Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptomics analysis of gene expressions of EC and HSPC in zebrafish CHT

ABSTRACT: RNA isolated from sorted cells from zebrafish CHT using HiSeq4000 (Illumina) in paired-read mode.

ORGANISM(S): Danio rerio

PROVIDER: GSE98426 | GEO | 2017/08/20

SECONDARY ACCESSION(S): PRJNA385073

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Transcriptomics analysis of gene expressions and DNA 5mC enrichment levels in control and dnmt1 morphants zebrafish embryos

Project description:RNA and whole-genome DNA were isolated from control and dnmt1 morphants zebrafish cells using the TRIzol (Tiangen) reagent and phenol-chloroform extraction by following the manual, respectively. The cDNA library for RNA-seq and DNA library for MeDIP-seq were sequenced using HiSeq2000 (Illumina) in single-end read and paired-read mode, reapectively.

2017-09-05 | GSE93927 | GEO

Multi-dimensional transcriptome analysis of an intact hematopoietic organ for HSPC expansion [10x]

Project description:To investigate the peculiarity of CHT HSPCs, as well as the interaction of CHT niche and HSPCs at higher resolution, we performed scRNA-seq with zebrafish CHT.

2019-04-23 | GSE120503 | GEO

Transcriptomics analysis of gene expressions, m6A enrichment levels and ythdf2 binding targets in control and mettl3 or ythdf2 morphants zebrafish embryos

Project description:RNA was isolated from control and mettl3 or ythdf2 morphants zebrafish cells using the TRIzol (Invitrogen) reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN (RNA integrity number) of higher than 9. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2500 or HiSeq 3000 (Illumina) in paired-read mode, creating reads with a length of 101 or 151 bp. Sequencing chemistry v2 (Illumina) was used.

2017-09-08 | GSE89655 | GEO

The Caudal Hematopoietic Tissue is Differentially Required for Erythrocytes and Neutrophils from Definitive Hematopoiesis in Zebrafish

Project description:Neutrophils and erythrocytes are vital to the immune system and oxygen transport, respectively. However, the mechanisms by which hematopoietic niches support their development remain incompletely understood. In hematopoiesis research, zebrafish larvae are a common model for studying the development of definitive neutrophils and erythrocytes in the caudal hematopoietic tissue. In this study, we showed that erythrocytes predominantly reside inside the blood vessels of the CHT, while neutrophils stay outside. Ectopic vascular endothelium, induced by Bone Morphogenetic Protein 2b(Bmp2b) overexpression, attracts both cell types, with erythrocytes inside and neutrophils outside. CHT removal has minimal impact on definitive neutrophils from the ventral wall of the dorsal aorta (VDA) but severely affects definitive erythrocytes from the same source. Bulk RNA-sequencing identified epoa as a vital factor for erythrocyte generation within CHT endothelium. Overexpression of epoa through the lyve1b promoter, which is specifically expressed in vein, lymphatic vessels and CHT vein endothelial cells, rescued the erythrocyte reduction in epoa mutants. Our study reveals that the caudal hematopoietic tissue is differentially required for definitive erythrocytes and neutrophils.

2023-11-16 | GSE247730 | GEO

Heterozygous Gata2b versus wildtype Gata2b zebrafish embryo HSPC CD41

Project description:Comparison between wildtype and Gata2b heterozygous zebrafish HSPCs

2023-02-17 | E-MTAB-12577 | biostudies-arrayexpress

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. 18 samples were collected and analyzed. There are 3 biological replicates. There are 3 cell type populations: 1) Runx+ HSPC; 2) kdrl+ endothelial cells; 3) non-fluorescent negative cells. There are cell populations from dissociated Lycorine-treated embryo pools, and control DMSO-treated embryo pools.

2015-01-15 | E-GEOD-56015 | biostudies-arrayexpress

Multi-dimensional transcriptome analysis of an intact hematopoietic organ for HSPC expansion [RNA-seq]

Project description:To decode the complexed mechanism controlling HSC expansion, from the viewpoint of systems biology, we performed spatial transcriptome analysis by dissecting the whole hematopoietic organ, CHT.

2019-04-23 | GSE120509 | GEO

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

2015-01-15 | GSE56015 | GEO

Transcriptome analysis of 6 hours post fertilization mecp2-null versus wild type zebrafish embryos

Project description:RNA sequencing was performed on RNA isolated from groups of 6 hpf wild type and mecp2-null embryos (n=3 biological replicates per condition with 30 embryos pooled per replicate). DESeq2 analysis was performed using https://usegalaxy.org/ Whole embryo mRNA profile of 30 pooled mecp2-null or wild type 6 hpf zebrafish embryos, in triplicate, using the Illumina HiSeq4000 platform

2016-09-01 | E-GEOD-80348 | biostudies-arrayexpress

RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28-20 hours post fertilization

Project description:The goal of this study is to perform RNAseq in different sub-types of the zebrafish embryonic dorsal aorta (DA) at 28-30 hpf using TgBAC(runx1P2:Citrine);Tg(kdrl:mCherry) double-transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit (QIAGEN, Cat No. 74034). High quality RNA (RIN > 8.0) was sent for RNAseq to the Wellcome Trust Centre for Human Genetics (WTCHG). 2.2 ng of total RNA was used to generate SMARTer libraries for low-input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities, trimmed where 20% of the bases were below quality score 20, and filtered to exclude adapters using Trimmomatic (Version 0.32). Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method (version 1.4.5-p1). To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads (QC-passed reads count) has been obtain using Samtools mapping statistics (flagstat tool).

2019-06-06 | GSE132259 | 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