Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Cultured ex vivo human brain tissue maintains cell-type transcriptional identities

ABSTRACT: There is growing recognition of the need for human-based models of the nervous system and its diseases. We used single-nucleus RNA sequencing of six patient samples to determine how well various cell types maintain their transcriptional identities over two weeks in organotypic slice culture. Patient samples included two pediatric temporal lobectomies, one adult frontal cortex, two glioblastomas, and one medulloblastoma. For each patient sample, we compared day 0 (flash-frozen at collection) to day 14 (organotypic slice culture) tissue. We found generally high correlations between day 0 and day 14 transcriptional profiles across cell types, especially in tumour cells, microglia, oligodendrocytes, and endothelial cells. This holds significant promise for the use of ex vivo human brain tissue in mechanistic studies and therapeutic screens.

ORGANISM(S): Homo sapiens

PROVIDER: GSE328077 | GEO | 2026/04/16

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Maintenance of Brain Tumor Profile on Organotypic Brian Slice Culture (OBSC)

Project description:Maintenance of Brain Tumor Profile on Organotypic Brian Slice Culture (OBSC)

| PRJNA955884 | ENA

Maintenance of Brain Tumor Profile on Organotypic Brian Slice Culture (OBSC)

Project description:Maintenance of Brain Tumor Profile on Organotypic Brian Slice Culture (OBSC)

| PRJNA955876 | ENA

Gene expression in response to axotomy in organotypical slices co-cultures

Project description:Brain slice cultures offer advantages over other in vitro methods, as they mimic numerous in vivo aspects. For most purposes, slices of the developing brain, termed organotypic slice cultures , preserve a high degree of cellular differentiation and tissue organization. The entorhino-hippocampal connection (EHP) is the main entrance of information to the hippocampus proper and the dentate gyrus. Also it has some specific features that make them particularly interesting in studies of axonal regeneration: (i) the culture method obviates the need for extensive animal surgery and requires less time than other in vivo approaches; (ii) the EHP is reproduced easily in vitro in cultures with a degree of laminar specificity similar to that found in vivo; (iii) the EHP is myelinated both in vitro and in vivo; and (iv) most of the cellular and molecular barriers to axon regeneration are present after the axotomy of the EHP in vitro. Altogether this model is useful to evaluate axon regeneration and putative estrategies to promote axonal growth. Keywords: organotypic slice cultures; axonal lession; gene expression

2011-02-25 | GSE20528 | GEO

Gene expression in response to axotomy in organotypical slices co-cultures

2011-02-25 | E-GEOD-20528 | biostudies-arrayexpress

Prostate cancer organotypic slice cultures (OSC) treated with E2 or DHT

Project description:Organotypic slice cultures from prostate cancer patients were generated and treated with or without 17b-estradiol or DHT to study estrogen and androgen signalling pathways.

2020-10-06 | GSE142287 | GEO

Vehicle and sAPPalpha-treated hippocampal slice cultures

Project description:Gene expression changes induced by alpha-secretase cleaved amyloid precursor protein (sAPPalpha) in organotypic hippocampal slice cultures of male, postnatal day 15 mice (C57B6/SJL). Hippocampal slice cultures were treated with phosphate buffered saline (GSM26700, GSM26701, GSM26702) or 1 nM sAPPalpha (GSM26703, GSM26704, GSM26705) for 24 h. Each sample consists of total RNA isolated from 8-12 slices from 4 mice. Data were analyzed with MAS 5.0 and scaled to 2500. sAPPalpha induces the amyloid sequestration protein transthyretin, insulin-like growth factor 2, insulin-like growth factor binding protein 2, and other genes involved in protective pathways such as apoptosis inhibition, detoxification, and retinol transport. Keywords = Alzheimer's disease Keywords = neuroprotection Keywords = sAPPalpha

2004-07-30 | GSE1555 | GEO

Annorade mRNA Sequencing Qualified the Transcriptome Analysis of Fresh and Warmed Tissue of Hepatocellular Carcinoma

Project description:Purpose: The aim of this study was to create a patient-derived slice model by combining cryopreservation technique with precision-cut slice culture method and explore its effectivity of predicting anti-cancer drug sensitivity in vitro. Methods: We prepared 0.3 mm thick tissue slices by a microtome and maintain its cell viability by cryopreservation technique. Slices were cultured individually in the presence or absence of regorafenib (REG) for 72 hours. Alterations in morphology and gene expression were assessed by histological and genetic analysis. Overall viability was also analyzed in tissue slices by CCK-8 quantification assay and fluorescent staining. Tissue morphology and cell viability could be evaluated to quantify drug effects. Results: Histological and genetic analysis showed that no significant alterations in morphology and gene expression were induced by vitrification‑based cryopreservation. The viability of warmed HCC tissues was up to 90% of the fresh tissues. The viability and proliferation could be retained for at least four days in filter culture system. The positive drug responses in precision-cut slice culture in vitro were evaluated by tissue morphology and cell viability. Conclusion: In summary, the successful application of precision-cut HCC slice culture combining cryopreservation technique in a systematic drug screen demonstrates the feasibility and utility of slice culture method for drug response.

2022-01-21 | GSE194095 | GEO

Single cell RNAseq analysis of organotypic brain slice microglia

Project description:Single cell RNAseq analysis of organotypic brain slice microglia

| PRJNA648000 | ENA

RNA-seq analysis of neonatal mouse cochlear supporting cells [Treated AK]

Project description:This study examined transcripts that are enriched in neonatal mouse cochlear supporting cells at postnatal day 1 and postnatal day 6 after inhibition of the Notch signaling pathway. Cochleas from postnatal day 0 and postnatal day 5 were cultured for 24 hours in the gamma secretase inhibitor DAPT or DMSO as a vehicle control. Supporting cells were purified by FACS sorting for GFP fluorescence from the cochleas of transgenic mice in which a BAC including the LFng locus drives the expression of GFP. Two replicates of GFP+ supporting cells were compared with all other cochlear cell types that were GFP-. We performed this experiment at two different ages, postnatal day 0+24 hours culture and postnatal day 5 + 24 hours culture. (corresponding to P1 and P6).

2016-07-01 | GSE83340 | GEO

Transcription profiling of mouse vehicle and sAPPalpha-treated hippocampal slice cultures

Project description:Gene expression changes induced by alpha-secretase cleaved amyloid precursor protein (sAPPalpha) in organotypic hippocampal slice cultures of male, postnatal day 15 mice (C57B6/SJL). Hippocampal slice cultures were treated with phosphate buffered saline (GSM26700, GSM26701, GSM26702) or 1 nM sAPPalpha (GSM26703, GSM26704, GSM26705) for 24 h. Each sample consists of total RNA isolated from 8-12 slices from 4 mice. Data were analyzed with MAS 5.0 and scaled to 2500. sAPPalpha induces the amyloid sequestration protein transthyretin, insulin-like growth factor 2, insulin-like growth factor binding protein 2, and other genes involved in protective pathways such as apoptosis inhibition, detoxification, and retinol transport. See Stein, TD, Anders, NJ, DeCarli, C, Chan, SL, Mattson, MP, and Johnson JA. Neutralization of transthyretin reverses the neuroprotective effects of secreted APP in APPSw mice resulting in tau phosphorylation and loss of hippocampal neurons: support for the amyloid hypothesis. J Neurosci. in press.

2007-10-10 | E-GEOD-1555 | biostudies-arrayexpress

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