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SRP039511
Sus scrofa
90 Downloadable Samples
Illumina HiSeq 2000
Description
We sequenced liver mRNA from 23 individual pigs (5 prefed and 18 fasted) taken at 4 separate time points to evaluate the change in gene expression over the course of hemorrhagic shock and resuscitation in response to a carbohydrate prefed state. Overall design: Examination of mRNA levels in liver biopsies from pigs at 4 timepoints throughout hemorrhagic shock and resuscitation
Publication Title
Fed state prior to hemorrhagic shock and polytrauma in a porcine model results in altered liver transcriptomic response.
Sample Metadata Fields
Specimen part, Cell line, Subject, Time
View Samples- Homo sapiens
- 22 Downloadable Samples
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
In this experiments different treatments were applied to lung cancer cell lines
Publication Title
Ingenuity network-assisted transcription profiling: Identification of a new pharmacologic mechanism for MK886.
Sample Metadata Fields
No sample metadata fields
View Samples- Rattus norvegicus
- 15 Downloadable Samples
- Affymetrix Rat Gene 1.0 ST Array (ragene10st)
Description
Neuronal differentiation of PC12 cells in response to NGF is a prototypical model in which signal duration determines a biological response. Sustained ERK activity induced by NGF, as compared to transient activity induced by EGF, is critical to the differentiation of these cells. To characterize the transcriptional program activated preferentially by NGF, we compared global gene expression profiles between cells treated with NGF and EGF for 2-4 hrs, when sustained ERK signaling in response to NGF is most distinct from the transient signal elicited by EGF. This analysis identified 69 genes that were preferentially upregulated in response to NGF.
Publication Title
Global expression analysis identified a preferentially nerve growth factor-induced transcriptional program regulated by sustained mitogen-activated protein kinase/extracellular signal-regulated kinase (ERK) and AP-1 protein activation during PC12 cell differentiation.
Sample Metadata Fields
Specimen part, Cell line, Time
View Samples- Homo sapiens
- 6 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
We propose the hypothesis that loss of estrogen receptor function which leads to endocrine resistance in breast cancer, also results in de-differentiation from an epithelial to a mesenchymal phenotype that is responsible for increased aggressiveness and metastatic propensity. siRNA mediated silencing of the estrogen receptor in MCF7 breast cancer cells resulted in estrogen/tamoxifen resistant cells (pII) with altered morphology, increased motility with rearrangement and switch from an actin to a vimentin based cytoskeleton, and ability to invade simulated components of the extracellular matrix. Phenotypic profiling using an Affymetrix Human Genome U133 plus 2.0 GeneChip indicated fold changes 3 in approximately 2500 identifiable unique sequences, with about 1270 of these being up-regulated in pII cells. Changes were associated with genes whose products are involved in cell motility, loss of cellular adhesion and interaction with the extracellular matrix. Selective analysis of the data also showed a shift from luminal to basal cell markers and increased expression of a wide spectrum of genes normally associated with mesenchymal characteristics, with consequent loss of epithelial specific markers. Over-expression of several peptide growth factors and their receptors are indicative of an increased contribution to the higher proliferative rates of pII cells as well as aiding their potential for metastatic activity. Signalling molecules that have been identified as key transcriptional drivers of epithelial to mesenchymal transition were also found to be elevated in pII cells. We suggest that these data support our hypothesis that induced loss of estrogen receptor in previously antiestrogen sensitive cells is a trigger for the concomitant loss of endocrine dependence and onset of a series of possibly parallel events that changes the cell from an epithelial to a mesenchymal type. Inhibition of this transition through targeting of specific mediators may be a useful supplementary strategy to circumvent the effects of loss of endocrine sensitivity.
Publication Title
Estrogen receptor silencing induces epithelial to mesenchymal transition in human breast cancer cells.
Sample Metadata Fields
Cell line
View Samples- Homo sapiens
- 16 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Ischaemic preconditioning is a method of protecting tissue against ischaemia-reperfusion injury. It is an innate protective mechanism that increases a tissue's tolerance to prolonged ischaemia when it is first subjected to short burst of ischaemia and reperfusion. It is thought to provide this protection by increasing the tissue's tolerance to ischaemia, therby reducing oxidative stress, inflammation and apoptosis in the preconditioned tissue.
Publication Title
Transcriptional responses in the adaptation to ischaemia-reperfusion injury: a study of the effect of ischaemic preconditioning in total knee arthroplasty patients.
Sample Metadata Fields
Specimen part, Time
View Samples- Mus musculus
- 16 Downloadable Samples
- NextSeq 500
Description
AIM: To detect differences in transcriptional profiles after knocking down Brca1, Bard1 or Wdr5, compared to a negative control in early reprogramming to pluripotency. DESCRIPTION: RNA-seq profiles of early reprogramming mouse embryonic fibroblasts (MEFs) transduced with lentivirus containing doxycycline-inducible OSKM factors to induce pluripotency . Before starting reprogramming, OSKM-MEFs were transfected with different siRNAs and then they were reprogrammed for 3 or 6 days. Overall design: The control sample consists of cells transfected with non-targeting siRNA. The other samples were transfected with either siBrca1, siWdr5 or siBard1. For every knockdown there is a biological replicate.
Publication Title
The corepressor NCOR1 and OCT4 facilitate early reprogramming by suppressing fibroblast gene expression.
Sample Metadata Fields
Cell line, Subject
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Objective: To quantify changes in adipogenic gene expression in the presence of ritonavir (RTV) or tenofovir (TDF), and determine whether conjugated linoleic acid (CLA) isomers (cis9,trans11 or trans10,cis12) can mitigate detrimental effects of antiretoviral drugs.
Publication Title
Microarray Analysis Reveals Altered Lipid and Glucose Metabolism Genes in Differentiated, Ritonavir-Treated 3T3-L1 Adipocytes.
Sample Metadata Fields
Specimen part, Cell line, Treatment
View Samples- Vitis vinifera
- 4 Downloadable Samples
- Affymetrix Vitis vinifera (Grape) Genome Array (vitisvinifera)
Description
Oxidative stress can arise when in vitro propagated plants developed under low light conditions are exposed to high light during transfer to ex vitro conditions. In such a situation, among the many potential stresses to which the transferred plant can be exposed, oxidative stress is commonly experienced, most likely brought about by absorption of light energy in excess of that required for very low levels of photosynthetic metabolism. In vitro propagated grapevine when transferred to ex vitro conditions with a 4 fold increase in PPFD shows an initial inhibition of PET accompanied by an accumulation of H2O2, suggesting a signal for the upregulation in gene expression and antioxidant enzyme activity, which peaked at 48h after transfer of in vitro grapevine to ex vitro growing conditions.
Publication Title
Comparative transcriptomic profiling of Vitis vinifera under high light using a custom-made array and the Affymetrix GeneChip.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Mus musculus
- 3 Downloadable Samples
- NextSeq 500
Description
AIM: To find molecular signatures associated to the siRNA-mediated knockdowns in order to be able to identify similarities among different knockdowns. DESCRIPTION: Each sample includes biological triplicates for 35 siRNA-mediated knockdowns targeting 30 chromatin-associated proteins during in early reprogramming to iPS at day 6. A daily timecourse from reprogramming cells, without treatment from MEFs until day 6 is also included in triplicate. Overall design: RNA was harvested for all samples in bulk and the CELSeq2 method was used to prepare the RNAseq libraries
Publication Title
The corepressor NCOR1 and OCT4 facilitate early reprogramming by suppressing fibroblast gene expression.
Sample Metadata Fields
Cell line, Subject
View Samples- Homo sapiens
- 52 Downloadable Samples
- Illumina HiSeq 1000
Description
We report differences in mRNA gene expression in rectal biopsies from MSM compared to controls and for MSM timed with episodes of CRAI. Overall design: Rectal biopsies were obtained from MSM at two study timepoints: 1. after who abstaining from CRAI for >72 hours and 2.after engaing in CRAI within the last 24 hours. Rectal biopsies were also obtained from men who never engaged in AI.
Publication Title
Short Communication: Anatomic Site of Sampling and the Rectal Mucosal Microbiota in HIV Negative Men Who Have Sex with Men Engaging in Condomless Receptive Anal Intercourse.
Sample Metadata Fields
Specimen part, Subject
View Samples