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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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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

Project description:To understand relapse mechanisms related to AML patients treated with venetoclax plus azacitidine therapy, we performed CITE-seq on paired diagnosis and relapse specimens from an AML patient treated with the therapy.

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CITE-seq analysis of mouse LSK cells

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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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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Human Early Postnatal Thymus [CITE-seq]

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Comprehensive Benchmarking of CITE-seq versus DOGMA-seq Single Cell Multimodal Omics

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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Autonomous neutrophil ageing in the lung governed by the pulmonary microbiome

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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Project description:Single-cell RNA-sequencing (scRNA-Seq) is widely used to characterize immune cell populations. However, mRNA levels correlate poorly with expression of surface proteins, which are well established to define immune cell types. CITE-Seq (cellular indexing of transcriptomes and epitopes by sequencing) utilizes oligonucleotide-tagged antibodies to simultaneously analyze surface phenotypes and transcriptomes. Considering the high costs of adding surface phenotyping to scRNA-Seq, we aimed to determine which of 188 tested CITE-Seq antibodies can detect their antigens on human peripheral blood mononuclear cells (PBMCs), a commonly interrogated cell population in immunology, and find the optimal concentration for staining. The recommended concentration was optimal for 76 antibodies, whereas staining quality of 7 antibodies improved when the concentration was doubled. 33 and 8 antibodies still worked well when the concentration was reduced to 1/5 or 1/25, respectively. 64 antigens were not detected at any antibody concentration. Optimizing the antibody panel by removing antibodies not able to detect their target antigens and adjusting concentrations of the remaining antibodies could enable a cost reduction of almost 50%. In conclusion, our data are a resource for building an informative and cost-effective panel of CITE-Seq antibodies and use them at their optimal concentrations in future CITE-seq experiments on human PBMCs.

2022-09-18 | GSE213282 | GEO

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