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SRP074233
Mus musculus
8 Downloadable Samples
Illumina HiSeq 2500
Description
Purpose: To identify the impact of thermoneutral housing as opposed to standard housing on gene expression profiles in the mouse peripheral blood mononuclear cells (PBMCs), focusing on proinflammatory immune responses and high-fat diet induced non-alcoholic fatty liver disease pathogenesis. Methods: Expression profiles from PBMCs collected from C57Bl6 mice fed chow or high-fat diet for 8 weeks, following 2 weeks at either standard or thermoneutral housing conditions. Sequencing was performed in duplicate, the Illumina HiSeq 2500. Transcripts that passed quality filters were analyzed at the gene level, using Strand NGS for accurate alignment and quantification. Results: We mapped approximately 20million reads per sample to the mm10 genome using annotations produced by Ensembl, which represented 36186 transcripts. Approximately 14000 genes exhibited reasonable expression in at least one experimental condition. The primary focus was the effect of housing temperature while holding diet consistent (i.e. thermoneutral vs standard, both on high-rat diet), where ~2700 genes exhibited differential regulation. Conclusions: We present the transcriptomic profile of PBMCs from mice fed chow of high-fat diets, following either standard or thermoneutral housing. We obseve an augmented proinflammatory immune response. Overall design: PBMC expression profiles were characterized following eight weeks of chow or high-fat diet, following two weeks of standard or thermoneutral housing.
Publication Title
Modulation of ambient temperature promotes inflammation and initiates atherosclerosis in wild type C57BL/6 mice.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 29 Downloadable Samples
Affymetrix Human Genome U133A Array (hgu133a)
Description
Gene expression profiles were recorded from rectal suction specimens of Cystic Fibrosis (CF) patients, carrying the CF-specific D508 mutated CFTR-allele. These profiles were compared with gene expression profiles from rectal suction specimens of non-CF subjects (control).
Publication Title
The CF-modifying gene EHF promotes p.Phe508del-CFTR residual function by altering protein glycosylation and trafficking in epithelial cells.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 126 Downloadable Samples
- Affymetrix Human Exon 1.0 ST Array [transcript (gene) version (huex10st)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Toward Signaling-Driven Biomarkers Immune to Normal Tissue Contamination.
Sample Metadata Fields
Disease, Disease stage
View Samples- Mus musculus
- 17 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Here we characterize and optimize both systems to increase their utility for preclinical studies. We show that TH-MYCN mice develop tumors in the paraspinal ganglia, but not in the adrenal, with cellular and gene expression patterns similar to human NB. In addition, we present a new ultrasound guided, non-invasive orthotopic xenograft method. This injection technique is rapid, provides accurate targeting of the injected cells and leads to efficient engraftment. We also demonstrate that tumors can be detected, monitored and quantified prior to visualization using ultrasound, MRI and bioluminescence. Finally we develop and test a standard of care chemotherapy regimen. This protocol, which is based on current treatments for neuroblastoma, provides a baseline for comparison of new therapeutic agents.
Publication Title
Preclinical models for neuroblastoma: establishing a baseline for treatment.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 28 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
Nasopharyngeal carcinoma (NPC) is a common cancer in southern China and South East Asia where more than 50,000 new cases are diagnosed each year.
Publication Title
The ATM tumour suppressor gene is down-regulated in EBV-associated nasopharyngeal carcinoma.
Sample Metadata Fields
Disease, Disease stage
View Samples- Homo sapiens
- 12 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
YAP knockdown in HUVEC elicits proliferation and cell cycle preogression defects. YAP deficient cells caused arrest in G1 and defects in S-phase entry. The microarray analysis was conducted to identify potential YAP targets that are involved in HUVEC cell cycle regulation
Publication Title
YAP regulates S-phase entry in endothelial cells.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Homo sapiens
- 18 Downloadable Samples
- Affymetrix Human Gene 2.0 ST Array (hugene20st)
Description
The transcriptional co-regulator IRF2BP1 gets de-SUMOylated after EGF treatment in Hela cells. SUMOylation of IRF2BP1 occurs at position K579.
Publication Title
Transient deSUMOylation of IRF2BP proteins controls early transcription in EGFR signaling.
Sample Metadata Fields
Cell line, Treatment
View Samples- Mus musculus
- 162 Downloadable Samples
- Illumina HiSeq 2500
Description
We report the transcriptome of single pancreatic cells at embryonic day e13.5 Overall design: Single cells mRNA of wild-type mouse pancreata at embryonic day 13.5
Publication Title
Single cell transcriptomic profiling of mouse pancreatic progenitors.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Homo sapiens
- 43 Downloadable Samples
- Illumina HiSeq 2500
Description
Purpose: To determine effects of arsenic on gene expression in polarized primary human bronchial epithelial (HBE) cells and impact on transcriptional response to Pseudomonas aeruginosa infection Methods: mRNA profiles of HBE cells from 6 donors exposed to 0, 5, 10 or 50 ug/L total arsenic +/- Pseudomonas aeruginosa (48 samples) were generated using Illumina sequencing, aligned in CLC Genomics workbench and analyzed for DE in EdgeR Findings: 20-30 million reads were mapped per sample and transcripts were identifed that were significantly differentially expressed in response to arsenic and Pseudomonas aeruginosa Overall design: Gene expression profiles of HBE cells from 6 donors exposed to three concentrations of arsenic +/- Pseudomonas were generated using mRNA sequencing
Publication Title
Arsenic alters transcriptional responses to Pseudomonas aeruginosa infection and decreases antimicrobial defense of human airway epithelial cells.
Sample Metadata Fields
Sex, Specimen part, Subject
View Samples- Mus musculus
- 6 Downloadable Samples
- Illumina MouseRef-8 v2.0 expression beadchip
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Coassembly of REST and its cofactors at sites of gene repression in embryonic stem cells.
Sample Metadata Fields
Cell line, Treatment
View Samples