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Effects of fixation on natural microbial community metatranscriptomes

ABSTRACT: Testing the short term and long term effects of fixation on natural marine microbial community metatranscriptomes

PROVIDER: PRJEB23003 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR2820010_1.fastq.gz	Fastqsanger.gz
	ERR2820010_2.fastq.gz	Fastqsanger.gz
	ERR2820011_1.fastq.gz	Fastqsanger.gz
	ERR2820011_2.fastq.gz	Fastqsanger.gz
	ERR2820012_1.fastq.gz	Fastqsanger.gz

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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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