Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

FixNCut: Single-cell genomics through reversible tissue fixation and dissociation

ABSTRACT: The use of single-cell technologies for clinical applications requires disconnecting sampling from downstream processing steps. Early sample preservation can further increase robustness and reproducibility by avoiding artifacts introduced during specimen handling. We present FixNCut, a methodology for the reversible fixation of tissue followed by dissociation that overcomes current limitations. We applied FixNCut to human and mouse tissues to demonstrate the preservation of RNA integrity, sequencing library complexity, and cellular composition, while diminishing stress-related artifacts. Besides single-cell RNA sequencing, FixNCut is compatible with multiple single-cell and spatial technologies, making it a versatile tool for robust and flexible study designs.

ORGANISM(S): Mus musculus Homo sapiens

PROVIDER: GSE229944 | GEO | 2024/03/11

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

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

FixNCut: Single-cell genomics through reversible tissue fixation and dissociation

Project description:FixNCut: Single-cell genomics through reversible tissue fixation and dissociation

| PRJNA956865 | ENA

FixNCut: single-cell genomics through reversible tissue fixation and dissociation.

Project description:The use of single-cell technologies for clinical applications requires disconnecting sampling from downstream processing steps. Early sample preservation can further increase robustness and reproducibility by avoiding artifacts introduced during specimen handling. We present FixNCut, a methodology for the reversible fixation of tissue followed by dissociation that overcomes current limitations. We applied FixNCut to human and mouse tissues to demonstrate the preservation of RNA integrity, sequencing library complexity, and cellular composition, while diminishing stress-related artifacts. Besides single-cell RNA sequencing, FixNCut is compatible with multiple single-cell and spatial technologies, making it a versatile tool for robust and flexible study designs.

| S-EPMC10979608 | biostudies-literature

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

Project description:We performed single-cell transcriptome analysis (using 10x genomics 3' scRNA-seq v3.1 chemistry) in the sea anemone Nematostella vectensis (Cnidaria).

2021-04-01 | GSE166977 | GEO

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

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

RNA-seq of human head and neck squamous cell carcinoma (HNSCC) to compare different tissue dissociation methods [bulkRNA]

Project description:Tissue dissociation, mechanical and/or enzymatic, is a method of disaggregating 3D connective tissue to release cells for downstream single cell analysis. Without proper controls for tissue dissociation experiments, potential artifacts can be mistaken for baseline tissue data. We hypothesized that enzymatic (collagenase/hyaluronidase) compared to mechanical dissociation leads to dissociated related artifacts not found in endogenous tumor tissue. To distinguish artifacts between enzymatic and mechanical dissociation, we compared separate enzymatic and mechanical dissociated samples with baseline samples from healthy and tumor patient whole blood, melanoma and head and neck squamous cell carcinoma (HNSCC) tumor tissues in flow cytometry, RNA sequencing and CODEX experiments. In bulk sorted tumor tissue, there is a significant difference between enzymatic and mechanical digested samples in cell stress, heat shock proteins and cell death related genes. These genes were also significantly upregulated in enzymatic over mechanical samples in the single cell RNA sequencing HNSCC tissue data. Fibroblasts and CD39+CD103+ CD8 T cells from tumor tissue, appear to require enzymatic digestion for efficient release from tissue compared to the mechanical digested samples. CD39+CD103+ CD8 tumor infiltrating lymphocytes (TILs) show different phenotypes depending on dissociation technique and tumor tissue. In tumor tissue, CD3+CD8+CD69+ T cells and gene expression were elevated in the enzymatic samples over the mechanical and baseline frozen tissue. Tissue dissociation techniques and tissue analysis from downstream applications have the potential for dissociation related artifacts that can mislead both protein and RNA sequencing data analysis in cancer research.

2023-09-19 | GSE243360 | GEO

Single-cell RNA-seq of human head and neck squamous cell carcinoma (HNSCC) to compare different tissue dissociation methods

2023-09-19 | GSE243359 | GEO

Fixation effects on variant-calling in a clinical resequencing panel

Project description:Formalin fixation is the standard method for preservation of tissue for diagnostic purposes, including pathological review and molecular assays. However, this method is known to cause artifacts that can affect the accuracy of molecular genetic tests. We assessed the applicability of alternative fixatives to determine whether these perform significantly better on next-generation sequencing assays, and whether adequate morphology is retained for primary diagnosis, in a prospective study using a clinical-grade laboratory-developed targeted resequencing assay. We examined and quantified several parameters relating to sequencing quality and variant-calling from tumor and normal colon epithelial tissues. We identify one alterative fixative, Sakura Universal Molecular Fixative that suppresses many formalin-related artifacts while retaining adequate morphology for pathological review.

| EGAS00001003507 | EGA

Cell fixation and preservation for droplet-based single cell transcriptomics

Project description:Cell fixation and preservation for droplet-based single cell transcriptomics

| PRJNA350512 | ENA