer
Publication Title
Comparison of global gene expression of gastric cardia and noncardia cancers from a high-risk population in china.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 60 Downloadable Samples
- Affymetrix Human Genome U133A 2.0 Array (hgu133a2)
Description
In the current study we focused on biallelic loss and its relation to expression of mRNA and miRNA in ESCC using arrays of 500K SNP, mRNA, and miRNA in 30 cases from a high-risk region of China. Our main results are the followings: 1) 77 genes had biallelic loss in at least 10% of ESCC samples, and most of them are located on chromosome 3p (gene number, n=42), 9p (n=14), 5q (n=10) and 4p (n=7); 2) 52 of 77 genes had signals in both tumor and matched normal on Affymetrix Hu 133 array whereas 79% of them (n=41) showed lower expression levels in patients with biallelic loss (group 1) than that without biallelic loss (group 2) and 19% (n=10) of genes showed higher expression levels in group1 than in group2; 3) 70 miRNAs targeting 35 genes were analyzed, and expression levels of 50 miRNAs (71%) were high while expression levels of their targets were low, and 20 miRNA (29%) showed low expression while their target genes showed high expression; 4) 60 miRNAs target 32 affected genes showed that 43% of (n=26) miRNA expression level were low in group 1 than in group 2 and 57% (n=34) miRNA showed higher expression levels in group 1 than in group 2; and the expression patterns of miRNA and genes affected are complex when comparison the two groups of patients.
Publication Title
Integrative genomics analysis of genes with biallelic loss and its relation to the expression of mRNA and micro-RNA in esophageal squamous cell carcinoma.
Sample Metadata Fields
Specimen part, Disease
View Samples- Homo sapiens
- 117 Downloadable Samples
- Affymetrix Human Genome U133A 2.0 Array (hgu133a2)
Description
Barretts esophagus (BE) is a metaplastic precursor lesion of esophageal adenocarcinoma (EA), the most rapidly increasing cancer in western societies. While the prevalence of BE is increasing, the vast majority of EA occurs in patients with undiagnosed BE. Thus, we sought to identify genes that are altered in BE compared to the normal mucosa of the esophagus, and which may be potential biomarkers for the development or diagnosis of BE.
Publication Title
Global changes in gene expression of Barrett's esophagus compared to normal squamous esophagus and gastric cardia tissues.
Sample Metadata Fields
Specimen part
View Samples- Saccharomyces cerevisiae
- 6 Downloadable Samples
- Illumina Genome Analyzer II
Description
Using RNA-seq, we analyzed the transcriptomes of isogenic haploid (MATa) and tetraploid (MATaaaa) budding yeast strains in the Sigma 1278b background and identified genes whose regulation was altered by ploidy. Overall design: Analysis of poly(A)+ RNA from 2 biological replicates of haploid (MATa) and tetraploid (MATaaaa) strains.
Publication Title
Control of transcription by cell size.
Sample Metadata Fields
Sex, Specimen part, Cell line, Subject
View Samples- Mus musculus
- 10 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Astrogliosis is a hallmark of the response to brain ischemia, comprised of changes in gene expression and morphology. Hsp72 protects from cerebral ischemia, and although several mechanisms of protection have been investigated, effects on astrocyte activation are unknown. To identify potential mechanisms of protection, gene expression was assessed in mice subjected to middle cerebral artery (MCAO) or sham surgery, of either wildtype (WT) or Hsp72-overexpressing (Hsp72Tg) mice. After stroke, both genotypes exhibited genes related to cell death, stress response, and immune response. Furthermore, genes indicative of astrocyte activation, including cytoskeletal proteins and cytokines, were upregulated. To measure astrocyte activation after stroke, detailed histological and morphological analyses were performed in the cortical penumbra after stroke using unbiased stereology. Consistent with other reports, we observed a marked and persistent increase in glial fibrillary acidic protein (GFAP ) as soon as 3 hours after MCAO. In contrast, vimentin immunoreactivity appeared 12-24 hours after stroke, peaked at 72 hours, and returned to baseline after 30 days. Surprisingly, no change in overall astrocyte number was observed based on glutamine synthetase (GS) immunoreactivity. To determine if Hsp72Tg mice exhibited altered astrocyte activation compared to WT controls, morphological evaluation by fractal analysis was used. Overexpression of Hsp72 reduced astrocyte cell area, arbor area, and to a lesser extent fractal dimension, 72 hours following stroke. In conclusion, in vivo overexpression of Hsp72 alters gene expression following stroke, including genes involved in astrocyte activation, and decreases astrocyte activation acutely following MCAO. Thus, modulation of astrogliosis may be a neuroprotective mechanism exerted by Hsp72 after ischemia.
Publication Title
Effects of heat shock protein 72 (Hsp72) on evolution of astrocyte activation following stroke in the mouse.
Sample Metadata Fields
Sex, Treatment
View Samples- Arabidopsis thaliana
- 83 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
The organs of multicellular species are comprised of cell types that must function together to perform specific tasks. One critical organ function is responding to internal or external change but little is known about how responses are tailored to specific cell types or coordinated among them on a global level. Here we use cellular profiling of five Arabidopsis root cell types in response to a limiting resource, nitrogen, to uncover a vast and predominantly cell-specific response that was largely undetectable using traditional methods. These methods reveal a new class of cell-specific nitrogen responses. As a proof-of-principle, we dissected one cell-specific response circuit that mediates nitrogen-induced changes in root branching from pericycle cells. Thus, cellular response profiling links gene modules to discrete functions in specific cell types.
Publication Title
Cell-specific nitrogen responses mediate developmental plasticity.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 2 Downloadable Samples
- IlluminaHiSeq2000
Description
We''ve developed a new Method to Analyze RNA following Intracellular Sorting (MARIS) allowing us to carry out gene expression studies on cells sorted based on intracellular immunoflourescence. The purpose of this study is to determine the degree of bias that MARIS introduces on gene expression. We report RNA-seq gene expression data from human embryonic stem cells differentiated to a stage in which insulin-expressing cells are present. Gene expression data using RNA isolated from live cells is compared to gene expression data using RNA isolated from MARIS processed cells (fixed, permeabilized, antibody stained and mock sorted) to determine the degree of correlation in gene expression between these two biologically identical samples. Overall design: Human embryonic stem cells are differentiated to a stage in which insulin-expressing cells are present and split into two biologically identical samples. RNA is immediately isolated from one sample using the RNeasy protocol (live sample). RNA is isolated from the second sample following MARIS (processed sample) with all cells collected after the sort in order to keep the cell type composition between the live and processed samples the same.
Publication Title
MARIS: method for analyzing RNA following intracellular sorting.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 30 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Reactive astrogliosis is characterized by a profound change in astrocyte phenotype in response to all CNS injuries and diseases. To better understand the reactive astrocyte state, we used Affymetrix GeneChip arrays to profile gene expression in populations of reactive astrocytes isolated at various time points after induction using two different mouse injury models, ischemic stroke and neuroinflammation.
Publication Title
Genomic analysis of reactive astrogliosis.
Sample Metadata Fields
Sex, Specimen part, Treatment
View Samples