Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA371453 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:To investigate the effects of transgenic lines L6 and L7 tomato fruits on total expression profile of MCF-7 breast cancer cells, we treated MCF-7 cells with 1 ug/ml of tomato fruit extract for 24 hours and compare it with wild type tomato fruit extract Objectives for this study included the identification of genes that were up or down-regulated at the transcriptional level in MCF-7 cells treated with transgenic lines L6 and L7 tomatofruit extract and compare it to wild type tomato fruit extract.
2017-06-12 | GSE94548 | GEO
Project description:The transformation of the ovary into a fruit after successful completion of pollination and fertilization has been associated with many changes at transcriptomic level. These changes are part of a dynamic and complex regulatory network that is controlled by phytohormones, with a major role for auxin. One of the auxin-related genes differentially expressed upon fruit set and early tomato fruit development is Solanum lycopersicum ARF9 (SlARF9). To explore the physiological role of SlARF9 in tomato fruit set and development, we generated transgenic tomato lines in which the gene was overexpressed or silenced, and used microarray analysis to identify possible transcriptomic changes associated with the fruit developmental phenotypes observed in the transgenic lines.
2014-11-26 | GSE63637 | GEO
Project description:Purpose: We used transcriptome sequencing to study the regulated mechanism of VvSUC11,VvSUC12,or VvSUC27 on tomato fruit growth. Methods: the 35S:: VvSUC11, VvSUC12, and VvSUC27 constructs were introduced into transgenic tomatoes (Micro-Tom) by the Agrobacterium-mediated transformation, 5 DPA (days after anthesis) fruit was collected, 3 replicates per group. Extract total RNA, detect RNA quality, library preparation, sequencing, and analyze data. Results:Reads were obtained for each sample using Illumina Hiseq X Ten sequencing. After discarding the low-quality reads, corresponding to over 40 million clean reads obtained from sequencing were mapped on the reference genome of Solanum lycopersicum. High Pearson's correlation coefficients of FPKM distribution between the three biological replicates for each sample were detected (1> R2 > 0.99, P < 0.001) , reflecting the robustness of our library preparation from tomato RNA samples. Compared with WT lines, there were 2459 DEGs in the VvSUC11-overexpressing lines, of which 1283 genes were upregulated and 1176 genes were downregulated. Whereas, there were 1369 DEGs in VvSUC12-overexpressing lines, including 544 upregulated and 825 downregulated genes. In the meanwhile,there were 1777 DEGs in VvSUC27-overexpressing lines, including 623 upregulated and 1154 downregulated genes.
2020-11-16 | GSE161505 | GEO
Project description:Marek's disease virus (MDV) is a highly contagious alphaherpesvirus with widespread incidence in the poultry industry. The double stranded DNA virus infects chickens and turkeys causing a lymphoproliferative disease known as Marek's disease (MD). Infected and susceptible birds develop T cell lymphomas that cause peripheral nerve degeneration, partial or complete paralysis and immunosuppression. Previously, our lab performed scRNA seq of splenic-derived cells from MD resistant Line 6 (L6) and MD susceptible Line 7 (L7) during MDV infection to identify major immune cell subsets. In this study we extend this previous analysis by adding scRNA seq of a first-generation (F1) L6 x L7 population to characterize allele specific expression in individual immune cell types. The joint analysis of scRNA seq of the L6, L7 and F1 cross provide a deeper understanding of how genetic variation impacts gene expression variation in immune cell types and identify regulatory mechanism playing a key role in MD resistance.
2025-02-04 | GSE278696 | GEO
Project description:The transformation of the ovary into a fruit after successful completion of pollination and fertilization has been associated with many changes at transcriptomic level. These changes are part of a dynamic and complex regulatory network that is controlled by phytohormones, with a major role for auxin. One of the auxin-related genes differentially expressed upon fruit set and early tomato fruit development is Solanum lycopersicum ARF9 (SlARF9). To explore the physiological role of SlARF9 in tomato fruit set and development, we generated transgenic tomato lines in which the gene was overexpressed or silenced, and used microarray analysis to identify possible transcriptomic changes associated with the fruit developmental phenotypes observed in the transgenic lines. The transcript profiling analysis was done using pericarp tissue from fruits, 3-4mm in diameter, with each sample containing the pericarp of two fruits. For each seperate transgenic line, tissues were pooled from 2-3 plants (T2), resulting in a total of 6 samples for SlARF9-OE, 7 samples for SlARF9-RNAi, and 2 samples for wild type. The transcript profiling analysis was carried out using affymetrix EUTOM3 tomato exon array.
2014-11-26 | E-GEOD-63637 | biostudies-arrayexpress
Project description:To evaluate the role of seeds in fruit quality, we induced parthenocarpy in tomato by regulating ovule-specific auxin synthesis or responsiveness using the INO promoter from A. thaliana, which is expressed in the outer layer of the integuments during early stages of ovule development. We compared these to fruit where the same coding regions were expressed from the DeFH9 promoter which is expressed in carpel tissues during early stages of ovule development. Expression of auxin synthesis or responsiveness genes by both of these promoters produced seedless parthenocarpic tomato fruit. We compared fruit samples using the Affymetrix tomato GeneChip (GPL4741) to determine how gene regulation and expression differed between wild-type and transgenic fruit. Experiment Overall Design: Wild-type fruit with seeds was compared with transgenic lines INO-IaaM, DefH9-IaaM, INO-RolB, and DefH9-RolB. To find genes with seed-specific expression, we also compared the control with wild-type fruit from which seeds had been manually removed. We had three biological replicates for each treatment and control except DefH9-RolB, for which only two replicates were available. Each CEL file from the microarray represents one plant from each line.
2009-09-15 | E-GEOD-14358 | biostudies-arrayexpress
Project description:Comparison of gene expression, in immature green fruit (15dpa), between transgenic tomato (S. lycopersicum cv. '.T63') lines expressing constitutively the transcription factors AtGLK1 (At2g20570) or AtGLK2 (At5g44190) regulated by the CaMV35S (p35S) to 'T63' lines expressing only the CaMV35S promoter construct (TControl) with no AtGLK sequences. The goal is to describe the effect on fruit transcriptome imposed by the presence of the transgens and relate defined transcriptome changes to the biochemical and morphological phenotypes observed in transgenic fruits
2012-06-29 | E-MEXP-3652 | biostudies-arrayexpress
Project description:The tomato (Solanum lycopersicum) MADS-box transcription factor RIPENING INHIBITOR (RIN) acts as a master regulator of tomato fruit ripening. We previously identified a direct RIN target gene Solyc07g052960, which encodes a putative GRAS family protein belonging to the SHORT-ROOT (SHR) branch, but its role was unknown. RNA interference (RNAi)-mediated gene silencing reduced Solyc07g052960 expression in transgenic fruits, but the fruits appeared to ripen normally. However, the transgenic fruits at the ripening stage showed a marked decrease of the expression levels of several ripening-induced genes, especially involved in cell wall modification and secondary metabolism. This suggests that Solyc07g052960 participates in the regulation of these processes as one component of the RIN-activated transcriptional cascade regulating fruit ripening in tomato. For a preliminary screening, we monitored global gene expression in tomato fruits from untransformed control (Ailsa Craig [AC] cultivar) and three transgenic lines with Solyc07g052960 knockdown by RNAi (lines T-7, T-22 and T-23) at the ripening (pink coloring) stage using microarray without biological replication.
2014-03-01 | E-GEOD-45658 | biostudies-arrayexpress
Project description:The steroid hormone brassinosteroids (BRs) play considerable roles in plant development and defence. Harnessing the extensive knowledge on Arabidopsis BR signalling network for improving productivity in crop species requires first to identify the conserved network components and their function in the target species. To investigate the function of SlBIM1a, the tomato closest homolog of AtBIM1, which is highly expressed in the developing fruit, we generated transgenic tomatoes, which overexpress or down-regulate SlBIM1a gene. Main alterations were observed in SlBIM1a overexpressing lines, which displayed a severe plant and fruit dwarfism. To unravel the molecular basis of phenotypical modifications in SlBIM1a overexpressing fruits, a microarray (Agilent) analysis was performed on Pro35S:SlBIM1aOX and WT fruits harvested at 15 DPA.
2020-10-26 | E-MTAB-9502 | biostudies-arrayexpress
Project description:To evaluate the role of seeds in fruit quality, we induced parthenocarpy in tomato by regulating ovule-specific auxin synthesis or responsiveness using the INO promoter from A. thaliana, which is expressed in the outer layer of the integuments during early stages of ovule development. We compared these to fruit where the same coding regions were expressed from the DeFH9 promoter which is expressed in carpel tissues during early stages of ovule development. Expression of auxin synthesis or responsiveness genes by both of these promoters produced seedless parthenocarpic tomato fruit. We compared fruit samples using the Affymetrix tomato GeneChip (GPL4741) to determine how gene regulation and expression differed between wild-type and transgenic fruit. Keywords: genetic modification
2009-08-31 | GSE14358 | GEO