Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Labelling transcriptional response to dissociation in zebrafish larvae using scSLAMseq

ABSTRACT: Transcriptional response to dissociation is known to cause artefacts in single cell data sets. We used 4sU to label newly made transcripts during dissociation in order to to later remove them from the data set

ORGANISM(S): Danio rerio

PROVIDER: GSE218169 | GEO | 2022/12/20

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Labelling transcriptional response to dissociation using SLAMseq

Project description:Transcriptional response to dissociation is known to cause artefacts in single cell data sets. We used 4sU to label newly made transcripts during dissociation in order to to later remove them from the data set

2022-12-20 | GSE202880 | GEO

Labelling transcriptional response to dissociation in mouse hippocampus using scSLAMseq

2022-12-20 | GSE202783 | GEO

Enzymatic dissociation induces transcriptional and proteotype bias in brain cell populations

Project description:Different cell isolation techniques exist for transcriptomic and proteotype profiling of brain cells. Here, we provide a systematic investigation of the influence of different cell isolation protocols on transcriptional and proteotype profiles in mouse brain tissue by taking into account single-cell transcriptomics of brain cells, proteotypes of microglia and astrocytes, and flow cytometric analysis of microglia. We show that standard enzymatic digestion of brain tissue at 37°C induces profound and consistent alterations in the transcriptome and proteotype of neuronal and glial cells, as compared to an optimized mechanical dissociation protocol at 4°C. These findings emphasize the risk of introducing technical biases and biological artefacts when implementing enzymatic digestion-based isolation methods for brain cell analyses.

2020-10-26 | GSE143796 | GEO

Effects of labelling fetal MSC with MRI Particles: MGIO and Ferucarbotran

Project description:Cell tracking is enabled by incubating ex vivo cells with commercially/clinically available MRI particulate label, such as ferucarbotran. However, the uptake by non-phagocytic cells, such as mesenchymal stem cell (MSC) is poor, and the detection by MRI is impeded. MGIO is a new label that is efficiently taken up by MSC. The proliferation and differentiation capacity of labelled cells are usually assessed to determine cytotoxicity. In this study, we compared the global gene expression profiles of mock-labelled, ferucarbotran-labelled and MGIO-labelled fetal MSC. Experiment Overall Design: Fetal MSC were labelled at passage 5, washed with PBS to remove excess labels, detached by trypsin, pelleted by centrfugation and lysed for RNA extraction with the RNeasy mini kit (Qiagen) in triplicates.

2009-02-08 | E-GEOD-13975 | biostudies-arrayexpress

ACME dissociation: a versatile cell fixation-dissociation method for single-cell transcriptomics

Project description:ACME dissociation: a versatile cell fixation-dissociation method for single-cell transcriptomics

| PRJNA631686 | ENA

ACME dissociation: a versatile cell fixation-dissociation method for single-cell transcriptomics

Project description:ACME dissociation: a versatile cell fixation-dissociation method for single-cell transcriptomics

| PRJNA702503 | ENA

Enzymatic dissociation induces transcriptional and proteotype bias in brain cell populations

Project description:Different cell isolation techniques exist for transcriptomic and proteotype profiling of brain cells. Here we show that standard enzymatic digestion of brain tissue at 37°C induces profound alterations in the transcriptome and proteotype of specific brain cells, as compared to cold mechanical dissociation. These findings emphasize the need to consider intrinsic bias and biological artefacts when implementing enzymatic digestion-based isolation methods for brain cell analyses.

2021-09-08 | PXD015592 | Pride

Hippocampal transcriptomic responses to enzyme‐mediated cellular dissociation

Project description:Single-neuron gene expression studies may be especially important for understanding nervous system structure and function because of the neuron-specific functionality and plasticity that defines functional neural circuits. Cellular dissociation is a prerequisite technical manipulation for single-cell and single cell-population studies, but the extent to which the cellular dissociation process affects neural gene expression has not been determined. This information is necessary for interpreting the results of experimental manipulations that affect neural function such as learning and memory. The goal of this research was to determine the impact of chemical cell dissociation on brain transcriptomes. We compared gene expression of microdissected samples from the dentate gyrus (DG), CA3, and CA1 subfields of the mouse hippocampus either prepared by a standard tissue homogenization protocol or subjected to a chemical cellular dissociation procedure. We report that compared to homogenization, chemical cellular dissociation alters about 350 genes or 2% of the hippocampal transcriptome. While only a few genes canonically implicated in long-term potentiation (LTP) and fear memory change expression levels in response to the dissociation procedure, these data indicate that sample preparation can affect gene expression profiles, which might confound interpretation of results depending on the research question. This study is important for the investigation of any complex tissues as research effort moves from subfield level analysis to single cell analysis of gene expression.

2017-06-15 | GSE99765 | GEO

ACME dissociation: a versatile cell fixation-dissociation method for single-cell transcriptomics

Project description:Single-cell sequencing technologies are revolutionizing biology, but are limited by the need of dissociating fresh samples that can only be fixed at later stages. We present ACME (ACetic-MEthanol) dissociation, a species-versatile cell dissociation approach that fixes cells as they are being dissociated. ACME-dissociated cells have high RNA integrity, can be cryopreserved multiple times, can be sorted by Fluorescence-Activated Cell Sorting (FACS) and are permeable, enabling combinatorial approaches of single-cell transcriptomics. ACME is based on cheap reagents and it can be done in most labs and even sampling trips. As a proof of principle, we have performed SPLiT-seq with ACME cells to obtain around ~35K cells from two planarian species and identified all previously described cell types in similar proportions. This technique allows fixed, dissociated cells to be obtained from diverse organisms that can be cryopreserved and subjected to combinatorial barcoding methods for single-cell transcriptomics and thus will accelerate our knowledge of cell types across the tree of life.

2020-06-03 | GSE150259 | GEO

Effects of labelling fetal MSC with MRI Particles: MGIO and Ferucarbotran

2009-02-01 | GSE13975 | 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