RNA-seq of CSMD1 enhancer CRISPRi in LUHMES cells and differentiated neurons
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB32901 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR3357650_1.fastq.gz | Fastqsanger.gz | |||
| ERR3357650_2.fastq.gz | Fastqsanger.gz | |||
| ERR3357651_1.fastq.gz | Fastqsanger.gz | |||
| ERR3357651_2.fastq.gz | Fastqsanger.gz | |||
| ERR3357646_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 12 |
Similar Datasets
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
Project description:This is RNA-seq from LUHMES cells and differentiated neurons with and without CSMD1 enhancer CRISPRi
| PRJEB32825 | ENA
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:Study of MeCP2 in LUHMES-derived neurons
| PRJNA517116 | ENA
Project description:CSMD1 gene, mapping to human chromosomal region 8p23, encodes a transmembrane protein with an extracellular region containing 14 CUB and 28 sushi domains, a transmembrane domain and a cytoplasmic domain with a putative tyrosine phosphorylation site.The loss of CSMD1 has been found to be associated with enhanced cell proliferation, migration and poor prognosis in head and neck squamous cell carcinoma (HNSCCs), lung squamous cell carcinoma (SCCs), melanoma, and breast cancer, suggesting its role as a tumor suppresser.However, its role in hypertrophic scar has not been uncovered. So we decided using fibroblasts to see its transcriptomes changing after CSMD1 knockdown.
2021-08-18 | GSE176551 | GEO
Project description:Differential transcriptome analysis in LUHMES cells overexpressing human wild-type alpha-synuclein or GFP
2022-03-31 | GSE191302 | GEO
Project description:Infertility in men and women is a common and complex genetic trait with shared biological bases between the sexes. We performed a series of rare variant analyses across 73,185 women and men to identify genes that contribute to primary gonadal dysfunction and identified CSMD1 as a strong candidate in both sexes. CSMD1 is a complement regulatory protein on chromosome 8p23. In order to interpret and support our genetic findings, we performed detailed transcriptomic and protein-based experiments which found CSMD1 enriched at the germ-cell/somatic-cell interface in both male and female gonads. We then performed a battery of tests on Csmd1 knockout mice. Knockout males show increased rates of infertility, and present testes with severe histological degeneration and significantly increased deposition of complement C3 protein. Knockout females show significant reduction in ovarian quality and breeding success, as well as impaired branching of the mammary glands. Furthermore, double knockout of Csmd1 and C3 leads to an unexpected and non-additive reduction in breeding success, suggesting that CSMD1 and the complement pathway play an important role in the normal postnatal development of the gonads in both sexes.
2019-09-04 | GSE136769 | GEO
Project description:Identification of toxicants that underlie neurological diseases is a neglected area awaiting a valid strategy to identify such toxicants. We sought biomarkers that respond to known neurotoxicants in LUHMES immortalized neurons and evaluated these biomarkers for use in screening libraries of environmental toxicants. LUHMES immortalized human dopaminergic neurons were surveyed by RNA sequencing following challenge with Parkinsonian toxicants rotenone, 6-hydroxydopamine, MPP+, and ziram (zinc dimethyldithiocarbamate; Zn2+DDC2), as well as additional toxicants paraquat, MS275, and methylmercury. The metallothionein gene MT1G was the most dynamic gene expression response to all seven toxicants. Multiple toxicants also increased transcripts for SLC30A1 and SLC30A2 zinc secretion transporters, the SLC7A11 xCT cystine/glutamate antiporter important for glutathione synthesis, DNA damage Inducible Transcript 3 (DDIT3), and secreted growth factors FIBIN and CXCL12, whereas several toxicants decreased expression of the Apelin growth factor (APLN). These biomarker genes showed advantages in sensitivity by responding to many toxicants at sub-cytotoxic concentrations. Since several of these biomarker genes and prior neurological disease studies implicated disruption of metal distribution, we tested metal chelator thiram (dimethyldithiocarbamate, DDC), Zn2+DDC2, and several other metals and metal chelates for cytoxicity and induction of MT1G expression. Metals and chelators that caused dynamic increases in MT1G expression caused cytotoxicity, whereas Ni2+DDC2 caused MT1G increase, but no cytotoxicity. These results bolster prior work suggesting that neurons are characteristically sensitive to depletion of glutathione or to disruption of cellular metal distribution and provide biomarkers to search for such neurotoxicants in chemical libraries.
2020-08-11 | GSE150005 | GEO
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
Project description:Assess the on- and off-target effects of dox-inducible CRISPR/Cas9 and CRISPRi constructs in a human iPS cell line. Transcript quantification of 3 cell lines, each plus or minus doxycycline and with or without specific single guide RNAs (sgRNAs), with 2 biological replicates each.
2016-01-19 | E-GEOD-76980 | biostudies-arrayexpress