Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A high-resolution transcriptome map of the sea urchin embryo

ABSTRACT: The sea urchin S. purpuratus is a model organism for study of the genomic control circuitry underlying embryonic development. We examined the complete repertoire of genes expressed in the S. purpuratus embryo, up to late gastrula stage, by means of high-resolution custom tiling arrays covering the whole genome. We detected complete spliced structures even for genes known to be expressed at low leveles in only a few cells. At least 11,000 to 12,000 genes are used in embryogenesis. These include most of the genes encoding transcription factors and signaling proteins, as well as some classes of general cytoskeletal and metabolic proteins, but only a minor fraction of genes encoding immune functions and sensory receptors. Thousands of small asymmetric transcripts of unknown function were also detected in intergenic regions throughout the genome. The tiling array data were used to correct and authenticate several thousand gene models during the genome annotation process. Keywords: high-resolution tiling array, sea urchin, embryo Keywords: other

ORGANISM(S): Strongylocentrotus purpuratus

PROVIDER: GSE6031 | GEO | 2006/10/23

SECONDARY ACCESSION(S): PRJNA97757

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Deep conservation of cis-regulatory elements and chromatin organization in echinoderms uncover ancestral regulatory features of animal genomes [Hi-C]

Project description:we generated new reference genome assemblies for two species belonging to two different echinoderm classes: the bat sea star Patiria miniata and the purple sea urchin Strongylocentrotus purpuratus

2024-11-30 | GSE281901 | GEO

An ancestral Wnt-Brachyury feedback loop and vertebrate-specific recruitment of mesoderm-determining target genes revealed by comparative Brachyury target screens

Project description:Transcription factor brachyury plays a key role during mesoderm development in vertebrates. In this study we study study the effect of this transcription factor in the purple sea urchin S. purpuratus.

2022-08-01 | GSE198320 | GEO

Response to elevated pCO2 in Strongylocentrotus purpuratus larvae

2013-01-01 | GSE37522 | GEO

Gene expression alterations in SoxC knockdown sea urchin embryos

2015-12-16 | GSE76067 | GEO

GRIP-seq data for S. purpuratus, 24hpf embryos

Project description:This is the inaugural dataset for the new GRIP-seq method to map cis-regulatory regions genome-wide. This dataset is for the purple sea urchin embryo, S. purpuratus, at 24 hours post fertilization. There are two experimental samples using an anti-Pol(II) antibody to pull down regulatory region-promoter complexes and one control using IgG alone. Full details of the GRIP-seq methodology are available in the linked manuscript. Bam index (bai) files and tiled data (tdf) files are also available at http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-3607/files/

2016-06-14 | E-MTAB-3607 | biostudies-arrayexpress

Select microRNAs are essential for early development in the sea urchin.

Project description:microRNAs (miRNAs) are small noncoding RNAs that mediate post-transcriptional gene regulation and have emerged as essential regulators of many developmental events. The transcriptional network during early embryogenesis of the purple sea urchin, Strongylocentrotus purpuratus, is well described and would serve as an excellent model to test functional contributions of miRNAs in embryogenesis. We examined the loss of function phenotypes of the major components of the miRNA biogenesis pathway. Inhibition of de novo synthesis of Drosha and Dicer in the embryo led to consistent developmental defects, a failure to gastrulate, and embryonic lethality, including changes in the steady state levels of transcription factors and signaling molecules involved in germ layer specification. We annotated and profiled small RNA expression from the ovary and several early embryonic stages by deep sequencing followed by computational analysis. All miRNAs have dynamic accumulation profiles through early development as do a large population of putative piRNAs (piwi-interacting RNAs). Defects in morphogenesis caused by loss of Drosha can be rescued with four miRNAs which permits a strong miRNA functional assay. Taken together our results indicate that post-transcriptional gene regulation directed by miRNAs is functionally important for early embryogenesis and is an integral part of the early embryonic gene regulatory network in S. purpuratus. Small RNA expression profiling in early sea urchin development

2012-02-17 | E-GEOD-35876 | biostudies-arrayexpress

Gene expression alterations in SoxC knockdown sea urchin embryos

Project description:Transcription factor SoxC is required for all neural development in purple sea urchin S. purpuratus embryos. To begin to develop a gene regulatory network for neural development, we used RNA-Seq to compare transcript populations in SoxC knockdown and control embryos. SoxC function was knocked down by morpholino oligo injection. RNA from about 1000 embryos were collected for both control and knockdown samples.

2015-12-16 | E-GEOD-76067 | biostudies-arrayexpress

Synergistic effects of temperature and pCO2 on growth, development and gene expression of Strongylocentrotus purpuratus larvae

Project description:Transcriptional profiling of purple sea urchin (Strongylocentrotus purpuratus) larvae cultured under four different seawater conditions: (i)13°C/400 µatm pCO2, (ii)13°C/1100 µatm pCO2, (iii)18°C/400 µatm pCO2 (iv)18°C/1100 µatm pCO2. The goal was to determine the effects of temperature and CO2, both important climate change variables, on gene expression

2013-01-01 | GSE39125 | GEO

Response to elevated pCO2 in Strongylocentrotus purpuratus larvae

Project description:Transcriptional profiling of purple sea urchin (Strongylocentrotus purpuratus) larvae cultured under three different seawater CO2 concentrations 400, 800, 1200 M-BM-5atm. The goal was to determine the effects of CO2, an important climate change variable, on global gene expression Larvae were cultured under three different seawater CO2 concentrations 400, 800, 1200 M-BM-5atm, each with four replicate cultures, and sampled at two developmental stages (gastrula and pluteus)

2013-01-01 | E-GEOD-37522 | biostudies-arrayexpress

Floc'hlay2020 - SeaUrchin_model_ginsim

Project description:Multilevel logical model encompassing the Nodal and BMP pathways together with key transcription factors setting the dorsal-ventral axis in the sea urchin P. lividus embryo. This model accounts for the specification of wild-type ventral ectoderm, ciliary band and dorsal ectoderm, and further recapitulates sophisticated mutant phenotypes.

2021-01-06 | MODEL2002190001 | BioModels

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