Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

All -in-one generation and multiomic profiling of human whole brain organoid on a microfluidic plate

ABSTRACT: We demonstrate an all-in-one microfluidic plate (AIOMP) that enables reproducible generation of homogenous hBOs with a facile procedure on a single device. The hBOs are fully biologically characterized using comprehensive proteome analysis.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Stem Cell, Cell Culture

SUBMITTER: Wang Yu

LAB HEAD: Rui Hu

PROVIDER: PXD045839 | Pride | 2026-01-12

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	21080304_WY_Chip-1.raw	Raw
	21080304_WY_Chip-2.raw	Raw
	21080304_WY_Chip-3.raw	Raw
	21080304_WY_S-1.raw	Raw
	21080304_WY_S-2.raw	Raw

Items per page:

1 - 5 of 8

Publications

All-in-one generation and multiomic profiling of human whole brain organoid on a millifluidic plate.

Zhao Wen W Wang Yu Y Chen Tao T Shen Min M Wang Jibo J Huang Xuemei X Zhu Lili L Yu Ting T Zhang Zhentao Z Yang Yunhuang Y Liu Maili M Wang Dong D Huang Weihua W Hu Rui R Chen Pu P

Materials today. Bio 20251209

Human brain organoids (hBOs) have been recently regarded as neurobiologically relevant brain models and exponentially exploited in a variety of neuroscience research. However, the current gold-standard method for generating hBOs is intricate and laborious, resulting in hBOs with morphological variability and inconsistent batch-to-batch reproducibility. Despite several studies reporting simplified hBO culture methods, few of those methods was biologically validated with multiomic profiling, which ...[more]

PMID: 41497900

Similar Datasets

Adaptiven mechanism of antibiotic resistant Staphylococus aureus to host environment

Project description:Antibiotic-resistant bacteria can escape from the killing of host immune and settle in the host to form persistent infections. In this study, we investigated the environmental adaptation mechanism of resistant Staphyloccus aureus (S. aureus) to host environment by Data-independent acquisition based quantitative proteomics and functional validation. The detection of growth curve and MIC indicated that ciprofloxacin-resistant S. aureus (Cip-R) showed survival advantage over sensitive strain. Cip-R also exhibited stronger adhesion and invasion ability than sensitive bacteria. Cip-R stimulation resulted in the production of stronger inflammatory factors of the host cells. Proteomics study combined with biochemical validations showed that Cip-R obtains adaptability to host via up-regulation of TCA cycle and down-regulation of ribosome metabolism and protein folding to maintain energy to support their survival. Thus, this study will help us to further explain the growth strategy of resistant bacteria to adapt to the host environment, and provide important information for the development of new antibacterial drugs.

2022-05-31 | PXD029584 | Pride

A high-resolution single-cell multiomic atlas of the human fetal lung - Organoid

Project description:Individual TFs were overexpressed in fetal lung tip organoids from a doxycycline-inducible construct for 3 days, and organoids were maintained in the self-renewing (tip cell-promoting) medium throughout to rigorously assay the lineage-determining competence of the TF, followed by scRNA-seq. ASCL1, NEUROD1, and NEUROG3 were selected as key neuroendocrine regulators. We also selected the GHRL+ NE-specific RFX6 and NKX2.2, the pan-NE PROX1, and, as controls, the basal cell-specific TFs DeltaNTP63, TFAP2A, PAX9, and mNeonGreen-3xNLS.

2022-01-27 | E-MTAB-11267 | biostudies-arrayexpress

A Kinetic Pump Integrated Microfluidic Plate (KIM-Plate) with High Usability for Cell Culture-Based Multiorgan Microphysiological Systems.

Project description:Microphysiological systems (MPSs), including organ-on-a-chip (OoC), have attracted attention as a novel method for estimating the effects and side effects of drugs in drug discovery. To reproduce the dynamic in vivo environment, previous MPSs were connected to pump systems to perfuse culture medium. Therefore, most MPSs are not user-friendly and have poor throughput. We aimed to develop a kinetic pump integrated microfluidic plate (KIM-Plate) by applying the stirrer-based micropump to an open access culture plate to improve the usability of MPSs. The KIM-Plate integrates six multiorgan MPS (MO-MPS) units and meets the ANSI/SBS microplate standards. We evaluated the perfusion function of the kinetic pump and found that the KIM-Plate had sufficient agitation effect. Coculture experiments with PXB cells and hiPS intestinal cells showed that the TEER of hiPS intestinal cells and gene expression levels related to the metabolism of PXB cells were increased. Hence, the KIM-Plate is an innovative tool for the easy coculture of highly conditioned cells that is expected to facilitate cell-based assays in the fields of drug discovery and biology because of its usability and high throughput nature.

| S-EPMC8471412 | biostudies-literature

Harnessing microfluidic streak plate technique to investigate the gut microbiome of Reticulitermes chinensis.

Project description:The termite gut microbiome is a model system to investigate microbial interactions and their associations with host. For decades, extensive research with molecular tools and conventional cultivation method has been carried out to define the microbial diversity in termite gut. Yet, many bacterial groups of the termite gut microbiome have not been successfully cultivated in laboratory. In this study, we adapted the recently developed microfluidic streak plate (MSP) technique for cultivation of termite gut microbial communities at both aerobic and anaerobic conditions. We found that 99 operational taxonomic units (OTUs) were cultivable by MSP approach and 18 OTUs were documented first time for termite gut microbiota. Further analysis of the bacterial diversities derived by culture-dependent MSP approach and culture-independent 16S rRNA gene typing revealed that both methods have bias in recovery of gut microbiota. In total 396 strains were isolated with MSP technique, and potential new taxa at species and/or genus levels were obtained that were phylogenetically related to Burkholderia, Micrococcus, and Dysgonomonas. Results from this study indicate that MSP technique is applicable for cultivating previously unknown and new microbial groups of termite gut microbiota.

| S-EPMC6436436 | biostudies-literature

Injection molded open microfluidic well plate inserts for user-friendly coculture and microscopy.

Project description:Open microfluidic cell culture systems are powerful tools for interrogating biological mechanisms. We have previously presented a microscale cell culture system, based on spontaneous capillary flow of biocompatible hydrogels, that is integrated into a standard cell culture well plate, with flexible cell compartment geometries and easy pipet access. Here, we present two new injection molded open microfluidic devices that also easily insert into standard cell culture well plates and standard culture workflows, allowing seamless adoption by biomedical researchers. These platforms allow culture and study of soluble factor communication among multiple cell types, and the microscale dimensions are well-suited for rare primary cells. Unique advances include optimized evaporation control within the well, manufacture with reproducible and cost-effective rapid injection molding, and compatibility with sample preparation workflows for high resolution microscopy (following well-established coverslip mounting procedures). In this work, we present several use cases that highlight the usability and widespread utility of our platform including culture of limited primary testis cells from surgical patients, microscopy readouts including immunocytochemistry and single molecule fluorescence in situ hybridization (smFISH), and coculture to study interactions between adipocytes and prostate cancer cells.

| S-EPMC6917835 | biostudies-literature

Integrated microfluidic array plate (iMAP) for cellular and molecular analysis.

Project description:Just as the Petri dish has been invaluable to the evolution of biomedical science in the last 100 years, microfluidic cell assay platforms have the potential to change significantly the way modern biology and clinical science are performed. However, an evolutionary process of creating an efficient microfluidic array for many different bioassays is necessary. Specifically for a complete view of a cell response it is essential to incorporate cytotoxic, protein and gene analysis on a single system. Here we present a novel cellular and molecular analysis platform, which allows access to gene expression, protein immunoassay, and cytotoxicity information in parallel. It is realized by an integrated microfluidic array plate (iMAP). The iMAP enables sample processing of cells, perfusion based cell culture, effective perturbation of biologic molecules or drugs, and simultaneous, real-time optical analysis for different bioassays. The key features of the iMAP design are the interface of on-board gravity driven flow, the open access input fluid exchange and the highly efficient sedimentation based cell capture mechanism (?100% capture rates). The operation of the device is straightforward (tube and pump free) and capable of handling dilute samples (5-cells per experiment), low reagent volumes (50 nL per reaction), and performing single cell protein and gene expression measurements. We believe that the unique low cell number and triple analysis capabilities of the iMAP platform can enable novel dynamic studies of scarce cells.

| S-EPMC4143330 | biostudies-other

Low-input and multiplexed microfluidic assay reveals epigenomic variation across cerebellum and prefrontal cortex

Project description:There has been an extensive effort underway to profile epigenetic features at the genome-wide scale using primary ex vivo tissues. Cell-type specificity of epigenomes calls for enrichment to obtain a homogenous cell population from a small quantity of tissues. Thus technologies that permit both ultralow input and high throughput are desired for profiling an array of histone marks. Here we demonstrate a simple microfluidic technology, SurfaceChIP-seq, for profiling genome-wide histone modifications using as few as 30 cells per assay and with up to 8 assays running in parallel. We applied the technology to study epigenomic landscapes in neurons and glia in prefrontal cortex and cerebellum of mouse brain. The data revealed extensive epigenomic difference in the two regions on important functional elements such as promoters and enhancers.

2018-03-30 | GSE99757 | GEO

Ultrasensitive Multiparameter Phenotyping of Rare Cells Using an Integrated Digital-Molecular-Counting Microfluidic Well Plate.

Project description:Integrated microfluidic cellular phenotyping platforms provide a promising means of studying a variety of inflammatory diseases mediated by cell-secreted cytokines. However, immunosensors integrated in previous microfluidic platforms lack the sensitivity to detect small signals in the cellular secretion of proinflammatory cytokines with high precision. This limitation prohibits researchers from studying cells secreting cytokines at low abundance or existing at a small population. Herein, the authors present an integrated platform named the "digital Phenoplate (dPP)," which integrates digital immunosensors into a microfluidic chip with on-chip cell assay chambers, and demonstrates ultrasensitive cellular cytokine secretory profile measurement. The integrated sensors yield a limit of detection as small as 0.25 pg mL-1 for mouse tumor necrosis factor alpha (TNF-α). Each on-chip cell assay chamber confines cells whose population ranges from ≈20 to 600 in arrayed single-cell trapping microwells. Together, these microfluidic features of the dPP simultaneously permit precise counting and image-based cytometry of individual cells while performing parallel measurements of TNF-α released from rare cells under multiple stimulant conditions for multiple samples. The dPP platform is broadly applicable to the characterization of cellular phenotypes demanding high precision and high throughput.

| S-EPMC8349899 | biostudies-literature

Indirect fabrication of versatile 3D microfluidic device by a rotating plate combined 3D printing system.

Project description:In the past decade, 3D-printing technology has been applied in the field of microfluidics to fabricate microfluidic devices for wide-ranging areas of study including chemistry, biology, medicine, and others. However, these methods face several limitations such as insufficient resolution and long fabrication time. In this study, versatile microfluidic devices with different functions were indirectly fabricated by a rapid sacrificial template printing process using a photocurable fluoropolymer with chemical durability. The Pluronic® F127 hydrogel as a sacrificial template was rapidly patterned on substrates by a non-lithographic printing process using a computer-controlled 3D-printing system. Viscous fluoropolymer was cast on the non-deformable template that was consequently removed by applying heat and negative pressure after UV curing. The chemical-resistant and transparent microchannels were oblate-hemispherical on the cross section. They were tested by performing a heterogeneous catalytic reaction as well as a photochemical reaction. The microchannels with controlled heights were devised to induce convection for functioning as a micromixer with asymmetric flows. Moreover, upon printing the Pluronic® F127 on both sides of the PFPE (perfluoropolyether-urethane dimethacrylate) membrane substrate, the 3D hybrid microfluidic device was embedded with a permeable membrane between the lower and upper channels, which is useful for gas-liquid chemical processes.

| S-EPMC9089432 | biostudies-literature

Spatial multiomic insights into acute cocaine exposure

Project description: Not available

| S-BSST1255 | biostudies-other