We aimed to provide a molecular description of Lynch syndrome-associated urothelial cancer in relation to molecular subtypes of sporadic bladder cancer. Whole genome mRNA expression profiles of 41 tumors and immunohistochemical stainings against FGFR3, KRT5, CCNB1, RB1, and CDKN2A (p16) of 37 tumors from Lynch syndrome patients were generated. Pathological data, microsatellite instability, anatomic location, and overall survival data was analyzed and compared with data from sporadic bladder cancer.
Molecular subtype classification of urothelial carcinoma in Lynch syndrome.
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View SamplesThis SuperSeries is composed of the SubSeries listed below.
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Specimen part
View SamplesWe used full genome microarrays to profile the full lifetime of the mouse placenta from embryonic day 8.5 (e8.5), at the time of chorioallantoic fusion, until postnatal day 0 (P0).
Genomic evolution of the placenta using co-option and duplication and divergence.
Specimen part
View SamplesSuperSeries contain expression data from the nuclei of cell types involved in patterning events, with focus on root apical stem cell formation, at 16-cell stage, early globular stage and late globular stage in the early Arabidopsis embryo (atlas). Expression data comparing nuclear and cellular RNA isolated from whole 16-cell stage Arabidopsis embryos is also included.
Transcriptome dynamics revealed by a gene expression atlas of the early Arabidopsis embryo.
Specimen part
View SamplesWe used full genome microarrays to profile the full lifetime of the mouse placenta from embryonic day 8.5 (e8.5), at the time of chorioallantoic fusion, until postnatal day 0 (P0). For these samples, at each stage the fetal placenta and maternal decidual tissues were dissected and profiled separately (See series 1).
Genomic evolution of the placenta using co-option and duplication and divergence.
Specimen part
View SamplesThe establishement of the first plant tissues occurs during embryo development. Indeed, cell types that will form the Arabidopsis root stem cell niche are first specified during 16-cell (16C), early globular (EG) and late globular (LG) stage of embryonic development. While some regulatory factors are known, we do not yet understand the genetic networks underlying the specification of these cell types. One main reason for this is the difficulties in adapting genome-wide approaches to the cellular level. Here, we have adapted such an approach (INTACT) to generate microarray-based cell type-specific transcriptomic profiles at 16C to LG stage for use in determining the role of the transcriptome in cell specification and differentiation during root stem cell niche formation.
Transcriptome dynamics revealed by a gene expression atlas of the early Arabidopsis embryo.
Specimen part
View SamplesStudies in mouse have led to enormous progress in our understanding of early human development. The identification of genes and the signaling pathways involved in mouse embryogenesis have helped us to better understand fertilization, morulation, gastrulation, organogenesis and embryonic development in mammals.
Global expression profiling reveals genetic programs underlying the developmental divergence between mouse and human embryogenesis.
Specimen part
View Samples[Hela cells]: We performed cdr2 knockdown with a pool of 4 cdr2-specific siRNAs to test whether cdr2 may regulate c-myc target genes as cells passage through mitosis.
The onconeural antigen cdr2 is a novel APC/C target that acts in mitosis to regulate c-myc target genes in mammalian tumor cells.
Cell line
View SamplesGene expression profiling has provided critical insights into the molecular pathways underlying development of model organisms, however little information is available on regulated gene expression during human embryogenesis. We have now filled this important gap of knowledge by performing genome-wide microarray analysis of the Homo sapiens gene expression during the 4-9th week, a period when most organs develop.
Gene expression atlas for human embryogenesis.
Specimen part
View SamplesWe sought to test whether vaccine-induced immune responses could protect rhesus macaques (RMs) against upfront heterologous challenges with an R5 simian-human immunodeficiency virus, SHIV-2873Nip. We immunized the RMs with recombinant Env proteins heterologous to the challenge virus. For induction of immune responses against Gag, Tat, and Nef, we explored a strategy of immunization with overlapping synthetic peptides (OSP). The immune responses against Gag and Tat were finally boosted with recombinant proteins. The vaccinees and a group of ten control animals were given five low-dose intrarectal (i.r.) challenges with SHIV-2873Nip. All controls and seven out of eight vaccinees became systemically infected; there was no significant difference in viremia levels of vaccinees vs. controls. Prevention of viremia was observed in one vaccinee which showed strong boosting of virus-specific cellular immunity during virus exposures. The protected animal showed no challenge virus-specific neutralizing antibodies in the TZM-bl or A3R5 cell-based assays and had low level ADCC activity after the virus exposures. Microarray data strongly supported a role for cellular immunity in the protected animal. Our study represents a case of protection against heterologous tier 2 SHIV-C by vaccine-induced, virus-specific cellular immune responses.
Multimodality vaccination against clade C SHIV: partial protection against mucosal challenges with a heterologous tier 2 virus.
Specimen part, Time
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