Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

9 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70

ABSTRACT: It has been recently shown that SNRNP70, a major component of the spliceosome, as well as other splicing regulators are found in axons. To investigate the role of SNRNP70 in axons, we generated a zebrafish null mutant and found motor connectivity defects that can be partially rescued upon transgenic overexpression of cytoplasmic-only human SNRNP70 (cyt-hSNRNP70). To understand the molecular function of the cytoplasmic pool of this splicing protein, we performed this RNA-seq experiment with the aim to identify mRNA transcripts whose expression is regulated by the cytoplasmic pool of SNRNP70. To do that, we crossed heterozygous mutant animals that are also positive for the cyt-SNRNP70 transgene. We then split embryos into four groups: (i) sibling, (ii) siblings/cyt-hSNRNP70, (iii) null, (iv) null/cyt-hSNRNP70. Total RNA was extracted from each one of the four groups (three biological replicates per sample) and sequenced.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Danio rerio

SUBMITTER: Nikolas Nikolaou

PROVIDER: E-MTAB-12301 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Gene expression profiling of neurons with Rbfox1 and Rbfox3 knockdown and rescue with cytoplasmic or nuclear Rbfox1 isoform [RNA-seq]

Project description:Human genetic studies have identified the neuronal RNA binding protein, Rbfox1, as a candidate gene for autism spectrum disorders. While Rbfox1 functions as a splicing regulator in the nucleus, it is also alternatively spliced to produce cytoplasmic isoforms. To investigate cytoplasmic Rbfox1, we knocked down Rbfox proteins in mouse neurons and rescued with cytoplasmic or nuclear Rbfox1. Transcriptome profiling showed that nuclear Rbfox1 rescued splicing changes induced by knockdown, whereas cytoplasmic Rbfox1 rescued changes in mRNA levels. iCLIP-seq of subcellular fractions revealed that in nascent RNA Rbfox1 bound predominantly to introns, while cytoplasmic Rbox1 bound to 3' UTRs. Cytoplasmic Rbfox1 binding increased target mRNA stability and translation, and overlapped significantly with miRNA binding sites. Cytoplasmic Rbfox1 target mRNAs were enriched in genes involved in cortical development and autism. Our results uncover a new Rbfox1 regulatory network and highlight the importance of cytoplasmic RNA metabolism to cortical development and disease. In this data set, we included the data from RNA-seq experiments. We performed RNA-seq to profile gene expression and splicing changes. The expression levels of Rbfox1 and Rbfox3 in cultured mouse hippocampal neurons were reduced by siRNAs. The reduction of Rbfox1 and 3 was rescued by expression of cytoplasmic or nuclear Rbfox1 splice isoform. The gene expression and splicing profiles were compared between different treatments. Eight samples were analyzed.

2015-12-10 | E-GEOD-71916 | biostudies-arrayexpress

Expression data from early Zebrafish embryos after knockdown of mir-34

Project description:microRNAs play crucial roles in the early development of an organism. However the regulation of transcription through the action of microRNAs during the initial embyonic development has not been studied. We used microarrays to detail the effect of maternal microRNA mir-34 in regulation of zygotic trancription during the initial stages of Zebrafish embryonic development from one cell stage through the maternal-zygotic transition up to 24 hours post fertilization. Zebrafish embryos were selected at specific stages of early embryonic development (1, 7, and 24 hours post fertilization). RNA was extracted and hybridized to Affymetrix microarrays. The embryos were injected with anti-microRNA LNA and were kept for constant monitoring for the indicated time points. A mockLNA was injected as a control. The embryos were visualized for any visible developmental abnormalities.

2013-04-03 | E-GEOD-32360 | biostudies-arrayexpress

Gene expression profiling of neurons with Rbfox1 and Rbfox3 knockdown and rescue with cytoplasmic or nuclear Rbfox1 isoform [RNA-seq]

2015-12-10 | GSE71916 | GEO

Free circular introns with an unusual branchpoint in neuronal projections

Project description:In eukaryotic cells, most introns are degraded soon after splicing in the nucleus but some persist either due to lack of splicing (detained/retained introns) or because they contain important functional elements, for example, sno/scaRNAs. Few introns are detectable outside the nucleus. To hunt for interesting new phenomena in cytoplasmic introns and splicing, we conducted a multimodal study of total RNA within projections (axons, dendrites, glial projections) of rat hippocampal neurons and discovered a class of free circular introns enriched in distal projections.

2019-04-18 | GSE129924 | GEO

The polyA+ transcriptomes of mouse embryonic stem cells and their derived neural precursors from strand-specific RNA-Seq

2012-08-01 | GSE38990 | GEO

The polyA+ transcriptomes of mouse embryonic stem cells and their derived neural precursors from strand-specific RNA-Seq

Project description:We have examined the nuclear (nuc) and cytoplasmic (cyt) polyA+ transcriptomes of undifferentiated mouse embryonic stem cells (un) and cells differentiated to neural precursors (d5) using strand-specific RNA-Seq. The 46C mouse embryonic stem cell line was used for this study. Two cell types were examined: undifferentiated mouse embryonic stem cells (un) and cells differentiated to neural precursors (d5). For each cell type, cells were fractionated to nuclear and cytoplasmic components. RNAs were extracted from each component and were fragmented enzymatically for library construction. For each cell type and component, strand-specific RNA-Seq libraries were generated using at least two different fragmentation protocols.

2012-08-01 | E-GEOD-38990 | biostudies-arrayexpress

RNA-seq of sfpq-/- zebrafish embryos and siblings at 24 hpf

Project description:RNA was extracted from whole zebrafish embryos at 24 hpf to examine changes in gene expression and splicing in sfpq null mutants

2021-01-27 | E-MTAB-9113 | biostudies-arrayexpress

U2AF1 plays a critical role in global co-transcriptional splicing (Fraction chrRNA-seq)

Project description:In order to measure the impact of U2AF1 on co-transcriptional splicing, we treated HeLa cells with control siRNA or U2AF1 siRNA. To measure co-transcriptional splicing, we fractionated HeLa cells into cytosolic (Cyt), nucleoplasm (NP), and chromatin/particle (Chr) fractions. We purified total RNA from Chr compartment, spiked in with in vitro transcribed EGFP and FireFly luciferase RNA for data normalization, depleted ribosomal RNAs, and constructed two independent libraries for RNA-seq.

2023-05-27 | GSE175671 | GEO

Rpb9 plays a critical role in global co-transcriptional splicing in mouse ESC (Fraction chrRNA-seq)

Project description:To define the function of Rpb9 on co-transcriptional splicing, we used auxin-inducible Rpb9 degron system in mouse embryonic stem cells (mESCs) with auxin treatment for 3 hours to sufficiently deplete Rpb9. To measure co-transcriptional splicing, we fractionated mESCs cells (spiked in with Drosophila S2 cells for data normalization) into cytosolic (Cyt), nucleoplasm (NP), and chromatin/particle (Chr) fractions. We purified total RNA from Chr compartment, depleted ribosomal RNAs, and constructed two independent libraries for RNA-seq, which showed excellent reproducibility.

2023-05-27 | GSE175670 | GEO

Rpb9 plays a critical role in global co-transcriptional splicing (Fraction RNA-seq)

Project description:In order to measure the impact of Rpb9 on co-transcriptional splicing, we treated HeLa cells with control siRNA or siRpb9, and for comparative analysis, we also depleted Rpb1 and confirmed by Western blotting the knockdown efficiency in all cases. To measure co-transcriptional splicing, we fractionated HeLa cells into cytosolic (Cyt), nucleoplasm (NP), and chromatin/particle (Chr) fractions. We purified total RNA from each compartment, spiked in with in vitro transcribed EGFP and FireFly luciferase RNA for data normalization, depleted ribosomal RNAs, and constructed two independent libraries for RNA-seq, which showed excellent reproducibility .

2023-11-15 | GSE162235 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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