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Genome-wide analysis of gene expression of livers of wild type and IL-4/IL-13-/- mice after carbon tetrachloride-induced injury

ABSTRACT: Global analysis of differentially expressed genes of livers of wild type and IL-4/IL-13-/- two days after carbon tetrachloride treatment. Total RNA obtained from isolated livers from vehicle and carbon tetrachloride administered wild type and IL-4/IL-13-/- mice.

ORGANISM(S): Mus musculus

SUBMITTER: Sharon Goh

PROVIDER: E-GEOD-45002 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Eosinophils secrete IL-4 to facilitate liver regeneration.

Goh Y P Sharon YP Henderson Neil C NC Heredia Jose E JE Red Eagle Alex A Odegaard Justin I JI Lehwald Nadja N Nguyen Khoa D KD Sheppard Dean D Mukundan Lata L Locksley Richard M RM Chawla Ajay A

Proceedings of the National Academy of Sciences of the United States of America 20130528 24

The liver is a central organ for the synthesis and storage of nutrients, production of serum proteins and hormones, and breakdown of toxins and metabolites. Because the liver is susceptible to toxin- or pathogen-mediated injury, it maintains a remarkable capacity to regenerate by compensatory growth. Specifically, in response to injury, quiescent hepatocytes enter the cell cycle and undergo DNA replication to promote liver regrowth. Despite the elucidation of a number of regenerative factors, th ...[more]

PMID: 23716700

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Genome-wide analysis of gene expression of livers of wild type and IL-4/IL-13-/- mice after carbon tetrachloride-induced injury

Project description:Global analysis of differentially expressed genes of livers of wild type and IL-4/IL-13-/- two days after carbon tetrachloride treatment.

2013-06-05 | GSE45002 | GEO

Carbon tetrachloride and Acetaminophen hepatotoxicity study

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Carbon tetrachloride and Acetaminophen hepatotoxicity study

Project description:Differential gene expression in mice liver after carbon tetrachloride and acetaminophen administration. Livers from control mice were compared with drug treated mice livers at different time points. Keywords: Time-course Mice (Mus musculus) belonging to control and carbon tetrachloride and acetaminophen-administered groups (n=4) were sacrificed. The livers were snap frozen in liquid nitrogen, and subsequently stored at -80ÂºC till further use. Liver samples were homogenized and total RNA was extracted with TRI reagent. 25 ug of total RNA was converted into labeled cDNA using CyScribe first strand cDNA labeling kit. The Cy5 and Cy3 labeled cDNAs were resuspended in Cyscribe Hyb buffer containing 10ug/ml sheared Salmon sperm DNA and 10ug/ml Yeast tRNA. The labeled samples were hybridized to the arrays and incubated for 16-18hrs at 42ÂºC. Fluorescent array images were collected for both Cy3 and Cy5 with molecular dynamics III scanner supported with ImageQuant v5.0. Image intensity data were extracted and analyzed with ArrayVision v8.0 analysis software. Background corrected data was LOWESS normalized and log ratios were calculated using Avadis v4. Further, mean log ratios were calculated for duplicate spots. Replicate experiments were carried out in dye swap manner for each time point.

2010-06-11 | E-GEOD-4874 | biostudies-arrayexpress

Carbon tetrachloride (CCl4) induced liver fibrosis

Project description:Carbon tetrachloride (CCl4) induced liver fibrosis

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Transcription profiling of mouse CD4+ GFP- (Teff) and CD4+ GFP+ (Treg) T cells treated with IL-2

Project description:To obtain the molecular signature of the effect that the IL-2 therapeutic dose induces on T cells in vivo, we performed gene array analysis. Since it was critical to perform this analysis on highly purified Tregs and Teffs, and also because activated Teffs can acquire CD25 expression, we used GFP-Foxp3 knock-in mice which allow for the purification of Tregs and Teffs based on the GFP expression. Illumina gene array was carried out on FACS sorted CD4+ GFP+ (Tregs) and CD4+ GFP- (Teffs) of mice that received either PBS or the curative schedule of IL-2, 2 hours after the last injection.<br><br>Further raw data files are available on the FTP site for this experiment.

2011-01-06 | E-MEXP-2530 | biostudies-arrayexpress

Gene expression profiles of rat liver tissues after carbon tetrachloride administration

Project description:Liver cirrhosis (LC) is pathologically characterized with abnormality and necrosis of hepatic cells, proliferation of fibrous tissue, nodular regeneration and pseudolobule formation. We used Rat Genome 230 2.0 microarray to further highlight the rat liver tissues after carbon tetrachloride administration

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Gene expression profiles of rat liver tissues after carbon tetrachloride treatment

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Qualitative modeling identifies IL-11 as a novel regulator in maintaining self-renewal in human pluripotent stem cells

Project description:A systems biology approach in which qualitative modeling based on combining boolean networks and in silico perturbation experiments were employed to identify 15 pluripotency regulating cytokines or cytokine related genes. IL-11 was validated as a novel factor capable of maintaing the undifferentiated state of human embryonic stem cells in the absence of exogenously added bFGF to the culture acting via a different mechanims than bFGF. Transcriptomic microarray data of eight overexpression and knock-down experiments were used for qualitative modeling based on boolean networks to predict novel factors - mainly cytokines - that maintain pluripotent human embryonic stem cells in the absence of bFGF in culture. The culture was maintained for at least 9 passages using and stained positive for alcaline phosphatase staining, OCT3/4, SOX2, NANOG, TRA1-60. Microarray based gene expression profiling showed that the IL-11 treatment occupies an intermediate state, between bFGF treatment and the negative control which is no cytokine treatment as judged by hierarchical clustering. Moreover, KEGG pathway analysis indicates common and additional distinct mechanisms of bFGF and IL-11 dependant pluripotency dependant mechanisms.

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Next Generation Sequencing (NGS) Facilitates Quantitative Analysis of Differentially Expressed Genes in Liver Regeneration After Combined Treatment With Ethanol And Carbon Tetrachloride

Project description:Purpose: The goals of this study are to use NGS-derived liver transcriptome profiling (RNA-seq) and identify differentially expressed genes in regenerating livers that were treated with ethanol and carbon tetrachloride. Methods: Liver mRNA profiles were generated from ethanol/CCl4-treated floxed homozytoes and Ctgf conditional knockout mice by deep sequencing, in duplicate, using Illumina GAIIx. qRT–PCR validation was performed using SYBR Green assay. Results: Ctgf deficiency was associated with 220 downregulated genes and 29 upregulated genes whereas Yap1 null livers had 351 downregulated genes and 287 upregulated genes after ethanol/CCl4 induced liver damage Conclusions: This study provides detailed analysis of liver transcriptomes in absence of Ctgf or Yap1 genes during ethanol/CCl4-induced injury, with biologic replicates, generated by RNA-seq technology.

2020-12-03 | GSE123309 | GEO

Mus musculus

Project description:Genome-wide analysis of gene expression of livers of wild type and IL-4/IL-13-/- mice after carbon tetrachloride-induced injury

| PRJNA192814 | ENA

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