Journal: EMBO Molecular Medicine

Article Title: Adipogenesis and insulin sensitivity in obesity are regulated by retinoid-related orphan receptor gamma

doi: 10.1002/emmm.201100172

Figure Lengend Snippet: Functional siRNA screen of potential RORγ target genes identified by microarray analysis of 3T3-L1 cells overexpressing RORγ. 3T3-L1 cells were transfected with siRNA pools, differentiated and fluorescently stained to assess the percentage of differentiated cells ( n = 4). Nuclear run-on assay for transcriptional activity of genes in undifferentiated 3T3-L1 cells infected with control or RORγ-overexpressing lentivirus. 32P-labelled mRNA was hybridized to cDNA from the indicated genes on a slot blot and analysed by autoradiography. Expression of Mmp3 mRNA in 3T3-L1 preadipocytes overexpressing RORγ by transient transfection or viral infection. MMP3 promoter constructs with potential ROR response elements (RREs) cloned into a luciferase reporter vector. Luciferase assay in 3T3-L1 preadipocytes overexpressing RORγ or control vector 48 h after transfection normalized to renilla luciferase activity. Activation of IL17 promoter was used as a control ( n = 4). Chromatin immunoprecipitation of RORγ in 3T3-L1 cells using anti-HA antibody 6 days after infection with RORγ or control lentivirus. DNA was quantified by qPCR using specific primers for RRE1 and RRE2 and normalized to input ( n = 3). Fluorescent staining of differentiated 3T3-L1 adipocytes expressing RORγ or control vector during differentiation treated with or without 20 µM of MMP3 inhibitor 2 days before and after induction of differentiation (scale: 100 µm). The results shown are representative of three independent experiments. Values represent means ± SD, * p ≤ 0.05 and ** p ≤ 0.01, *** p ≤ 0.001.

Article Snippet: mRNA was isolated and transcribed into cDNA using the Multi-MACS cDNA kit (Miltenyi). mRNA expression was assessed by real-time PCR using SybrGreen (Invitrogen) according to the manufacturer's protocol. mRNA expression was normalized to 36b4 or Gapdh.

Techniques: Functional Assay, Microarray, Transfection, Staining, Nuclear Run-on Assay, Activity Assay, Infection, Control, Dot Blot, Autoradiography, Expressing, Construct, Clone Assay, Luciferase, Plasmid Preparation, Activation Assay, Chromatin Immunoprecipitation

Journal: Experimental and Therapeutic Medicine

Article Title: Expression of platelet-derived growth factor in the vascular walls of patients with lower extremity arterial occlusive disease

doi: 10.3892/etm.2015.2275

Figure Lengend Snippet: Reagents used in the study.

Article Snippet: Multi-functional DNA Gel Extraction kit II (Spin-Column) , BioTeke Corporation, Beijing, China.

Techniques: RNA Extraction, Gel Extraction

Journal: Cell

Article Title: Longitudinal Multi-omics Reveals Subset-Specific Mechanisms Underlying Irritable Bowel Syndrome

doi: 10.1016/j.cell.2020.08.007

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: ​ REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and Virus Strains Bifidobacterium longum ATCC ATCC 55813 Lachnospiraceae sp. 2_1_58FAA BEI Resources HM-161, HMP ID 0991 Lachnospiraceae sp. 1_4_56FAA BEI Resources HM-154, HMP ID 0988 Hungatella hathewayi DSM DSM 13479 Chemicals, Peptides, and Recombinant Proteins RNAlater stabilization solution Invitrogen AM7020 Tryptamine hydrochloride Millipore Sigma CAS# 343–94-2 Hypoxanthine Millipore Sigma CAS# 68–94-0 Critical Commercial Assays Amplex Red Xanthine/Xanthine Oxidase Assay Kit Thermo Fisher {"type":"entrez-protein","attrs":{"text":"A22182","term_id":"89506","term_text":"pir||A22182"}} A22182 Deposited Data Mendeley dataset, supplemental data I-VI This paper https://doi.org/10.17632/29n2z5r5ph.3 Microbiome data This paper European Nucleotide Archive, PRJEB37924 Metabolomics data This paper MetaboLights repository, MTBLS1396 Transcriptome and methylome data This paper Gene Expression Omnibus, {"type":"entrez-geo","attrs":{"text":"GSE146853","term_id":"146853"}} GSE146853 Experimental Models: Organisms/Strains Germ-free mice Taconic Farms Swiss Webster Software and Algorithms Maaslin2 Huttenhower lab http://huttenhower.sph.harvard.edumaaslin BURST Knights lab https://zenodo.org/record/806850 SHOGUN Knights lab https://github.com/knights-lab/SHOGUN Other Code used for metagenome and metabolome data analysis This study https://gitlab.com/rubenmars/ibs-multi-omics-code Code used for correlation networks This study https://github.com/mhoutti/ibs_network Open in a separate window KEY RESOURCES TABLE Longitudinal sampling limits heterogeneity seen in cross-sectional microbiome studies Alteration in the gut microbiome and microbial metabolites underlie IBS and symptom flares Data integration reveals effect of microbial metabolites on gastrointestinal function Purine starvation is identified as a possible therapeutic target in IBS

Techniques: Recombinant, Expressing, Software