Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcritomic analysis in untreated and sodium arsenite treated (96-120 hours post fertilization hpf) in pooled (12-15) zebrafish larval livers 5 days post fertilization (dpf): wild-type TAB5 compared to as3mt mutant larvae

ABSTRACT: Transcritomic analysis in untreated and sodium arsenite treated (96-120 hours post fertilization hpf) in pooled (12-15) zebrafish larval livers 5 days post fertilization (dpf): wild-type TAB5 compared to as3mt mutant larvae

PROVIDER: PRJNA951412 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR24043269_1.fastq.gz	Fastqsanger.gz
	SRR24043269_2.fastq.gz	Fastqsanger.gz
	SRR24043270_1.fastq.gz	Fastqsanger.gz
	SRR24043270_2.fastq.gz	Fastqsanger.gz
	SRR24043271_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 52

Similar Datasets

Transcritomic analysis in untreated and sodium arsenite treated (96-120 hours post fertilization; hpf) in pooled (12-15) zebrafish larval livers 5 days post fertilization (dpf): wild-type TAB5 compared to as3mt mutant larvae

Project description:This study was carried out to compare the changes in gene expression in 5 dpf zebrafish larval livers in response to mutation of the arsenic methylation gene (as3mt) - 8 bp deletion in exon 3 with and without 1 mM sodium arsenite treatment (96-120 hpf)

2023-05-01 | GSE228752 | GEO

Gene expression analysis in untreated or 1 mM iAs (6-120 hours post fertilization; hpf), pooled (10) whole larvae 5 days post fertilization (dpf): wild-type TAB14 compared to as3mt mutant larvae [whole lavae]

Project description:This study was carried out to compare the changes in gene expression in whole larvae 120 hours post fertilization zebrafish larvae in response to whole body mutation of the arsenic methylation gene (as3mt) - 8 bp deletion in exon 3 with and without 6-120 hpf exposure to 1 mM sodium arsenite (iAs).

2023-05-01 | GSE228753 | GEO

Gene expression analysis in untreated or 1 mM iAs (6-120 hours post fertilization hpf), pooled (10) whole larvae 5 days post fertilization (dpf): wild-type TAB14 compared to as3mt mutant larvae [whole lavae]

Project description:Gene expression analysis in untreated or 1 mM iAs (6-120 hours post fertilization hpf), pooled (10) whole larvae 5 days post fertilization (dpf): wild-type TAB14 compared to as3mt mutant larvae [whole lavae]

| PRJNA951414 | ENA

Exposure of zebrafish larvae to 3g and 5g hyper gravity between 5-6 days post-fertilization.

Project description:The general objective of the study was to determine modulation of gene expression by environmental factors, with a special emphasis on bone formation. For this reason, the specific period of treatment was chosen between 5-6 days post-fertilization (dpf), when bone formation and calcification are taking place. Zebrafish larvae were placed at 5 dpf into a Large Diameter Centrifuge and brought to a gravitational force of 3g or 5g for 24 hours. We show that this treatment causes a clear increase of bone formation, as illustrated by cranial skeleton staining of the bone matrix by Alizarin Red, by morphometric analysis of the resulting images and by gene expression studies of selected genes. Thus, a whole genome micro-array experiment was conducted to identify genes that may be involved in the observed effect on bone formation.

2015-02-27 | E-MTAB-3289 | biostudies-arrayexpress

Determining the effects of hepatic As3mt overexpression on the response to arsenic in the liver of zebrafish larvae

Project description:This study was carried out to compare changes in gene expression in 120 hpf livers that overexpress as3mt in hepatocytes between after 24-hour exposure to 1.0 and 1.5 mM iAs. Tg(fabp10a:As3mt) untreated = CL 1 AS3MT 0; Tg(fabp10a:As3mt) iAs treated = CL 1 AS3MT 1 or CL 1 AS3MT 1.5.

2021-08-31 | GSE156419 | 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

Gene expression profile at single cell level of the enteric nervous system (ENS) of 5 days post fertilization (dpf) zebrafish

Project description:Gene expression profile at single cell level of the enteric nervous system (ENS) of 5 days post fertilization (dpf) zebrafish

| PRJNA936083 | ENA

Analysis of the transcriptome of undifferentiated SH-SY5Y neuroblastoma cells following AS3MT knockout with CRISPR/Cas9.

Project description:Aims/Hypothesis: AS3MT is a risk gene for schizoprhenia and the role in neuronal cell lines has not been established. Using CRISPR/Cas9 generated two AS3MT knockout lines (B6/C6) and age matched wild type controls (D2/D3) in SH-SY5Y neuroblastoma cells and characterised the transcriptional response following knockout. We carried out two independent sequencing runs, including independent cell culturing, RNA extraction, library prep, and sequencing and identify considerable overlap of differentially expressed genes identifying a robust transcriptional response following AS3MT knockout. We identified a number of genes involved in cellular adhesions, ribosomal function, cell-cell contact, and neuronal development, as well as a significant enrichment of previously associated schizophrenia genes, including ZNF80a and DRD2.

2021-10-04 | GSE182157 | GEO

Runx+ HSPC, kdrl+ endothelial, and negative cells sorted from DMSO- or Lycorine-treated 3 dpf zebrafish embryos

Project description:The zebrafish is a powerful model for the study of hematopoietic stem and progenitor cells (HSPC). We have developed a novel HSPC-specific transgenic line (Runx1+23:GFP). We have used this line in time-lapse live imaging studies to track the migration of HSPC during development. We have also performed a chemical genetic screen to find small molecules that modulate HSPC numbers during development. Treating embryos from 2-3 days post fertilization (2-3 dpf) then fixing for in situ staining with HSPC probes cmyb and runx1, we found the compound lycorine increased HSPC numbers. Applying this compound during time-lapse live imaging showed increased accumulation of Runx+ HSPC in the caudal hematopoietic tissue (CHT). Treatment from 2-3 dpf, then washing off the compound, had a sustained effect on the size of the HSPC with Runx+ numbers higher at 5 and 7 dpf. We have performed microarray analysis to elucidate the molecular changes within HSPC and endothelial cells after Lycorine treatment. We treated Runx1+23:GFP;kdrl:DsRed2 embryos from 2-3 dpf with 75 uM lycorine in 1% DMSO. We then dissociated the embryos and sorted the Runx+ GFP cells, the kdrl+ DsRed2 cells, and the non-fluorescent negative cells from the total embryo as a comparator population. Total RNA was amplified and biotin labled for hybridization on Affymetrix microarrays.

2015-01-15 | GSE56015 | GEO

Gene expression profiling of zebrafish embryos at 5 days post fertilization [Agilent Arrays]

Project description:We compared Agilent custom made expression microarrays with Illumina deep sequencing for RNA analysis of zebrafish embryos 5 days post fertilization, showing as expected a high degree of correlation of expression of a common set of 15,927 genes. This microarray study was designed to determine the gene expression profile of zebrafish embryos 5 days post fertilization. We also have compared expression with embryos that were injected with Mycobacterium marinum in the yolk at 2 hours post fertilization. After injections embryos were transferred into fresh egg water and incubated at 28M-BM-0C. 150 embryos of mock-injected embryos or 200 embryos injected with 12 CFU bacteria were snap-frozen in liquid nitrogen, and total RNA was isolated using TRIZOL reagent. The samples were analyzed in a technical duplicate using a dye swap experiment in order to check for dye bias.

2013-08-01 | E-GEOD-44226 | biostudies-arrayexpress

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