Browse
Submit Data
Databases
API
Help

Dataset Information

31 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Protocol for whole-brain immunostaining of the turquoise killifish after tissue clearing.

ABSTRACT: Distribution of cells and proteins in whole organs, such as the brain, can provide another level of insight into molecular and cellular functions. Here, we describe a whole-brain immunostaining method using the turquoise killifish, an emerging model for aging research. We optimized a protocol for tissue clearing and whole-brain immunostaining to the turquoise killifish brain. This protocol provides a comprehensive procedure from brain dissection to whole-brain imaging and image processing. For complete details on the use and execution of this protocol, please refer to Eunjeong Do (2020) and Lee et al. (2021).

SUBMITTER: Lee S

PROVIDER: S-EPMC8176364 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Determining glioma cell invasion and proliferation in ex vivo organotypic mouse brain slices using whole-mount immunostaining and tissue clearing.

Project description:The ex vivo organotypic brain slice invasion model is commonly used to study the growth dynamics of gliomas, primary brain tumors that are known for their invasive behavior. Here, we describe a protocol where the ex vivo organotypic mouse brain slice invasion model is combined with whole-mount immunostaining, tissue clearing, and 3D reconstruction, to visualize and quantify the invasion of glioma cells. In addition, we describe an approach to determine the proliferation rate of the cells within this model. For complete details on the use and execution of this protocol, please refer to Uceda-Castro et al. (2022).

| S-EPMC9508478 | biostudies-literature

Transcriptomes of aging brain, heart, muscle, and spleen from female and male African turquoise killifish.

Project description:The African turquoise killifish is an emerging vertebrate model organism with great potential for aging research due to its naturally short lifespan. Thus far, turquoise killifish aging 'omic' studies have examined a single organ, single sex and/or evaluated samples from non-reference strains. Here, we describe a resource dataset of ribosomal RNA-depleted RNA-seq libraries generated from the brain, heart, muscle, and spleen from both sexes, as well as young and old animals, in the reference GRZ turquoise killifish strain. We provide basic quality control steps and demonstrate the utility of our dataset by performing differential gene expression and gene ontology analyses by age and sex. Importantly, we show that age has a greater impact than sex on transcriptional landscapes across probed tissues. Finally, we confirm transcription of transposable elements (TEs), which are highly abundant and increase in expression with age in brain tissue. This dataset will be a useful resource for exploring gene and TE expression as a function of both age and sex in a powerful naturally short-lived vertebrate model.

| S-EPMC10570339 | biostudies-literature

Modified CLARITY Achieving Faster and Better Intact Mouse Brain Clearing and Immunostaining.

Project description:CLARITY is a hydrogel embedding clearing method that has the advantages of transparency, different tissue compatibility and immunostaining compatibility. However, there are also some limitations to CLARITY as it requires a long time to achieve transparency, and the electrophoresis clearing is complex. Therefore, we aimed to simplify the electrophoresis system and shorten the processing time of CLARITY. In our study, we developed a non-circulation electrophoresis system to achieve easier manipulation of electrophoresis clearing. We modified the original CLARITY protocol in hydrogel embedding methods, clearing buffer and immunostaining. When comparing brains processed by our modified method or the original protocol, we found our modifications permit faster and more efficient clearing and labeling. Moreover, we developed a new clearing method named Passive pRe-Electrophroresis CLARITY (PRE-CLARITY) and a new immunostaining method named Centrifugation-Expansion staining (CEx staining). PRE-CLARITY achieved faster clearing and higher transparency, and CEx staining accomplished intact mouse brain labeling faster. With our modifications to CLARITY, we accomplished intact mouse brain clearing and immunostaining within one week, while this requires weeks to months with the original CLARITY. Our studies would allow high-content tracing and analysis of intact brain or other large-scale samples in a short time.

| S-EPMC6646319 | biostudies-literature

A clearing-free protocol for imaging intact whole adipose tissue innervation in mice.

Project description:Here we provide a clearing-free protocol for processing intact, whole mount subcutaneous white adipose tissue (scWAT) for immunofluorescence as an alternative to current clearing-based approaches. We use a combination of Z-depth reduction and autofluorescence quenching techniques to fluorescently label, image, and quantify adipose tissue innervation effectively throughout intact mouse tissues without the need for optical clearing or light sheet microscopy. This protocol has been optimized and validated for adipose neurovascular labeling. For complete details on the use and execution of this protocol, please refer to Willows et al. (2021).

| S-EPMC8784403 | biostudies-literature

Whole-Brain Analysis of Cells and Circuits by Tissue Clearing and Light-Sheet Microscopy.

Project description:In this photo essay, we present a sampling of technologies from laboratories at the forefront of whole-brain clearing and imaging for high-resolution analysis of cell populations and neuronal circuits. The data presented here were provided for the eponymous Mini-Symposium presented at the Society for Neuroscience's 2018 annual meeting.

| S-EPMC6706004 | biostudies-literature

Project description:Age-related vision loss caused by retinal neurodegenerative pathologies is becoming more prevalent in our ageing society. To understand the physiological and molecular impact of ageing on retinal homeostasis, we used the short-lived African turquoise killifish, a model known to naturally develop central nervous system (CNS) ageing hallmarks and vision loss. Bulk and single-cell RNA-sequencing (scRNAseq) of three age groups (6-, 12-, and 18-week-old) identified transcriptional ageing fingerprints in the killifish retina, unveiling pathways also identified in the aged brain, including oxidative stress, gliosis, and inflammageing. These findings were comparable to observations in the ageing mouse retina. Additionally, transcriptional changes in genes related to retinal diseases, such as glaucoma and age-related macular degeneration, were observed. The cellular heterogeneity in the killifish retina was characterized, confirming the presence of all typical vertebrate retinal cell types. Data integration from age-matched samples between the bulk and scRNAseq experiments revealed a loss of cellular specificity in gene expression upon ageing, suggesting potential disruption in transcriptional homeostasis. Differential expression analysis within the identified cell types highlighted the role of glial/immune cells as important stress regulators during ageing. Our work emphasizes the value of the fast-ageing killifish in elucidating molecular signatures in age-associated retinal disease and vision decline. This study contributes to the understanding of how age-related changes in molecular pathways may impact CNS health, providing insights that may inform future therapeutic strategies for age-related pathologies.

| S-EPMC11320354 | biostudies-literature

Project description:Age-related vision loss caused by retinal neurodegenerative pathologies is becoming more prevalent in our ageing society. To understand the physiological and molecular impact of ageing on retinal homeostasis, we used the short-lived African turquoise killifish, a model known to naturally develop central nervous system (CNS) ageing hallmarks and vision loss. Bulk and single-cell RNA-sequencing (scRNA-seq) of three age groups (6-, 12-, and 18-week-old) identified transcriptional ageing fingerprints in the killifish retina, unveiling pathways also identified in the aged brain, including oxidative stress, gliosis, and inflammageing. These findings were comparable to observations in ageing mouse retina. Additionally, transcriptional changes in genes related to retinal diseases, such as glaucoma and age-related macular degeneration, were observed. The cellular heterogeneity in the killifish retina was characterised, confirming the presence of all typical vertebrate retinal cell types. Data integration from age-matched samples between the bulk and scRNA-seq experiments revealed a loss of cellular specificity in gene expression upon ageing, suggesting potential disruption in transcriptional homeostasis. Differential expression analysis within the identified cell types highlighted the role of glial/immune cells as important stress regulators during ageing. Our work emphasises the value of the fast-ageing killifish in elucidating molecular signatures in age-associated retinal disease and vision decline. This study contributes to the understanding of how age-related changes in molecular pathways may impact CNS health, providing insights that may inform future therapeutic strategies for age-related pathologies.

| S-EPMC10979842 | biostudies-literature

Intranuclear immunostaining-based FACS protocol from embryonic cortical tissue.

Project description:Cell sorting can be used to purify cell populations for cell type-specific molecular probing. Fluorescence-activated cell sorting (FACS) coupled with high-throughput sequencing affords molecular signature identification for specific cell types. FACS has many challenges that limit comprehensive cell purification from the brain, leading to incomplete molecular characterization. Here, we present the intranuclear immunostaining-based FACS protocol with several modified steps, which allows optimized nuclei/cell sorting from mouse or human embryonic cortical tissue for distinct downstream molecular investigation of basal intermediate progenitors.

| S-EPMC7859298 | biostudies-literature

Widespread sex dimorphism across single-cell transcriptomes of adult African turquoise killifish tissues.

Project description:The African turquoise killifish (Nothobranchius furzeri), the shortest-lived vertebrate that can be bred in captivity, is an emerging model organism for aging research. Here, we describe a multitissue, single-cell gene expression atlas of female and male blood, kidney, liver, and spleen. We annotate 22 cell types, define marker genes, and infer differentiation trajectories. We find pervasive sex-dimorphic gene expression across cell types. Sex-dimorphic genes tend to be linked to lipid metabolism, consistent with clear differences in lipid storage in female vs. male turquoise killifish livers. We use machine learning to predict sex using single-cell gene expression and identify potential markers for molecular sex identity. As a proof of principle, we show that our atlas can be used to deconvolute existing bulk RNA sequencing (RNA-seq) data to obtain accurate estimates of cell type proportions. This atlas can be a resource to the community that could be leveraged to develop cell-type-specific expression in transgenic animals.

| S-EPMC10842523 | biostudies-literature

Circular RNAs in the ageing African turquoise killifish

Project description:In this work we took 9 samples from brain and 6 samples from muscle of the African turquoise killifish (Nothobranchius furzeri) at 3.5, 8.5 and 14 weeks. Total RNA was sequenced and circRNAs were detected.

2019-07-31 | GSE134065 | GEO

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