Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: LUHMES epigenetic data

PROVIDER: PRJNA1076600 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR27970100.fastq.gz	Fastqsanger.gz
	SRR27970101.fastq.gz	Fastqsanger.gz
	SRR27970102.fastq.gz	Fastqsanger.gz
	SRR27970103_1.fastq.gz	Fastqsanger.gz
	SRR27970104_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 58

Similar Datasets

Neuronal differentiation of LUHMES cells is accompanied by substantial changes of the proteome

Project description:To study mechanisms of neurodegenerative diseases, neuronal cell lines are important model systems and are often differentiated into postmitotic neuron-like cells to resemble more closely primary neurons obtained from brains. One such cell line is the Lund Human Mesencephalic (LUHMES) cell line which can be differentiated into dopamine-like neurons and is frequently used to study mechanisms of Parkinson’s disease (PD) and neurotoxicity. Neuronal differentiation of LUHMES cells is commonly verified by measurement of selected neuronal markers, but little is known about proteome-wide protein abundance changes during differentiation. Using mass spectrometry and label-free quantification (LFQ) we compared the proteome of differentiated and undifferentiated LUHMES cells as well as of cultured primary murine midbrain neurons, which are mainly dopaminergic. Neuronal differentiation induced substantial changes of the LUHMES cell proteome (18.4% reveal protein abundance changes of more than 4-fold), with proliferation-related proteins (e.g. MCMs) being strongly down-regulated and neuronal and dopaminergic proteins being up to 1000-fold upregulated, such as L1CAM and SNCA. Several of these proteins, including MAPT and SYN1, may be useful new markers to experimentally validate neuronal differentiation of cultured LUHMES cells. Primary midbrain neurons were more closely related to differentiated than to undifferentiated LUHMES cells with respect to the abundance of proteins related to neurodegeneration or to genetic forms of PD. In summary, our comparative proteomic analysis demonstrates that differentiated LUHMES cells are a suitable model for studies on PD and neurodegeneration and provides a resource of the proteome-wide changes during neuronal differentiation.

2020-09-24 | PXD020044 | Pride

Project description:LUHMES baseline Konstanz

| PRJEB23589 | ENA

RNA-seq of CSMD1 enhancer CRISPRi in LUHMES cells and differentiated neurons

Project description:we performed lentiviral CRISPR interference (CRISPRi) by recruiting dCas9 fused with the KRAB domain to the CSMD1 enhancer (fam3) in the neuronal precursor cell line – Lund human mesencephalic (LUHMES). Given that the expression of CSMD1 was not detectable in LUHMES cells we differentiated these cells into neurons. Differentiated neurons with CRISPRi of CSMD1 enhancer showed significantly higher expression of CSMD1 than control.

2022-06-30 | E-MTAB-8027 | biostudies-arrayexpress

Transcriptome and proteome analysis in LUHMES cells overexpressing alpha-synuclein

Project description:Differential transcriptome analysis in LUHMES cells overexpressing human wild-type alpha-synuclein or GFP

2022-03-31 | GSE191302 | GEO

Time-course enhancer profiling of a human neuronal cell line

Project description:We characterized the transcribed active enhancers of a human neuronal cell line derived from fetal mesencephalon (LUHMES) during differentiation by native elongating transcript-cap analysis of gene expression (NET-CAGE). Raw data files starting from 'Total' are conventional CAGE method outputs, and those starting from 'Nascent' are NET-CAGE method outputs.

2025-01-19 | E-MTAB-13588 | biostudies-arrayexpress

Transcriptome and proteome analysis in LUHMES cells overexpressing alpha-synculein

Project description:LUHMES cells share many characteritics with human dopamingeric neurons in the substantia nigra, the cells whose demise is responsible for the motor symptoms in Parkinson’s disease (PD). LUHMES cells can therefore be used bona fide as a model to study pathophysiological processes involved in PD. Previously, we showed that LUHMES cell degenerate after six days upon overexpression of wild type alpha-synuclein. In the present study we performed a transcriptome and proteome expression analysis in alpha-synuclein-overexpressing cells and GFP-expressing control cells in order to identify genes and proteins that are differentially regulated upon overexpression of alpha-synuclein. The analysis was performed four days after the initiation of alpha-synuclein or GFP overexpression, before the cells died in order to identify processes that preceded cell death.

2022-05-19 | PXD028322 | Pride

Time-course transcriptome analysis of a human neuronal cell line

Project description:RNA-seq analysis on a human neuronal cell line derived from fetal mesencephalon (LUHMES) from day 0 to day 6.

2021-07-31 | E-MTAB-8908 | biostudies-arrayexpress

Systematic characterization of LUHMES cell-based Parkinson’s disease models reveals potential novel drug targets.

Project description:Parkinson's disease (PD) encompasses incurable and progressive loss of dopaminergic neurons in patients and the research for effective disease-modifying treatments are still ongoing. In this study, using a systems biology-based approach we show that 6-OHDA treatment of alpha-synuclein-overexpressing LUHMES cells can be used as a physiologically relevant model of PD. RNAseq analysis in these LUHMES-based disease models validate genes including HMOX1 and IGF2R in common with previously identified PD genes. We further confirm that quercetin and rutin can partially alleviate cell death in this model and show that the expression of genes related to PD as well as those related to mitochondria and energy metabolism are back to basal levels in control cells upon quercetin or rutin pre-treatment. When RNAseq analysis was performed on drug-pretreated LUHMES PD models, protein folding, misfolded protein binding and unfolded protein response pathways were found to be affected. We believe these findings offer new avenues of innovative therapeutic strategies for PD.

2026-01-01 | GSE287941 | GEO

Time-course transcriptome analysis of a human neuronal cell line with RFX2 KO

Project description:RNA-seq analysis on a human neuronal cell line derived from fetal mesencephalon (LUHMES) wild type and RFX2 knockout from day 0 to day 6.

2024-01-31 | E-MTAB-11546 | biostudies-arrayexpress

Long-term treatment with bortezomib induces specific methylation changes in differentiated neuronal cells

Project description:Genome-wide patterns of DNA methylation were quantified using the Illumina Infinium HumanMethylationEPIC BeadChip in DNA samples extracted from LUHMES cell line cells repeatedly treated with bortezomib (BTZ).

2022-08-03 | GSE202792 | 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