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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Ketogulonigenium vulgare cells: co-culture mode vs. mono-culture mode

ABSTRACT: Transcriptional profiling of K. vulgare cells co-cultured with Bacillus megaterium compared to K. vulgare mono-cultured cells. Differentially expressed genes in co-cultured and mono-cultured K. vulgare cells were analyzed. The aim was to investigate the mechanisms of B. megaterium stimulating K. vulgare propagation on global gene expression. Two-condition experiment: co-cultured K. vulgare and B. megaterium cells vs. mono-cultured K. vulgare cells. Biological replicates: 3 co-cultured replicates, 3 mono-cultured replicates.

ORGANISM(S): Bacillus megaterium

SUBMITTER: Zhu Yibo

PROVIDER: E-GEOD-37594 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Ketogulonigenium vulgare cells: co-culture mode vs. mono-culture mode

Project description:Transcriptional profiling of K. vulgare cells co-cultured with Bacillus megaterium compared to K. vulgare mono-cultured cells. Differentially expressed genes in co-cultured and mono-cultured K. vulgare cells were analyzed. The aim was to investigate the mechanisms of B. megaterium stimulating K. vulgare propagation on global gene expression.

2012-04-26 | GSE37594 | GEO

Ketogulonicigenium vulgare cells: Acid-stressed vs. Control

Project description:Transcriptional profiling of K. vulgare cells, co-cultured with Bacillus megaterium, comparing control untreated cells with cells treated with pH 4.0 for 2 h. Differentially expressed genes in acid-stressed cells were analyzed. The aim was to investigate the mechanisms of K. vulgare in response to acid stress on global gene expression. Two-condition experiment, acid-stressed (pH 4.0) cells vs. control cells. Biological replicates: 3 control replicates, 3 acid-stressed replicates.

2014-10-23 | E-GEOD-33105 | biostudies-arrayexpress

Ketogulonigenium vulgare cells: co-culture mode vs. mono-culture mode

Project description:Ketogulonigenium vulgare cells: co-culture mode vs. mono-culture mode

| PRJNA162307 | ENA

Ketogulonicigenium vulgare cells: Acid-stressed vs. Control

2014-10-23 | GSE33105 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of LSEC and Hepa1-6 mono- and co-cultured

Project description:Purpose: investigating paracrine effects of mono- and/or co-cultured LSEC and Hepa1-6 Method: mRNA profiles of mono- and co-cultured LSEC and Hepa1-6 were generated by deep sequencing. Results: The RNA-seq data confirmed that extracellular matrix-encoding genes were up-regulated by co-cultured LSEC with Hepa1-6.

2023-01-31 | GSE202457 | GEO

Exosome Transfer from Stromal to Breast Cancer Cells Regulates Therapy Resistance Pathways [set 2]

Project description:Stromal communication with cancer cells can influence treatment response. We show that stromal and breast cancer (BrCa) cells utilize paracrine and juxtacrine signaling to drive chemotherapy and radiation resistance. Upon heterotypic interaction, exosomes are transferred from stromal to BrCa cells. RNA within exosomes, which are largely non-coding transcripts and transposable elements, stimulates the pattern recognition receptor RIG-I to activate STAT1-dependent anti-viral signaling. In parallel, stromal cells also activate NOTCH3 on BrCa cells. The paracrine anti-viral and juxtacrine NOTCH3 pathways converge as STAT1 facilitates transcriptional responses to NOTCH3 and expands therapy resistant tumor-initiating cells. Primary human and/or mouse BrCa analysis support the role of anti-viral/NOTCH3 pathways in NOTCH signaling and stroma-mediated resistance, which is abrogated by combination therapy with gamma secretase inhibitors. Thus, stromal cells orchestrate an intricate cross-talk with BrCa cells by utilizing exosomes to instigate anti-viral signaling. This expands BrCa subpopulations adept at resisting therapy and re-initiating tumor growth. Breast cancer cells lines and MRC5 fibroblasts were mono-cultured or co-cultured together. Cell types were separated by FACS and gene expression changes were examined using the Affymetrix Human Gene 1.0ST arrays. The effect of tumor-stromal cell interaction on different breast cancer cell types was analyzed using biological replicates. Gene expression changes resulting from knockdown of STAT1 was also investigated.

2014-10-24 | E-GEOD-60995 | biostudies-arrayexpress

Exosome Transfer from Stromal to Breast Cancer Cells Regulates Therapy Resistance Pathways [set 1]

2014-10-24 | E-GEOD-60994 | biostudies-arrayexpress

Human carcinoma-associated fibroblasts (CAF): co-culture with cancer cells vs. CAF only

Project description:Gene expression profiling of CAF co-cultured with human oral squamous cell carcinoma (OSCC) cells compared with mono-cultured CAF. To identify key molecular regulators expressed by carcinoma-associated fibroblasts (CAF) that promote cancer cell invasion, microarrays were performed by comparing co-cultured OSCC cells and CAF with monoculture controls. comparison 1: CAF co-cultured with OSCC vs. mono-cultured CAF comparison 2: OSCC co-cultured with CAF vs. mono-cultured OSCC 1.7X10(5) YD-10B OSCC cells and 1.7X10(5) CAF were seeded in the upper chamber and lower chamber, respectively, of 6-transwell plates containing collagen-coated 1 micrometer pore transmembrane filters (Becton Dickinson, Franklin Lakes, NJ, USA). Monoculture control samples were generated by culturing only CAF or OSCC on the same side of the filter as in the co-culture design.

2010-06-21 | E-GEOD-18532 | biostudies-arrayexpress

LncRNAs expression profiles in the livers of 20-month-old male HBx transgenic mice and C57BL/6 wild-type mice

Project description:The hepatitis B virus X protein (HBx) has been implicated as an oncogene in both epigenetic modifications and genetic regulation during hepatocarcinogenesis, but the underlying mechanisms are not entirely clear. Long non-coding RNAs (lncRNAs), which regulate gene expression with little or no protein-coding capacity, are involved in diverse biological processes and in carcinogenesis. We asked whether HBx could promote hepatocellular carcinoma (HCC) by regulating the expression of lncRNAs.In this study, we investigated the alteration in expression of lncRNAs induced by HBx using microarrays, and our results indicate that HBx transgenic mice have a specific profile of liver lncRNAs compared with wild-type mice. For these experiments, six each of 20-month-old male HBx-transgenic mice and wild-type C57BL/6 mice were sacrificed and the livers were removed. Every three livers were pooled as one sample; therefore, each group was represented by two samples. The total RNA was extracted from the four samples and used for microarray experiments. Mouse LncRNA Array (4 x 44K, ArrayStar, Rockville, MD) were used to monitor the expression level of approximately 14000 lncRNAs identified from the NCBI RefSeq, UCSC, RNAdb2.0, NRED, Fantom3.0 and UCRs. LncRNAs differentially expressed were identified by comparing expression levels in HBx-transgenic mice and wild-type mice.

2013-11-04 | E-GEOD-42185 | biostudies-arrayexpress

LncRNAs expression profiles in the livers of C57Bl/6 mice after partial hepatectomy

Project description:Liver regeneration has important implications because many therapeutic strategies for the surgical treatment of liver diseases, such as removal of liver tumors and liver transplantation, depend on the ability of the liver to regenerate physically and functionally. Recent studies reported that lncRNAs control cell proliferation in hepatocellular carcinoma (HCC). However, the role of lncRNAs in liver regeneration and the overall mechanisms remain largely unknown. To address this issue, we carried out a genome-wide lncRNA microarray analysis during liver regeneration in mice after 2/3 partial hepatectomy (PH) at various time points. The results revealed differential expression of thousands of lncRNAs during liver regeneration. Six-week-old male wildtype C57Bl/6 mouse liver samples were obtained at 0, 1.5, 12, and 24 hours after 2/3 PH, and three mice were analyzed for each time point. Total RNA was isolated using Trizol.Mouse Stringent LncRNA Array (4 x 44K, ArrayStar, Rockville, MD) were used to monitor the expression level of approximately 14000 lncRNAs identified from the NCBI RefSeq, UCSC, RNAdb2.0, NRED, Fantom3.0 and UCRs. LncRNAs differentially expressed were identified by comparing expression levels during liver regeneration in mice after 2/3 partial hepatectomy (PH) at various time points.

2013-04-24 | E-GEOD-43687 | biostudies-arrayexpress

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