Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Laminariales

ABSTRACT: RNA-seq, computational analysis of the secretome of brown algae

PROVIDER: PRJDB5131 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	DRR068675_1.fastq.gz	Fastqsanger.gz
	DRR068675_2.fastq.gz	Fastqsanger.gz
	DRR068676_1.fastq.gz	Fastqsanger.gz
	DRR068676_2.fastq.gz	Fastqsanger.gz
	DRR068677_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 14

Similar Datasets

A high-resolution transcriptome map of Ectocarpus siliculosus

Project description:Brown algae (Phaeophyceae) are complex photosynthetic organisms with a very different evolutionary history to green plants, to which they are only distantly related. These seaweeds are the dominant species in rocky coastal ecosystems and they exhibit many interesting adaptations to these, often harsh, environments. The brown algae are also important because they are one of only a very small number of eukaryotic lineages that have evolved complex multicellularity. This work used whole genome tiling array approach to generate a comprehensive transcriptome map of the filamentous seaweed Ectocarpus siliculosus (Dillwyn) Lyngbye, a model organism for the brown algae. Keywords: high-resolution tiling array, brown algae, ectocarpus

2010-04-07 | GSE19912 | GEO

A high-resolution transcriptome map of Ectocarpus siliculosus

2010-04-07 | E-GEOD-19912 | biostudies-arrayexpress

Proteomic and genomic analysis of the marine fungus Paradendryphiella salina

Project description:We set out to investigate the genetic adaptions of the known marine fungus Paradendryphiella salina CBS112865 to the degradation of brown macro-algae, expecting to find a repertoire of carbohydrate active enzymes highly specialized to the degradation of algal polysaccharides. We performed whole genome, transcriptome sequencing and shotgun proteomic analysis of the secretome of P. salina growing on three species of brown algae and under carbon starvation. The genome comparison to close terrestrial fungal relatives, revealed P. salina to have a similar, but reduced carbohydrate active enzyme (CAZyme) profile, except for the presence of three putative alginate lyase 7 genes, most likely acquired via ancient horizontal gene transfer event from a marine bacterium and a polysaccharide lyase 8 gene with similarity to ascomycete chondroitin AC lyases. The proteomic analysis revealed both PL7 and PL8 enzymes to be highly abundant in the algal fermentations together with enzymes necessary for degradation of laminarin, cellulose, lipids and peptides. Our findings indicate that the base CAZyme repertoire of saprobic and plant pathogenic ascomycetes with the necessary addition of alginate lyases provide the fungi with the enzymatic capabilities to thrive on brown algae polysaccharides and even cope with the algal defense mechanisms.

2019-11-13 | PXD012152 | Pride

ClariomS Array to Investigate Vaspin Transgenic Mice: Assessing the Impact of (Brown) Adipocyte Vaspin Expression on Thermoregulation and Brown Adipose Tissue Thermogenesis

Project description:Vaspin previously was identified as part of the secretome of activated brown adipose tissue in mice. For microarray analysis and to determine the effect of adipocyte-sepcific vaspin overexpression on transcriptional changes during acute cold exposure, brown adipose tissue of female vaspin transgenic mice on C57BL/6N background (published in 10.3389/fendo.2023.1146454; VasTg) and wild type control mice were investigated after acute 6 h cold exposure of 8°C.

2024-08-31 | E-MTAB-14068 | biostudies-arrayexpress

Neisseria gonorrhoeae F62

Project description:Computational Analysis of Bacterial RNA-Seq Data

| PRJNA194150 | ENA

Benchmarking differential expression, imputation and quantification methods for proteomics data

Project description:Data analysis is a critical part of quantitative proteomics studies in interpreting biological questions. Numerous computational tools including protein quantification, imputation, and differential expression (DE) analysis were generated in the past decade. However, searching optimized tools is still an unsolved issue. Moreover, due to the rapid development of RNA-Seq technology, a vast number of DE analysis methods are created. Applying these newly developed RNA-Seq-oriented tools to proteomics data is still a question that needs to be addressed. In order to benchmark these analysis methods, a proteomics dataset constituted the proteins derived from human, yeast, and drosophila with different ratios were generated. Based on this dataset, DE analysis tools (including array-based and RNA-Seq based), imputation algorithms, and protein quantification methods were compared and benchmarked. This study provided useful information on analyzing quantitative proteomics datasets. All the methods used in this study were integrated into Perseus which are available at https://www.maxquant.org/perseus.

2022-11-16 | PXD029891 | JPOST Repository

Identification of microRNAs in response to blue light irridiation by high-throughput sequencing in Saccharina japonica

Project description:Blue light (BL) is an important environmental factor that plays critical role in algae growth and development. Saccharina japonica, as a typical brown alga, showed greatly affected by BL. However, little has been known about the regulation pathway of BL response in algae. microRNAs (miRNAs) participated in great number of life process regulation and may be also involved in the BL response in plants. To identify miRNAs from S. japonica and characterize their probable roles in BL response, we sequenced and compared small RNA libraries under BL irradiation and dark conditions. 20 potential novel miRNAs were identified from S. japonica. Bioinformatics analysis of the miRNAs indicated that their potential targets were involved in various biological processes. Based on differential expression analysis and qRT-PCR experiment, some probable miRNAs related to BL responses were selected for further verification of their function, such as miR398. Our results demonstrated that miRNAs might play vital roles in metabolism of S. japonica, including BL responses.

2017-06-12 | GSE36704 | GEO

Paraglaciecola sp. L1A13 strain:brown algae | isolate:brown algae

Project description:Paraglaciecola sp. L1A13 strain:brown algae | isolate:brown algae Genome sequencing

| PRJNA595826 | ENA

Cobetia sp. L2A1 strain:brown algae | isolate:brown algae

Project description:Cobetia sp. L2A1 strain:brown algae | isolate:brown algae Genome sequencing

| PRJNA595828 | ENA

Polaribacter sp. L3A8 strain:brown algae | isolate:brown algae

Project description:Polaribacter sp. L3A8 strain:brown algae | isolate:brown algae Genome sequencing

| PRJNA595830 | ENA