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Effect of methanol fixation on single cell RNA sequencing of the murine dentate gyrus.

ABSTRACT: Effect of methanol fixation on single cell RNA sequencing of the murine dentate gyrus.

PROVIDER: PRJNA970711 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR24478455_1.fastq.gz	Fastqsanger.gz
	SRR24478455_2.fastq.gz	Fastqsanger.gz
	SRR24478456_1.fastq.gz	Fastqsanger.gz
	SRR24478456_2.fastq.gz	Fastqsanger.gz
	SRR24478457_1.fastq.gz	Fastqsanger.gz

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Effect of methanol fixation on single cell RNA sequencing of the murine dentate gyrus.

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Single-cell transcriptome of cerebral organoids with and without methanol fixation

Project description:To study how methanol fixation affects single-cell transcriptomic measurement, two cerebral organoids were dissociated. Cell suspension of each organoid was split into two aliquots. Methanol fixation was applied to one of the two aliquots. Single-cell RNA-seq with 10x Genomics was applied to the two aliquots separately.

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Single-Cell Transcriptome Analysis of Acute Myeloid Leukemia Cells Using Methanol Fixation and Cryopreservation

Project description:Introduction: The application of single-cell RNA sequencing has greatly improved our under-standing of various cellular and molecular mechanisms involved in physiological and pathophysi-ological processes. However, obtaining living cells for this technique can be difficult under certain conditions. To solve this problem, the methanol fixation method appeared as a promising alternative for routine clinical use. Materials and Methods: In this study, we selected two AML samples that had been fixed in methanol for 12–18 months. Once the cells were rehydrated, these samples were subjected to single-cell RNA sequencing. We then compared the results obtained from these samples with those obtained from the same samples cryopreserved in DMSO. Results: We used a previously validated methanol fixation protocol to perform scRNA-seq on DMSO cryopreserved cells and cells fixed in methanol for more than one year. Preliminary results show that methanol fixation induces some genetic and transcriptional modification compared with DMSO cryopreservation but remains a valuable method for single-cell analysis of primary human leukemia cells. Conclusions: The initial findings from this study highlight certain resemblances in methanol fixation over a 12-month period and cryopreservation with DMSO, along with associated transcriptional level modifications. However, we observed genetic degradation in the fixation condition when extending beyond one year. Despite certain study limitations, it is evident that short-term methanol fixation can be effec-tively used for leukemia blast samples. Its ease of implementation holds the potential to simplify the integration of this technique into routine clinical practice.

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