Global changes in gene expression in Caco-2 cell line by treatment with extract from iodine-biofortified carrot and lettuce
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Magdalena Łój
PROVIDER: E-GEOD-71605 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Whole genome microarray data were analyzed to describe the changes in gene transcription profile in human Caco-2 cancer cells under the influence of the extract from iodine-biofortified and non-fortified carrot and lettuce. These iodine-biofortified vegetables can be used as a functional food.
2015-08-01 | GSE71605 | GEO
Project description:Cultivated carrot (Daucus carota L. ssp. sativus) was domesticated from wild carrot (Daucus carota L. ssp. carota) with radical different traits. The aim of this study was to compare the root transcriptomes between cultivated and wild carrots for SNP discovery, inferring domestication process, and identifying domestication genes. Six cultivated carrots representing main European carrot root types and five wild carrot populations from widely dispersed sites were used. The root transcriptomes were sequenced with multiplexing paried-end sequencing in Illumina Genome Analyzer IIx.
2013-10-24 | E-MTAB-1340 | biostudies-arrayexpress
Project description:Bolting is a key process in the growth and development of lettuce (Lactuca sativa L.). High temperature can induce earlier bolting which decreases in both quality and production of lettuce. However, knowledge underlying lettuce bolting is still lacking. To better understand the molecular basis of bolting, a comparative proteomics analysis was conducted on lettuce stems in the bolting period induced by high temperature (33 °C) compared with a control (20 °C) using iTRAQ-based proteomics, phenotypic measures, and biological verifications. High temperature induced lettuce bolting, while control temperature did not. Of the 6656 proteins identified, 758 proteins significantly altered their expression level induced by high-temperature relative to the control, of which 409 were up-regulated and 349 down-regulated. Proteins with abundance level change were mainly involved in photosynthesis, carbohydrate metabolism, stress response, hormone synthesis, and signal transduction. These differential proteins were mainly enriched in pathways associated with photosynthesis and tryptophan metabolism involving in auxin (IAA) biosynthesis. Among the differentially expressed proteins associated with photosynthesis and tryptophan metabolism were up-regulated. Moreover, in gibberellin (GA) biosynthesis pathway, 10 of main enzymes of P450 were up-regulated. Proteins related to SAUR and GRP, implicated in IAA and GA signal transduction were up-regulated, and the phosphorylation and ubiquitination related proteins regulating IAA and GA signal transduction were also induced. These findings indicate that a high temperature enhances the function of photosynthesis, IAA and GA synthesis and signal transduction to promote the process of bolting, which is in line with the physiology and transcription levels of IAA and GA metabolism. Our data provide a first comprehensive dataset for gaining novel understanding of the molecular basis underlying lettuce bolting induced by high temperature. It is potentially important for further functional analysis and genetic manipulation for molecular breeding to breed new cultivar of lettuce to restrain early bolting, which is vital for improving vegetable quality.
2019-11-12 | PXD008610 | Pride
Project description:Using a 3'-tiling microarray covering the whole F. graminearum genes, we carried out genome-wide expression analyses of both a wild type and a FgVelB deletion strainn of F. graminearum at a sexual stage (3 days after perithecial induction on carrot agar) Our study is the first report elucidating regulatory pathways controlled by FgVelB in Fusarium graminearum. A total of 4 chips were used for microarray. Total RNAs were extracted from perithecia and/or ground mycelia formed on carrot agar cultures of a self-fertile wild-type and a self-sterile FgVelB-deleted strain of F. graminearum with two biological replicates.
2012-08-02 | E-GEOD-36638 | biostudies-arrayexpress
Project description:Perchlorate, which is a ubiquitous and persistent ion, competitively interferes with iodide accumulation in the thyroid, causing iodine deficiency, which may result in reduced thyroid hormone synthesis and secretion. Human studies suggest that perchlorate presents very little risk in healthy individuals; however, the precautionary principle demands that the sensitive populations of iodine deficient adults and mothers require extra consideration. In an attempt to determine if the effects on gene expression were similar, we compared the thyroidal effects of perchlorate (10 mg/kg) treatment for 14 days in drinking water with those caused by 8 weeks of Iodine-deficiency in rats. The thyroids were collected (N=3 each group) and total mRNA was analyzed using the Affymetrix Rat Genome 230 2.0 GeneChip®. Changes in gene expression were compared with appropriate control groups. We compared the 2-fold gene changes due to I-deficiency with changes due to perchlorate treatment. 189 transcripts were changed by the Iodine-deficient diet and 722 transcripts were changed by the perchlorate treatment. 34% of the transcripts changed by the I-deficient diet were also changed by perchlorate and generally in the same direction. three specific transporter genes, AQP1, NIS, & SLC22A3 were changed by both treatments, indicating that the membrane specific changes were similar. Iodine-deficiency primarily caused changes in retinol and calcium signaling pathways and perchlorate primarily caused changes related to the accumulation of extracellular matrix proteins. This study provides evidence that perchlorate, at least at this dose level, changes more genes and changes different genes compared to iodine deficiency. Changes in gene expression due to I-deficiency compared to normal diet for 2 months. Changes in gene expression due to perchlorate in the drinking water compared to normal drinking water for 1 or 14 days. Feeding study in rats.
2010-11-04 | E-GEOD-25144 | biostudies-arrayexpress
Project description:Asynchronized and nonuniform seed germination is causing obstacles to the large-scale cultivation of carrot (Daucus carota L.). In the present study, the combination of high voltage electrostatic field treatment (EF) with hydropriming (HYD), namely hydro-electro hybrid priming (HEHP), significantly improved all germination indicators of carrot seeds, and the promoting effect was superior to that of the HYD treatment. A TMT-based proteomic analysis was conducted on the carrot seeds, and the maximum number of differentially abundant proteins (DAPs) appeared between CK and HEHP. KEGG analysis revealed that the upregulated DAPs were mainly enriched in the pathways related to protein synthesis and degradation such as “ribosome” and “proteasome”, while the downregulated DAPs were mainly enriched in photosynthesis-related pathways. Furthermore, the maximum DAPs were annotated in carbohydrate metabolism. Some proteins identified as key enzymes of the glyoxylate cycle, the tricarboxylate cycle, glycolysis and the pentose phosphate pathway showed enhanced abundance in priming treatments. The activities of several key enzymes involved in carbohydrate metabolism were also enhanced by the priming treatments, especially the HEHP treatment. Real-time quantitative PCR (qRT-PCR) analysis revealed that the effect of priming is mainly reflected before sowing. In conclusion, the optimal effect of HEHP is to regulate the synthesis and degradation of proteins in seeds to meet the requirements of germination and initiate the utilization of seed storage reserves and respiratory metabolism. The present work expanded the understanding of the response mechanism of carrot seed germination to priming and the biological effects of high voltage electrostatic field.
2022-04-04 | PXD030133 | Pride
Project description:Global changes in gene expression in Caco-2 cell line by treatment with extract from iodine-biofortified carrot and lettuce
| PRJNA291607 | ENA
Project description:Raw RNAseq data of hydroponically grown crops (cai xin, lettuce, and spinach) subjected under 31 different conditions. Comparative analysis of gene expression across species and stress conditions were carried out.
2024-04-30 | E-MTAB-14018 | biostudies-arrayexpress
Project description:Leafy green vegetables, such as lettuce, have been increasingly implicated in outbreaks of foodborne illnesses due to contamination by Escherichia coli O157:H7. While E. coli can survive in soils, colonize plants, and survive on produce, very little is known about the interaction of E. coli with the roots of growing lettuce plants. In these studies a combination of microarray analyses and microbial genetics were used to gain a comprehensive understanding of bacterial genes involved in the colonization and growth of E. coli K12 on lettuce roots using a hydroponic assay system. Here we report that after three days of interaction with lettuce roots, 193 and 131 genes were significantly up-regulated and down-regulated at least 1.5 fold, respectively. Forty-five out of the 193 up-regulated genes (23%) were involved in protein synthesis and were highly induced. Genes involved in stress response, attachment and biofilm formation were up-regulated in E. coli when they interacted with lettuce roots under conditions of hydroponic growth. In particular crl, a gene regulating the cryptic csgA gene for curli production, was significantly up regulated. The crl, csgA and fliN mutants had a reduced capacity to attach to roots as determined by bacterial counts and by confocal laser scanning microscopy. Our microarray data showed that E. coli K12 increased the synthesis of proteins indicated that a dramatic change was induced in the physiology of the microorganism. This study indicates that E. coli K12 can efficiently colonize lettuce roots by using attachment and biofilm modulation genes and can readily adapt to the rhizosphere of lettuce plants. Further studies are needed to better characterize this interaction in pathogenic strains of this species. Escherichia coli MG1655 strains were grown in the lettuce rhizosphere for three days. Transcriptional profiling of E. coli was compared between cells grown with and without rhizosphere . Three biological replicates of each treatment were prepared, and six microarray slides were used.
2011-11-17 | E-GEOD-33735 | biostudies-arrayexpress
Project description:The draft genome of L. sativa (lettuce) cv. Tizian was sequenced in two Illumina sequencing runs, mate pair and shotgun. This entry contains the RAW sequencing data.
2018-02-09 | E-MTAB-6347 | biostudies-arrayexpress