Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

13 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single-cell RNA-Seq data of zebrafish blood cells

ABSTRACT: 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.

INSTRUMENT(S): Illumina HiSeq 2500, Illumina HiSeq 4000

ORGANISM(S): Danio rerio

SUBMITTER: Emmanouil Athanasiadis

PROVIDER: E-MTAB-5530 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

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

Analysis of single CD41 cell transcriptomes from Zebrafish

Project description:Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes, and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.

2016-01-08 | E-MTAB-3947 | biostudies-arrayexpress

Single-cell RNA sequencing of spleen-derived LCK-expressing cells from adult zebrafish

Project description:Transcriptome data from individual lck:GFP expressing cells isolated from spleens of two adult Zebrafish. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T-cells and NK-like and a minor one of myeloid-like cells. Single cell transcriptomes are matched with FACS index sorting data (GFP, forward and side light scatter and dead cell staining)

2016-11-01 | E-MTAB-4617 | 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

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

Transcriptomic profile 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 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.

2021-12-23 | GSE145564 | GEO

A Novel Perivascular Cell Population in the Zebrafish Brain

Project description:Purpose: RNA-seq analysis from isolated zebrafish fluorescent granular perithelial (FGP) cells in adult brains compared to endothelial cells or entire fish. Method: FGPs and endothelium were isolated by FACS sorting using transgenic line Tg(kdrl:mCherry);Tg(mrc1a:eGFP).

2017-05-15 | GSE97421 | GEO

Single-cell transcriptional analysis reveals ILC-like cells in zebrafish

Project description:Transcriptome data from zebrafish single cells from guts from either from Tg(lck:EGFP) rag1-/-mutant or wild-type zebrafish were isolated and single cell suspensions were prepared as described in protocol section. Three zebrafish, per each condition (i.e. zebrafish intraperitoneally injected with PBS, lyophilised Anisakis simplex or inactivated Vibrio anguillarum), were used to collect the total of 12,000 lck+ cells (4000 per zebrafish) for 10x experiment.

2018-11-16 | E-MTAB-7159 | biostudies-arrayexpress

Differentially expressed genes in zebrafish vascular development

Project description:The goal of this experiment was to identify using tissue specific transgenic zebrafish (Fli:EGFP), genes of interest important for embryonic vascular development. Keywords: time course, GFP cell isolation, zebrafish The experiment contained 6 samples. A18, A24 = total RNA isolated from 18 and 24 hpf zebrafish embryo; B2, C and D2=RNA isolated from GFP positive cells sorted at 18, 24 and 28 hpf respectively from Tg(Fli1:EGFP) embryos; E2 = RNA isolated from GFP positive cells sorted at 18 hpf from Tg(Flk:GRCFP) embryos.

2010-05-22 | E-GEOD-12516 | biostudies-arrayexpress

RNA-SEQ analysis of single cells extracted from the metanephric mesenchyme of Embryonic day 11.5 (E11.5) Crym-EGFP transgenic mice.

Project description:We used micro-dissection with FACS sorting techniques to isolate single cells from the metanephric mesenchyme of the E11.5 developing kidney. A subset of these single cell populations is analysed individually via Fluidigm single cell analysis. This analysis will determine the transcriptional profile of each cell type, identify compartment specific transcripts, compartment specific transcript isoforms and cell-type specific long-noncoding RNAs. In addition the unbiased nature of RNA-SEQ will potentially identify novel transcripts that have not been annotated in the database. Kidneys are harvested from Tg(Crym-EGFP)GF82Gsat mice. Single cells are extracted from E11.5 metanephric mesenchyme using manual micro-dissection techniques. A subset of these cells is analyzed individually via Fluidigm single cell analysis. The long term goal is to generate a transcriptional atlas of the developing kidney.

2014-08-01 | E-GEOD-59129 | biostudies-arrayexpress

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