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Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of mouse liver after Con, Veh, Dex treatments reveals glucocorticoid signalling synchronizes the liver transcriptiome

ABSTRACT: Mouse liver RNA was extracted using Trizol (Invitrogen) and Qiagen RNeasy kits. RNA was checked with an Agilent Bioanalyzer for evidence of sub-genomic DNA and degradation. Targets were produced using standard Affymetrix protocols. Each sample represents data from a single mouse liver.

ORGANISM(S): Mus musculus

SUBMITTER: Akhilesh Basi Reddy

PROVIDER: E-GEOD-564 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Glucocorticoid signaling synchronizes the liver circadian transcriptome.

Reddy Akhilesh B AB Maywood Elizabeth S ES Karp Natasha A NA King Verdun M VM Inoue Yusuke Y Gonzalez Frank J FJ Lilley Kathryn S KS Kyriacou Charalambos P CP Hastings Michael H MH

Hepatology (Baltimore, Md.) 20070601 6

<h4>Unlabelled</h4>Circadian control of physiology is mediated by local, tissue-based clocks, synchronized to each other and to solar time by signals from the suprachiasmatic nuclei (SCN), the master oscillator in the hypothalamus. These local clocks coordinate the transcription of key pathways to establish tissue-specific daily metabolic programs. How local transcriptomes are synchronized across the organism and their relative contribution to circadian output remain unclear. In the present stud ...[more]

PMID: 17538967

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Liver treatments Con, Veh, Dex

Project description:Mouse liver RNA was extracted using Trizol (Invitrogen) and Qiagen RNeasy kits. RNA was checked with an Agilent Bioanalyzer for evidence of sub-genomic DNA and degradation. Targets were produced using standard Affymetrix protocols. Each sample represents data from a single mouse liver. Keywords: other

2004-06-30 | GSE564 | GEO

Gene expression profile in the liver of insulin-deficient mice with icv leptin administration

Project description:Analysis of gene expression in the liver of insulin-deficient mice regulated by icv leptin administration. Control group received icv PBS administration. Icv leptin administration ameliorates hyperglycemia in insulin-deficient mice. Our transcriptome data provides important aspects of the leptin’s anti-type 1 diabetes action. Mice were harvested 10 days after icv leptin administration (25ng/0.11uL/hour). Liver samples were quickly removed, frozen in liquid nitrogen and subsequently stored at –80ºC. RNAs were extracted by Qiagen mRNA extract kits (RNeasy plus). gDNA was eliminated in this procedure by gDNA eliminator column, which is included in Qiagen mRNA extract kits. Genomics and Microarray Core Facility at UT-Southwestern (http://microarray.swmed.edu/) checked RNA quality with Bioanalyzer Chip and processed the samples for hybridization with Illumina Mouse-6 V2 BeadChip (Illumina Inc., San Diego, CA).

2013-09-03 | E-GEOD-48598 | biostudies-arrayexpress

Network Modeling of Liver Metabolism to Predict Plasma Metabolite Changes During Short-Term Fasting in the Laboratory Rat: Liver Transcriptome Changes in Study 3

Project description:Purpose: The purpose of this study is to measure the changes in liver transcriptome in response to short-term fasting between 7 and 13 h where the rats were dosed with 2 ml/kg of saline vehicle at 0 h Methods: Total RNA was isolated from the liver, using TRIzol Reagent (Thermo Fisher Scientific, Waltham, MA) and the direct-zol RNA Mini Prep kit (Zymo Research, Irvine, CA). The isolated RNA samples were then submitted to the Vanderbilt University Medical Center VANTAGE Core (Nashville, TN) for RNA quality determination and sequencing. Total RNA quality was assessed using a 2100 Bioanalyzer (Agilent, Santa Clara, CA). At least 200 ng of DNase-treated total RNA with high RNA integrity was used to generate poly-A-enriched mRNA libraries, using KAPA Stranded mRNA sample kits with indexed adaptors (Roche, Indianapolis, IN). Library quality was assessed using the 2100 Bioanalyzer (Agilent), and libraries were quantitated using KAPA library Quantification kits (Roche). Pooled libraries were subjected to 75-bp paired-end sequencing according to the manufacturer’s protocol (Illumina HiSeq3000, San Diego, CA). Results: No genes were were found to be differentially expressed with a false discovery rate less than 0.1 Conclusions: There were no significant changes in liver gene expression between 7 and 13 h of fasting

2019-03-19 | GSE123987 | GEO

Network Modeling of Liver Metabolism to Predict Plasma Metabolite Changes During Short-Term Fasting in the Laboratory Rat: Liver Transcriptome Changes in Study 1

Project description:Purpose: The purpose of this study is to measure the changes in liver transcriptome in response to short-term fasting between 5 and 10 h where the rats were dosed with 6 ml/kg of polyethylene glycol vehicle at 0 h Methods: Total RNA was isolated from the liver, using TRIzol Reagent (Thermo Fisher Scientific, Waltham, MA) and the direct-zol RNA Mini Prep kit (Zymo Research, Irvine, CA). The isolated RNA samples were then submitted to the Vanderbilt University Medical Center VANTAGE Core (Nashville, TN) for RNA quality determination and sequencing. Total RNA quality was assessed using a 2100 Bioanalyzer (Agilent, Santa Clara, CA). At least 200 ng of DNase-treated total RNA with high RNA integrity was used to generate poly-A-enriched mRNA libraries, using KAPA Stranded mRNA sample kits with indexed adaptors (Roche, Indianapolis, IN). Library quality was assessed using the 2100 Bioanalyzer (Agilent), and libraries were quantitated using KAPA library Quantification kits (Roche). Pooled libraries were subjected to 75-bp single-end sequencing according to the manufacturer’s protocol (Illumina HiSeq3000, San Diego, CA). Results: No genes were were found to be differentially expressed with a false discovery rate less than 0.1 Conclusions: There were no significant changes in liver gene expression between 5 and 10 h of fasting

2019-03-19 | GSE123935 | GEO

Transcriptomics analysis of gene expression in wildtype and FTO knockout mouse liver

Project description:Fto conditional knockout mutation was generated using phage-based Escherichia coli homologous recombination systems. Construct targeting the third exon of mouse Fto gene was introduced into ES cell by homologous recombination. The mice with homozygous targeted allele were crossed to Albumin-Cre for deletion the third exon of mouse Fto gene in liver. Total RNA was isolated from Liver Tissue using the TRIzol (Invitrogen) reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 (Illumina) in paired-read mode, creating reads with a length of 101 bp. Sequencing chemistry v2 (Illumina) was used.

2022-01-26 | GSE125785 | GEO

Network Modeling of Liver Metabolism to Predict Plasma Metabolite Changes During Short-Term Fasting in the Laboratory Rat: Liver Transcriptome Changes in Study 2

Project description:Purpose: The purpose of this study is to measure the changes in liver transcriptome in response to short-term fasting between 5 and 10 h where the rats were dosed with 2 ml/kg of corn oil vehicle at 0 h Methods: Total RNA was isolated from the liver, using TRIzol Reagent (Thermo Fisher Scientific, Waltham, MA) and the direct-zol RNA Mini Prep kit (Zymo Research, Irvine, CA). The isolated RNA samples were then submitted to the Vanderbilt University Medical Center VANTAGE Core (Nashville, TN) for RNA quality determination and sequencing. Total RNA quality was assessed using a 2100 Bioanalyzer (Agilent, Santa Clara, CA). At least 200 ng of DNase-treated total RNA with high RNA integrity was used to generate poly-A-enriched mRNA libraries, using KAPA Stranded mRNA sample kits with indexed adaptors (Roche, Indianapolis, IN). Library quality was assessed using the 2100 Bioanalyzer (Agilent), and libraries were quantitated using KAPA library Quantification kits (Roche). Pooled libraries were subjected to 150-bp paired-end sequencing according to the manufacturer’s protocol (Illumina NovaSeq6000, San Diego, CA). Results: Conclusions: There were 100 genes that could be mapped to the rat metabolic network iRno, with significant changes in expression between 5 and 10 h of fasting in the top 10% by effect size parameter b (b > 0.6).

2019-03-19 | GSE124004 | GEO

Characterization of Glucocorticoid Receptor (GR) in Mouse Liver

2015-12-11 | GSE75682 | GEO

Characterization of Glucocorticoid Receptor (GR) in Mouse Liver

Project description:We proposed an experiment that determines liver gene regulation profiles in GRLKO. By comparison to the wide type C57BL/6 mouse, we determined the contribution of GR on liver gene expression either at basal level or after Dexamethasone (DEX) injection. WT and GR knockout mice were divided into two groups, one with dexamethasone treatment and one with out. Each group has four replicates.

2015-12-11 | E-GEOD-75682 | biostudies-arrayexpress

Direct RNA sequencing experiment of humanized liver mice with metabolic treatments

Project description:To make the human liver accessible to metabolic treatments, we employed a liver-specific humanized mouse model in which approximately 50% of the mouse hepatocytes were replaced by human ones. To capture transcriptomes reflecting pathophysiology and therapeutic development of metabolic diseases, we subjected the humanized mice to dietary intervention and the key metabolic transcriptional factor agonist treatments. We then performed rna exoression profiling analysis using data obtained from nanopore direct RNA sequencing of these humanized mice.

2024-01-23 | GSE224278 | GEO

RNA-seq study on time of day specific Glucocorticoid action in mouse liver and lung tissues

Project description:Glucocorticoids are critical regulators of energy metabolism and immunity and major drug targets in inflammatory disease. It is also known that the circadian clock regulates both metabolism and immunity. This experiment is part of wider study to understand the coupling between circadian clock components and Glucocorticoid receptor in multiple mouse tissues. Here, RNA-seq analysis was performed in vehicle and dexamethasone (a synthetic Glucocorticoid) treated WT mouse liver and lung tissues at two circadian times, to understand time of the day variation in Glucocorticoid regulated genes. Mice were treated at ZT6 (6 hours after lights on, 1:30pm) or at ZT18 (6 hours after lights off, 1:30am) with dexamethasone (1 mg/kg intraperitoneal) or vehicle (methylcyclodextrin 1mg/kg intraperitoneal) for 2 hours before sacrifice by cervical dislocation. Lung and liver tissue were lysed and total RNA prepared using SV Total RNA Isolation System (Promega). Quality and integrity of total RNA samples were assessed by 2100 Bioanalyzer or a 2200 TapeStation (Agilent Technologies) according to the manufacturer’s instructions. RNA sequencing (RNA-seq) libraries were generated using the TruSeq® Stranded mRNA assay (Illumina, Inc.) according to the manufacturer’s protocol. Then paired-end sequenced (101 + 101 cycles, plus indices) on an Illumina HiSeq2500 instrument.

2018-11-13 | E-MTAB-7020 | biostudies-arrayexpress

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