Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Protocol for Dissection and Dissociation of Zebrafish Telencephalon for Single-Cell Sequencing.

ABSTRACT: Single-cell sequencing (sc-Seq) is a powerful tool to investigate the molecular signatures of cell types in a complex mixture of cells. A critical step in sc-Seq is preparing a single-cell suspension with a high number of viable cells. Here, we show how to dissect zebrafish telencephalon and how to dissociate it into a single-cell suspension. This is followed by flow cytometry-based sorting to enrich for neural progenitor stem cells. Our technique typically yields 70,000 live cells from one zebrafish telencephalon. For complete details on the use and execution of this protocol, please refer to Cosacak et al. (2019).

SUBMITTER: Cosacak MI

PROVIDER: S-EPMC7263268 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Protocol for Dissection and Dissociation of Zebrafish Telencephalon for Single-Cell Sequencing.

Cosacak Mehmet Ilyas MI Bhattarai Prabesh P Kizil Caghan C

STAR protocols 20200529 1

Single-cell sequencing (sc-Seq) is a powerful tool to investigate the molecular signatures of cell types in a complex mixture of cells. A critical step in sc-Seq is preparing a single-cell suspension with a high number of viable cells. Here, we show how to dissect zebrafish telencephalon and how to dissociate it into a single-cell suspension. This is followed by flow cytometry-based sorting to enrich for neural progenitor stem cells. Our technique typically yields 70,000 live cells from one zebr ...[more]

PMID: 32835293

Similar Datasets

A single-cell transcriptome atlas of the maturing zebrafish telencephalon.

Project description:The zebrafish telencephalon is composed of highly specialized subregions that regulate complex behaviors such as learning, memory, and social interactions. The transcriptional signatures of the neuronal cell types in the telencephalon and the timeline of their emergence from larva to adult remain largely undescribed. Using an integrated analysis of single-cell transcriptomes of approximately 64,000 cells obtained from 6-day-postfertilization (dpf), 15-dpf, and adult telencephalon, we delineated nine main neuronal cell types in the pallium and eight in the subpallium and nominated novel marker genes. Comparing zebrafish and mouse neuronal cell types revealed both conserved and absent types and marker genes. Mapping of cell types onto a spatial larval reference atlas created a resource for anatomical and functional studies. Using this multiage approach, we discovered that although most neuronal subtypes are established early in the 6-dpf fish, some emerge or expand in number later in development. Analyzing the samples from each age separately revealed further complexity in the data, including several cell types that expand substantially in the adult forebrain and do not form clusters at the larval stages. Together, our work provides a comprehensive transcriptional analysis of the cell types in the zebrafish telencephalon and a resource for dissecting its development and function.

| S-EPMC10234298 | biostudies-literature

Single-cell sequencing of 12 months old zebrafish telencephalon

Project description:Zebfrafish brains were injected with neutral cell tracking dye. Zebrafish telencephalon were dissociated and dye postive cells were sorted by FACS and single-cell sequencing performed from these cells.

2021-09-23 | GSE161834 | GEO

Single-cell sequencing of 12 months old zebrafish telencephalon

Project description:Single-cell sequencing of 12 months old zebrafish telencephalon

| PRJNA679600 | ENA

Enrichment and single-cell sequencing of the ventricular cells from zebrafish telencephalon

2022-06-24 | GSE186874 | GEO

An Optimized Tissue Dissociation Protocol for Single-Cell RNA Sequencing Analysis of Fresh and Cultured Human Skin Biopsies.

Project description:We present an optimized dissociation protocol for preparing high-quality skin cell suspensions for in-depth single-cell RNA-sequencing (scRNA-seq) analysis of fresh and cultured human skin. Our protocol enabled the isolation of a consistently high number of highly viable skin cells from small freshly dissociated punch skin biopsies, which we use for scRNA-seq studies. We recapitulated not only the main cell populations of existing single-cell skin atlases, but also identified rare cell populations, such as mast cells. Furthermore, we effectively isolated highly viable single cells from ex vivo cultured skin biopsy fragments and generated a global single-cell map of the explanted human skin. The quality metrics of the generated scRNA-seq datasets were comparable between freshly dissociated and cultured skin. Overall, by enabling efficient cell isolation and comprehensive cell mapping, our skin dissociation-scRNA-seq workflow can greatly facilitate scRNA-seq discoveries across diverse human skin pathologies and ex vivo skin explant experimentations.

| S-EPMC9096112 | biostudies-literature

A single-cell transcriptome atlas of the zebrafish telencephalon

Project description:Wild-type zebrafish telencephalon single-cell RNA-sequencing from 6 dpf, 15 dpf, and adult.

2022-09-02 | GSE212314 | GEO

Dissection of Influenza Infection In Vivo by Single-Cell RNA Sequencing.

Project description:The influenza virus is a major cause of morbidity and mortality worldwide. Yet, both the impact of intracellular viral replication and the variation in host response across different cell types remain uncharacterized. Here we used single-cell RNA sequencing to investigate the heterogeneity in the response of lung tissue cells to in vivo influenza infection. Analysis of viral and host transcriptomes in the same single cell enabled us to resolve the cellular heterogeneity of bystander (exposed but uninfected) as compared with infected cells. We reveal that all major immune and non-immune cell types manifest substantial fractions of infected cells, albeit at low viral transcriptome loads relative to epithelial cells. We show that all cell types respond primarily with a robust generic transcriptional response, and we demonstrate novel markers specific for influenza-infected as opposed to bystander cells. These findings open new avenues for targeted therapy aimed exclusively at infected cells.

| S-EPMC7185763 | biostudies-literature

Transcriptomic profile of early zebrafish PGCs by single cell sequencing.

Project description:Single cell RNA-seq is a powerful and sensitive way to capture the genome-wide gene expression. Here, single cell RNA-seq was utilized to study the transcriptomic profile of early zebrafish PGCs (primordial germ cells) at three different developmental stages. The three stages were 6, 11 and 24 hpf (hours post fertilization). For each developmental stage, three zebrafish PGCs from one embryo were collected, and 9 samples in total were used in this experiment. Single cell RNA-seq results showed that 5099-7376 genes were detected among the 9 samples, and the number of expressed genes decreased as development progressed. Based on the gene expression pattern, samples from 6 and 11 hpf clustered closely, while samples from 24 hpf were more dispersed. By WGCNA (weighted gene co-expression network analysis), the two biggest modules that had inverse gene expression patterns were found to be related to PGC formation or migration. Functional enrichment analysis for these two modules showed that PGCs mainly conducted migration and cell division in early development (6/11 hpf) and translation activity became active in late development (24 hpf). Differentially expressed gene analyses showed that more genes were downregulated than upregulated between two adjacent stages, and genes related to PGC formation or migration reported by previous studies decreased significantly from 11 to 24 hpf. Our results provide base knowledge about zebrafish PGC development at the single cell level and can be further studied by other researchers interested in biological development.

| S-EPMC6693734 | biostudies-literature

Dissociation of microdissected mouse brain tissue for artifact free single-cell RNA sequencing.

Project description:Single-cell RNA sequencing (scRNA-seq) provides the transcriptome of individual cells and addresses previously intractable problems including the central nervous system's transcriptional responses during health and disease. However, dissociating brain cells is challenging and induces artificial transcriptional responses. Here, we describe an enzymatic dissociation method for mouse brain that prevents dissociation artifacts and lowers technical variations with standardized steps. We tested this protocol on microdissected brain tissue of 3-week- to 24-month-old mice and obtained high-quality scRNA-seq results. For complete details on the use and execution of this protocol, please refer to Safaiyan et al. (2021).

| S-EPMC8196224 | biostudies-literature

Molecular organization of neuronal cell types and neuromodulatory systems in the zebrafish telencephalon.

Project description:The function of neuronal networks is determined not only by synaptic connectivity but also by neuromodulatory systems that broadcast information via distributed connections and volume transmission. To understand the molecular constraints that organize neuromodulatory signaling in the telencephalon of adult zebrafish, we used transcriptomics and additional approaches to delineate cell types, to determine their phylogenetic conservation, and to map the expression of marker genes at high granularity. The combinatorial expression of GPCRs and cell-type markers indicates that all neuronal cell types are subject to modulation by multiple monoaminergic systems and distinct combinations of neuropeptides. Individual cell types were associated with multiple (typically >30) neuromodulatory signaling networks but expressed only a few diagnostic GPCRs at high levels, suggesting that different neuromodulatory systems act in combination, albeit with unequal weights. These results provide a detailed map of cell types and brain areas in the zebrafish telencephalon, identify core components of neuromodulatory networks, highlight the cell-type specificity of neuropeptides and GPCRs, and begin to decipher the logic of combinatorial neuromodulation.

| S-EPMC10808507 | biostudies-literature

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