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SRP057793
Homo sapiens
149 Downloadable Samples
IlluminaHiSeq2000
Description
No description.
Publication Title
Genomic and transcriptomic comparison of post-radiation versus sporadic sarcomas.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 73 Downloadable Samples
- Illumina HiSeq 2000
Description
No description.
Publication Title
Genomic and transcriptomic comparison of post-radiation versus sporadic sarcomas.
Sample Metadata Fields
Sex, Age, Specimen part, Disease, Disease stage
View Samples- Homo sapiens
- 45 Downloadable Samples
Affymetrix Human Exon 1.0 ST Array [CDF: Brainarray Version 13.0 (huex10st)
Description
We compare the genetic profiles of the primary tumors of uveal melanoma or metastasis to their corresponding xenografts that have been passaged over time.
Publication Title
Patient-derived xenografts recapitulate molecular features of human uveal melanomas.
Sample Metadata Fields
Disease
View Samples- Homo sapiens
- 63 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
A high percentage of uveal melanoma patients develop metastatic tumors that predominately occur in the liver. To identify genes associated with metastasis in this pathology, we studied 63 molecular profiles derived from gene expression microarrays performed from enuceated primary tumors.
Publication Title
High PTP4A3 phosphatase expression correlates with metastatic risk in uveal melanoma patients.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Saccharomyces cerevisiae
- 3 Downloadable Samples
- Affymetrix Yeast Genome S98 Array (ygs98)
Description
Prolonged cultivation (>25 generations) of Saccharomyces cerevisiae in aerobic, maltose-limited chemostat cultures led to profound physiological changes. Maltose hypersensitivity was observed when cells from prolonged cultivations were suddenly exposed to excess maltose. This substrate hypersensitivity was evident from massive cell lysis and loss of viability. During prolonged cultivation at a fixed specific growth rate, the affinity for the growth-limiting nutrient (i.e., maltose) increased, as evident from a decreasing residual maltose concentration. Furthermore, the capacity of maltose-dependent proton uptake increased up to 2.5-fold during prolonged cultivation. Genome-wide transcriptome analysis showed that the increased maltose transport capacity was not primarily due to increased transcript levels of maltose-permease genes upon prolonged cultivation. We propose that selection for improved substrate affinity (ratio of maximum substrate consumption rate and substrate saturation constant) in maltose-limited cultures leads to selection for cells with an increased capacity for maltose uptake. At the same time, the accumulative nature of maltose-proton symport in S. cerevisiae leads to unrestricted uptake when maltose-adapted cells are exposed to a substrate excess. These changes were retained after isolation of individual cell lines from the chemostat cultures and nonselective cultivation, indicating that mutations were involved. The observed trade-off between substrate affinity and substrate tolerance may be relevant for metabolic engineering and strain selection for utilization of substrates that are taken up by proton symport.
Publication Title
Prolonged maltose-limited cultivation of Saccharomyces cerevisiae selects for cells with improved maltose affinity and hypersensitivity.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus, Xenopus laevis
- 19 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Cue-directed axon guidance depends partly on local translation in growth cones. Many mRNA transcripts are known to reside in developing axons yet little is known about their subcellular distribution or, specifically, which transcripts are in growth cones.
Publication Title
Subcellular profiling reveals distinct and developmentally regulated repertoire of growth cone mRNAs.
Sample Metadata Fields
Specimen part
View Samples- Bos indicus, Bos taurus
- 6 Downloadable Samples
- Affymetrix Bovine Genome Array (bovine)
Description
This trial was undertaken to examine the perhipheral cellular and antibody response of cattle following infestation with the cattle tick, Rhipicephalus microplus. The information from the Affymetrix gene expression data is used to complement other measurements of immune function such as cellular subset composition and antibody response in cattle of high (Brahman) and low (Holstein-Friesian) resistance to the cattle tick.
Publication Title
Immunological profiles of Bos taurus and Bos indicus cattle infested with the cattle tick, Rhipicephalus (Boophilus) microplus.
Sample Metadata Fields
Sex
View Samples- Saccharomyces cerevisiae
- 15 Downloadable Samples
- Affymetrix Yeast Genome S98 Array (ygs98)
Description
Aerobic, glucose-limited chemostat cultures of Saccharomyces cerevisiae grown with six different nitrogen sources were subjected to transcriptome analysis. The use of chemostats enabled an analysis of nitrogen-source-dependent transcriptional regulation at a fixed specific growth rate. A selection of preferred (ammonium and asparagine) and non-preferred (leucine, phenylalanine, methionine and proline) nitrogen sources was investigated. For each nitrogen source, distinct sets of genes were induced or repressed relative to the other five nitrogen sources. A total number of 131 of such signature transcripts were identified in this study. In addition to signature transcripts, genes were identified that showed a transcriptional co-response to two or more of the six nitrogen sources. For example, 33 genes were transcriptionally up-regulated in leucine-, phenylalanine- and methionine-grown cultures, which was partly attributed to the involvement of common enzymes in the dissimilation of these amino acids. In addition to specific transcriptional responses elicited by individual nitrogen sources, their impact on global regulatory mechanisms such as nitrogen catabolite repression (NCR) could be monitored. NCR-sensitive gene expression in the chemostat cultures showed that, ammonia and asparagine were rich nitrogen sources. By this criterion, leucine, proline and methionine were poor nitrogen sources and phenylalanine showed an intermediate NCR response.
Publication Title
Transcriptional responses of Saccharomyces cerevisiae to preferred and nonpreferred nitrogen sources in glucose-limited chemostat cultures.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 6 Downloadable Samples
- Illumina HiSeq 2000
Description
Purpose: To study the mechanisms involved in the regulation by NFIX on neural stem cell development and to examine the transcriptome changes associated with the loss of NFIX in neural stem cells. Methods: Subventricular zones of 10-day-old wild-type and Nfix KO mice were sectioned and dissociated into single cells. Cells were cultured in proliferation condition for 10 days. RNA was purified and poly-A selected to build the library for RNA-seq. Conclusions: Our study represents the first detailed analysis of transcriptome changes in primary monolayer-cultured neural stem cells associated with the loss of NFIX. Overall design: Cells dissociated from 10-day-old wild-type and nuclear factor I-X (Nfix KO) mice subventricular zone were cultured in DMEM/F12 with B27, Glutamine, EGF and bFGF for 10 days. RNA was harvested with Norgen RNA purification micro kit and then prepared with illumina TruSeq kit. Samples from 6 mice (3 vs. 3) were loaded on one lane. 50-cycle single-read run was performed on Hiseq 2000. The sequence reads were analyzed by TopHat 2.0.7 followed by Cufflinks 1.3.0 with the mm9 UCSC annotation files.
Publication Title
Loss of NFIX Transcription Factor Biases Postnatal Neural Stem/Progenitor Cells Toward Oligodendrogenesis.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 29 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Systems biology of interstitial lung diseases: integration of mRNA and microRNA expression changes.
Sample Metadata Fields
Specimen part, Disease
View Samples