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TranscriptomicsRibosome Profiling over a Zebrafish Developmental Timecourse
To experimentally-validate the non-coding status of annotated lncRNAs, we performed ribosome profiling over a developmental timecourse that matched our previously-published (Pauli et al. 2012) developmental transcriptome. We find that many previously-annotated lncRNAs appear to be translated, but in...
ORGANISM(S): Danio rerio 
2013-05-23 | E-GEOD-46512 | biostudies-arrayexpress
ProteomicsA molecular network of conserved factors keeps ribosomes dormant in the egg
Ribosomes are produced in large quantities during oogenesis and stored in the egg. However, the egg and early embryo are translationally inactive. How translation is activated during embryogenesis is poorly understood. Using mass-spectrometry and cryo-EM analyses of ribosomes isolated from zebrafish...
ORGANISM(S): Danio rerio (Zebrafish) (Brachydanio rerio) Xenopus laevis (African clawed frog) 
2022-11-03 | PXD026866 | Pride
Cryo-em Cross-linking Xenopus Mass-spectrometry Ribosome Zebrafish 
TranscriptomicsDifferential gene expression profiling in the presence and absence of cohesin in Drosophila salivary glands (gene expression data)
Analysis of differential gene expression in third instar Drosophila salivary glands in the absence versus presence of cohesin. ABSTRACT: Developmental abnormalities observed in Cornelia de Lange Syndrome (CdLS) have been genetically linked to mutations in the cohesin machinery. These findings raise ...
ORGANISM(S): Drosophila melanogaster 
2010-12-22 | E-GEOD-21844 | biostudies-arrayexpress
TranscriptomicsA direct role for cohesin in genome-wide gene regulation and Ecdysone-response in Drosophila salivary gland
Developmental abnormalities observed in Cornelia de Lange Syndrome (CdLS) have been genetically linked to mutations in the cohesin machinery. These findings raise the possibility that cohesin, in addition to its canonical function of mediating sister chromatid cohesion, might also be involved in reg...
ORGANISM(S): Drosophila melanogaster 
2011-03-22 | E-GEOD-21874 | biostudies-arrayexpress
TranscriptomicsComprehensive identification of long non-coding RNAs expressed during zebrafish embryogenesis [RNA_seq]
Long non-coding RNAs (lncRNAs) comprise a diverse class of transcripts that structurally resemble mRNAs but do not encode proteins. Recent genome-wide studies in human and mouse have annotated lncRNAs expressed in cell lines and adult tissues, but a systematic analysis of lncRNAs expressed during ve...
ORGANISM(S): Danio rerio 
2011-11-17 | E-GEOD-32898 | biostudies-arrayexpress
UnknownA molecular network of conserved factors keeps ribosomes dormant in the egg
Not available
EMPIAR-11274 | biostudies-other
ProteomicseIF4E1b is a non-canonical eIF4E required for maternal mRNA dormancy
Maternal mRNAs are essential for protein synthesis during oogenesis and early embryogenesis. To adapt translation to specific needs during development, maternal mRNAs are translationally repressed by shortening the polyA tails. While mRNA deadenylation is associated with decapping and degradation in...
ORGANISM(S): Danio rerio (Zebrafish) (Brachydanio rerio) 
2024-04-12 | PXD042434 | Pride
P-bodies / translational regulation / zebrafish 
GenomicsComprehensive identification of long non-coding RNAs expressed during zebrafish embryogenesis [ChIP_Seq]
Long non-coding RNAs (lncRNAs) comprise a diverse class of transcripts that structurally resemble mRNAs but do not encode proteins. Recent genome-wide studies in human and mouse have annotated lncRNAs expressed in cell lines and adult tissues, but a systematic analysis of lncRNAs expressed during ve...
ORGANISM(S): Danio rerio 
2011-11-17 | E-GEOD-32899 | biostudies-arrayexpress
TranscriptomicsA high resolution sequencing and modeling identifies distinct dynamic RNA regulatory strategies
To monitor the relative regulatory contributions of RNA production, processing and degradation, we sampled RNA from mouse DCs every 15 minutes, for the first 3 hours of their response to LPS (13 samples in total), following a short (10 minute) metabolic labeling pulse with 4sU preceding the sampled ...
ORGANISM(S): Mus musculus 
2014-12-16 | E-GEOD-56977 | biostudies-arrayexpress
ProteomicsIdentification of Tmem81 and Izumo1-associated proteins in zebrafish sperm by IP-MS/MS
Supporting MS data for paper (doi: ) by Deneke, Blaha et al (2024), titled “A conserved fertilization complex bridges sperm and egg in vertebrates”. Related to Figure 3B, Figure S4B-C.
ORGANISM(S): Danio rerio (Zebrafish) (Brachydanio rerio) 
2024-10-25 | PXD054632 | Pride
Ip-ms Sperm Zebrafish Fertilization 
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