Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA sequencing of ex vivo microtumor models embedded in different matrices and constructed from either control or Arpc4-knockout cells.

ABSTRACT: The loss of Arpc4 resulted in reduced expression of other Arp2/3 complex components, rendering the Arp2/3 complex nonfunctional. The ex vivo microtumor(3D) models were composed of either control or Arpc4 knockout (KO) KC 8025 cells embedded in different matrices containing three condition:25% collagen I, 25% collagen I + 75% Matrigel, and 75% Matrigel for 5 days. To identify genes affected by Arpc4 knockout in this model, RNA-seq analysis was performed on bulk samples. 8025 cell line was derived from primary cells isolated from genetically engineered p48Cre/+; LSL-KrasG12D/+ (KC).

ORGANISM(S): Mus musculus

PROVIDER: GSE305670 | GEO | 2025/12/21

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

RNA-seq analysis of ex vivo microtumor models comprising control or Arpc4 knockout (KO) PDAC cells

Project description:The loss of Arpc4 resulted in reduced expression of other Arp2/3 complex components, rendering the Arp2/3 complex nonfunctional. The ex vivo microtumor(3D) models were composed of either control or Arpc4 knockout (KO) KP 8025 cells, mouse primary pancreatic stellate cells (PSCs), and bone marrow-derived macrophages. To identify genes affected by Arpc4 knockout in this model, RNA-seq analysis was performed on bulk samples. R254 cell line which was derived from primary cells isolated from genetically engineered p48Cre/+; LSL-KrasG12D/+; p53flox/flox (KPC) mice, and 8025 cell line which was derived from primary cells isolated from genetically engineered p48Cre/+; LSL-KrasG12D/+ (KC) mice were also conducted with RNA seq.

2025-12-21 | GSE284423 | GEO

Effects of O2 concentration on endeometrial organoids within collagen-based gel (70% type I collagen and 30% matrigel)

Project description:We investgated effect of O2 concentration on gene expression of EMO within collagen-based gel (70% type I collagen and 30% matrigel).

2023-11-12 | GSE247420 | GEO

RNA-seq of wildtype mouse small intestinal organoids grown in Matrigel or in/on collagen.

Project description:We aimed to analyse the effect of different extra-cellular matrices on the growth of small intestinal organoids. Small intestinal crypts of wildtype mice were harvested and grown under standard Matrigel organoid conditions. After establishment of organoids (passaged 1-2), organoids were grown in Matrigel, on collagen or in a drop of collagen. Growth in a droplet of collagen requires addition of Wnt3a, therefore all samples are either provided with standard culture conditions (ENR) or with ENR+50%Wnt3a-CM (WENR). Samples were grown in specified matrix for at least 1-2 passages before RNA was purified.

2021-04-01 | E-MTAB-10082 | biostudies-arrayexpress

Activation of adult human pancreatic ductal and ductal progenitor-like cells requires extracellular matrix protein signaling [bulkRNA-seq]

Project description:Ductal progenitor-like cells are a subpopulation of ductal cells in the adult human pancreas that have the potential to contribute to regenerative medicine. However, the microenvironmental cues that regulate their activation are poorly understood. Here, we establish a 3-dimensional suspension culture system containing six defined soluble factors in which primary human ductal and ductal progenitor-like cells can survive but do not proliferate. Expansion and polarization occur when cells are provided with a low concentration (5% v/v) of Matrigel, a sarcoma cell product enriched in many extracellular matrix (ECM) proteins. Screening of ECM proteins identified that collagen IV is capable of partially recapitulating the effects of Matrigel. Inhibition of integrin α1β1, a major collagen IV receptor, negates collagen IV- and Matrigel-stimulated effects. These results demonstrate that collagen IV is a key ECM protein that stimulates the expansion and polarization of human ductal and ductal progenitor-like cells via integrin α1β1 receptor signaling.

2023-05-31 | GSE233344 | GEO

Activation of adult human pancreatic ductal and ductal progenitor-like cells requires extracellular matrix protein signaling [scRNA-seq]

2023-06-05 | GSE233785 | GEO

Tear protein profile in eyes with keratoconus after one year of intrastromal corneal ring and corneal crosslinking: a pilot study

Project description:Keratoconus (KC) is a corneal ectasia characterized by structural changes, resulting in progressive thinning and biomechanical weakening that can lead to worsening visual acuity due to irregular astigmatism. Corneal collagen Crosslinking (CXL) and Intracorneal Ring Segment (ICRS) are widely used treatments in KC disease, but the alterations they cause in biomechanical mediators are still poorly understood. The aim of this study was to analyze the tear proteome profile before and after treatments to identify biomarkers altered by surgery.

2022-10-14 | PXD035655 | Pride

Effects of substrates on gene expression of human endometrial organoids

Project description:To investigate the effects of different substrates on human endometrial organoids , we compared the transcriptomes of EMO cultured within Matrigel and collagen-based gels.

2023-11-11 | GSE237245 | GEO

Mechanosensitive calcium channels and integrins coordinate the reprogramming of colorectal cancer cells into a fetal-like state

Project description:Plate-based scRNA-seq data of murine CRC organoids that were embedded in either Matrigel-or Collagen I matrices and harvested after 1 day.

2025-09-23 | GSE279558 | GEO

Expression data of MB114 Endothelial cells during in vitro angiogenesis on Matrigel

Project description:MB114 cells cultured on Matrigel for 1, 5, 15, 25 hours Keywords: time course experiment

2007-05-20 | GSE7507 | GEO

Gene expression analysis of cultures of acinar-enriched explants from KC Fgfr2+/+ and Fgfr2f/f mice in collagen provides insight into mutant Kras-driven trasformation of acinar cells

Project description:This study used RNA-sequencing of cultures of acinar-enriched epithalial explants from KC Fgfr2+/+ and Fgfr2f/f mice in collagen to study mutant Kras-induced malignant trasformation of acinar cells in the presence and absence of Fgfr2.

2025-01-13 | GSE278148 | 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