Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A microfluidics workflow for spatial analysis of microenvironmental gradient impact on cancer cell phenotypes

ABSTRACT: Despite the physiological and pathophysiological significance of microenvironmental gradients, tools for generating such gradients and analysing their impact on cellular phenotypes are lacking. Here we present an integrated microfluidics-based workflow for mimicking extracellular pH gradients characteristic of solid tumors, and studying their multifactorial impact on cancer cells. Our microfluidics device generates a pH gradient across cancer cell 3D cultures in an extracellular matrix. The gradient, validated using pH-sensitive fluorophores can be rapidly controlled to represent spatiotemporal microenvironmental changes, and the device allows high resolution live imaging of, e.g., cell motility and chemotaxis. The device can be reopened, allowing immunofluorescence analysis of phenotypes and spatially resolved analysis of gene expression changes across the pH gradient. The workflow is easily adaptable for other gradients and multiple cell types, making it broadly applicable for integrated analysis of roles of microenvironmental gradients in biology.

ORGANISM(S): Homo sapiens

PROVIDER: GSE242233 | GEO | 2024/05/07

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

A microfluidics workflow for spatial analysis of microenvironmental gradient impact on cancer cell phenotypes

Project description:A microfluidics workflow for spatial analysis of microenvironmental gradient impact on cancer cell phenotypes

| PRJNA1012322 | ENA

Inducible defense response of C. cinerea against its fungiverous nematode A. avenae in microfluidics device

Project description:The fungal toxin-encoding genes are highly upregulated in the vegetative mycelium upon challenge with the predator. Our recent studies in microfluidics have shown that latter induction is spatially restricted to parts of the vegetative mycelium that is in direct contact with the predator. In order to dissect the defensome of a multicellular fungus against a predator, here, we performed RNA - sequencing of mushroom Coprinopsis cinerea upon challenged with fungivorous nematode Aphelenchus avenae in Microfluidics device at three different time points. We analyzed hyphae that were collected from a microfluidics device where they have been in direct contact with or cultivated without A. avenae.

2018-11-30 | E-MTAB-7005 | biostudies-arrayexpress

An integrated CUT&RUN quality control workflow for histone modifications and transcription factors

Project description:An integrated CUT&RUN quality control workflow for histone modifications and transcription factors

| PRJNA722185 | ENA

Proteomic survey for search of biomarkers of colon tumors

Project description:To the search of new colon tumor biomarkers in the transition from normal colon (NC) mucosa to adenoma (AD) and adenocarcinoma (AC), we integrated microarray data with the results of a high-throughput proteomic workflow. In proteomic study, we used a modified isoelectric focusing protocol on strips with an immobilized pH gradient to separate peptides labeled with iTRAQ (isobaric tags for relative and absolute quantitation) tags followed by liquid chromatography–tandem mass spectrometry analysis.

2016-12-14 | PXD005274 | Pride

CO2/HCO3- perturbations of simulated large-scale gradients in a novel scale-down device cause fast transcriptional responses in Corynebacterium glutamicum

Project description:The exploration of scale-down models to imitate the influence of large scale bioreactor inhomogeneities on cellular metabolism is a topic with increasing relevance. While gradients of substrates, pH, or dissolved oxygen are often investigated, oscillating CO2/HCO3- levels, a typical scenario in large industrial bioreactors, is rarely addressed. Hereby, we investigate the metabolic and transcriptional response in Corynebacterium glutamicum wild type as well as the impact on L-lysine production in a model strain exposed to pCO2 gradients of (75-315) mbar. A novel three-compartment cascade bioreactor system was developed and characterized that offers high flexibility for installing gradients and residence times to mimic industrial-relevant conditions, and provides the potential of accurate carbon balancing. The phenomenological analysis of cascade fermentations imposed to the pCO2 gradients at industry-relevant residence times of about 3.55 min did not significantly impair the process performance, with growth and product formation being similar to control conditions. However, transcriptional analysis disclosed up to 66 differentially expressed genes already after 3.55min under stimulus exposure, with the overall change in gene expression directly correlateable to the pCO2 gradient intensity and the residence time of the cells.

2014-05-15 | E-MTAB-2585 | biostudies-arrayexpress

Optimization of mESC ChIP-re-ChIP workflow

Project description:Optimization of mESC ChIP-re-ChIP workflow

| PRJNA1014115 | ENA

Combination of digital microfluidics and magnetic bead-based intact proteoform elution for top-down nanoproteomics of single C. elegans

Project description:While most nanoproteomics approaches for the analysis of low-input samples are based on bottom-up LC-MS workflows, top-down approaches enabling proteoform characterization are still underrepresented. Using mammalian cell proteomes, we here established a facile one-pot sample preparation protocol based on protein aggregation on magnetic beads and intact proteoform elution using 40% v/v formic acid. Performed on a digital microfluidics device, the workflow enabled sensitive analysis of single Caenorhabditis elegans nematodes, increasing the number of proteoform identifications compared to in-tube sample preparation by 46%. Label-free quantification of single nematodes grown under different conditions allowed to identify changes in abundance of proteoforms not distinguishable by bottom-up proteomics. The workflow presented here will help to elucidate cellular changes on the proteoform level in other samples of limited availability.

2023-06-19 | PXD039883 | Pride

A computational workflow for the analysis of 3’ Tag-Seq data

Project description:RNA-sequencing (RNA-seq) is a ubiquitous tool to profile genome-wide changes in gene expression. RNA-seq uses high-throughput sequencing technology to quantify the amount of RNA in a biological sample. With the increasing popularity of RNA-seq, many variations on the protocol have been proposed to extract unique and relevant information from biological samples. 3’ Tag-Seq (also called TagSeq, 3′ Tag-RNA-Seq, and Quant-Seq 3′ mRNA-Seq) is one RNA-seq variation, where the 3’ end of the transcript is selected and amplified to yield one copy of cDNA from each transcript in the biological sample.We present a simple, easy to use, and publicly available computational workflow to analyze 3’ Tag-Seq data. The workflow begins by trimming sequence adapters from raw FASTQ files. The trimmed sequence reads are checked for quality using FastQC, aligned to the reference genome, and read counts are obtained using STAR. Differential gene expression analysis is performed using DESeq2, based on differential analysis of gene count data. The outputs of this workflow are MA plots, tables of differentially expressed genes, and UpSet plots.This protocol is intended for users specifically interested in analyzing 3’ Tag-Seq data. As such, transcript length-based normalizations are not performed within the workflow. Future updates to this workflow could include custom analyses based on the gene counts table as well as data visualization enhancements.

2022-10-13 | GSE200778 | GEO

Study of workflow development

Project description:ViralFlow: an automated workflow for SARS-CoV-2 genome assembly, lineage assignment, mutations and intrahost variants detection

| PRJEB47823 | ENA

A microfluidics-enabled automated workflow of sample preparation for MS-based immunopeptidomics

Project description:Mass spectrometry (MS)-based immunopeptidomics is an attractive antigen discovery method with growing clinical implications, especially for personalized cancer immunotherapies. However, the current experimental approach to extract HLA-I-restricted peptides requires a bulky sample source, which remains a challenge for obtaining clinical tumor samples. We present an innovative streamlined workflow that requires a low sample volume. The workflow integrates the immunoaffinity purification (IP) and C18 peptide cleanup steps on a single microfluidics platform with automated liquid handling and minimal sample transfers, resulting in higher assay sensitivity. We also demonstrate how state-of-the-art data-independent acquisition (DIA) MS method further enhances the depth and reproducibility of tandem mass spectrometry (MS2) spectra-based peptide sequencing. As a result, over 4,000 and 5,000 HLA-I restricted peptides can be reliably identified from as low as 0.2 million human RA957 cells and a melanoma tissue of merely 5 mg, respectively. We also identified multiple known immunogenic tumor-associated antigens and hundreds of peptides derived from non-canonical protein sources. The presented workflow is a powerful tool for identifying the immunopeptidome of sparse samples.

2023-05-12 | PXD040858 | Pride

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