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ScRNA-seq studies

ABSTRACT: scRNA-seq studies

PROVIDER: PRJNA648132 | ENA |

REPOSITORIES: ENA

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			Action	DRS
		Other
	SRR12299417.fastq.gz	Fastqsanger.gz
	SRR12299418.fastq.gz	Fastqsanger.gz
	SRR12299419.fastq.gz	Fastqsanger.gz
	SRR12299420.fastq.gz	Fastqsanger.gz

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RNA-seq studies

Project description:RNA-seq studies

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scRNA-seq data of mouse splenocytes

Project description:We generated scRNA-seq data of mouse spenocytes that correspond to a previously published scATA-seq data.

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Single cell RNA-seq analysis links respiratory dysfunction to an extracellular matrix-specific damage response

Project description:Energy metabolism and extracellular matrix function are closely connected to orchestrate and maintain tissue organization, but the crosstalk is poorly understood. Here, we used scRNA-seq analysis to uncover the importance of respiration for extracellular matrix homeostasis in mature cartilage. Genetic inhibition of respiration in cartilage results in the expansion of a central area of 1-month-old mouse femur head cartilage showing disorganized chondrocytes and increased deposition of extracellular matrix material. scRNA-seq analysis identified a cluster-specific decrease in mitochondrial DNA-encoded respiratory chain genes and a unique regulation of extracellular matrix-related genes in nonarticular chondrocyte clusters. These changes were associated with alterations in extracellular matrix composition, a shift in the collagen/non-collagen protein content and an increase of collagen crosslinking and ECM stiffness. The results demonstrate, based on findings of the scRNA-seq analysis, that respiration is a key factor contributing to ECM integrity and mechanostability in cartilage and presumably also in many other tissues.

2022-02-17 | PXD027109 | Pride

RNA sequencing/Gene expression studies of G⍺13 signaling in lymphoma [scRNA-seq]

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Inferring TF activation order in time series scRNA-Seq studies.

Project description:Methods for the analysis of time series single cell expression data (scRNA-Seq) either do not utilize information about transcription factors (TFs) and their targets or only study these as a post-processing step. Using such information can both, improve the accuracy of the reconstructed model and cell assignments, while at the same time provide information on how and when the process is regulated. We developed the Continuous-State Hidden Markov Models TF (CSHMM-TF) method which integrates probabilistic modeling of scRNA-Seq data with the ability to assign TFs to specific activation points in the model. TFs are assumed to influence the emission probabilities for cells assigned to later time points allowing us to identify not just the TFs controlling each path but also their order of activation. We tested CSHMM-TF on several mouse and human datasets. As we show, the method was able to identify known and novel TFs for all processes, assigned time of activation agrees with both expression information and prior knowledge and combinatorial predictions are supported by known interactions. We also show that CSHMM-TF improves upon prior methods that do not utilize TF-gene interaction.

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HSPC scRNA seq

Project description:HSPC scRNA seq

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scRNA-seq of pluripotent stem cell derived human intestinal organoids

Project description:Here, we used single cell RNA-sequencing (scRNA-seq) to profile pluripotent stem cell derived human intestinal organoids (HIOs) grown in matrigel or a non-adhesive alginate hydrogel after 28 days of in vitro growth. Additionally, we used scRNA-seq to profile HIOs derived in the presence of Neuregulin 1 (NRG1) and/or EGF after 40 days of in vitro growth.

2021-05-21 | E-MTAB-10268 | biostudies-arrayexpress

[10x] scRNA-seq of mouse Plasmodium-specific CD4+ T cells

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2020-10-14 | E-MTAB-9317 | biostudies-arrayexpress

scRNA-seq of early brain organoid development from pluripotency

Project description:To study developmental trajectories in brain organoids, we conducted scRNA-seq and scATAC-seq in parallel on a dense timecourse of early development.

2022-08-18 | E-MTAB-12001 | biostudies-arrayexpress

Eosinophils scRNA-seq from healthy and asthmatic donors

Project description:scRNA-seq data from human eosinophils purified from blood samples. Samples include three healthy patients and three asthmatic donors.

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