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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Human hepatic stellate cell line LX-2 activated under acidic culture condition

ABSTRACT: We found that the number of tumor-infiltrating myofibroblasts was positively correlated to tumor acidification status in hepatocellular carcinoma (HCC). Hepatic stellate cells (HSCs), the predominant precursors of liver myofibroblasts, were activated and transdifferentiated into myofibroblasts under acidic culture condition. To identify the molecular phenotype of LX-2 cells in acidic culture conditions, we further conducted a gene expression profile analysis. LX-2 cells cultured in pH 7.2 or pH 6.2 medium separately for six days was used in gene expression microarray analysis.

ORGANISM(S): Homo sapiens

SUBMITTER: Wenxin Qin

PROVIDER: E-GEOD-49301 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Human hepatic stellate cell line LX-2 activated under acidic culture condition

Project description:We found that the number of tumor-infiltrating myofibroblasts was positively correlated to tumor acidification status in hepatocellular carcinoma (HCC). Hepatic stellate cells (HSCs), the predominant precursors of liver myofibroblasts, were activated and transdifferentiated into myofibroblasts under acidic culture condition. To identify the molecular phenotype of LX-2 cells in acidic culture conditions, we further conducted a gene expression profile analysis.

2013-07-29 | GSE49301 | GEO

Transcription profiling of human LX-2 cells cultured on Matrigel

Project description:we performed transcriptional analysis of the human hepatic stellate cell line, LX-2, cultured on Matrigel.

2010-10-01 | E-MEXP-2584 | biostudies-arrayexpress

Super-Enhancer-mediated Control of Liver Fibrosis by BET Bromodomain Proteins

Project description:Here, we investigate the role of enhancers in myofibroblasts, a cell type that dominates the pathogenesis and progression of tissue fibrosis. We reveal that bromodomain and extra-terminal family members (BETs), an important group of epigenetic readers, are critical for super-enhancer-mediated pro-fibrotic gene expression in hepatic stellate cells (HSCs, lipid-containing liver-specific pericytes), upon activation during liver fibrogenesis give rise to myofibroblasts2-4. We observe significantly enriched localization of BETs to hundreds of super-enhancers associated with genes involved in multiple pro-fibrotic pathways. This unique loading pattern consequentially serves as a molecular mechanism by which BETs modulate pro-fibrotic gene expression in myofibroblasts. Strikingly, suppression of BET-enhancer interaction using small-molecule inhibitors such as JQ1 dramatically blocks activation of HSCs into myofibroblasts and significantly compromises the proliferation of activated HSCs. Identification of BRD2, BRD3, BRD4, PolII, PolIIs2p and PolIIs5p binding sites in human stellate LX2 cells that were treated with DMSO (0.1%) or JQ1 (500nM) for 16 hrs.

2015-12-11 | E-GEOD-58680 | biostudies-arrayexpress

Gene expression in INA6 multiple myeloma cells in an acidic condition

Project description:We found the epigenetic regulation of gene expression in MM cells in acidic conditions. We further looked into gene expression in MM cells in acidic conditions using a cDNA microarray. INA6 cells were cultured for 12 hours, at pH7.4 or pH6.8 in the absence or presence of valproiate at 100 ug/mL. The total RNA was isolated using RNeasy Mini kit.

2013-11-22 | E-GEOD-52611 | biostudies-arrayexpress

RNA sequencing of the hepatic stellate cell line LX-2 treated with either DMSO or Aramchol after 24 or 48 hours.

Project description:To investigate whether Aramchol might reduce liver fibrosis in part directly inhibiting HSCs, we treated LX-2 cells with Aramchol, 10 µM for 24 or 48 hours, then performed RNA sequencing. Sequencing libraries were made with the TruSeq Stranded mRNA Library Prep Kit by manufacturers suggestions. Sequencing parameters are as follows: poly-A RNA enrichment, 175 bp paired reads ran on HiSeq2500 Illumina instrument. Mapping of raw sequencing reads was performed using STAR (2.4.0c) to the UCSC GRCh37/hg19 reference genome.

2021-05-19 | E-MTAB-9870 | biostudies-arrayexpress

ChIP-on-chip of OmpR binding in Salmonella enterica serovar Typhimurium strain SL1344 and E.scherichia coli strain CSH50 at pH 7 and pH 4.5 including analysis of OmpR binding in SL1344 in the absence and presence of novobiocin (25 M-NM-<g/ml)

Project description:OmpR is a DNA binding protein belonging to the OmpR/EnvZ two component system. This system is known to sense changes in osmolarity in Escherichia coli. Recently, OmpR in Salmonella enterica serovar Typhimurium was found to be activated by acidic pH and DNA relaxation. In this study, ChIP-on-chip was employed to ascertain the genome-wide distribution of OmpR in Salmonella Typhimurium and Escherichia coli in acidic and neutral pH. In addition we investigated the affect of DNA relaxation on OmpR binding in Salmonella Typhimurium. Analysis of OmpR binding at pH 7 and pH 4.5 in E-minimal medium in both SL1344 and CSH50. Three independent biological replicates at each pH 7 and pH 4.5 was performed. This was done in each strain background. DNA was immunopreciptated using an anti-FLAG anitbody which binds to flag-tagged OmpR in both strains. Two control M-bM-^@M-^XmockM-bM-^@M-^Y experiments were performed under the same culture condtions in each strain background; DNA was immunopreciptated using normal mouse IgG antibody. To analyse the effect of DNA relaxation onOmpR binding SL1344 was maintained in the exponential growth phase in LB broth with and without treatment with the drug novobiocin (25 M-NM-<g/ml) for 40 min. This was peformed on two independent occasions. In all cases the experimental immunoprecipitated DNA was hybridised against the input DNA.

2014-03-27 | E-GEOD-49914 | biostudies-arrayexpress

Microarray analysis of T-cell death-associated gene 8 (TDAG8)-mediated gene expression in mouse Lewis lung carcinoma (LLC) cells.

Project description:We previously identified an extracellular pH-sensing G protein-coupled receptor T cell death associated gene 8 (TDAG8) as an extracellular pH sensor of tumor cells that promotes cell growth/survival in vitro and tumor development in vivo. To determine genes regulated by TDAG8 in vitro, mouse Lewis lung carcinoma (LLC) cells stably expressing TDAG8 (TDAG8-LLC cells) and control vector (control LLC cells) were cultured under acidic conditions. Transcriptome microarray analysis using Affymetrix GeneChip Mouse Genome 430 2.0 Arrays was performed with total RNA prepared from these cells. To determine genes regulated by TDAG8 in vitro, mouse Lewis lung carcinoma (LLC) cells stably expressing TDAG8 (TDAG8-LLC cells) and control vector (control LLC cells) were cultured under acidic conditions. Transcriptome microarray analysis using Affymetrix GeneChip Mouse Genome 430 2.0 Arrays was performed with a mixture of equal amounts of total RNA samples from four independent cell cultures.

2012-11-01 | E-GEOD-31776 | biostudies-arrayexpress

Transcriptomic analysis of Mtb Erdman, MtbΔvirS and MtbΔvirSComplement upon acidic stress of pH4.5

Project description:Since VirS was shown to be upregulated in acidic conditions and MtbΔvirS displayed defect in growth at pH4.5, we performed microarray at pH 6.6 and pH 4.5 to study the role of VirS in regulating gene expression at acidic pH.

2019-05-23 | GSE118508 | GEO

The Rfg1 and Bcr1 transcription factors regulate acidic pH-induced filamentous growth in Candida albicans

Project description:To investigate the function of Rfg1 in sensing acidic pH and regulating filamentation in C. albicans, we performed the global gene expression profile analysis of WT and rfg1/rfg1 mutant.We reveal that Rfg1 is an essential acidic pH sensor in C. albicans. Rfg1 regulates filamentous growth in acidic pH condition via co-regulation of Rim101-Phr1 pathway, cAMP signaling pathway,and the transcription factors Bcr1, Efg1, Flo8, and Hgc1.

2023-03-24 | GSE227654 | GEO

High-throughput sequencing of methylated cytosine enriched by modification-dependent restriction endonuclease MspJI

Project description:In this study, we combine MspJI digestion and electrophoretic band selection with next generation high-throughput sequencing technology to detect 5-methylcytosines in Arabidopsis genome. By developing a bioinformatics workflow to attribute the CNNR sites recognized by MspJI to the reference genome, we fulfilled the systematic assessment of this method. According to the assessment, here we provide the method for generating a detailed map of plant methylome that could be feasible, reliable and economical in methylation investigation. Extracting the MspJI digested fragments, constructing sequencing library according to the Illumina protocol and sequencing with Illumina HiSeq2000. Repeatability and reproducibility studies were performed between two samples from the same individual. Specificity and sensitivity of the method was examined by comparing our data with WGBS data downloaded from GEO (GSE15922: GSM399600). **The WGBS seq data ('aerial_tissues_BS_seq_CNNR.gff') was generated from the GSM399600 Sample supplementary files ('aerial_tissues_BS_seq_alignment_batch-*.gff.gz') and was utilized to do comparative study with our MspJI-seq data including sensitivity and specificity analysis.

2013-05-01 | E-GEOD-46428 | biostudies-arrayexpress

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