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Understanding the transcriptional consequences of Lamin A deficiency within the immune compartment of the lung using single cell RNA sequencing.

ABSTRACT: Understanding the transcriptional consequences of Lamin A deficiency within the immune compartment of the lung using single cell RNA sequencing.

PROVIDER: PRJNA609172 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11195870_1.fastq.gz	Fastqsanger.gz
	SRR11195870_2.fastq.gz	Fastqsanger.gz
	SRR11195871_1.fastq.gz	Fastqsanger.gz
	SRR11195871_2.fastq.gz	Fastqsanger.gz
	SRR11195872_1.fastq.gz	Fastqsanger.gz

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Understanding the transcriptional consequences of Lamin A deficiency within the immune compartment of the lung using single cell RNA sequencing.

Project description:To understand the transcriptional consequences of Lamin A deficiency within the immune compartment of the lung we conducted single cell RNA sequencing on sorted immune cells from WT vs. Lmna-flox/flox Vav1-cre-/- mice (in duplicate, 2 mice per group).

2023-07-24 | GSE146080 | GEO

Understanding the transcriptional consequences of the Progeria LmnaG609G mutation within the immune compartment of the lung using single cell RNA sequencing.

Project description:To understand the transcriptional consequences of Progeria LmnaG609G mutation within the immune compartment of the lung we conducted single cell RNA sequencing on sorted immune cells from WT vs. LmnaG609G/G609G mice (in duplicate, 2 mice per group).

2024-08-01 | GSE183249 | GEO

Understanding the transcriptional consequences of the Progeria LmnaG609G mutation within the immune compartment of the lung using single cell RNA sequencing.

Project description:Understanding the transcriptional consequences of the Progeria LmnaG609G mutation within the immune compartment of the lung using single cell RNA sequencing.

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Distinct structural and functional heterochromatin partitioning of lamin B1 and lamin B2 revealed using genome-wide Nicking Enzyme Epitope targeted DNA sequencing.

Project description:Gene expression is regulated by chromatin DNA methylation and other features, including histone post-translational modifications (PTMs), chromatin remodelers, and transcription factor occupancy. A complete understanding of gene regulation will require the mapping of these chromatin features in small cell number samples. Here we describe a novel genome-wide chromatin profiling technology, named as Nicking Enzyme Epitope targeted DNA sequencing (NEED-seq). NEED-seq offers antibody-targeted controlled nicking by Nt.CviPII-pGL fusion to study specific protein-DNA complexes in formaldehyde fixed cells, allowing for both visual and genomic resolution of epitope bound chromatin. When applied to nuclei, NEED-seq yielded genome-wide profile of chromatin associated proteins and histone PTMs. Additionally, NEED-seq of lamin B1 and B2 demonstrated their association with heterochromatin. Lamin B1 and B2 associated domains (LAD) segregated to three different states, and states with stronger LAD correlated with heterochromatic marks. Hi-C analysis displayed A and B compartment with equal lamin B1 and B2 distribution, although methylated DNA remained high in B compartment. LAD clustering with Hi-C resulted in subcompartments, with lamin B1 and B2 partitioning to facultative and constitutive heterochromatin respectively and were associated with neuronal development. Thus, lamin B1 and B2 show structural and functional partitioning in mammalian nucleus.

2025-01-16 | GSE261834 | GEO

CscoreTool-M infers 3D sub-compartment probabilities within cell population

Project description:Motivation: Computational inference of genome organization based on Hi-C sequencing has greatly aided the understanding of chromatin and nuclear organization in three dimensions (3D). However, existing computational methods fail to address the cell population heterogeneity. Here we describe a probabilistic modeling-based method called CscoreTool-M that infers multiple 3D genome sub-compartments from Hi-C data. Results: The compartment scores inferred using CscoreTool-M represents the probability of a genomic region locating in a specific sub-compartment. Compared to published methods, CscoreTool-M is more accurate in inferring sub-compartments corresponding to both active and repressed chromatin. The compartment scores calculated by CscoreTool-M also help to quantify the levels of heterogeneity in sub-compartment localization within cell populations. By comparing proliferating cells and terminally differentiated non-proliferating cells, we show that the proliferating cells have higher genome organization heterogeneity, which is likely caused by cells at different cell-cycle stages. By analyzing 10 sub-compartments, we found a sub-compartment containing chromatin potentially related to the early-G1 chromatin regions proximal to the nuclear lamina in HCT116 cells, suggesting the method can deconvolve cell cycle stage-specific genome organization among asynchronously dividing cells. Finally, we show that CscoreTool-M can identify sub-compartments that contain genes enriched in housekeeping or cell-type-specific functions. Availability: https://github.com/scoutzxb/CscoreTool-M

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CscoreTool-M infers 3D sub-compartment probabilities within cell population

Project description:CscoreTool-M infers 3D sub-compartment probabilities within cell population

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Lamin and Lamin B receptor knockout

Project description:influence of lamin B rereceptor knockout and lamin A/C knockout on gene expression in cultured myoblast cells and in striated muscle tissue knockout samples are obtained by mating of heterozygous animals. Homozygous KO and wt animals of one litter are compared. Two boilogical replicates of KO samples are processed in parallel. wt samples are used as controls. One wt sample is processed per KO litter. Where appropriate two wt samples are used as biological replicates.

2013-01-28 | E-GEOD-37076 | biostudies-arrayexpress

Lamin and Lamin B receptor knockout

Project description:influence of lamin B rereceptor knockout and lamin A/C knockout on gene expression in cultured myoblast cells and in striated muscle tissue

2013-01-28 | GSE37076 | GEO

Lamin B1 and LAP2β resist cytoskeletal force to maintain lamin A/C meshwork organization and preserve nuclear integrity

Project description:The nuclear lamins are extremely long-lived proteins in most cell types. As a consequence, lamin function cannot be effectively dissected with temporal precision using standard knock-down approaches. Here, we apply the auxin inducible degron (AID) system to rapidly deplete each lamin isoform within one cell cycle and reveal the immediate impacts of lamin loss on the nucleus . Surprisingly, neither acute lamin A/C (LA/C), lamin B1 (LB1), nor lamin B2 (LB2) depletion altered nuclear shape or induced nuclear blebbing, indicating that acute lamin loss is not sufficient to alter nuclear morphology. LB1 depletion is immediately followed by LA/C meshwork disorganization due to actin cytoskeletal forces on the lamina, yet neither LA/C nor LB1 depletion induced nuclear rupturing. We found that the abundant inner nuclear membrane protein LAP2β protects nuclear integrity in the absence of LB1, as depletion of both LB1 and LAP2β induced severe LA/C disorganization and frequent nuclear rupturing. Depolymerization of the actin cytoskeleton halts nuclear rupture in LAP2β- and LB1-depleted nuclei. We conclude that both LB1 and LAP2β resist cytoskeletal force to maintain regular lamin A/C meshwork organization and preserve nuclear integrity.

2025-02-17 | GSE289252 | GEO

Cancer stem cell subpopulations within the CD44high human breast cancer stem cell compartment

Project description:The CD44hi compartment in human breast cancer is enriched in tumor-initiating cells, however the functional heterogeneity within this subpopulation remains poorly defined. From a human breast cancer cell line with a known bi-lineage phenotype we have isolated and cloned two CD44hi populations that exhibited mesenchymal/Basal B and luminal/Basal A features, respectively. Rather than CD44+/CD24-,Basal B (G4) cells, only CD44hi/CD24lo, epithelioid Basal A (A4) cells retained a tumor-initiating capacity in NOG mice, form mammospheres and exhibit resistance to standard chemotherapy. Microarray data obtained from Affymetrix Human Gene 1.0 ST Array Five replicates of A4 and 5 replicates of G4

2012-06-11 | E-GEOD-32455 | biostudies-arrayexpress

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