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SRP089712
Mus musculus
86 Downloadable Samples
Illumina HiSeq 2000
Description
We analyzed Purkinje cell transcriptome dynamics in the developing mouse cerebellum during the first three postnatal weeks, a key developmental period equivalent to the third trimester in human cerebellar development. Our study represents the first detailed analysis of developmental Purkinje cell transcriptomes and provides a valuable dataset for gene network analyses and biological questions on genes implicated in cerebellar and Purkinje cell development. Overall design: Laser capture microdissection was employed to obtain a highly enriched population of cerebellar Purkinje cells. Deep sequencing was performed on RNA isolated from 1000 Purkinje cells at five developmental timepoints (postnatal days P0, P4, P8, P14 and P21) in triplicate.
Publication Title
A gene expression signature in developing Purkinje cells predicts autism and intellectual disability co-morbidity status.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Homo sapiens
- 33 Downloadable Samples
Affymetrix Human Genome U133A 2.0 Array (hgu133a2)
Description
To characterize gene expression in esophageal squamous cell carcinoma, we examined gene expression in tumor and matched normal adjacent tissue from 17 ESCC patients from a high-risk region of China.
Publication Title
Genome wide analysis of DNA copy number neutral loss of heterozygosity (CNNLOH) and its relation to gene expression in esophageal squamous cell carcinoma.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 12 Downloadable Samples
- Illumina HiSeq 2500
Description
Purpose: The goals of this study are to compare the effects of 5% and 20% oxygen culture on human embryonic stem cells, inlcuding the impact on their transcriptomes. Overall design: mRNA profiles of two human embryonic stem cell lines (MEL1 and MEL2) cultured long term at 5% and 20% oxygen.
Publication Title
Oxygen Regulates Human Pluripotent Stem Cell Metabolic Flux.
Sample Metadata Fields
Cell line, Subject
View Samples- Mus musculus
- 23 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Temporal genome profiling of DSS colitis
Publication Title
Temporal genomewide expression profiling of DSS colitis reveals novel inflammatory and angiogenesis genes similar to ulcerative colitis.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 56 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Background
Publication Title
Excessive Cytolytic Responses Predict Tuberculosis Relapse After Apparently Successful Treatment.
Sample Metadata Fields
Time
View Samples- Homo sapiens
- 3 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Despite wide scale vaccination with Mycobacterium bovis BCG, the prevalence of tuberculosis remains high, reflecting the global variable efficacy of this vaccine against adult pulmonary TB. Characterisation of different immune responses to M. tuberculosis and M. bovis BCG would increase understanding of pathology following M. tuberculosis infection or reactivation, and would facilitate the rational design of a new vaccine. Gene expression profiling was conducted on samples from diluted whole blood cultures from three healthy donors following incubation with live mycobacteria for six days. Approximately 8,000 gene entities were at least two-fold up- or down- regulated by the mycobacteria, and both mycobacteria induced similar expression changes in approximately 2,300 genes. Strikingly, many genes exhibited qualitatively different expression patterns, with over 1,000 genes up-regulated in response to M. bovis BCG but not changed by M. tuberculosis. Gene Ontology analysis revealed that the genes which failed to upregulate in M. tuberculosis-infected cultures included a large proportion of genes with lysosomal function. The inhibited up-regulation of expression of IFN--inducible protein 30, acid phosphatase 2, cathepsin B and GM2 ganglioside activator was verified in samples from six biologically independent donors by qRT-PCR. The failure to up-regulate these genes in response to M. tuberculosis may constitute an immune evasion mechanism, preventing intracellular killing and antigen presentation.
Publication Title
Excessive Cytolytic Responses Predict Tuberculosis Relapse After Apparently Successful Treatment.
Sample Metadata Fields
Specimen part
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- Mus musculus
- 15 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
We have identified genes that are differentially expressed between the bladders of UPII-SV40Tag mice and their age-matched wild-type littermates at 3, 6, 20, and 30 weeks of age. These are ages that correspond to premalignant, carcinoma in situ, and early-stage and later stage invasive UCC, respectively
Publication Title
Identification of genes correlated with early-stage bladder cancer progression.
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