The differences of the transcriptional profile between wide-type maize and transgenic ZmPIS maize (drought tolerance) by the assay of digital gene expression profile data
Ontology highlight
ABSTRACT:
ORGANISM(S): Zea mays
SUBMITTER: Xiuxia Liu
PROVIDER: E-GEOD-31944 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:The present study profiled and analyzed gene expression of the maize ear at four key developmental stages. Based on genome-wide profile analysis, we detected differential mRNA of maize genes. Some of the differentially expressed genes (DEGs) were predicted to be potential candidates of maize ear development. Several well-known genes were found with reported mutants analyses, such as, compact plant2 (ct2), zea AGAMOUS homolog1 (zag1), bearded ear (bde), and silky1 (si1). MicroRNAs such as microRNA156 were predicted to target genes involved in maize ear development. Antisense transcripts were widespread throughout all the four stages, and are suspected to play important roles in maize ear development. Thus, identification and characterization of important genes and regulators at all the four developmental stages will contribute to an improved understanding of the molecular mechanisms responsible for maize ear development. Seeds of the maize inbred line 18-599 (Maize Research Institute, Sichuan Agricultural University, Chengdu, China) were grown in a growth chamber at 24°C/18°C (day/night) with 12 h illumination per day. Ears were collected as described previously [10] at four developmental stages: the growth point elongation, spikelet differentiation, floret primordium differentiation, and the floret organ differentiation phases. In brief, ears were manually collected at the four developmental stages. All the samples were harvested and immediately frozen in liquid nitrogen, and stored at -80°C until used for RNA isolation.
2015-04-30 | E-GEOD-49805 | biostudies-arrayexpress
Project description:A genome-wide transcriptome analysis showed that altering ZmPIN1a expression led to wide-ranging gene expression changes. When comparing overexpression lines A17 with the WT, 2975 genes were differentially expressed with 793 up-regulated and 2182 down-regulated in the leaves, and 2129 genes were differentially expressed with 938 up-regulated and 1191 down-regulated in the roots. GO analysis indicated that these differentially expressed genes participate in multiple biological processes from hormone signaling to metabolism. The local biosynthesis, PAT and signaling of auxin were altered; some was directly employed in plant developments such as AUX/IAA, ARFs and genes related to PAT. The genes involved in ethylene, GA, BR CK and ABA metabolism and signaling were altered as well. These phytohormones were also confirmed as key regulators in plant development and abiotic stress responses. Some of the differentially expressed genes between A17 and WT were identified as Arabidopsis root morphology and development mutant genes. These mutants were abnormal in their plant hormone synthesis and signaling, calcium-mediated signaling, MAP kinase signaling, transcription factors, membrane transporters etc. This finding suggested that ZmPIN1a overexpression led to a change of the auxin signaling transduction and even the metabolism of auxin and the metabolism and signaling of other hormones. These events led to changes in the expression of numerous genes and resulted in the modification of plant morphology, especially the root architecture. Maize (Zea mays L.) inbred line DH4866, its ZmPIN1a sense transgenic lines A17 and antisense transgenic lines a55 were used in this study. The transcriptome by altering ZmPIN1a expression was done by comparing the transcriptome of WT and transgenic lines both in root and leaf of V3 stage plants.
2014-05-06 | E-GEOD-57291 | biostudies-arrayexpress
Project description:Purpose: AURKA plays an important role in breast cancer development. Exploring the gene expression profiles regulated by AURKA will facilitate to understand the mechanism which is responsible for AURKA induced breast cancer development. Results: We found that 350 genes were significantly up-regulated during AURKA overexpression in MCF-10A cells, 346 genes were significantly down-regulated during AURKA overexpression in MCF-10A cells. Conclusions: Our study indicated that 696 differentially expressed genes might contribute to AURKA induced breast cancer development. MCF-10A cells overexpressed AURKA or the empty vector were subjected to RNA extraction. The resulted RNA samples were performed RNA-sequencing analyses of gene expression profiles.
2015-10-28 | E-GEOD-57931 | biostudies-arrayexpress
Project description:Versatile roles of REVOLUTA (REV), a Class III homeodomain-leucine zipper (HD-ZIP III) transcription factor, have been mainly depicted in Arabidopsis and Populus. In this study, we investigated the functions of its tomato homolog, namely SlREV. Over-expression of a microRNA166-resistant version of SlREV (35S::REVRis) not only resulted in vegetative abnormities such as curly leaves and fasciated stems, but also caused dramatic reproductive alterations including continuous production of flowers at pedicel abscission zone (AZ) and ectopic fruit formation on receptacles. Microscopic analysis showed that meristem-like structures continuously emerged out from the exodermises of pedicel AZs and ectopic carpels formed between the first and the second whorl of floral buds in 35S::REVRis plants. Therefore, we performed Illumina’s digital gene expression (DGE) system, a tag-based transcriptome sequencing methodTranscriptional data to dicover differential expressed genes in early buds (1-2 mm floral buds at stage 6-8) of overexpression line SlREVRis-1. The result suggests that SlREV may regulate genes related to meristem maintenance and cell differentiation in the development of flower pedicel abscission zone, and modulate genes in homodomain and MADS-box families and hormone pathways during fruit formation. These results reveal important roles of SlREV in tomato. 1-2 mm floral buds at stage 6-8 were sampled from three individual plants of 35S::REVRis-1 and corresponding WT control. Three aliquots of RNA from transgenic or WT plants were pooled. Then, the digital expression profile were generated by Illumina Cluster Station and Illumina HiSeq™ 2000 System (BGI Inc.).
2014-06-10 | E-GEOD-58305 | biostudies-arrayexpress
Project description:Friable embryogenic callus (FEC) has been considered as the most suitable materials for efficient genetic transformation of cassava. Due to heavy genotype dependence on FEC induction and being amenable to somaclonal variation, the production and maintaining of reliable FEC is a limitation factor for cassava genetic transformation. Identification of key elements involving in biological processes from somatic embryos (SEs) to the FEC at different stages will provide critical insights for FEC improvement. Cytological observation showed the dramatic change of subcellular structures among SEs, fresh FEC (FFEC) and old FEC (OFEC). Decrease of sucrose and increase of fructose and glucose were detected in OFEC. A total of 6871 differentially expressed genes (DEGs) were identified from SEs, FFEC and OFEC by RNA-seq. Analysis of the DEGs showed that FEC induction was accompanied by the process of dedifferentiation, whereas the epigenetics modification occurred during the continuous subculturing process. The cell structure was reconstructed, mainly including the GO terms of "cell periphery" and "external encapsulating structure"; in parallel, the internal mechanisms were changed correspondingly, including the metabolisms of process (glycolysis) and compounds(alanine, aspartate, and glutamate). The significant reduction of genomic DNA methylation in OFEC indicates altered gene expression via chromatin modification. These results indicate that the induction and long-term subculture of FEC is a complicated biological process involving changes of genome modification, gene expression and subcellular reconstruction. The findings will be useful for improving FEC induction and maintenance from farmer-preferred cassava cultivars that are recalcitrant to genetic transformation, hence improving cassava through genetic engineering. Two-week-old SEs cultured on GD, FFEC emerging from SEs, and 9-month-old OFEC were used for analysis. Each sample was mixtured from six indepedent replicates and were collected for RNA extraction respectively.
2015-09-05 | E-GEOD-72717 | biostudies-arrayexpress
Project description:To study the function of chromatin regulators in hybrid gene expression, the histone deacetylase gene OsHDT1 was over-expressed or inactivated by RNAi in an elite rice parent. Digital analysis of gene expression using high throughput sequencing technology revealed several differential gene expression patterns in the hybrid, including additivity, nonadditivity and overdominance, etc. Alteration of OsHDT1 levels affected many genes specifically in the hybrid. In addition, we show that increased OsHDT1 could suppress overdominance gene expression, providing evidence of overdominance gene action in heterosis. These results not only support the overdominance hypothesis to explain heterosis, but also provide evidence that variation in the levels of single trans-acting regulatory proteins such as chromatin factors is important to establish differential gene expression pattern in the hybrid. High throughput sequencing technology was used to analyse gene differencial expression of 15 days old rice seedling of 5 samples, MH63(MH), ZS97(ZS), SY63(SY,hybrids of MH and ZS), overexpression of OsHDT1 in SY(FU), RNAi of OsHDT1 in SY(FR).
2012-01-01 | E-GEOD-27240 | biostudies-arrayexpress
Project description:Schistosoma japonicum is one of the remarkable platyhelminths that are endemic in the South Asian countries. The parasite is dioecious and can parasitize inside host blood stream for many years. Rapid reproduction by producing large number of eggs and count-react or active manipulating host anti-parasite responses are the strategies that benefit the long term parasitization of the parasite. Currently, Praziquantel is the only commercial drug that is effective against the worms but not the eggs of parasite in the host and no vaccine available to prevent human or animal schistosomiasis. Development of novel antiparasite reagents and immune-prevention measures rely on the deciphering of parasite biology. The decoding of the genomic sequence of the parasite has made it possible to dissect the biological functions of genes that govern the development of the parasite inside the hosts. In this study, the polyadenylated RNA from male and female S. japonicum was isolated and deep sequenced. By comparative analysis on the transcriptomic differences of the two sexes of the parasite, potential genes or gender-specific biological pathways can be targeted. Messenger RNA from male and female S. japonicum parasite was selectively purified from total RNA using oligo-(dT) conjugated magnetic beads. Complementary DNA (cDNA) was synthesized guided by oligo-(dT) as a primer.
2011-12-01 | E-GEOD-26845 | biostudies-arrayexpress
Project description:We report the application of Solexa/Illumina's digital gene expression (DGE) sequencing approaches to investigate inactivated Vibrio harveyi--induced transcriptome changes in Lateolabrax japonicas, a non model vertebrate species. Totally 3.44 and 3.22 million raw tags were measured. Then, gene annotation was performed by tags mapping analysis and the 169,950 non-redundant consensus sequences from RNA-seq based transcriptome analysis were used as reference transcript database. Tag mapping indicated that Vibrio harveyi--challenged adult Lateolabrax japonicas express over 70% of all genes represented in transcript databases. Meanwhile, totally 1224 consensus sequences exhibited significant difference after the bacterial challenge, in which 1183 transcripts can be well annotated, while approximately 41 transcripts have low sequence homology to the existing known sequences in public databases, suggesting that they might be putative novel immune-relevant genes in Lateolabrax japonicus closely related to the immunity for bacterial challenge. Our present study would greatly benefit to give deep insight into the immunogenetics in fish species, and clinical application in fish diseases. Examination of differentially expressed transcripts in baterial- and mock challenged fish.
2011-06-12 | E-GEOD-21712 | biostudies-arrayexpress
Project description:4,392 differentially expressed genes were generated by DGE analysis, and 3,074 had good comparability with known gene sequences in existing species. 1,152 differentially expressed sequences were mapped to the reference canonical pathways in the KEGG database, and were assigned to 110 KEGG pathways, 11 pathways less then with the transcriptome database. Differentially expressed genes were classed according to their function, which includes phytohormones, growth and developmental processes, defense, peroxidase and P450-related genes. Pathway analysis also revealed that the principal secondary metabolites in the C. odorata cuttings were phytohormones and flavonoids. Examination of 2 different stage of adventitious root formation
2012-11-16 | E-GEOD-42283 | biostudies-arrayexpress
Project description:Cassava mosaic disease caused by cassava begomoviruses is the most serious disease of cassava in Africa. However, the molecular mechanisms leading to symptom development of infected cassava plants are poorly understood. Here a high throughput digital gene expression profiling (DGE) based on Illumina Solexa sequencing technology was used to investigate the global transcriptional response of cassava to the African cassava mosaic virus infection. Results showed that 3,210 genes were differentially expressed in virus-infected cassava leaves. Gene Ontology (GO) term and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that photosynthesis related genes were most affected, which was consistent with the chlorotic symptom on the infected leaves. The upregulation of chlorophyll degradation genes, e.g. the genes encoding chlorophyllase and pheophorbide a oxygenase, as well as the downregulation of the major apoproteins genes in light harvesting complex II (LHCII) identified by the DGE analysis were confirmed by qRT-PCR. Together with the reduction of chlorophyll b content and fewer grana stacks in the infected leaf cells, this study reveals that the degradation of chlorophyll plays an important role during ACMV symptom development for the first time. Meanwhile, we believe that the non-lethal effect on photosystem is a trick for virus to avoid fierce host immune response and a result of the long-term co-evolution. This study will provide a road map for future investigations into virus symptom development. ACMV-infected cassava leaves mixture from three independent replicates were collected for RNA extractions at 20 dpi. Control samples were harvested from empty agrobacteria treated leaves incubated under the same conditions.
2014-04-01 | E-GEOD-47224 | biostudies-arrayexpress