Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single-cell RNA sequencing of zebrafish thyroid cells

ABSTRACT: Single-cell RNA sequencing of zebrafish thyroid cells

PROVIDER: PRJNA551501 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR9609653_1.fastq.gz	Fastqsanger.gz
	SRR9609653_2.fastq.gz	Fastqsanger.gz
	SRR9609654_1.fastq.gz	Fastqsanger.gz
	SRR9609654_2.fastq.gz	Fastqsanger.gz

Items per page:

1 - 4 of 4

Similar Datasets

Single-cell RNA sequencing of zebrafish thyroid cells

Project description:The thyroid gland is responsible for supplying the thyroid hormones to the body. The gland is an endocrine organ with an intricate structure enabling production, storage and release of the thyroid hormones. The gland is composed of numerous spherical follicles of varying sizes, surrounded by thyroid follicular epithelial cells, or thyrocytes. The thyrocytes surrounding the follicles generate the thyroid hormones in a multi-step process. Though the machinery responsible for the production of thyroid hormones by thyrocytes is well established, it remains unknown if all the thyrocytes resident in the thyroid gland are equally capable of generating thyroid hormones. In other words, the extent of molecular homogeneity between individual thyrocytes has not yet been investigated. To obtain an unbiased picture into the molecular heterogeneity present in zebrafish thyrocytes, we performed droplet based next-generation sequencing of individual thyrod gland cells. Using unsupervised clustering, we could identify all the major cell types present in the thyroid gland. Moreover, we could define sub-populations within the major cell-types, demonstrating the presence of molecular heterogeneity within nominally homogenous cell-populations.

2019-12-31 | GSE133466 | GEO

Single cell RNA sequencing of normal thyroid

Project description:Single cell RNA sequencing of normal thyroid

| PRJNA756232 | ENA

Single-cell RNA sequencing of zebrafish pancreatic cells

Project description:Single-cell RNA sequencing of zebrafish pancreatic cells

| PRJNA509469 | ENA

Single cell RNA sequencing of normal thyroid

Project description:We performed single-cell RNA-sequencing of 54,762 cells derived from normal thyroid tissue from 7 patients, revealing distinct cell types including epithelial cells, fibroblasts, endothelial cells, smooth muscle cells/pericytes, and various immune cells.

2022-12-28 | GSE182416 | GEO

Single-cell RNA sequencing of lck-GFP transgenic zebrafish

Project description:The present study was conducted in the frame of the EU-funded Graphene Flagship project. The aim is to evaluate the impact of graphene oxide (GO) on the (innate) immune system using zebrafish as a model. We previously performed single-cell RNA-sequencing of germ-free zebrafish embryos exposed to GO plus the microbial metabolite butyrate (BA). Here, we performed a follow up experiment using germ-free lck-GFP transgenic fish in which the zebrafish were exposed to GO plus BA at 5 dpf. The embryos were then dissociated and subsequently sorted on lck and submitted for single-cell RNA-sequencing using 10x Genomics.

2022-07-23 | E-MTAB-11991 | biostudies-arrayexpress

Single-cell RNA sequencing of germ-free zebrafish embryos

Project description:The present study was conducted in the frame of the EU-funded Graphene Flagship project. We previously evaluated the impact of graphene oxide (GO) on the gut microbiome in adult zebrafish by performing 16S rRNA gene sequencing in wild-type versus AhR-deficient zebrafish. Here, we performed single-cell RNA-sequencing (10x Genomics) on whole (dissociated) germ-free (GF) zebrafish embryos exposed at 5 dpf to GO plus the microbial metabolite butyrate to gain insight into the impact on specific cell populations in GF zebrafish.

2022-07-22 | E-MTAB-11984 | biostudies-arrayexpress

Single-cell RNA-Seq of mouse thyroid organoid

Project description:The thyroid gland regulates metabolism and growth via secretion of thyroid hormone by thyroid follicular cells (TFCs). Loss of TFCs, by cellular dysfunction, autoimmune destruction or surgical resection, underlies hypothyroidism. Recovery of thyroid hormone levels by transplantation of mature TFCs derived from stem cells in vitro holds great therapeutic promise. However, the utilization of in vitro derived tissue for regenerative medicine is restricted by the efficiency of differentiation protocols to generate mature organoids. Here, to improve the differentiation efficiency for thyroid organoids, we utilized single-cell RNA-Seq to chart the molecular steps undertaken by individual cells during the in vitro transformation of mouse embryonic stem cells to TFCs. Our single-cell atlas of mouse organoid systematically and comprehensively identifies, for the first time, the cell-types generated during production of thyroid organoids. Using pseudotime analysis, we identify molecular pathways that regulate thyroid maturation in vitro. Our study highlights the potential of single-cell molecular characterization in understanding and improving thyroid maturation, and paves the way for identification of therapeutic targets against thyroid disorders.

2021-05-26 | GSE163818 | GEO

Transcriptional profiling of pax2a-Low and pax2a-High thyroid follicular cells in zebrafish

Project description:Thyroid follicular cells (TFCs) are responsible for generation, storage and release of thyroid hormone. Single-cell analysis of zebrafish thyroid gland demonstrated transcriptional heterogeneity within the TFC population (Gillotay et al., bioRxiv, 2020. doi: 10.1101/2020.01.13.891630. GEO dataset for single-cell RNA-Seq.: GSE133466). Particularly, TFC displayed transcriptional heterogeneity in the expression of pax2a, a transcription factor involved in differentiation and maturation of TFCs. To validate the genetic heterogeneity, we generated a pax2a knock-in line, in which mKO2 expression is driven by endogenous pax2a locus. Using Tg(tg:nls-EGFP); pax2a:mKO2-Knock-in, we sorted for TFCs (GFP+) and separated the pax2a-Low (mKO2-Low) and pax2a-High (mKO2-High) populations for NGS.

2020-06-25 | GSE153197 | GEO

Gene expression profile at single cell level of thyroid cells from thyroid cancer tissues

Project description:We performed single-cell RNA sequencing (scRNA-seq) on 3 normal thyroid, 7 papillary thyroid cancer (PTC), and 5 anaplstic thyroid cancer (ATC) cases. We used scRNA-seq to analyze serirne/glycine metabolism in thyroid tumors.

2023-10-17 | GSE232237 | GEO

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

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