Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptome profiling and co-expression network analysis of 96 Haematococcus pluvialis samples

ABSTRACT: Haematococcus pluvialis is a microalga known for producing the red carotenoid, astaxanthin. Key research areas to improve productivity include optimizing vegetative biomass, enhancing astaxanthin content, and controlling secondary cell wall formation. In this study, RNA-seq was conducted on 96 H. pluvialis samples under various treatments and time points, generating 96.7 GB of high-quality data (2,080,511,173 clean reads, quality score > 30). Gene expression was quantified as transcripts per million (TPM), and genes with similar expression patterns were clustered. A co-expression network, constructed with a soft threshold of β=7 (R² > 0.9), identified 39 co-expression modules, each averaging 732 genes. Additionally, the re-annotation process provided functional descriptions for around 8,600 previously uncharacterized genes. Gene functional classification analysis revealed their involvement in metabolic pathways related to genetic information processing and primary/secondary metabolite metabolism. This dataset provides a valuable resource for exploring the molecular mechanisms involved in critical processes such as growth regulation, astaxanthin accumulation, and secondary cell wall synthesis in H. pluvialis.

ORGANISM(S): Haematococcus lacustris

PROVIDER: GSE289633 | GEO | 2025/06/27

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Comparative analysis of transcriptome profiles of G. hirsutum L. acc. TM-1 and its immature fber mutant during fiber secondary cell wall development stages

2014-06-30 | GSE49617 | GEO

Histone H3K4 methyltransferase ATX1 positively regulates secondary wall biosynthesis in interfascicular fibers in Arabidopsis

Project description:Secondary wall thickening in the sclerenchyma cells is strictly controlled by a complex network of transcription factors in vascular plant. However, little is known about the epigenetic mechanism regulating secondary cell wall biosynthesis. Genome-wide analysis revealed that the up-regulation of genes involved in secondary wall formation during stem development is largely coordinated by increasing level of H3K4 tri-methylation. In this study, we identified that ARABIDOPSIS HOMOLOG of TRITHORAX1 (ATX1), a H3K4-histone methyltransferase, positively regulates secondary wall deposition mainly through activating the expression of secondary wall NAC master switch genes, SECONDARY WALL-ASSOCIATED NAC DOMAIN PROTEIN1 (SND1) and NAC SECONDARY WALL THICKENING PROMOTING FACTOR1 (NST1).

2020-11-29 | GSE153705 | GEO

Comparative analysis of transcriptome profiles of G. hirsutum L. acc. TM-1 and its immature fber mutant during fiber secondary cell wall development stages

Project description:To gain novel insights into the molecular mechanisms of fiber secondary cell wall development, fiber transcriptomes of the immature fiber mutant (im) with defective secondary cell wall development and its near-isogenic line, TM-1 (wild-type) were compared using cDNA microarray technology. The expression profiling was performed at 5 developmental time points: 13, 16, 19, 22, and 25dpa. Secondary cell wall development related genes were identified by differentially expressed gene analysis. And these genes could be used as potential candidate genes for manipulation to improve fiber quality. Cotton plants were grown under field condition. Flowers were tagged and cotton bolls were collected during Fiber development stages. Total RNA was isolated from fiber bearing ovules of wild-type, TM-1 and immature fiber mutant (im) collected at various (13, 16, 19, 22 and 25 dpa) fiber development stages. A total of 15 hybridizations with three biological replicates including a swap-dye experiment for each fiber developmental stage were employed.

2014-06-30 | E-GEOD-49617 | biostudies-arrayexpress

Expression data from VND7 induction line

Project description:Plants typically contain two different types of cell walls: a primary wall that is being deposited around all growing cells, and a secondary wall that is produced in cells with specialized functions once they have ceased to grow. In Arabidopsis, VND7 is a transcription factor that is sufficient to activate secondary cell wall synthesis. To artificially turn on the secondary cell wall synthesis, VND7 was fused to the activation domain of the herpes virus VP16 protein and the glucocorticoid receptor (GR) domain. Thus, the transgenic plants harbouring the constructs can then be treated with dexamethasone (DEX), a glucocorticoid derivative, to induce the secondary cell wall formation. We used microarrays to investigate the global program of gene expression during the secondary cell wall development and identified up- and down-regulated genes associated with this process.

2016-02-22 | GSE77153 | GEO

Transcriptome analysis of secondary cell wall development in Medicago truncatula

Project description:Global transcriptional profiling has been successfully used to identify genes and regulatory pathways in secondary cell wall thickening. A systematic microarray assay of secondary cell wall development along stem maturation in Medicago truncatula was conducted to identify genes and pathways that are involved in lignin/cellulose biosynthesis of secondary wall development.

2016-06-28 | E-MTAB-3909 | biostudies-arrayexpress

Salicylic acid treatment and overexpression of a novel polyamine transporter gene for astaxanthin production in Phaffia rhodozyma

Project description:Phaffia rhodozyma is an ideal microbial astaxanthin resource. However, the low productivity of astaxanthin in this yeast obstructs the process of industrial production. Although P. rhodozyma is isolated from plant material and the phytohormone has proved to be an effective stimulator for microbial production, the effects and mechanisms of phytohormones on astaxanthin synthesis in P. rhodozyma have been rarely reported. In this study, a concentration of down to 0.5 mg/L exogenous salicylic acid (SA) could promote biomass, astaxanthin content and yield by 20.8%, 95.8% and 135.3% in P. rhodozyma, respectively. Further transcriptomic analysis showed that SA could discriminate well the transcriptomic profile of P. rhodozyma cells. The differently expressed genes (DEGs) in P. rhodozyma cells between the SA-treatment and the SA-free groups were identified, and involved in astaxanthin and its competitive metabolite synthesis, material supply, biomolecules metabolism and transportation, anti-stress and signal transductions at a global-cell level. A regulation mechanism of astaxanthin synthesis induced by SA, including perception and transduction of the SA signal, expression regulations of the downstream genes by transcription factors, and cellular stress response to the SA, is put forward in this study. The polyamine transporter gene (PT), as an up-regulated DEG, was overexpressed in the P. rhodozyma to obtain the transformant Prh-PT-006. It was found that biomass, astaxanthin content and yield of the Prh-PT-006 under 0.5 mg/L SA treatment could reach 6.6 g/L, 0.35 mg/g DCW and 2.3 mg/L, 24.5%, 143.1% and 199.0% higher than the wild strain at the SA-free condition, respectively. The result will provide the engineering targets for constructing strains with high-yield of astaxanthin, and help to accelerate the industrialization process of microbial astaxanthin.

2023-10-16 | GSE242572 | GEO

Differential transcriptomic expression of an imprved astaxanthin production

Project description:The differential expression of the high-yield astaxanthin Phaffia rhodozyma BPAX-A1 with the wild-type Phaffia rhodozyma CBS6938 was obtained and analysed to understand metabolic changes leading to an improved astaxanthin production.

2023-09-14 | GSE213476 | GEO

Ectopic expression of MYB46 identifies transcriptional regulatory genes in secondary wall biosynthesis in Arabidopsis

Project description:MYB46 functions as a transcriptional switch that turns on the genes necessary for secondary wall biosynthesis. Elucidating the transcriptional regulatory network immediately downstream of MYB46 is crucial to our understanding of the molecular and biochemical processes involved in the biosynthesis and deposition of secondary walls in plants. The transcription factors identified here may include direct activators of secondary wall biosynthesis genes. The current study discovered novel hierarchical relationships among the transcription factors involved in the transcriptional regulation of secondary wall biosynthesis and generated several testable hypotheses. To gain insights into the MYB46-mediated transcriptional regulation, we first established an inducible secondary wall thickening system in Arabidopsis by expressing MYB46 under the control of dexamethasone inducible promoter. Then, we used ATH1 GeneChip microarray to obtain a series of time-course transcriptome profiles with regard to the induction of secondary wall development.

2010-05-27 | E-GEOD-16143 | biostudies-arrayexpress

cDNA microarray expression profile during fiber elongation between G. hirsutum and G. barbadense

Project description:Sea-island cotton (Gossypium barbadense L.) has superior fiber quality properties such as length, fineness and strength, while Upland cotton (Gossypium hirsutum L.) is characterized by high yield. To reveal features of Upland cotton and Sea-island cotton fiber cells, differential genes expression profiles during fiber cell elongation and in secondary wall deposits were established using cDNA microarray technology. This research provides a valuable genomic resource to deepen our understanding of the molecular mechanisms of cotton fiber development, and may ultimately lead to improvements in cotton fiber quality and yield.

2012-05-24 | GSE18028 | GEO

NST1 over-expression vs wild type

Project description:In plants, secondary wall thickenings play important roles in various biological processes, although the factors regulating these processes remain to be characterized. We show that expression of chimeric repressors derived from NAC SECONDARY WALL THICKENINGS PROMOTING FACTOR1 (NST1) and NST2 in Arabidopsis resulted in an anther dehiscence defect due to loss of secondary wall thickening in anther endothecium. Plants with double, but not single, T-DNA-tagged lines for NST1 and NST2, had the same anther-indehiscent phenotype as transgenic plants that expressed the individual chimeric repressors, indicating that NST1 and NST2 are redundant in regulating secondary wall thickening in anther walls. The activity of the NST2 promoter was particularly strong in anther tissue, while that of the NST1 promoter was detected in various tissues in which lignified secondary walls develop. Ectopic expression of NST1 or NST2 induced ectopic thickening of secondary walls in various above-ground tissues. Epidermal cells with ectopic thickening of secondary walls had structural features similar to those of tracheary elements. However, among genes involved in the differentiation of tracheary elements, only those related to secondary wall synthesis were clearly upregulated. None of the genes involved in programmed cell death was similarly affected. Our results suggest NAC transcription factors as possible regulators of secondary wall thickening in various tissues. Keywords: transgenic vs wt comparison

2005-09-29 | GSE3363 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data