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Bulk RNA-seq dataset of uninjured vs injured larval zebrafish hearts at 48 hours post injury on 5 days post fertilisation

ABSTRACT: Bulk RNA-seq dataset of uninjured vs injured larval zebrafish hearts at 48 hours post injury on 5 days post fertilisation

PROVIDER: PRJEB46994 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR6501830_1.fastq.gz	Fastqsanger.gz
	ERR6501830_2.fastq.gz	Fastqsanger.gz
	ERR6501831_1.fastq.gz	Fastqsanger.gz
	ERR6501831_2.fastq.gz	Fastqsanger.gz
	ERR6501832_1.fastq.gz	Fastqsanger.gz

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Bulk RNA-seq dataset of uninjured vs injured larval zebrafish hearts at 48 hours post injury on 5 days post fertilisation

Project description:This experiment sought to understand the transcriptomic changes that occur in the larval zebrafish heart following injury. 600 hearts were laser injured at 3 days post fertilisation, extracted 48 hours later and pooled into three groups of 200. RNA was extracted from the whole heart(s) and sent for sequencing along with 3 groups of 200 uninjured hearts, extracted and processed identically. RNA sequencing, quality control and alignment was performed by the commercial company GENEWIZ.

2021-10-01 | E-MTAB-10860 | biostudies-arrayexpress

RNA sequencing on uninjured and injured cardiac regions of B6 and C3H strains

Project description:Purpose: To analyze gene expression in calcific (C3H) and non-calcific (B6) hearts Methods: B6 and C3H mice were induced cardiac injury by rapid freeze thaw of cardiac tissue (cryo-injury). A left thoracotomy was performed at the level of 2nd intercostal space and the exposed beating heart was frozen for 10 seconds by gently pressing a pre-cooled steel rod of 1mm diameter in dry ice. Freezing of cardiac tissue was confirmed by the rapid discoloration of the tissue. Seven days after injury, injured and uninjured regions from same heart were used for RNA sequence. Results: In contrast to only 70 odd genes that were differentially upregulated following injury in non-calcified mouse hearts (B6) about 960 genes were upregulated in C3H hearts following injury induced calcification. Out of the 960 differentially upregulated genes, only 35 were found to be common or upregulated in both C3H and B6 hearts after injury illustrating of the overlapping but dramatically different magnitude of the injury response. Families of genes regulating diverse aspects of an injury response including inflammation, extracellular matrix proteins, cell proliferation and collagen production were differentially expressed between the calcific and non-calcific hearts after injury. The mean expression of osteogenic genes (osteogenic signature) was significantly higher in injured C3H hearts compared to uninjured C3H hearts. The osteogenic signature was not higher in injured B6 hearts compared to control uninjured B6 hearts. Conclusions: Calcific hearts compared to non-calcific hearts responded to injury with a dramatically different transcriptional program.

2016-11-07 | GSE87837 | GEO

Transcriptomic analysis of injured and uninjured knee joints from Trem2 KO mice [bulk RNA-seq]

Project description:Trem2 is a single-pass transmembrane receptor of the immunoglobulin superfamily and is primarily expressed in myeloid cells. Cells from injured and uninjured knee joints of wildtype C57BL/6 mice and Trem2 KO mice were sequenced to determine if Trem2 plays a role in macrophage differentiation or function after joint injury.

2022-07-18 | GSE200842 | GEO

bulk RNAseq of uninjured and 18 hours post-methyl bromide lesion FACS Horizontal basal cells (HBCs)

Project description:RNAseq analysis of uninjured vs 18hpl injured HBCs show heterogeneous modulation of pathways associated with quiescent stem cell activation. HBCs are the trp63 expressing, quiescent basal stem cell in the olfactory epithelium.

2017-06-08 | GSE92779 | GEO

Skeletal muscle injury-responsive macrophage subsets in larval zebrafish

Project description:Single-cell RNA-sequencing (scRNA-seq) was applied to identify and characterise macrophage subsets that responded to larval zebrafish muscle injury. The Tg(mpeg1:mCherry) transgenic zebrafish line was utilised to isolate mCherry-expressing macrophages by FACS. Following needle-stab muscle injury of a 4 days post fertilisation (dpf) larvae, the wound site was dissected out at 1, 2, and 3 days post injury (dpi) for macrophage isolation. Macrophages isolated from 4 dpf-uninjured larvae were also included. This analysis led to the identification of 8 discrete clusters of macrophages, one of which corresponded to uninjured macrophages. The 7 wound-present macrophage subsets highlighted greater macrophage heterogeneity than previously described in an in vivo skeletal muscle injury context.

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Transcriptomic analysis of injured and uninjured knee joints from Trem2 KO mice [bulk RNA-seq]

Project description:Transcriptomic analysis of injured and uninjured knee joints from Trem2 KO mice [bulk RNA-seq]

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Transcriptomic profile of endogenous Tregs in mouse injured bone, muscle, skin and heart tissues compared to healthy spleen Tregs

Project description:We aimed to identify the changes in gene expression profile of Tregs isolated from the injured bone, muscle, skin and heart, compared to healthy (uninjured) spleen Tregs. The bone injury consisted of calvarial bone defects, the muscle injury involved volumetric muscle loss defect in the quadriceps and the skin injury involved full-thickness punch-biopsy wounds. The heart injury was performed using the left coronary artery ligation to induce myocardial infarction (MI). The Tregs accumulating within the injured tissues were isolated and purified by fluorescence activated cell sorting (FACS), at 7 days post-injury (which is the peak of Treg accumulation within these tissues post-injury).

2024-05-31 | GSE228871 | GEO

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