The host & gut microbiome orchestrate smoking cessation-induced weight gain
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina NovaSeq 6000
ORGANISM(S): Mus musculus
SUBMITTER: Uria Mor
PROVIDER: E-MTAB-10869 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Gene expression in adipose and other tissues of polygenic Fat and Lean mice.<br>
2011-11-04 | E-MEXP-3091 | biostudies-arrayexpress
Project description:Treatment with insulin-like growth factor-I (IGF-I) during feed deprivation attenuates the weight loss response in both mammals and fish, therefore the reduction in plasma IGF-I concentrations during fasting likely serves as a signal that contributes to the catabolic response. To better understand the physiological mechanisms responsible for this effect rainbow trout were administered IGF-I during a 2 wk period of feed deprivation and changes in gene expression in white muscle were determined using microarray analysis. Weight loss was reduced by 15% (P<0.05) in IGF-I treated fish. A total of 440 transcripts were identified as differentially regulated (P<0.05) between saline and IGF-I treated fish. Genes related to protein degradation were down-regulated and included protease and peptidase genes and genes involved in ubiquitin-proteasome and cathepsin-mediated proteolytic pathways. IGF-I increased expression of myosin binding protein H and coronin-1C, while decreasing expression of other myofibrillar and cytoskeleton-associated genes like troponin-C and parvalbumin-2. Polyadenylate-binding protein 2, a transcription factor that positively regulates myoD and myogenin expression, was upregulated with IGF-I treatment. Additional genes that were differentially regulated are associated with lipid and carbohydrate metabolism, mitochondrial biogenesis and electron transport, gene transcription, signal transduction and regulation of apoptosis. In summary, these data suggest that IGF-I plays a central role in regulating protein degradation, especially via the ubiquitin-proteasomal pathway, and that reductions in protein degradation and the subsequent effects on other physiological systems are largely responsible for the IGF-I-induced reduction in weight loss. Eight approximately 1-year old full-sibling rainbow trout families were housed in individual tanks, according to family, at the National Center for Cool and Cold Water. Each fish was pit-tagged at 7-months of age. At the beginning of the study, fish were anesthetized with tricaine methanesulfonate (MS-222), weighed, and an osmotic pump was surgically inserted into the peritoneal cavity of each fish (n=4 fish/family/treatment, N=16 fish). The osmotic pump contained either recombinant human IGF-I, which released hormone at 25 ug/kg/day, or saline, which was the vehicle used to resuspend IGF-I. Feed was withheld 2-days prior to surgery and for the experimental 2 week period. Fish were harvested using as overdose of MS-222, weighed, and white muscle samples were removed, frozen in liquid N, and stored at -80 C until analysis. Muscle RNA was isolated from muscle of the two families that exhibited the greatest difference in weight loss between IGF-I and saline treatments; families 64 and 107. Hybridizations were performed using a dye-swap design with an IGF-I and saline treated fish within the same family, therefore a total of 16 slides were hybridized using Alexa 647 and Alexa 555 dyes.
2015-02-01 | E-GEOD-31765 | biostudies-arrayexpress
Project description:This experiment compares gene expression in kidneys of control and ACTH treated mice. <br>Kidney RNA was prepared from 6 mice: three controls and three ACTH treated and processed by the microarray team at Ark Genomics and the Roslin Institute. <br>RNAs were processed through standard Affymetrix protocols, with one round of cDNA amplification. Processed RNAs were hybridised to Affymetrix Mouse Genome 430 2.0 GeneChip, and data were extracted through the GCOS software. <br>CEL files were made available for further data processing via RMA in Bioconductor.
2009-03-31 | E-MEXP-1761 | biostudies-arrayexpress
Project description:Analysis of angiotensin II effect on left ventricle at gene expression level. The hypothesis tested in the present study was that angiotensin II treatment may affect gene expression in left ventricle in a strain specific manner. Results provide important information about which genes respond to angiotensin II in C57Bl/6N male mice compared to their C57Bl/6J counterparts. Total RNA obtained from isolated left ventricles from C57Bl/6J and C57Bl/6N mice subjected to 48 hours of angiotensin II infusion, via osmotic mini-pumps (500ng/kg/h) implanted sub-cutaneously, compared to sham operated controls.
2014-12-12 | E-GEOD-53269 | biostudies-arrayexpress
Project description:Engrailed homeoproteins are expressed in adult dopaminergic neurons of the substantia nigra. In Engrailed1 heterozygous mice, these neurons start dying at 6 weeks, are more sensitive to oxidative stress and progressively develop traits similar to those observed following an acute and strong oxidative stress inflected to wild-type neurons. These changes include DNA strand breaks and the modification (intensity and distribution) of several nuclear and nucleolar heterochromatin marks. Engrailed1 and Engrailed2 are biochemically equivalent transducing proteins previously used to antagonize dopaminergic neuron death in Engrailed heterozygous mice and in mouse models of Parkinson disease. Accordingly, we show that, following an acute oxidative stress, a single Engrailed2 injection restores all nuclear and nucleolar heterochromatin marks, decreases the number of DNA strand breaks and protects dopaminergic neurons against apoptosis. RNA-seq data for differentially expressed genes in the SNpc of En1+/- mice, En2 infused mice and 6-OHDA/En2 injection experiments.
2015-09-24 | E-GEOD-72321 | biostudies-arrayexpress
Project description:Rationale. Lung inflammation in premature infants contributes to development of bronchopulmonary dysplasia (BPD), a chronic lung disease with long-term sequelae. Pilot studies administering budesonide suspended in surfactant have found reduced BPD without apparent adverse effects as occur with systemic dexamethasone therapy. Objectives. To determine effects of budesonide on differential genes expression in human fetal lung Methods. We prepared RNA from 3 samples of human fetal lung at 23 weeks gestation before (preculture, PC) and after 4 days culture as explants with (Bud) or without (Way) budesonide (30 nM) and performed RNAseq on the 9 samples.
2016-06-30 | E-GEOD-83888 | biostudies-arrayexpress
Project description:Population control for the scRNA-seq based analysis a well-established fraction of mouse subcutaneous adipose-derived stromal vascular fraction (SVF) cells that is generally considered to harbour adipogenic stem and progenitor cells (ASPCs). We collected Lin- (CD31- CD45- TER119-) CD29+ CD34+ SCA1+ cells from the mouse subcutaneous SVF of transgenic mice, in which red fluorescent protein (RFP) is induced in Dlk1-expressing cells upon feeding with tamoxifen. While CD29, CD34, and SCA1 are generally expected to enrich for stem cells, DLK1 has previously been suggested to specifically mark pre-adipocytes.
2018-05-01 | E-MTAB-5818 | biostudies-arrayexpress
Project description:Angiotensin II (Ang II) mediated signaling plays a key role in the development of hypertension associated target organ damages. However, the gene expression changes regulated by Ang II in the early stage of acute cerebral, cardiac, renal, vascular injury remain unclear. we investigated Ang IIâ??mediated gene expression alteration associated with the development of early cerebral, cardiac, renal, vascular injury by microarray assay in a mouse model. All mice were euthanized by an overdose of pentobarbital on days 1, 3 and 7 of Angiotensin II treatment. Total RNA was isolated with TRIzol (Invitrogen) from brains, hearts, kidneys and vessels (n=1-3 per group) at each time point according to manufacturerâ??s instructions. Gene expression profiling was performed using Affymetrix GeneChip mouse Genome 430 2.0 array according to the manufacturerâ??s instructions (Affymetrix, Inc., Santa Clara, CA). On the GeneChip Mouse Genome 430 2.0 Array, over 45,000 probe sets analyze the expression level of over 39,000 transcripts and variants from over 34,000 well characterized mouse genes.
2014-07-16 | E-GEOD-59437 | biostudies-arrayexpress
Project description:We analysed a well-established fraction of mouse subcutaneous adipose-derived SVF cells that is generally considered to harbour adipose stem and progenitor cells (ASPCs). To study the molecular characteristics and the subpopulation structure of ASPCs, we performed three replicate scRNA-seq experiments. We collected Lin- (CD31- CD45- TER119-) CD29+ CD34+ SCA1+ cells from the mouse subcutaneous SVF of transgenic mice, in which red fluorescent protein (RFP) is induced in Dlk1-expressing cells upon feeding with tamoxifen. While CD29, CD34, and SCA1 are generally expected to enrich for stem cells, DLK1 has previously been suggested to specifically mark pre-adipocytes. The submission includes the raw data of all sequenced cells, while we only processed 208 high quality single cells. RFP status is indicated in the processed files.
2018-05-01 | E-MTAB-5802 | biostudies-arrayexpress
Project description:Adipose tissue dysfunction in obese humans is associated with disrupted metabolic homeostasis, insulin resistance, and type 2 diabetes mellitus (T2DM). In a mouse model that has preserved insulin sensitivity despite increased adiposity, we used unbiased three-dimensional integration of proteome profiles, metabolic profiles, and gene regulatory networks to understand adipose tissue proteome-wide changes and their metabolic implications. Multiple-dimensional liquid chromatography tandem mass spectrometry and extended multiplexing TMT labeling (24 biological samples) was used to analyze proteomes of epididymal adipose tissues isolated from wildtype (Csf2+/+) and GM-CSF driven dendritic cell deficient (Csf2-/-) mice that were fed low fat, high fat, or high fat plus cholesterol diets for 8 weeks. The peripheral metabolic health (as measured by body weight, adiposity, plasma fasting glucose, insulin, triglycerides, phospholipids, total cholesterol levels, and glucose and insulin tolerance tests) deteriorated with diet for both genotypes, while mice lacking Csf2 were protected from insulin resistance. Regardless of diet, 30, mostly mitochondrial metabolism proteins participating in amino acid and branched chain amino acid pathways were altered, between Csf2-/- and Csf2+/+ mice. Tissue DHTKD1 levels were >4-fold upregulated and plasma 2-aminoadipoate (2-AA) levels were >2 fold reduced in Csf2-/- mice. GM-CSF driven dendritic cells play a detrimental role in insulin sensitivity via lysine metabolism involving Dhtkd1/2-AA axis.
2018-08-06 | PXD008660 | Pride