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GSE19926
Mus musculus
8 Downloadable Samples
Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
acLDL loading of mouse peritoneal macrophage is an in vitro foam cell model.
Publication Title
Cholesterol accumulation regulates expression of macrophage proteins implicated in proteolysis and complement activation.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 73 Downloadable Samples
Illumina HiSeq 2500
Description
CD33-/- and/or TREM2-/- mice were crossed with the 5xFAD mouse model of Alzheimer's disease to generate single and double CD33/TREM2 knock-out mice on 5xFAD background. Transcriptome and gene expression analyses were performed to analyze the impact of CD33 and/or TREM2 knock-out on the transcriptome of microglia in the context of amyloid pathology. The results revealed that CD33 and/or TREM2 knock-out reprogrammed microglial gene expression signatures in 5xFAD mice in an age-dependent manner. Differential gene expression in 5xFAD;CD33-/- microglia depended on the presence of TREM2. These data suggest that TREM2 acts downstream of CD33. Overall design: Microglia were isolated from brains of WT, 5xFAD, 5xFAD;CD33-/-, 5xFAD;TREM2-/-, and 5xFAD;CD33-/-;TREM2-/- mice at 4 and 8 months of age, using FACS sorting for CD11b and CD45. RNA was extracted using the RNeasy Plus Micro Kit (Qiagen). Libraries were prepared using the TruSeq Stranded mRNA LT Prep Kit (Illumina) and sequenced on an Illumina HiSeq 2500 sequencer using single-end 50. Reads were aligned to mouse genome mm10 using the STAR aligner. Read counts for individual genes were obtained using HTSeq.
Publication Title
TREM2 Acts Downstream of CD33 in Modulating Microglial Pathology in Alzheimer's Disease.
Sample Metadata Fields
Age, Cell line, Subject
View Samples- Mus musculus
- 12 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
Background: High density lipoprotein (HDL) protects the artery wall by removing cholesterol from lipid-laden macrophages. However, recent evidence suggests that it might also inhibit atherogenesis by combating inflammation. Methods and Results: To identify potential anti-inflammatory mechanisms, we challenged macrophages with lipopolysaccharide (LPS), an inflammatory microbial ligand for Toll-like receptor 4 (TLR4). HDL inhibited the expression of 33% (301 of 911) of the genes normally induced by LPS, microarray analysis revealed. One of its major targets was the type I interferon response pathway, a family of potent viral immunoregulators controlled by TLR4 and the TRAM/TRIF signaling pathway. Unexpectedly, HDLs ability to inhibit gene expression was independent of cellular cholesterol stores. Moreover, it was unaffected by downregulation of two ATP-binding cassette transporters, ABCA1 and ABCG1, that promote cholesterol efflux. To examine the pathways potential in vivo relevance, we used mice deficient in apolipoprotein (apo) A-I, HDLs major protein. After infection with Salmonella (a Gram-negative bacterium that expresses LPS), apoA-Ideficient mice had 6-fold higher plasma levels of interferon-beta-a key regulator of the type I interferon response than did wild-type mice. Conclusions: HDL inhibits a subset of LPS-stimulated macrophage genes that regulate the type I interferon response, and its action is independent of sterol metabolism. These findings raise the possibility that regulation of macrophage genes by HDL might link innate immunity and cardioprotection.
Publication Title
High-density lipoprotein suppresses the type I interferon response, a family of potent antiviral immunoregulators, in macrophages challenged with lipopolysaccharide.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 10 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Ikaros mediates gene silencing in T cells through Polycomb repressive complex 2.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Mus musculus
- 6 Downloadable Samples
Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
The Ikaros zink finger transcription factor is a critical regulator of the hematopietic system, and plays an important role in the regulation of the development and function of several blood cell lineages.
Publication Title
Ikaros mediates gene silencing in T cells through Polycomb repressive complex 2.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 4 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
We used microarrays to analyze gene expression changes in the Ikaros null ILC87 T cell tumor line after re-expression of Ikaros.
Publication Title
Ikaros mediates gene silencing in T cells through Polycomb repressive complex 2.
Sample Metadata Fields
Cell line
View Samples- Arabidopsis thaliana
- 20 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Seven-day-old white-light-grown Arabidopsis seedlings were exposed for 15 minutes to polychromatic radiation with decreasing short-wave cut-off in the UV range, transferred back to the standard growth chamber and samples were taken 1 and 6 hours after the start of irradiation.
Publication Title
Genome-wide analysis of gene expression reveals function of the bZIP transcription factor HY5 in the UV-B response of Arabidopsis.
Sample Metadata Fields
Age, Time
View Samples- Mus musculus
- 8 Downloadable Samples
- Affymetrix Mouse Gene 2.1 ST Array (mogene21st)
Description
Lamin A/C was ablated in pancreatic acinar cells using Elastase1 driven, Cre-ErT mediated, LoxP recombination, causing excision of exons 10 and 11 of the Lmna gene
Publication Title
Lamin A/C Maintains Exocrine Pancreas Homeostasis by Regulating Stability of RB and Activity of E2F.
Sample Metadata Fields
Sex
View Samples- Arabidopsis thaliana
- 16 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Seven-day-old white-light-grown wild-type, cop1-4 or hy5-1 mutant Arabidopsis seedlings were exposed for fifteen minutes to polychromatic radiation with decreasing short-wave cut-off in the UV range (WG305 = +UV-B, WG327 = -UV-B) and samples were taken 1 h after the onset of irradiation.
Publication Title
CONSTITUTIVELY PHOTOMORPHOGENIC1 is required for the UV-B response in Arabidopsis.
Sample Metadata Fields
Age, Time
View Samples- Mus musculus
- 23 Downloadable Samples
- NextSeq 500
Description
Histological resolution of the murine pancreas occurs within one week after injury. Whether histological resolution constitutes pancreatic recovery at a molecular level is not known. We performed RNA-sequencing on the recovering pancreas to determine the transcriptomic profile within the histologically recovered pancreas. We show that although there is histological resolution one week after injury in mice, compared to baseline (non-injured pancreas), there are still numerous differentially expressed genes (DEGs) at one and even two weeks after injury. Overall, the findings suggest the actual recovery takes longer than initially thought given the differential transcriptomic profile in the pancreas two weeks after injury compared to the baseline pancreas. There is also the possibility of a novel emerging pancreatic transcriptome upon recovery. Overall design: Acute pancreatitis was induced by caerulein hyperstimulation in both male and female C57BL/6 mice. Total RNA was extracted from the head of the murine pancreas in mice at baseline (non-injured; n=8), day 7 (post-injury; n=8), and day 14 (post-injury; n=7). Total stranded RNA libraries (ribo-depleted) were generated and sequenced on the Illumina NextSeq 500 NGS platform. RNA-seq data was analyzed for differentially expressed genes between baseline and day 7 and between baseline and day 14.
Publication Title
Pancreatic gene expression during recovery after pancreatitis reveals unique transcriptome profiles.
Sample Metadata Fields
Sex, Specimen part, Cell line, Subject
View Samples