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SRP052708
Escherichia coli
11 Downloadable Samples
Illumina Genome Analyzer II, Illumina HiSeq 2500
Description
Characterization of the global transcriptome of bacterial strains carrying IncA/C plasmids, mapping of fitness compensatory mutations in strains carrying IncA/C plasmids and targeted pull-downs of DNA associated with proteins of interest.
Publication Title
No associated publication
Sample Metadata Fields
Specimen part, Disease, Cell line
View Samples SRP032280- Homo sapiens
- 1 Downloadable Sample
- IlluminaGenomeAnalyzerII
Description
RNAseq to determine baseline expression of kinome in MDA-MB-231 claudin-low breast cancer cell line
Publication Title
Dynamic reprogramming of the kinome in response to targeted MEK inhibition in triple-negative breast cancer.
Sample Metadata Fields
No sample metadata fields
View Samples SRP032344- Homo sapiens
- 1 Downloadable Sample
- IlluminaGenomeAnalyzerII
Description
RNAseq of SUM159PT claudin-low breast cancer cell line to determine baseline kinome expression
Publication Title
Dynamic reprogramming of the kinome in response to targeted MEK inhibition in triple-negative breast cancer.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 6 Downloadable Samples
Affymetrix Murine Genome U74A Version 2 Array (mgu74av2)
Description
Mice lacking topoisomerase II (Top II) are known to exhibit a perinatal death phenotype. In the current study, transcription profiles of the brains of wild type and top2 knockout mouse embryos were generated. Surprisingly, only a small number (1-4%) of genes were affected in top2 knockout embryos. However, the expression of nearly 30% of developmentally regulated genes was either up- or down-regulated.
Publication Title
Role of topoisomerase IIbeta in the expression of developmentally regulated genes.
Sample Metadata Fields
Sex, Specimen part
View Samples- Mus musculus
- 4 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
RNA from wt and SIN1 knock-out MEF cell lines were compared
Publication Title
mTORC2 Responds to Glutamine Catabolite Levels to Modulate the Hexosamine Biosynthesis Enzyme GFAT1.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 2 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Latent HIV-1 infection represents a barrier to virus eradication as latent HIV-1 is impervious to the effects of antiretroviral drugs and can avoid detection by the host immune system. Strategies to clear latent HIV-1 infection in patients have so far failed in clinical trials to increase the decay rate of the latent reservoir underscoring the need for continued study of HIV-1 latency. In this study, a genome-wide RNAi screen was performed to probe cellular factors involved in maintaining HIV-1 latency in HeLa cells latently infected with an HIV-1 reporter virus.
Publication Title
No associated publication
Sample Metadata Fields
Specimen part, Cell line
View Samples SRP011480- Zea mays
- 92 Downloadable Samples
- Illumina HiSeq 2000, Illumina Genome Analyzer IIx
Description
Maize exhibits levels of structural variation (SV) of non-repeat sequences that are unprecedented among higher eukaryotes. This SV includes hundreds of copy number variants (CNVs) and thousands of presence/absence variants (PAVs). Many of the PAVs contain intact, expressed, single-copy genes that are present in one haplotype but absent from another. The goal of this project is to test the hypothesis that differences in gene copy number (both gains and losses) contribute to the extraordinary phenotypic diversity and plasticity of maize. Maize is a good model for these studies because it exhibits a rapid decay of linkage disequilibrium (LD) and because a draft genome sequence of the B73 inbred and mapping populations are available. As a first step, the "Zeanome", a near-complete set of genes present in B73, other maize lines and the wild ancestor of maize (teosinte), is being defined using transcriptomic data.
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Saccharomyces cerevisiae
- 83 Downloadable Samples
- Illumina HiSeq 2000
Description
No description.
Publication Title
No associated publication
Sample Metadata Fields
Cell line
View Samples- Mus musculus
- 74 Downloadable Samples
- Illumina HiSeq 2500
Description
RNA-seq transcriptome profiles of genetically fate-mapped serotonin neurons, manually sorted from multiple anatomic domains, at both population and single cell resolution.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part, Cell line
View Samples- Zea mays
- 64 Downloadable Samples
- Illumina HiSeq 2000
Description
Heterosis which is the improved vigor of F1-hybrids compared to their parents is widely exploited in maize (Zea mays L.) breeding to produce elite hybrids of superior yield. The transcriptomes of the maize inbred lines B73 and Mo17 and their reciprocal hybrid offspring were surveyed in the meristematic zone, the elongation zone, cortex and stele tissues of primary roots, prior to the developmental manifestation of heterosis. Single parent expression (SPE) is consistent with the dominance model for heterosis in that it denotes genes that are expressed in only one parent but in both reciprocal hybrids. In primary root tissues, between 1,027 (elongation zone) and 1,206 (stele) SPE patterns were observed. As a consequence, hybrids displayed in each tissue >400 active genes more than either parent. Analysis of tissue-specific SPE dynamics revealed that 1,233 of 2,233 SPE genes displayed SPE in all tissues in which they were expressed while 1,000 SPE genes displayed in at least one tissue a non-SPE pattern. In addition, 64% (17,351/ 27,164) of all expressed genes were assigned to the two subgenomes which are the result of an ancient genome duplication. By contrast, only between 18 and 25% of the SPE genes were assigned to a subgenome suggesting that a disproportionate number of SPE genes are evolutionary young and emerged after genome duplication. We hypothesize that this phenomenon is associated with human selection of favorable maize genotypes which might primarily affect younger genes rather than genes whose functions have been conserved for millions of years.
Publication Title
Nonsyntenic genes drive highly dynamic complementation of gene expression in maize hybrids.
Sample Metadata Fields
No sample metadata fields
View Samples