Similar Datasets
Project description:We previously reported that Def (Digestive-organ expansion factor) was a pan-endodermal enriched factor that is essential for the growth of digestive organs in zebrafish using a def mutant line hi429 as model (Chen et al., 2005). To further elucidate Def function, we generated a Def over-expressed zebrafish line, namely Tg (fabp10a:def)-I, in which def expression was under the control of a liver-specific promoter fabp10a. We used microarrays to detail the global programme of gene expression in Tg (fabp10a:def)-I transgenic line compared with wild type zebrafish control, and identified distinct classes of differently regulated genes in Tg (fabp10a:def)-I line. Total RNA from the adult livers of three independent batches of 3-month-old Tg(fabp10a:def)-I and wild type (AB strain) male fish was extracted using TRIzol (Invitrogen), each batch with the liver samples from three fish mixed together. The samples were subjected to microarray hybridization and the data were generated for further analysis.
2013-02-28 | E-GEOD-41059 | biostudies-arrayexpress
Project description:We previously reported that Def (Digestive-organ expansion factor) was a pan-endodermal enriched factor that is essential for the growth of digestive organs in zebrafish using a def mutant line hi429 as model (Chen et al., 2005). To further elucidate Def function, we generated a Def over-expressed zebrafish line, namely Tg (fabp10a:def)-I, in which def expression was under the control of a liver-specific promoter fabp10a. We used microarrays to detail the global programme of gene expression in Tg (fabp10a:def)-I transgenic line compared with wild type zebrafish control, and identified distinct classes of differently regulated genes in Tg (fabp10a:def)-I line.
2013-02-28 | GSE41059 | GEO
Project description:in the present study, we evaluated whether microbiota modulation is able to restore hepatic steatosis induced by n-3 PUFA depletion in mice. For this purpose, mice were fed during three months with a n-3 PUFA-depleted diet (presenting a high n-6/n-3 PUFA ratio), and then supplemented with fructooligosaccharides (FOS, 0.25g/day/mice), a prebiotic, during the last ten days of the experiment (DEF/FOS). In the same time, some n-3 PUFA-depleted mice were returned on a control diet during the last 10 days of treatment (DEF/CT) to compare the effect of FOS supplementation to a restored intake in n-3 PUFA. Microarray analyses were performed to identify the molecular targets modified by FOS supplementation in the liver of n-3 PUFA depleted mice. These mice were compared to control mice (fed a control diet during the 112 days of experiment) and to n-3 PUFA-depleted mice (fed a n-3 PUFA-depleted diet during the 112 days of experiment) for which the results have been previously published (Pachikian B.D. et al. PLoS One. 2011;6(8):e23365, accession number GSE26986) Male C57Bl/6J mice (9 weeks old; Charles River, Brussels, Belgium) were housed in groups of 4 mice per cage at 22°C in a 12 h light/dark cycle and given free access to diet and water. After an acclimatisation period of 1 week, mice were fed a control (CT) (D08041805, Research Diets, New Brunswick, USA) or an n-3 PUFA-depleted diet (DEF) (D08041806, Research Diets, New Brunswick, USA) for 112 days ad libitum. The CT diet contained the following (percent w/w): casein 20, total carbohydrate 72.4 (including corn starch 44.2, sucrose 10, maltodextrin 13.2, cellulose 5), soybean oil 5, mineral mix 3.5 and vitamin mix 1. The depletion was induced by replacing the soybean oil with sunflower oil, which exhibited a higher n-6/n-3 PUFA ratio. The n-6/n-3 PUFA ratio was 6.9 and 127.2 for the CT diet and the DEF diet, respectively. Ten days before the end of the experiment, DEF mice were divided into three groups: DEF, DEF/FOS and DEF/CT mice. The DEF mice were still fed with the n-3 PUFA depleted diet (DEF). The DEF/FOS mice were still fed the DEF diet and were supplemented for 10 days with fructooligosaccharides (DEF/FOS). FOS (Beneo P95 gift from Orafti; Tienen, Belgium) was added to tap water in a concentration adequate to reach an intake of 0.25g of FOS per day. For DEF/CT mice, the DEF diet was replaced by the CT diet during the last 10 days of treatment. At the end of the study period, mice fed the CT (n=4), DEF (n=7), DEF/CT (n=8) or DEF/FOS diet (n=8) were anaesthetised (ketamine/xylazine i.p., 100 and 10 mg/kg of body weight, respectively). The liver tissue was immediately clamped in liquid N2 and kept at -80°C until analysis. All mice experiments were approved by the local animal ethics committee and the housing conditions were as specified by the Belgian Law of April 6, 2010 on the protection of laboratory animals (agreement n° LA 1230314).
2012-12-12 | E-GEOD-31727 | biostudies-arrayexpress
Project description:In order to identify transcript changes in response to DEF , we used human macrophages with or without DEF treatment. In order to study the effect of iron chelation on LPS-polarized macrophage transcriptome, we exposed DEF-treated or control macrophages to short time exposure to LPS. We then performed whole-genome transcriptome sequencing by RNA-sequencing (RNA-seq).
2019-07-09 | GSE128885 | GEO
Project description:Purpose: To understand the role of SUMOylation of c-Fos in the differential regulation of target genes and altered cellular pathways upon STm infection. To address this, we performed a RNA-seq experiment with stable over expressing WT-FOS or SUMO-def-FOS in f10 c-FOS-Knock out MEFs upon STm infection. Methods: Three biological replicates of c-FOS-KO-WT-FOS, c-FOS-KO-WT-FOS with salmonella infection, c-FOS-KO-SUMO-def-FOS and c-FOS-KO-SUMO-def-FOS with salmonella infection, cells were collected and total RNA was extracted according to kit's protocol. The total RNA was used to generate a cDNA library using Quantseq 3' mRNA kit. Results: Transcriptional profiling revealed that genes involved in immune response, proliferation, metastasis etc. are differentially regulated in salmonella infected c-FOS-KO-SUMO-def-FOS MEFs compare to salmonella infected c-FOS-KO-WT-FOS MEFs. Conclusions: Our study revealed the extensive transcriptomics analysis from c-FOS-KO-WT-FOS and c-FOS-KO-SUMO-def-FOS MEFs upon salmonella infection. We found that SUMOylation of c-Fos provides selectivity that causes differential regulation of target genes which are involved in immune response, proliferation etc. pathways of host. Together, our findings illuminate an important regulatory role played by SUMOylated c-Fos upon STm infection.
2022-05-08 | GSE201782 | GEO
Project description:The two-spotted spider mite, Tetranychus urticae, is one of the most significant mite pests in agriculture that can feed on more than 1,100 plant hosts, including model plants Arabidopsis thaliana and tomato, Solanum lycopersicum. In order to refine the involvement of jasmonic acid (JA) in mite-induced responses, we analyzed transcriptional changes in tomato JA signaling mutant defenseless1 (def-1) upon JA treatment and spider mite herbivory. We used microarray to assess global gene expression in Solanum lycopersicum def-1 cv. Castlemart upon jasmonic acid treatment and Tetranychus urticae attack. 1 month old def-1 tomato plants were subjected to Tetranychus urticae attack through application of 100 adult mites on a terminal leaflet of leaf 3 for 24 h or plants were sprayed with 1 mM jasmonic acid solution.
2015-01-05 | E-GEOD-61075 | biostudies-arrayexpress
Project description:To investigate the role of gene expression during Newcastle disease virus (NDV) infection.The NDV GM strain was used to infect DEF cells with 1moi, while an uninfected group was set up as a control.
2023-04-11 | GSE229335 | GEO
Project description:In the present study, we investigated the consequences of n-3 polyunsaturated fatty acids (PUFA) depletion on hepatic lipid metabolism in mice fed during three months with a diet presenting a high n-6/n-3 PUFA ratio to induce n-3 PUFA depletion. Microarray analyses were performed to identify the molecular targets involved in the development of hepatic steatosis associated with n-3 PUFA depletion. Male C57Bl/6J mice (9 weeks old) were housed in groups of four mice per cage at 22°C in a 12h light/dark cycle and given free access to diet and water. After an acclimatization period of 1 week, the mice were fed a control (CT) or an n-3 PUFA-depleted diet (DEF) for 3 months. At the end of the study period, mice (CT, n=6; DEF, n=7) were anesthetized after a 6h period of fasting. Some mice (CT: n=4 et DEF: n=7) were anesthetized without being starved. A fraction of the main liver lobe was fixed-frozen in isopentane and kept at -80°C for histological analysis. The excess tissue material was immediately clamped in liquid N2 and kept at -80°C. All mice experiments were approved by the local animal ethics committee, and the housing conditions were as specified by the Belgian Law of November 14, 1993 on the protection of laboratory animals (agreement n° LA 1230314).
2011-08-25 | E-GEOD-26986 | biostudies-arrayexpress
Project description:In this study, we assess potential differences in mechanism of action for two PAHs, benzo[a]pyrene (BAP) and dibenzo-[def,p]chrysene (DBC), in a primary human 3D bronchial epithelial culture (HBEC) model based on short-term biosignatures identified from global transcriptional profiling.
2020-03-18 | GSE128492 | GEO