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CITE-seq (cellular indexing of transcriptomes and epitopes by sequencing) of WT and RAS mutant specimens from acute myeloid leukemia (AML) patients.

ABSTRACT: CITE-seq (cellular indexing of transcriptomes and epitopes by sequencing) of WT and RAS mutant specimens from acute myeloid leukemia (AML) patients.

PROVIDER: PRJNA656531 | ENA |

REPOSITORIES: ENA

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			Action	DRS
		Other
	SRR12430452_1.fastq.gz	Fastqsanger.gz
	SRR12430452_2.fastq.gz	Fastqsanger.gz
	SRR12430453_1.fastq.gz	Fastqsanger.gz
	SRR12430453_2.fastq.gz	Fastqsanger.gz

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CITE-seq (cellular indexing of transcriptomes and epitopes by sequencing) of WT and RAS mutant specimens from acute myeloid leukemia (AML) patients.

Project description:To understand the role of RAS mutations in AML, we performed CITE-seq on diagnosis specimens from WT and RAS mutant AML patients.

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CITE-seq (cellular indexing of transcriptomes and epitopes by sequencing) of paired diagnosis and relapse specimens from acute myeloid leukemia (AML) patients treated with venetoclax plus azacitidine

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Project description:We performed cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) of the LSK compartment of TdT-reporter and TdT-fate mapping mice, in order to elucidate the heterogeneity and developmental trajectories within the MPP (lymphoid-primed multipotent progenitor) and HSC (hematopoietic stem cell) compartments.

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Human Early Postnatal Thymus [CITE-seq]

Project description:Within the thymus, regulation of the cellular cross-talk directing T cell development is dependent on spatial interactions within specialized niches. To create a holistic, spatially defined map of tissue niches guiding postnatal T cell development we employed the multidimensional imaging platform CO-detection by indEXing (CODEX), as well as Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) and Assay for Transposable-Accessible Chromatin (ATAC-seq). We generated age-matched 4–5-month-old postnatal thymus datasets for both male and female donors, and describe signaling and cell-cell interaction networks in sequential thymocyte developmental niches. Together, these data represent a unique age-matched spatial multiomic resource to investigate how sex-based differences in thymus regulation and T cell development arise, and provide an essential resource to understand the mechanisms underlying immune function and dysfunction in males and females.

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Project description:The recently developed transcription, epitopes, and chromatin accessibility by sequencing (TEA-seq) and similar DOGMA-seq single-cell trimodal omics assays provide unprecedented opportunities for understanding cell biology, but independent optimization, benchmarking and evaluation are lacking. We explored the utility, pros and cons of DOGMA-seq compared to the bimodal cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) assay in activated and stimulated human peripheral blood T cells. We identified an optimal incubation time and concentration of digitonin (DIG) for cell permeabilization and found that single-cell trimodal omics measurements after DIG permeabilization were generally better than after an alternative “low-loss lysis” (LLL) permeabilization condition. Next, we found that DOGMA-seq with optimized DIG permeabilization and its ATAC library provides more information, even though its mRNA and cell surface protein antibody-derived tag (ADT) libraries have slightly inferior quality, compared to CITE-seq. Finally, we recognized the additional value of DOGMA-seq for studying lineage-specific T helper cells.

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Project description:We used cellular indexing of transcriptomes and epitopes-based single cell RNA sequencing (CITE-scRNAseq) coupled with adoptive transfer approaches to determine tissue contribution to neutrophil diversity.

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