Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptomic profile of zebrafish liver cells in thioacetamide (TAA) model

ABSTRACT: Zebrafish transgenic lines Tg(fabp10a:dsRed), Tg(hand2:EGFP) and Tg(kdrl:ras-mCherry) in AB wild-type background were anesthetized with MS-222 and adult females were injected intraperitoneally with 500 mg/kg thioacetamide (TAA) or sterile water as a control 6 times over the course of 2 weeks. We have characterized transcriptomic profiles of FACS-isolated hepatocytes (dsRed+), stellate cells (EGFP+) and liver endothelial cells (mCherry+) from fishes treated with TAA or sterile water. Cells negative for the fluorescence were used as a control.

ORGANISM(S): Danio rerio

PROVIDER: GSE145564 | GEO | 2021/12/23

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Genome-wide chromatin accessibility profiles of zebrafish liver cells in thioacetamide (TAA) model

Project description:Zebrafish transgenic lines Tg(fabp10a:dsRed), Tg(hand2:EGFP) and Tg(kdrl:ras-mCherry) in AB wild-type background were anesthetized with MS-222 and adult females were injected intraperitoneally with 500 mg/kg thioacetamide (TAA) or sterile water as a control 6 times over the course of 2 weeks. We have characterized chromatin accessibility profiles of FACS-isolated hepatocytes (dsRed+), stellate cells (EGFP+) and liver endothelial cells (mCherry+) from fishes treated with TAA or sterile water. Cells negative for the fluorescence were used as a control.

2021-12-23 | GSE145563 | GEO

Single-cell transcriptional analysis reveals innate lymphoid cell (ILC)-like cells in zebrafish

Project description:Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tg(cd4-1:mCherry), Tg(lck:EGFP), Tg(mhc2dab:GFP, cd45:dsRed), AB.

2018-11-16 | E-MTAB-7117 | biostudies-arrayexpress

Zebrafish (Danio rerio) Schwann cell, oligodendrocyte lineage, and neuron RNA-sequencing

Project description:RNA-sequencing of cells collected from 72 hpf embryos: Schwann cells (Gt(foxd3:mCherry);Tg(sox10:mEGFP)), oligodendrocyte lineage cells (Tg(olig2:dsred);Tg(sox10:megfp)), and neurons (Tg(nbt:dsred))

2021-05-15 | GSE174486 | GEO

A time-course study of thioacetamide (TAA)-induced liver fibrosis in rats

Project description:The aim is to characterize rat liver fibrosis induced by thioacetamide (TAA). To induce hepatic fibrosis, Male Sprague Dawley rats (9-12 weeks of age and 380-420 g of weight upon arrival, supplied by Beijing Vital River laboratory animal Co., Ltd.) were treated with thioacetamide (TAA). Rat liver samples were collected from five groups of rats at week 1, 2, 4, 8 and 13 after TAA (300 mg/kg) administration three times per week while five control groups receive the same volume of 0.9% normal saline. Four biological replicates were used for each group.

2021-09-29 | E-MTAB-10547 | biostudies-arrayexpress

Single-cell RNA-Seq data of zebrafish blood cells

Project description:Transcriptome data from zebrafish single and bulk cells from blood and testes. Blood cells were collected from adult Tg(cd4:mCherry), Tg(cd41:EGFP), Tg(gata1a:GFP), Tg(lyz:DsRed2), Tg(mfap4:tdTomato), Tg(mpx:EGFP), Tg(runx1:mCherry), Tg(tal1:EGFP) and Tubingen Long Fin wild type fish.

2017-11-17 | E-MTAB-5530 | biostudies-arrayexpress

Endothelial Brg1-Notch Signaling Regulates Zebrafish Heart Regeneration

Project description:The goal of this study is to compare the NGS-derived heart transcriptome profiling (RNA-seq) between kdrl GFP positive endothelial cells of 4-HT induced Tg(ubi:loxp-DsRed-stop-loxp-DN-xBrg1; kdrl:CreER; kdrl:eGFP) (DNK) and Tg(ubi:loxp-DsRed-stop-loxp-DN-xBrg1; kdrl:eGFP) (CtrlK) injured hearts.

2022-07-09 | GSE154193 | GEO

Comparing the genome-wide chromatin accessibility of uhrf1 hi272 mutants and phenotypically wildtype whole zebrafish embryos at 120 hpf using ATAC-Seq.

Project description:The goal of this study is to study the chromatin accessibility differences between control and uhrf1 hi272 mutant 120 hpf zebrafish embryos (uhrf1 hi272+/-, Tg(fabp10a:CAAX-EGFP) using ATAC-Seq technique.

2020-06-23 | GSE151293 | GEO

Effect of endothelial specific inhibition of Brg1 on gene expression during zebrafish heart regeneration [RNA-seq]

Project description:To decipher the molecular action of endothelial Brg1 in the regulation of zebrafish heart regeneration, we applied Tg(kdrl:eGFP) to label cardiac endothelial cells including the endocardium, and achieved endothelium-specific over-expression of DN-xBrg1 by using the compound zebrafish line consisting of Tg(ubi:loxp-DsRed-STOP-loxp-DN-xBrg1; kdrl:CreER; kdrl:eGFP) (defined as DNK), while we used Tg(ubi:loxp-DsRed-STOP-loxp-DN-xBrg1; kdrl-eGFP) as control (CtrlK) in the presence of 4-HT starting at 3 days before ventricular resection. The kdrl:eGFP endothelial cells, which were sorted by FACS (fluorescence-activated cell sorting) from CtrlK and DNK hearts at 7 dpa, were subjected to RNA-seq analysis.

2023-04-03 | GSE200936 | GEO

Expression profiles of zebrafish transgenic line Tg(fabp10a:def)-I

Project description:We previously reported that Def (Digestive-organ expansion factor) was a pan-endodermal enriched factor that is essential for the growth of digestive organs in zebrafish using a def mutant line hi429 as model (Chen et al., 2005). To further elucidate Def function, we generated a Def over-expressed zebrafish line, namely Tg (fabp10a:def)-I, in which def expression was under the control of a liver-specific promoter fabp10a. We used microarrays to detail the global programme of gene expression in Tg (fabp10a:def)-I transgenic line compared with wild type zebrafish control, and identified distinct classes of differently regulated genes in Tg (fabp10a:def)-I line. Total RNA from the adult livers of three independent batches of 3-month-old Tg(fabp10a:def)-I and wild type (AB strain) male fish was extracted using TRIzol (Invitrogen), each batch with the liver samples from three fish mixed together. The samples were subjected to microarray hybridization and the data were generated for further analysis.

2013-02-28 | E-GEOD-41059 | biostudies-arrayexpress

Localized EMT reprograms glial progenitors to promote spinal cord repair [bulk RNA-seq]

Project description:mCherry/EGFP double positive cells were isolated from the spinal cords of Tg(ctgfa:mCherry; gfap:EGFP) zebrafish at 5 days post injury. Bulk spinal cord tissue at 5, 10, and 21 days post-injury were also sequenced.

2021-01-31 | GSE164943 | 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