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GSE33639
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- 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- Homo sapiens
- 33 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
The expression level for 15 887 transcripts in lymphoblastoid cell lines from 19 monozygotic twin pairs (10 male, 9 female) were analysed for the effects of genotype and sex. On an average, the effect of twin pairs explained 31% of the variance in normalized gene expression levels, consistent with previous broad sense heritability estimates. The effect of sex on gene expression levels was most noticeable on the X chromosome, which contained 15 of the 20 significantly differentially expressed genes. A high concordance was observed between the sex difference test statistics and surveys of genes escaping X chromosome inactivation. Notably, several autosomal genes showed significant differences in gene expression between the sexes despite much of the cellular environment differences being effectively removed in the cell lines. A publicly available gene expression data set from the CEPH families was used to validate the results. The heritability of gene expression levels as estimated from the two data sets showed a highly significant positive correlation, particularly when both estimates were close to one and thus had the smallest standard error. There was a large concordance between the genes significantly differentially expressed between the sexes in the two data sets. Analysis of the variability of probe binding intensities within a probe set indicated that results are robust to the possible presence of polymorphisms in the target sequences.
Publication Title
Replicated effects of sex and genotype on gene expression in human lymphoblastoid cell lines.
Sample Metadata Fields
Sex
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- Mus musculus
- 55 Downloadable Samples
- Illumina HiSeq 2000
Description
The goal of this study was to identify potential AMH-induced genes and regulatory networks controlling regression by RNA-Seq transcriptome analysis of differences in Müllerian Duct mesenchyme between males (AMH signaling on) and females (AMH signaling off) in purified fetal Müllerian Duct mesenchymal cells. This analysis found 82 genes up-regulated in males during MD regression and identified Osterix (Osx)/Sp7, a key transcriptional regulator of osteoblast differentiation and bone formation, as a novel downstream effector of AMH signaling during MD regression. Overall design: Müllerian Duct mesenchymal cells mRNA profiles from 2-7 embryonic day 14.5 embryos were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000.
Publication Title
<i>Osterix</i> functions downstream of anti-Müllerian hormone signaling to regulate Müllerian duct regression.
Sample Metadata Fields
Sex, Specimen part, Cell line, Subject
View Samples- Mus musculus
- 10 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
This study compared gene expression in murine bcr-abl positive acute lymphoblastic leukemia cells in vivo in allogeneic BMT recipients compared to syngneneic BMT recipients.
Publication Title
Differential gene expression in acute lymphoblastic leukemia cells surviving allogeneic transplant.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 9 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
The effect of CLA on gene expression in Caco-2 cells
Publication Title
Conjugated linoleic acid alters global gene expression in human intestinal-like Caco-2 cells in an isomer-specific manner.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Analysis of adult retinas from tripartite motif-containing domain 9 knockouts and wild type littermates. Trim9 belongs to the TRIM family of E3 ubiquitin ligases. Results provide insight into possible roles for Trim9 in the retina.
Publication Title
The Trim family of genes and the retina: Expression and functional characterization.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 8 Downloadable Samples
- Illumina HiSeq 2500
Description
Lamina propria and muscularis macrophages, were sorted at steady steate and 2h after oral exposure to an attenuated form of Salmonella, comparison among these populations showed that the muscularis macrophages quckly respond to the presence of intestinal bacteria, upregulating some important tissue protective genes. Overall design: intestinal macrophages from 3 mice were pooled into one RNA sample, the experiment was done control X infected and was repeated twice
Publication Title
Neuro-immune Interactions Drive Tissue Programming in Intestinal Macrophages.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Danio rerio
- 4 Downloadable Samples
- IlluminaHiSeq2000
Description
We used morpholinos and gene editing tools to inactivate the srsf5a gene. In contrast to srsf5a homozygous mutants that did not display any phenotypic traits, microinjection of sMOsrsf5a led to developmental defects. By using RNA sequencing on morphants and control embryos we were able to identify a plethora of morpholino inadvertant target. Overall design: Two biological replicates were used per conditions. Samples named CtrlMO consist in embryos injected with the control morpholino (5''-CCTCTTACCTCAGTTACAATTTATA-3'', Gene Tools). Samples named sMOsrsf5a consist in embryos injected with the morpholino against srsf5a (5''-GGATTCAGTCTCACCTCTCACTGCA-3'', Gene Tools).
Publication Title
Number of inadvertent RNA targets for morpholino knockdown in Danio rerio is largely underestimated: evidence from the study of Ser/Arg-rich splicing factors.
Sample Metadata Fields
No sample metadata fields
View Samples