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GSE69062
Mus musculus
16 Downloadable Samples
Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
CD38, a multi-functional membrane receptor and enzyme, consumes NAD+ to generate products such as cyclic-ADP-ribose. CD38 knockout mice show elevated tissue and blood NAD+ level. Chronic feeding of high-fat, high-sucrose diet to wild type mice leads to exercise intolerance and reduced metabolic flexibility. Loss of CD38 by genetic mutation protects mice from diet-induced metabolic deficit. These animal model results suggest that elevation of tissue NAD+ through genetic ablation of CD38 can profoundly alter energy homeostasis in animals that are maintained on a calorically-excessive Western diet.
Publication Title
Genetic Ablation of CD38 Protects against Western Diet-Induced Exercise Intolerance and Metabolic Inflexibility.
Sample Metadata Fields
Specimen part
View Samples- Arabidopsis thaliana
- 12 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Microarray expression profiling was used to identify genes expressed misexpressed in wild-type Arabidopsis seedlings treated with 5-aza-2 deoxyctidine (5AC) or trichostatin A (TSA), and in decrease in dna methylation1 (ddm1) mutant seedlings.
Publication Title
Changes in global gene expression in response to chemical and genetic perturbation of chromatin structure.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 33 Downloadable Samples
Illumina HiSeq 2500
Description
The goal of this study was to define relationships between peripheral blood miRNAs and mRNAs of women undergoing idiopathic preterm labor (PTL) and compare network level changes to control women that deliver at term.Using RNA Sequencing we have performed global miRNA and mRNA profiling in both monocytes and whole blood leukocytes of women who underwent PTL (N=15) matched to non-pathological controls (N=30) as a part of the Ontario Birth Study cohort. We have identified differentially expressed miRNAs, mRNAs and pathways associated with PTL. Intriguingly, we found perturbations in many cellular signaling pathways, particularly in interleukin signaling. We also predicted mRNA targets for specific miRNAs and used these predictions to build putative miRNA-mRNA networks. We identified 6 miRNAs significantly associated with PTL whose expression is negatively correlated with expression of 14 predicted mRNA targets that are also significantly associated with PTL. Overall design: miRNA and mRNA were quantified from whole blood and monocytes of women undergoing spontaneous preterm labor compared to nonlabor controls matched on gestational age
Publication Title
Comparative analysis of gene expression in maternal peripheral blood and monocytes during spontaneous preterm labor.
Sample Metadata Fields
Subject
View Samples- Macaca mulatta, Pan troglodytes, Homo sapiens
- 29 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Divergent whole-genome methylation maps of human and chimpanzee brains reveal epigenetic basis of human regulatory evolution.
Sample Metadata Fields
No sample metadata fields
View Samples- Macaca mulatta, Pan troglodytes, Homo sapiens
- 29 Downloadable Samples
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
We identified human-specific gene expression patterns in the brain by comparing expression with chimpanzee and rhesus macaque
Publication Title
Divergent whole-genome methylation maps of human and chimpanzee brains reveal epigenetic basis of human regulatory evolution.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 72 Downloadable Samples
- Illumina MouseRef-8 v2.0 expression beadchip
Description
Liposarcoma is a poorly understood malignancy of fat cells. Lipolysis, a central pathway of adipose tissue metabolism, has been implicated in cancer. Here, we generated tissue-specific single- and combined knockout mice for the two major lipases ATGL and HSL. Notably, double knockout (DAKO) mice developed late onset liposarcoma with complete penetrance, while single knockout mice appeared normal. DAKO whole transcriptome profiles differed from those of single knockout mice, revealing an early-onset tissue-specific response that persisted until the late-onset development of liposarcoma. Cancer-associated markers Gpnmb and G0s2 were among the most highly dysregulated genes in DAKO mice and also in human liposarcomas, suggesting a potential role for these proteins as liposarcoma-specific biomarkers. Taken together, our results demonstrate a novel epistatic interaction linking lipolysis with cancer. DAKO mice provide a promising model for studying early premalignant changes that lead to late-onset disease.
Publication Title
Epistatic interaction between the lipase-encoding genes Pnpla2 and Lipe causes liposarcoma in mice.
Sample Metadata Fields
Age, Specimen part
View Samples- Homo sapiens
- 12 Downloadable Samples
- Illumina HiSeq 2500
Description
The goal of the study was to compare transcriptome changes in HeLa cells after infection with recombinant Thogoto virus (wild-type, ML deletioin mutant or ML SW mutant not able to interact wiith TFIIB. While wild-type virus is able to inhibit inflammatory genes, ML deletion mutant and TFIIB-non-interacting mutant lose this effect on gene transcription. Overall design: Examination of transcriptome changes in HeLa cells under steady state or after THOV infection using Illumina HiSeq.
Publication Title
Viral targeting of TFIIB impairs de novo polymerase II recruitment and affects antiviral immunity.
Sample Metadata Fields
Cell line, Subject
View Samples- Homo sapiens
- 52 Downloadable Samples
- IlluminaHiSeq2000
Description
We carried out RNA-sequencing (RNA-seq) of adult human postmortem neocortical brain tissue, and then correlated those expression values with the fMRI signal in each brain region Overall design: Ten cortical regions were included in the analysis: pre-motor cortex - PMV (BA6), dorsolateral prefrontal cortex – DLPFC (BA9), middle temporal gyrus – pMTG (BA21), superior temporal gyrus – pSTG (BA22), angular gyrus - AG (BA39), supramarginal gyrus - SMG (BA40), pars opercularis - POP (BA44), pars triangularis - PTr (BA45), middle frontal gyrus – MFG (BA46) and pars orbitalis - POrB (BA47). For each brain region, three or more samples from left adult brain hemispheres were collected (ages range from 33 to 49) and only males were included to avoid the effect of sex
Publication Title
Correspondence between Resting-State Activity and Brain Gene Expression.
Sample Metadata Fields
No sample metadata fields
View Samples- Pseudomonas aeruginosa
- 26 Downloadable Samples
- Illumina HiSeq 2500
Description
We demonstrate that the versatile environmental bacterium Pseudomonas aeruginosa adapts a virulence phenotype after serial passage in Galleria mellonella as an invertebrate model host. The virulence phenotype was not linked to the acquisition of genetic variations and was sustained for several generations, despite cultivation of the ex vivo virulence-adapted P. aeruginosa cells under non-inducing rich medium conditions. Transcriptional reprogramming seemed to be induced by a host-specific food source as reprogramming was also observed upon cultivation of P. aeruginosa in medium supplemented with polyunsaturated long-chain fatty acids. Methods : mRNA profiles were generated for Pseudomonas aerugionsa samples derived from LB-cultures grown to an OD600 =2. The removal of ribosomal RNA was performed using the Ribo-Zero Bacteria Kit (Illumina) and cDNA libraries were generated with the ScriptSeq v2 Kit (Illumina) . The samples were sequenced in single end mode on an Illumina HiSeq 2500 device and mRNA reads were trimmed and mapped to the NC_008463.1 (PA14) reference genome from NCBI using Stampy pipeline with defaut settings. Overall design: Isolate CH2658 was subjected to in vivo and in vitro evolution experiments in this study. This isolate was obtained from the lab of G. Gastmeier, Charite Berlin, Germany. The in vivo passages (using G. mellonella) are named CH2658 I-IV corresponding to passages 1 4. The last passage CH2658 IV corresponds to the “evolved strain” and was passaged in LB (four days, two passages a day) to generate revertants which are referred to as CH2658 Rev1-4 corresponding to samples from day1-4. The last passage CH2658 Rev4 is called “revertant”. Additionally, the clinical isolate was passaged under in vitro conditions in the presence of linolenic acid (Roth) with (CH2658 Lil+P) and without paraffin (CH2658 Lil). As controls, CH2658 was passaged in LB (CH2658 LB) and in LB supplemented with paraffin (CH2658 LB+P). The in vitro passage experiment was conducted for four days and two passages a day.
Publication Title
Establishment of an induced memory response in Pseudomonas aeruginosa during infection of a eukaryotic host.
Sample Metadata Fields
Subject
View Samples- Pseudomonas aeruginosa
- 10 Downloadable Samples
- Illumina HiSeq 2500
Description
Purpose: The goal of this study was to use RNA Seq to explore whether and to what extent genetic heterogeneity would shape the transcriptional profile in the environment of the CF lung Methods : mRNA profiles were generated for Pseudomonas aerugionsa samples derived from explanted lung tissue or pure cultures isolated from the same lung regions by deep sequencing. To enrich the bacterial RNA MicrobeEnrich Kit (Ambion) was used. The removal of ribosomal RNA was performed using the Ribo-Zero Bacteria Kit (Illumina) and cDNA libraries were generated with the ScriptSeq v2 Kit (Illumina) . The samples were sequenced in single end mode on an Illumina HiSeq 2500 device and mRNA reads were trimmed and mapped to the PAO1 NC_002516 reference genome from NCBI using Stampy pipeline with defaut settings. Overall design: mRNA profiles either from Pseudomonas aeruginosa containing explanted lung tissue from a single patient from various regions of the lung or pure P. aeruginosa liquid cultures grown in LB at 37C from the same lung regions as the ex vivo samples were generated and deep sequenced using Illumina HiSeq 2500.
Publication Title
Genetically diverse Pseudomonas aeruginosa populations display similar transcriptomic profiles in a cystic fibrosis explanted lung.
Sample Metadata Fields
Subject
View Samples