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SRP076333
Drosophila melanogaster
154 Downloadable Samples
Illumina HiSeq 2000
Description
The goal was to study the effects of lead exposure on gene expression and identify the lead-responsive genes. After detecting 1,536 cis-eQTLs (FDR = 10%) and 952 trans-eQTLs, we focused our analysis on Pb-sensitive “trans-eQTL hotspots”. Overall design: 158 randomly selected Drosophila Synthetic Population Resource (A2) samples (control 79 samples and Pb-treated) without replicates
Publication Title
Identification of Splicing Quantitative Trait Loci (sQTL) in <i>Drosophila melanogaster</i> with Developmental Lead (Pb<sup>2+</sup>) Exposure.
Sample Metadata Fields
Cell line, Subject
View Samples- Rattus norvegicus
- 5 Downloadable Samples
Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
In obesity an increase in -cell mass occurs to cope with the rise in insulin demand. This -cell plasticity is essential to avoid the onset of hyperglycemia, although the molecular mechanisms that regulate this process remain unclear. This study analyzed the role of adipose tissue in the control of -cell replication. Using a diet-induced model of obesity, we obtained conditioned media from three different white adipose tissue depots. Only in the adipose tissue depot surrounding the pancreas did the diet induce changes that led to an increase in INS1E cells and the islet replication rate. To identify the factors responsible for this proliferative effect, adipose tissue gene expression analysis was conducted by microarrays and quantitative RT-PCR. Of all the differentially expressed proteins, only the secreted ones were studied. IGF binding protein 3 (Igfbp3) was identified as the candidate for this effect. Furthermore, in the conditioned media, although the blockage of IGFBP3 led to an increase in the proliferation rate, the blockage of IGF-I receptor decreased it. Taken together, these data show that obesity induces specific changes in the expression profile of the adipose tissue depot surrounding the pancreas, leading to a decrease in IGFBP3 secretion. This decrease acts in a paracrine manner, stimulating the -cell proliferation rate, probably through an IGF-I-dependent mechanism. This cross talk between the visceral-pancreatic adipose tissue and -cells is a novel mechanism that participates in the control of -cell plasticity. (Endocrinology 153: 177187, 2012)
Publication Title
Role of IGFBP-3 in the regulation of β-cell mass during obesity: adipose tissue/β-cell cross talk.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 2 Downloadable Samples
- IlluminaHiSeq2500
Description
Transcriptome of testes was examined for comparison of transcript abundance with that of sperm/seminal fluid (as sequenced in separate study) Overall design: Commercially available (Ambion) human testes RNA was prepared and sequenced in two replicates
Publication Title
Nuclease Footprints in Sperm Project Past and Future Chromatin Regulatory Events.
Sample Metadata Fields
No sample metadata fields
View Samples- Rattus norvegicus
- 11 Downloadable Samples
- Affymetrix Rat Expression 230A Array (rae230a)
Description
Background and Aims: It is well demonstrated that in the beta cell population of the pancreas there is a dynamic turnover, which results from the net balance of several processes; beta cell replication, apoptosis and neogenesis. These processes have been studied in partial pancreatectomy and glucagon-like peptide 1 treated animals, where an increase in pancreas regeneration has been observed. Similarly, sodium tungstate, which decreases hyperglycemia in several animal models of diabetes, promotes a rise in the beta cell mass of nSTZ and STZ animals. However, the molecular mechanisms underlying this pancreas regeneration remain unknown. Therefore the objective of this study is to identify which genes are up or down regulated in the increase of the beta cell population of STZ rats treated with sodium tungstate.
Publication Title
Molecular mechanisms of tungstate-induced pancreatic plasticity: a transcriptomics approach.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 119 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
Each infectious agent represents a unique combination of pathogen-associated molecular patterns that interact with specific pattern-recognition receptors expressed on immune cells. Therefore, we surmised that the blood immune cells of individuals with different infections might bear discriminative transcriptional signatures. Gene expression profiles were obtained for 131 peripheral blood samples from pediatric patients with acute infections caused by influenza A virus, Gram-negative (Escherichia coli) or Gram-positive (Staphylococcus aureus and Streptococcus pneumoniae) bacteria. Thirty-five genes were identified that best discriminate patients with influenza A virus infection from patients with either E coli or S pneumoniae infection. These genes classified with 95% accuracy (35 of 37 samples) an independent set of patients with either influenza A, E coli, or S pneumoniae infection. A different signature discriminated patients with E coli versus S aureus infections with 85% accuracy (34 of 40). Furthermore, distinctive gene expression patterns were observed in patients presenting with respiratory infections of different etiologies. Thus, microarray analyses of patient peripheral blood leukocytes might assist in the differential diagnosis of infectious diseases.
Publication Title
Gene expression patterns in blood leukocytes discriminate patients with acute infections.
Sample Metadata Fields
Sex, Age, Treatment, Race
View Samples- Homo sapiens
- 4 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
Plasmacytoid dendritic cells (pDCs) are key regulators of anti-viral immunity. They rapidly secrete IFN-alpha and cross-present viral antigens thereby launching adaptive immunity. Here we show that activated human pDCs inhibit replication of cancer cells, and kill them in a contact dependent fashion. Expression of CD2 distinguishes two pDC subsets with distinct phenotype and function. Both subsets secrete IFN-alpha and express Granzyme B and TRAIL. CD2high pDCs uniquely express lysozyme and can be found in tonsils and in tumors. Both subsets launch recall T cell response. However, CD2high pDCs secrete higher levels of IL12 p40, express higher levels of co-stimulatory molecule CD80 and are more efficient in triggering proliferation of nave allogeneic T cells. Thus, human blood pDCs are composed of subsets with specific phenotype and functions.
Publication Title
CD2 distinguishes two subsets of human plasmacytoid dendritic cells with distinct phenotype and functions.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 96 Downloadable Samples
- NextSeq 500
Description
Maternal plasama colected longitudinally were profiled using targeted sequencing (DriverMapâ„¢) (https://www.cellecta.com) to evaluate changes with gestational age and with labor in normal pregnancy. Overall design: The study included normal pregnancies with (TIL) (n=8) and without (TNL) (n=8) spontaneous labor at term. Half of the women in each group had 3 longitudinal samples taken from 12.1-40.3 weeks of gestation, while the other half of women had only one sample taken at term before delivery, for a total of 32 samples. Note that Sample_26 was considered contaminated and hence data for that sample was not included in downstream analyses.
Publication Title
Single cell transcriptional signatures of the human placenta in term and preterm parturition.
Sample Metadata Fields
Subject
View Samples- Mus musculus
- 18 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
The objective of this study is to assess the effects of the Serum Response Factor deletion on the cardiac gene expression program at different time points after the deletion (day 8 and day 25) and to compare the response of SRF-deficient heart and control heart to phenylephrine, an alpha-adrenergic agonist triggering cardiac hypertrophy.
Publication Title
Nicotinamide Riboside Preserves Cardiac Function in a Mouse Model of Dilated Cardiomyopathy.
Sample Metadata Fields
Sex
View Samples- Mus musculus
- 96 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Comparative analysis of resistant and susceptible macrophage gene expression response to Leishmania major parasite.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 48 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
We analyzed the transcriptional signatures of mouse bone marrow-derived macrophages (BMDM) at different times after infection with promastigotes of the protozoan parasite Leishmania major.
Publication Title
Comparative analysis of resistant and susceptible macrophage gene expression response to Leishmania major parasite.
Sample Metadata Fields
Specimen part
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