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GSE25014
Homo sapiens
22 Downloadable Samples
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Sickle cell disease is characterized by hemolysis, vaso-occlusion and ischemia reperfusion injury. These events cause endothelial dysfunction and vasculopathies in multiple systems
Publication Title
Global gene expression profiling of endothelium exposed to heme reveals an organ-specific induction of cytoprotective enzymes in sickle cell disease.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Escherichia coli str. k-12 substr. mg1655
- 8 Downloadable Samples
- Affymetrix E. coli Genome 2.0 Array (ecoli2)
Description
This study demonstrates simulated microgravity effects on E. coli K 12 MG1655 when grown on LB medium supplemented with glycerol. The results imply that E. coli readily reprograms itself to combat the multiple stresses imposed due to microgravity. Under these conditions it survives by upregulating oxidative stress protecting genes and simultaneously down regulating the membrane transporters and synthases to maintain cell homeostasis.
Publication Title
Effect of simulated microgravity on E. coli K12 MG1655 growth and gene expression.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 4 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Immortalized, amelanotic melanocytes isolted from skin of Balb/c express enzymatically-inactive tyrosinase due to a homozygous point mutation (TGT->TCT) in tyrosinase gene, resulting in a lack of melanin . To serve as a control cell line, pigmentation was restored in these cells by correcting the point mutation using an RNA-DNA oligonucleotide (kingly gift from Dr. Alexeev Y. Vitali).
Publication Title
Melanocyte-secreted fibromodulin promotes an angiogenic microenvironment.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 24 Downloadable Samples
- Illumina HumanHT-12 V4.0 expression beadchip
Description
Comparative analysis of RUNX1 and RUNX2 responsiveness in the presence or absence of E2
Publication Title
RUNX1 prevents oestrogen-mediated AXIN1 suppression and β-catenin activation in ER-positive breast cancer.
Sample Metadata Fields
Cell line, Treatment
View Samples- Homo sapiens
- 12 Downloadable Samples
- Illumina HumanHT-12 V4.0 expression beadchip
Description
Effect of RUNX1 depletion in the presence or absence of Estradiol
Publication Title
RUNX1 prevents oestrogen-mediated AXIN1 suppression and β-catenin activation in ER-positive breast cancer.
Sample Metadata Fields
Cell line, Treatment
View Samples- Mus musculus
- 32 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
Odorants are thought to activate sets of odorant receptors in vivo, but capturing sets of responsive receptors in vivo has never been accomplished.
Publication Title
In vivo identification of eugenol-responsive and muscone-responsive mouse odorant receptors.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 14 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Esophageal carcinoma is the third most common gastrointestinal malignancy worldwide and is generally unresponsive to therapy. African Americans have an increased risk for esophageal squamous cell cancer (ESCC), the subtype that shows marked variation in geographic frequency. To identify key genes involved in ESC carcinogenesis in African Americans we conducted microarray expression profiling and found a significant dysregulation of genes encoding stress response and drug-metabolizing enzymes, mainly in NRF2 pathway. The involvement of NRF2 mediated oxidative damage represent a key step in the evolution of African American ESCC. Loss of activity of these enzymes would confer increased sensitivity of esophageal cells to xenobiotics, such as alcohol and tobacco smoke, and may account for the high incidence of ESCC in this ethnic group. The differential expression profile also indicates an inflammatory component and tissue regeneration in ESCC tumorigenesis. Together, these findings suggest a remarkable interplay of genetic and environmental factors in the pathogenesis of African American ESCC.
Publication Title
African-American esophageal squamous cell carcinoma expression profile reveals dysregulation of stress response and detox networks.
Sample Metadata Fields
Race
View Samples- Mus musculus
- 6 Downloadable Samples
Illumina Genome Analyzer II
Description
Regulation of RNA levels is critical for the response to external stimuli and determined through the interplay between RNA production, processing and degradation. Despite the centrality of these processes, most global studies of RNA regulation do not distinguish their separate contributions and relatively little is known about how they are temporally integrated. Here, we combine metabolic labeling of RNA with advanced RNA quantification assays and computational modeling to estimate RNA transcription and degradation during the response of immune dendritic cells (DCs) to pathogens, a critical and tightly regulated step in innate immunity. We find that transcription regulation plays a major role in shaping most temporal changes in RNA levels, but that changes in degradation rate are important for shaping sharp ‘peaked’ responses. We find that transcription changes precede corresponding RNA changes by a small lag (15-30 min), which is shorter for induced than for repressed genes. Massively parallel sequencing of the entire RNA population – including non-polyadenylated transcripts – allows us to estimate RNA processing, and identify specific groups of transcripts, mostly cytokines and transcription factors, undergoing enhanced mRNA maturation. This suggests an additional role for splicing in regulating mRNA maturation. Our method provides a new quantitative approach to study key steps in the integrative process of RNA regulation. Overall design: Sequencing of 4sU-labeled RNA taken from a 7 samples time-series (one sample every 1 hour) during the response of DCs to LPS stimulation. 4-thiouridine was added 45 minutes prior to sample collection. Data presented here for six timepoints: 0, 1, 3-6 hrs. 2hr timepoint not included.
Publication Title
Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 381 Downloadable Samples
- Illumina HiSeq 2500
Description
Four Kcng4-cre;stop-YFP mouse retinas from two mice were dissected, dissociated and FACS sorted, and single cell RNA-seq libraries were generated for 384 single cells using Smart-seq2. Aligned bam files are generated for 383 samples as one failed to align. Overall design: Four mouse retinas (labeled 1la, 1Ra, and 2la, 2Ra respective from the two mice) were used, and 96 single cells from each were processed using Smart-seq2. Total 384 cells Smart-seq2 analysis of P17 FACS sorted retinal cells from the Kcng4-cre;stop-YFP mice (Kcng4tm1.1(cre)Jrs mice [Duan et al., Cell 158, 793-807, 2015] crossed to the cre-dependent reporter Thy1-stop-YFP Line#1 [Buffelli et al., Nature 424, 430-434, 2003])
Publication Title
Comprehensive Classification of Retinal Bipolar Neurons by Single-Cell Transcriptomics.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 64 Downloadable Samples
- Illumina HiSeq 2500, Illumina HiSeq 2000
Description
RNA-Seq is an effective method to study the transcriptome, but can be difficult to apply to scarce or degraded RNA from fixed clinical samples, rare cell populations, or cadavers. Recent studies have proposed several methods for RNA-Seq of low quality and/or low quantity samples, but their relative merits have not been systematically analyzed. Here, we compare five such methods using a comprehensive set of metrics, relevant to applications such as transcriptome annotation, transcript discovery, and gene expression. Using a single human RNA sample, we constructed and deeply sequenced 10 libraries with these methods and two control libraries. We find that the RNase H method performed best for low quality RNA, and can even effectively replace oligo (dT) based methods for standard RNA-Seq. SMART and NuGEN had distinct strengths for low quantity RNA. Our analysis allows biologists to select the most suitable methods and provides a benchmark for future method development. Overall design: Examination of 9 different RNA-Seq libraries starting from total RNA from 5 distinct methods; also 3 control RNA-Seq libraries
Publication Title
Comparative analysis of RNA sequencing methods for degraded or low-input samples.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples