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GSE65844
Triticum aestivum
53 Downloadable Samples
Affymetrix Wheat Genome Array (wheat)
Description
Allopolyploidy, entailing whole genome duplication (WGD) of merged divergent genomes of different species, often instigates transcriptome shock, whereby both total gene expression level and homeolog expression partitioning can be disrupted and remodeled. Little is known about the extent to which the parental expression-conserved genes will be disrupted/remodeled by allopolyploidization, nor the evolutionary relevancy of shock-induced expression repatterning. Here, by microarray-based gene expression profiling and gene-specific cDNA-pyrosequencing, we assessed transgenerational transcriptome shock in a synthetic allotetraploid wheat (AT2) with karyotype and basic morphology mimicking those of natural tetraploid wheat, Triticum turgidum. We show that the transcriptome shock in AT2 is exceptionally strong that it disrupted intrinsically conserved parental gene expression, and resulted in extensive expression nonadditivity in the newly formed allotetraploid plants. At total expression level, a substantial proportion of shock-induced novel expression, especially over-transgressive expression, was rapidly stabilized already in early generations of AT2. Extensive remodeling of homeolog expression occurred in AT2, including those genes that showed additive total expression, and which generated subgenome expression dominance, a pattern that mirrors T. turgidum. Thus, the shock-induced new patterns of gene expression at both the total expression level and subgenome homeolog partitioning showed evidence of evolutionary persistence. Complex relationships between homeolog expression remodeling and nonadditive total expression were observed in a tissue-specific manner.
Publication Title
No associated publication
Sample Metadata Fields
Specimen part
View Samples- Oryza sativa
- 12 Downloadable Samples
- Affymetrix Rice Genome Array (rice)
Description
To investigate possible genetic basis of alkali tolerance in rice, we generated an introgressed rice line (K83) with significantly enhanced tolerance to alkali stress than its recipient parental cultivar (Jijing88). By using microarray analysis, we examined global gene expression profiles in K83 and Jijing88, found more than 1,200 genes were constitutively differentially expressed in K83 compared with Jijing88, with 572 up- and 654 down-regulated. Upon alkali treatment, a total of 347 genes in K83 were found up- and 156 down-regulated in K83, compared with 591 and 187 respectively in Jijing88.
Publication Title
Transcriptome alteration in a rice introgression line with enhanced alkali tolerance.
Sample Metadata Fields
Specimen part
View Samples- Glycine max
- 4 Downloadable Samples
- Affymetrix Soybean Genome Array (soybean)
Description
Chinese soybean (Glycine max (L.) Merr.) cultivars Rsmv1 and Ssmv1 were used for soybean mosaic virus (SMV) resistance genes screening. The Rsmv1 cultivar was highly-resistant to SMV but the Ssmv1 cultivar was highly-susceptible.
Publication Title
No associated publication
Sample Metadata Fields
Specimen part
View Samples- Triticum aestivum
- 2 Downloadable Samples
- Affymetrix Wheat Genome Array (wheat)
Description
The three subgenomes (B, A and D) of common wheat (2n=6x=42) are largely intact, which makes extraction of the BBAA subgenomes as organismally independent genomes possible. Availability of such novel extracted tetraploid wheat (Extracted-tetra) provides a unique opportunity to study whether and to what extent the BBAA subgenomes of common wheat have been irreversibly modified, as well as its attendant biological consequences, during their evolutionary trajectory as allohexaploidy. We report here that the extracted-tetra is stable in karyotype but with severely deteriorated phenotypes. Microarray-based transcriptome analysis revealed a substantial portion of differentially expressed genes (down- or up-regulation) between extracted and natural tetraploid wheat, Triticum turgidum, which exceeded the transcriptome divergence at tetraploid level, implying reinforced effects of allopolyploidization and domestication at the allohexaploid level. Great majority of the differentially expressed genes showed additive expression in a resynthesized allohexaploid wheat (parented by Extracted-tetra), indicating transcriptome modifications to the BBAA subgenomes are largely irreversible. Analysis of a newly synthesized allohexaploid wheat (parented by T. turgidum) suggests that whereas most of the modified genes are accrued evolutionary changes, some showed immediate regulation post-allohexaploidization and evolutionary perseverance. Homeologue-specific pyrosequencing of 44 genes revealed either concordant or independent expression changes to the B and A homeologues. The Extracted-tetra vs.T. turgidum down-regulated genes showed enrichment for distinct GO categories.
Publication Title
No associated publication
Sample Metadata Fields
Specimen part
View Samples- Gallus gallus
- 65 Downloadable Samples
- Affymetrix Chicken Genome Array (chicken)
Description
Gene expression profiles of chicken preadipocytes were constructed using Chicken Genome Arrays to determine the gene expression patterns of preadipocytes derived from two chicken lines divergently selected for abdominal fat content.
Publication Title
No associated publication
Sample Metadata Fields
Specimen part
View Samples- Zea mays
- 20 Downloadable Samples
- Affymetrix Maize Genome Array (maize)
Description
Head smut of maize, which is caused by the Sporisorium reilianum f. sp. Zeae (Khn), has been a serious disease in maize. In order to find head smut resistant candidate genes, microarrays were used to monitor the gene expression profiles between disease resistant near isogenic lines (NIL) L282 and L43, highly resistant inbred line Q319 and highly susceptible inbred line Huangzao4 after 0 to7 days post inoculation of S.reiliana by artificial inoculation method.
Publication Title
No associated publication
Sample Metadata Fields
Specimen part, Time
View Samples- Gallus gallus
- 9 Downloadable Samples
- Affymetrix Chicken Genome Array (chicken)
Description
Excessive accumulation of lipids in the adipose tissue is a major problem in the present-day broiler industry. However, few studies have analyzed the expression of adipose tissue genes that are involved in pathways and mechanisms leading to adiposity in chickens. Gene expression profiling of chicken adipose tissue could provide key information about the ontogenesis of fatness and clarify the molecular mechanisms underlying obesity.
Publication Title
Profiling of chicken adipose tissue gene expression by genome array.
Sample Metadata Fields
Age
View Samples- Arabidopsis thaliana
- 6 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
To identify the target genes regulated by ANAC069, the expression profiles of OE (Overexpression of ANAC069) plants and KO (Knockout of ANAC069, SALK_095231C) plants under salt stress conditions were compared using Affymetrix Arabidopsis gene chips.
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Gallus gallus
- 6 Downloadable Samples
- Affymetrix Chicken Genome Array (chicken)
Description
A better understanding of the regulation of gene expression and lipid metabolism in the chicken will benefit producers, as well as scientists who use the chicken as a model organism for studies of developmental biology and human therapeutics.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Mus musculus
- 16 Downloadable Samples
- Illumina MouseRef-8 v2.0 expression beadchip
Description
Bile acids are not only physiological detergents facilitating nutrient absorption, but also signaling molecules regulating metabolic homeostasis. We reported recently that transgenic expression of CYP7A1 in mice stimulated bile acid synthesis and prevented Western diet-induced obesity, insulin resistance and hepatic steatosis. The aim of this experiment is to determine the impact of induction of hepatic bile acid synthesis on liver metabolism by determining hepatic gene expression profile in CYP7A1 transgenic mice. CYP7A1 transgenic mice and wild type control mice were fed either standard chow diet or high fat high cholesterol Western diet for 4 month. Hepatic gene expressions were measured by microarray analysis. Our results indicate that hepatic bile acid synthesis is closely linked to cholesterogenesis and lipogenesis, and maintaining bile acid homeostasis is improtant in hepatic metabolic homeostasis.
Publication Title
Regulation of cholesterol and bile acid homeostasis by the cholesterol 7α-hydroxylase/steroid response element-binding protein 2/microRNA-33a axis in mice.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples