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GSE40168
Homo sapiens
9 Downloadable Samples
Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
To uncover the chromosome 16 associated proteome and to take advantage of the generated knowledge to make progress in human biology in health and disease, a consortium of 15 groups was organized in four working groups: SRM and protein sequencing, antibody and peptide standard, clinical healthcare and biobanking and bioinformatics. According to a preliminary in silico study integrating knowledge from Ensembl, UniProt and GPM, Ramos B lymphocyte cells, MCF-7 epitelial cells and CCD18 fibroblast were selected as it is theoretically expected that any chromosome 16 protein coding gene is expressed in at least one of them. To define in detail the transcriptome of the above mentioned cell lines Affymetrix microarray based analyses were performed. Upon hybridization in Human ST 1.0 arrays, raw data were processed with RMA algorithm for background correction and normalization. Chromosome 16 gene expression pattern was then defined in each cell line and comparative analysis was done with R package statistics. Biological functions involving chromosome 16 genes were analysed with GO and functional networks were studied with Ingenuity Pathway Analysis. Expressed genes were compared with data from shotgun proteomic experiments to find the degree of correlation mRNA-protein. Expression of genes coding for proteins with weak or none MS evidence is shown. The integration of this information in decision-making process of the mass spectrometry group is discussed.
Publication Title
Spanish human proteome project: dissection of chromosome 16.
Sample Metadata Fields
Cell line
View Samples- Homo sapiens
- 18 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
Metazoan development depends on accurate execution of differentiation programs that allow pluripotent stem cells to adopt specific fates. Differentiation is brought about by global changes to chromatin architecture and transcriptional networks, yet whether other regulatory events support cell fate determination is less well understood. Using a human embryonic stem cell model, we identified the vertebrate-specific ubiquitin ligase Cul3KBTBD8 as an essential regulator of neural crest cell formation. Cul3KBTBD8 monoubiquitylates NOLC1 and its paralog TCOF1, whose mutation underlies the developmental disease Treacher Collins Syndrome that is characterized by a loss of cranial neural crest cells. Ubiquitylation of NOLC1 and TCOF1 drives formation of a platform that connects RNA polymerase I with ribosome modification enzymes, thereby altering the translational program of differentiating cells to support the generation of neural crest cells. We conclude that the dynamic regulation of ribosome function is an important feature of cell fate determination.
Publication Title
Cell-fate determination by ubiquitin-dependent regulation of translation.
Sample Metadata Fields
Cell line
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Bisphenol-A is a widespread endocrine disruptor chemical. In utero or perinatal exposure to bisphenol-A (BPA), leads to impaired glucose metabolism during adulthood. To investigate the consequences of the exposure to bisphenol-A during development in pancreatic beta-cell growth
Publication Title
Maternal Exposure to Bisphenol-A During Pregnancy Increases Pancreatic β-Cell Growth During Early Life in Male Mice Offspring.
Sample Metadata Fields
Sex, Specimen part
View Samples- Homo sapiens
- 960 Downloadable Samples
- Illumina HumanRef-8 v3.0 expression beadchip
Description
Statins reduce cardiovascular disease risk by lowering plasma low density lipoprotein (LDL)-cholesterol. To identify novel pathways that modulate statin response, we assessed the influence of simvastatin exposure on expression quantitative trait locus (eQTL) associations across the genome in 480 lymphoblastoid cell lines (LCLs). Cell lines were derived blood samples collected ant entry visit from participants in the Cholesterol and Pharmacogenomics (CAP) trial, who underwent a 6 week 40mg/day simvastatin trial. We identified 4590 cis-eQTLS that were independent of treatment status (FDR=1%) and six cis-eQTLS for which there was evidence of an interaction with treatment (FDR=20%). Genotypes and Phenotypes derived from these indivudals are available through dbGaP (Accession Number). eQTL results are available at: http://eqtl.uchicago.edu/cgi=bin/gbrowse/eqtl/
Publication Title
HNRNPA1 regulates HMGCR alternative splicing and modulates cellular cholesterol metabolism.
Sample Metadata Fields
Sex, Subject
View Samples- Mus musculus
- 46 Downloadable Samples
- Affymetrix Mouse Genome 430A 2.0 Array (mouse430a2)
Description
We performed affymetrix gene expression profiling on mammary tumors from eight well-characterized genetically engineered Mouse (GEM) models of human breast cancer.
Publication Title
Integrated miRNA and mRNA expression profiling of mouse mammary tumor models identifies miRNA signatures associated with mammary tumor lineage.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 4 Downloadable Samples
Illumina Genome Analyzer II
Description
MicroRNAs (miRNAs) are a class of small RNA molecules that regulate expression of specific mRNA targets. They can be released from cells, often encapsulated within extracellular vesicles (EVs), and therefore have the potential to mediate intercellular communication. It has been suggested that certain miRNAs may be selectively exported, although the mechanism has yet to be identified. Manipulation of the miRNA content of EVs will be important for future therapeutic applications. We therefore wished to assess which endogenous miRNAs are enriched in EVs and how effectively an overexpressed miRNA would be exported. Small RNA libraries from HEK293T cells and vesicles before or after transfection with a vector for miR-146 overexpression were analysed by deep sequencing. A subset of miRNAs was found to be enriched in EVs. The global expression data provided by deep sequencing confirms that specific miRNAs are enriched in EVs released by HEK293T cells. Overall design: Cells were transfected with a plasmid to direct overexpression of miR-146a. Extracellular vesicles were isolated by ultracentrifugation from untreated and transfected cells. RNA was isolated from one sample each of untreated and transfected cells and vesicles.Small RNA libraries were prepared for sequencing.
Publication Title
Selective extracellular vesicle-mediated export of an overlapping set of microRNAs from multiple cell types.
Sample Metadata Fields
Specimen part, Subject
View Samples- Drosophila melanogaster
- 140 Downloadable Samples
- Affymetrix Drosophila Genome 2.0 Array (drosophila2)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Suboptimal evolutionary novel environments promote singular altered gravity responses of transcriptome during Drosophila metamorphosis.
Sample Metadata Fields
Sex, Age
View Samples- Homo sapiens
- 68 Downloadable Samples
- Affymetrix Human X3P Array (u133x3p), Affymetrix Human Genome U95 Version 2 Array (hgu95av2)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Differentially expressed genes regulating the progression of ductal carcinoma in situ to invasive breast cancer.
Sample Metadata Fields
Specimen part, Disease, Disease stage
View Samples- Drosophila melanogaster
- 90 Downloadable Samples
- Affymetrix Drosophila Genome 2.0 Array (drosophila2)
Description
Genome-wide transcriptional profiling showed that reducing gravity levels in the International Space Station (ISS) causes important alterations in Drosophila gene expression intimately linked to imposed spaceflight-related environmental constrains during Drosophila metamorphosis. However, simulation experiments on ground testing space-related environmental constraints, show differential responses. Curiously, although particular genes are not common in the different experiments, the same GO groups including a large multigene family related with behavior, stress response and organogenesis are over represented in them. A global and integrative analysis using the gene expression dynamics inspector (GEDI) self-organizing maps, reveals different degrees in the responses of the transcriptome when using different environmental conditions or microgravity/hypergravity simulation devices
Publication Title
Suboptimal evolutionary novel environments promote singular altered gravity responses of transcriptome during Drosophila metamorphosis.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 38 Downloadable Samples
Affymetrix Human X3P Array (u133x3p), Affymetrix Human Genome U95 Version 2 Array (hgu95av2)
Description
We used gene expression profiling of human DCIS and IBC to discover uniquely expressed genes that may also regulate progression.
Publication Title
Differentially expressed genes regulating the progression of ductal carcinoma in situ to invasive breast cancer.
Sample Metadata Fields
Specimen part, Disease, Disease stage
View Samples