Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptome sequencing of hepatocytes (with or without GFP) during liver development in zebrafish

ABSTRACT: This study presents a comprehensive transcriptomic analysis of hepatocytes and non-hepatocytes during zebrafish liver development at 3 days post-fertilization (dpf), 7 dpf, and adult stages. Utilizing GFP-labeled hepatocytes from Tg(fabp10:GFP) zebrafish, cells were isolated via flow cytometry, followed by RNA sequencing to profile gene expression dynamics. High-quality sequencing data (Q30 > 90%) revealed distinct transcriptional patterns, with hepatocytes at 3 dpf exhibiting significant differences compared to 7 dpf and adult stages. Differential expression analysis identified over 10,000 genes per comparison, highlighting key regulators of liver growth. Functional enrichment analyses (GO and KEGG) underscored the importance of ATP metabolism, DNA replication, and cell cycle pathways, particularly in early developmental stages. Notably, genes such as TFDP1, SKP2, and CCNB1 were consistently differentially expressed across stages, suggesting their pivotal roles in hepatocyte proliferation and liver maturation. These findings provide a foundational resource for understanding the molecular mechanisms driving liver development and regeneration, with potential implications for liver disease research and therapeutic strategies.

ORGANISM(S): Danio rerio

PROVIDER: GSE299042 | GEO | 2026/05/01

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

FACS-Assisted Microarray Profiling Implicates Novel Genes and Pathways in Zebrafish Gastrointestinal Tract Development

Project description:Zebrafish (Danio rerio) gutGFP transgenic embryos [Tg(XlEef1a1:GFP)s854] were collected at 4 time points: 2 days post fertilization (dpf), 3, dpf, 4 dpf, 6 dpf. Embryos were dissociated into single cells and sorted by FACS based on GFP expression. RNA was extracted from the different cell populations (Stratagene), amplified (NuGEN Ovation), and hybridized to Affymetrix Zebrafish GeneChips. Keywords: Time course.

2009-07-10 | GSE12189 | GEO

Transcription profiling of Zebrafish single cell dissected and FACS sorted embryos to investigate gastrointestinal tract development implicates novel genes and pathways

2009-07-19 | E-GEOD-12189 | biostudies-arrayexpress

The CCCH-type zinc finger transcription factor Zc3h8 protects hepatocytes from degeneration by repressing the inflammatory response in zebrafish.

Project description:Transcriptional profile of hepatocytes during the cq5 mutant liver degeneration (middle stage-5.5 dpf, and later stage-7.5 dpf).

2017-12-31 | GSE106985 | GEO

Identification of Strip1-interacting partners in zebrafish head proteome

Project description:Zebrafish embryos expressing GFP-tagged wild type form of Strip1 were used for this study, embryos carrying the GFP-tagged mutant form of Strip1 or GFP only were used as negative controls. Co-immunoprecipitation was performed on 2 dpf head lysates using GFP-trap beads. Samples were prepared for mass spectrometry analysis using trypsin based on-bead digestion protocol.

2022-03-16 | PXD028131 | JPOST Repository

Activating transcription factor 6 is necessary and sufficient for alcoholic fatty liver disease in zebrafish

Project description:ATF6 is a key regulator of the unfolded protein response. Through use of zebrafish and cultured cells we demonstrate that ATF6 drives fatty liver disease by interaction with fatty acid synthase (FASN). Total small RNA from livers of 5 dpf larval zebrafish were collected: 2 batches of Tg(fabp10:nls-mCherry) control larvae, 2 batches of ethanol-treated Tg(fabp10:nls-mCherry) larvae, and 1 batch of Tg(fabp10:nAtf6-cherry; cmlc2:GFP). Each batch was purified for preparation of high-throughput sequencing libraries.

2014-05-01 | E-GEOD-56498 | biostudies-arrayexpress

RaynaNolen_2024_PFOS_Zebrafish_GEMs

Project description:Condition specific zebrafish metabolic models generated using the COBRA MetaboTools framework. The Wang et al., (2021) zebrafish genome-scale metabolic model (GEM) was constrained with experimental data from 5 days post fertilized (dpf) zebrafish to generate a 'base-model'. In turn this 5 dpf zebrafish base-model was constrained with experimental (transcriptomics and metabolomics) data from 5 dpf zebrafish exposed to the environmental pollutant perfluorooctane sulfonate (PFOS), at three levels - Low (0.06 uM), Medium (0.6 uM), and High (2 uM) PFOS. The MetaboTools framework was used to construct three condition-sepcific models: Low, Medium, and High PFOS. Key simulation predictions of effects on the carnitine shuttle and lipid metabolism were confirmed in wild-caught fish and dolphins (stranded animals) sampled from the northern Gulf of Mexico - published in Nolen et al., (2024) https://doi.org/10.1016/j.cbpc.2023.109817

2024-03-04 | MODEL2403010004 | BioModels

Effect of 17 M-NM-2-estradiol on developing zebrafish embryos

Project description:Estrogen signaling is important for vertebrate embryonic development. Here we have used zebrafish (Danio rerio) as a vertebrate model to identify estrogen regulated genes during the first 4 days of development. Zebrafish embryos were exposed to 1 M-BM-5M 17M-NM-2-estradiol from 3 hours post fertilization to 4 days post fertilization, harvested daily and subjected to RNA extraction for transcriptome analysis using microarrays. Estrogen responsive genes were analyzed with hierarchical clustering followed by gene function and tissue expression analysis. Markedly distinct sets of genes were up and down-regulated by estrogen treatment at different time points. Among these genes, only the well-known estrogenic marker vtg1 was co-regulated at all time points. Despite this, the biological functional categories targeted by estrogen were similar throughout zebrafish development. Estrogen responsive genes were enriched mainly in the liver, pancreas and brain. In conclusion, our data shows that in zebrafish distinct cohorts of E2 responsive genes are expressed in a tissue specific manner at different developmental stages. However, the biological pathways that are affected are conserved. 30 embryos were pooled as one sample and exposed to 1 M-NM-<M E2 or vehicle (0.1% DMSO) at approximately 3 hours post fertilization (hpf). At different time points, 1 dpf (24 hpf), 2 dpf (48 hpf), 3 dpf (72 hpf) and 4 dpf (104 hpf), embryos were collected for total RNA extractions. Time points 1 and 2 dpf were performed in biological triplicates of independent pools of RNA while time points 3 and 4 dpf were performed in quadruplicates.

2013-12-31 | E-GEOD-42766 | biostudies-arrayexpress

Zebrafish gonadal transcriptome analysis in response to heat

Project description:High temperature can induce masculinization in many fish species including zebrafish (Ospina-Alvarez & Piferrer PLoS One 3:e2837). Juvenile zebrafish exposed to high temperature during gonad differentiation period will result in male bias adult sex ratio. This experiment compared the zebrafish gonadal transcriptome between fishes that were exposed to high (36 oC) and control (28 oC) temperatures. Gene expression analysis using microarray were performed at juvenile (37 dpf) and adult (90 dpf) stages.

2017-02-13 | GSE51434 | GEO

Transcriptomic profiling of Tg(fabp10a:hUHRF1-EGFP)high zebrafish livers and control siblings at 5 dpf

Project description:Overexpression of high levels of human UHRF1 tagged with EGFP (hUHRF1-EGFP)high in zebrafish hepatocytes induces cellular senescence by 5 days post fertilization (dpf) and hepatocellular carcinoma by 15-20 dpf. The goal of this study is to compare the transcriptome profile of zebrafish livers with (hUHRF1-EGFP)high overexpression compared to WT siblings. RNAseq was performed on RNA extracted from pools of microdissected liveres by using RiboZero libary prep to capture all transcripts, including transposable elements, that are expressed in the livers.

2023-03-21 | GSE227735 | GEO

Systematic proteomics study on the early embryonic development of zebrafish

Project description:Quantitative proteomic data for 10 stages (including 4-cell, 256-cell, 1000-cell, Oblong, Dome, Bud, 16-hpf, 28-hpf, 3-dpf, 5-dpf) of early zebrafish development, each stage corresponds to two sets of biological repeats, and each set of biological repeats corresponds to two sets of technical repeats.

2023-01-10 | PXD039348 |

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