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SRP040273
Bos taurus
6 Downloadable Samples
Illumina HiSeq 2000
Description
The study aimed to uncover differential expression pattern of regulatory microRNAs in bovine granulosa cells derived from preovulatory dominant and subordinate follicles. Overall design: We used ovarian follicle samples of experimental heifers slaughtered at day 19 of the estrous cycle . Follicles were catagorized as preovulatory dominant follicles (PDF) and anovulatory subordinate follicles (SF). The granulosa cells were collected from each follicle and subjected to microRNA enriched total RNA isolation and used for miRNAs deep sequencing. A total of 6 samples (three biological replicated from PDF and 3 biological replicates from SF) were used for miRNA deep sequencing.
Publication Title
MicroRNA Expression Profile in Bovine Granulosa Cells of Preovulatory Dominant and Subordinate Follicles during the Late Follicular Phase of the Estrous Cycle.
Sample Metadata Fields
Subject
View Samples- Sus scrofa
- 12 Downloadable Samples
- Illumina HiSeq 2000
Description
Investigation of the transcriptome profile of lung dendritic cells (DCs) of two genetically different pig breeds (Pietrain and Duroc) after PRRSV infection in vitro and determination of the temporal changes in transcriptional profiles. Overall design: Pietrain and Duroc lung DCs were isolated and infected in vitro with PRRSV. Total cellular mRNA from non-infected (0 hours) and infected (3, 6, 9, 12 and 24 hours post infection) lung DCs was extracted and 12 lung DCs samples were used for the global transcriptome profile analysis (RNA-Seq).
Publication Title
Transcriptome profile of lung dendritic cells after in vitro porcine reproductive and respiratory syndrome virus (PRRSV) infection.
Sample Metadata Fields
Sex, Specimen part, Subject
View Samples- Oryza sativa
- 6 Downloadable Samples
Affymetrix Rice (Chinese Build) Gene 1.0 ST Array (rcngene10st)
Description
The experiments were performed to understand the molecular basis of plant growth promotion in rice by Rhodotorula mucilaginosa JGTA-S1, an endophytic yeast from Typha angustifolia
Publication Title
Early changes in shoot transcriptome of rice in response to Rhodotorula mucilaginosa JGTA-S1.
Sample Metadata Fields
Specimen part, Treatment, Time
View Samples- Drosophila melanogaster
- 6 Downloadable Samples
- Illumina HiSeq 2500
Description
SIN3 is a master transcriptional scaffold protein. SIN3 interacts with RPD3 and other accessory proteins to form a histone modifying complex. A single Sin3A gene encodes multiple isoforms of SIN3, of which SIN3 187 and SIN3 220 are the predominant isoforms. Previous studies demonstrated that SIN3 isoforms play non-redundant roles during fly development. In the current study, we sought to investigate the genes regulated by SIN3 187. Overall design: S2 cells and cells carrying a stable transgene of SIN3 187HA (SIN3 187HA cells) were treated with 0.07 µM CuSO4. CuSO4 treatment led to ectopic expression of SIN3 187HA. S2 cells were used as a control. Following induction, total mRNA was extracted. mRNA profiling of these samples were performed by deep sequencing using Illumina Hiseq2500. Three biological replicates were performed.
Publication Title
Genome-wide studies reveal novel and distinct biological pathways regulated by SIN3 isoforms.
Sample Metadata Fields
Cell line, Subject
View Samples- Homo sapiens
- 19 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Erg and AP-1 as determinants of glucocorticoid response in acute lymphoblastic leukemia.
Sample Metadata Fields
Specimen part, Disease, Disease stage, Cell line, Treatment, Subject, Time
View Samples- Homo sapiens
- 12 Downloadable Samples
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
The beneficial effects of glucocorticoids (GCs) in acute lymphoblastic leukemia (ALL) are based on their ability to induce apoptosis. Omics technologies such as DNA microarray analysis are widely used to study the changes in gene expression and have been successfully implemented in biomarker identification. In addition, time series studies of gene expression enable the identification of correlations between kinetic profiles of glucocorticoid receptor (GR) target genes and diverse modes of transcriptional regulation. This study presents a genome-wide microarray analysis of both our and published Affymetrix HG-U133 Plus 2.0 data in GCs-sensitive and -resistant ALL. GCs-sensitive CCRF-CEM-C7-14 cells were treated with dexamethasone at three time points (0 h, 2 h and 10 h). The treated samples were then compared to the control (0 h).
Publication Title
Erg and AP-1 as determinants of glucocorticoid response in acute lymphoblastic leukemia.
Sample Metadata Fields
Specimen part, Disease, Disease stage, Treatment, Subject, Time
View Samples- Homo sapiens
- 7 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
The beneficial effects of glucocorticoids (GCs) in acute lymphoblastic leukemia (ALL) are based on their ability to induce apoptosis. Omics technologies such as DNA microarray analysis are widely used to study the changes in gene expression and have been successfully implemented in biomarker identification. In addition, time series studies of gene expression enable the identification of correlations between kinetic profiles of glucocorticoid receptor (GR) target genes and diverse modes of transcriptional regulation. This study presents a genome-wide microarray analysis of both our and published Affymetrix HG-U133 Plus 2.0 data in GCs-sensitive and -resistant ALL. GCs-sensitive CCRF-CEM-C7-14 cells were treated with dexamethasone at three time points (0 h, 2 h and 10 h). The treated samples were then compared to the control (0 h).
Publication Title
Erg and AP-1 as determinants of glucocorticoid response in acute lymphoblastic leukemia.
Sample Metadata Fields
Specimen part, Cell line, Treatment, Time
View Samples- Mus musculus
- 50 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
Pglyrp1-/-, Pglyrp2-/-, Pglyrp3-/-, and Pglyrp4-/- mice are all more sensitive than wild type (WT) mice to dextran sulfate sodium (DSS)-induced colitis. The purpose of this study was to determine which genes are differentially induced by DSS treatment in the colon of Pglyrp1-/-, Pglyrp2-/-, Pglyrp3-/-, and Pglyrp4-/- mice compared to WT mice. The results demonstrate higher induction of proinflammatory gene expression in Pglyrp1-/-, Pglyrp2-/-, Pglyrp3-/-, and Pglyrp4-/- mice than in WT mice after DSS treatment. The majority of genes whose expression is increased in Pglyrp1-/-, Pglyrp2-/-, Pglyrp3-/-, and Pglyrp4-/- mice but not in WT mice are interferon-inducible genes. Thus, Peptidoglycan Recognition Proteins Pglyrp1, Pglyrp2, Pglyrp3, and Pglyrp4 protect mice from excessive inflammatory response and damage to the colon by limiting expression of interferon-inducible genes in the colon.
Publication Title
Peptidoglycan recognition proteins protect mice from experimental colitis by promoting normal gut flora and preventing induction of interferon-gamma.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 6 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Follistatin is a folliculogenesis regulating protein that has been found in relatively high concentration in the female ovarian tissues. Follistatin acts as an antagonist to the function of Activin, which is often found elevated in ovarian carcinogenesis and thus presents a possibility for therapeutic intervention in controlling ovarian cancer. Most of the ovarian cancer occurs in its ovarian surface epithelium (OSE) cells. Although breast cancer susceptibility gene 1 (BRCA1) is a known tumor suppressor for breast cancer but its role in ovarian cancer is beginning to unfold. We have shown that in ovarian carcinoma cells (SKOV3), stable overexpression of BRCA1 stimulates Follistatin secretion and simultaneously downregulates Activin expression. Moreover, knock down of BRCA1 in immortalized OSE (IOSE) cells from human ovarian tissue demonstrates downregulation of Follistatin secretion with simultaneous up regulation of Activin expression. IOSE cells generated from an ovarian cancer patient with BRCA1 mutation failed to secrete Follistatin in the medium. Our results indicate a novel function for BRCA1 in the form of regulation of the expression of Follistatin in the ovarian cells.
Publication Title
BRCA1 regulates follistatin function in ovarian cancer and human ovarian surface epithelial cells.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Drosophila melanogaster
- 22 Downloadable Samples
- Affymetrix Drosophila Genome 2.0 Array (drosophila2)
Description
Expression profiling following depletion of Mediator Cdk8 module subunits Cdk8, Cyclin C (CycC), Med12 and Med13 72 hours after dsRNA treatment of Drosophila melanogaster S2 cells. Results provide insight into the role of individual Cdk8 module subunits in regulation of transcription.
Publication Title
Cyclin-dependent kinase 8 module expression profiling reveals requirement of mediator subunits 12 and 13 for transcription of Serpent-dependent innate immunity genes in Drosophila.
Sample Metadata Fields
Specimen part
View Samples