Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Gene expression profiling of adult zebrafish caudal fin and tumor tissues

ABSTRACT: Using Agilent custom made expression microarrays we analyzed the difference of gene expression in caudal fin tissues of wild type fish and transgenic fish that can form melanomas. For this we used a transgenic line with forced expression of V600EBRAF that resulted in melanocyte hyperplasia, while expression of G12VHRAS resulted in malignant melanocyte neoplasia that initially grows radially (RGP) and then vertically (VGP)

ORGANISM(S): Danio rerio

PROVIDER: GSE76791 | GEO | 2016/01/13

SECONDARY ACCESSION(S): PRJNA308592

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Gene expression profiling of adult zebrafish caudal fin and tumor tissues

Project description:Using Agilent custom made expression microarrays we analyzed the difference of gene expression in caudal fin tissues of wild type fish and transgenic fish that can form melanomas. For this we used a transgenic line with forced expression of V600EBRAF that resulted in melanocyte hyperplasia, while expression of G12VHRAS resulted in malignant melanocyte neoplasia that initially grows radially (RGP) and then vertically (VGP) This microarray study was designed to determine the gene expression profile of zebrafish caudal fins in wild type or transgenic animals. Total RNA extracted from 3 pools of 10 caudal fins were used for WT, BRAF and RGP samples, whilst for VGP RNA was extracted from 3 pools of 6 caudal fin tumours.

2016-01-13 | E-GEOD-76791 | biostudies-arrayexpress

Effect of swim-training on caudal fin development in zebrafish larvae

Project description:Genome-wide microarray analysis of the effects of swim-training on caudal fin development in zebrafish larvae. Zebrafish were subjected to swim-training from 5 days post fertilization (dpf) until 10 dpf. Subsequently, we performed a genome-wide microarray analysis on the caudal fins of control and trained fish at 10 dpf. The goal of the project was to investigate the effects of swim-training on the gene expression level during caudal fin development in zebrafish larvae. Two-condition experiment: control vs trained fish. RNA was isolated from pooled caudal fins of 15 control fish (in duplo: pooled control samples (C2 and C3)) and of 15 trained fish (in duplo: pooled trained samples( T2 and T3)). Subsequently, each pooled RNA sample of control and trained caudal fins was labeled with Cy3 and Cy5 in order to correct for dye bias. We included a technical replicate of the labeled C2 and T2 samples.

2014-07-17 | E-GEOD-44395 | biostudies-arrayexpress

Effect of swim-training on caudal fin development in zebrafish larvae

2014-07-17 | GSE44395 | GEO

RNA-seq of proximal, middle, and distal caudal fin tissue of thyroid-ablated zebrafish (hypothyroid, HypoTH) and wild-type zebrafish (euthyroid, EuTH)

Project description:The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal, middle and distal adult fin tissue of hypothyroid zebrafish, with euthyroid sibling fish as control.

2022-04-12 | E-MTAB-9528 | biostudies-arrayexpress

Cellular diversity of the regenerating caudal fin

Project description:single cell transcriptomics of preinjury and regenerating caudal fin tissue revealed cell type consistency and cell-type-specific genetic program during regeneration

2020-08-12 | GSE137971 | GEO

RNA-seq data from adult zebrafish caudal fin regeneration

Project description:Adult zebrafish are able to regenerate many organs such as their caudal fin in only few days post amputation. To explore the landscape and dynamic of the genes involed in regeneration, we performed a global transcriptomic analysis using RNA-seq during zebrafish caudal fin regeneration.

2019-08-13 | GSE112498 | GEO

Small RNA and mRNA expression profiling during zebrafish caudal fin regeneration

Project description:Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors. MicroRNAs are short highly conserved non-coding genes that suppress expression of target genes and thereby control multiple genetic programs. Given their important regulatory roles and evolutionary conservation, we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration. We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing. The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing. Small RNA and mRNA gene expression profiling during 0 and 4 days post amputation.

2016-06-01 | E-GEOD-74415 | biostudies-arrayexpress

Small RNA and mRNA expression profiling during zebrafish caudal fin regeneration

2016-06-01 | GSE74415 | GEO

Zebra fish fin proteome - Proteome profile of zebrafish caudal fin based on one-dimensional gel electrophoresis LCMS/MS and two-dimensional gel electrophoresis MALDI MS/MS analysis

Project description:Fin

2011-05-05 | PRD000300 | Pride

Single-cell RNA sequencing of the cut and uncut caudal fin of zebrafish larvae

Project description:Purpose: The goal of this study was to establish the first detailed cell atlas of the regenerating caudal fin of zebrafish larvae. Intact and regenerating caudal fin were used for single-cell RNA-sequencing with the aim to provide the first integrated model of epimorphic regeneration in zebrafish larvae and demonstrate the diversity of the cells required for blastema formation. Methods: 150 of regenerating caudal fin (cut) and intact caudal fine (uncut) samples were dissociated and loaded into the 10x Genomics Chromium Platform, and sequenced using Illumina NovaSeq 6000. Conclusion: Our study constitutes a resource of the gene expression profile in intact and regenerating caudal fin of zebrafish larvae. We report the application of single-molecule-based sequencing technology for high-throughput profiling of both intact (uncut) and regenerating caudal fin samples (cut) at 24hpA. We confirmed the presence of macrophage subsets, previously described by our group to govern zebrafish fin regeneration, and identified a novel blastemal cell population.

2021-07-17 | GSE158851 | 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