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Single-cell reconstitution reveals persistence of clonal heterogeneity in the murine hematopoietic system [WES]

ABSTRACT: Single-cell reconstitution reveals persistence of clonal heterogeneity in the murine hematopoietic system [WES]

PROVIDER: PRJNA728047 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR14465162_1.fastq.gz	Fastqsanger.gz
	SRR14465162_2.fastq.gz	Fastqsanger.gz
	SRR14465163_1.fastq.gz	Fastqsanger.gz
	SRR14465163_2.fastq.gz	Fastqsanger.gz
	SRR14465164_1.fastq.gz	Fastqsanger.gz

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Single-cell reconstitution reveals persistence of clonal heterogeneity in the murine hematopoietic system [WES]

Project description:We transplanted a single HSC into irradiated mice, creating a clonal hematopoietic system. This allowed us to study mitotically stable allelic imbalances at peripheral compartments (T cells, B cells).

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Single-cell reconstitution reveals persistence of clonal heterogeneity in the murine hematopoietic system

Project description:Single-cell reconstitution reveals persistence of clonal heterogeneity in the murine hematopoietic system

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Single-cell reconstitution reveals persistence of clonal heterogeneity in the murine hematopoietic system [RNA-seq]

Project description:Single-cell reconstitution reveals persistence of clonal heterogeneity in the murine hematopoietic system [RNA-seq]

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Single-cell reconstitution reveals persistence of clonal heterogeneity in the murine hematopoietic system [RNA-seq]

Project description:We transplanted a single HSC into irradiated mice, creating a clonal hematopoietic system. Using RNA-Seq on the cDNA of the peripheral compartments (T cells, B cells), we studied mitotically stable transcriptional states of the alleles of the entire transcriptome on the differentiating HSC.

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Single-cell reconstitution reveals persistence of clonal heterogeneity in the murine hematopoietic system

Project description:This SuperSeries is composed of the SubSeries listed below.

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Project description:We present Tracking Recombination Alleles in Clonal Engraftment using sequencing (TRACE-Seq), a novel methodology that utilizes barcoded rAAV6 donor template libraries, carrying either in-frame silent mutations or semi-randomized nucleotide sequences outside the coding region, to track the in vivo lineage contribution of gene targeted HSPC clones. By targeting the HBB gene with a rAAV6 donor template library consisting of ~20,000 possible unique exon 1 in-frame silent mutations, we track the hematopoietic reconstitution of HBB targeted myeloid-only, lymphoid-only, and multi-lineage repopulating human HSPC clones in immunodeficient mice.

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TRACE-Seq Reveals Clonal Reconstitution Dynamics of Gene Targeted Human Hematopoietic Stem Cells

Project description:TRACE-Seq Reveals Clonal Reconstitution Dynamics of Gene Targeted Human Hematopoietic Stem Cells

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Clonal heterogeneity in melanoma

Project description:Genetic heterogeneity is an important feature of solid tumors, however it is often assumed that most cancer cell lines are genetically homogeneous. A disparity in genetic complexity between cell lines and the disease they model could result in problems such as in vitro preclinical experiments overstating the effectiveness of putative therapeutics. We therefore derived clonal sublines by single cell cloning of in house derived early passage melanoma cell lines (LM-MEL-series), and compared their genomes to each other and the parental cell line using Illumina 610-Quad SNP arrays.

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AThi oHSC ATlo oHSC WES - Identifying clonal differences or differences in mutation burden between autophagy engaging and non-engaging hematopoietic stem cells during mouse aging.

Project description:We performed paired WES from DNA isolated from AThi and ATlo hematopoietic stem cells (FACS sorted on the basis of GFP marker intensity, 33% GFPlo as ATHi, 33% GFPhi as ATlo) using tail DNA as an internal control to identify somatic mutations. Few mutations were called at a variant allele frequency of ≥ 5% in this bulk sequencing approach, in line with recent results obtained with more sensitive methods. We also observed a high degree of shared mutations between AThi and ATlo oHSCs within each biological replicate, and no conserved mutations across biological replicates. The majority of called mutations were intronic or synonymous single nucleotide variants with limited expected consequences for their encoded proteins. Taken together, these results indicate that differing autophagy levels in oHSCs are not explained by clonal divergence or differential mutagenic burden, nor do they point to mutagenic burden as a driver of oHSC dysfunction in 24-month-old mice. They also do not provide evidence for clonal evolution between AThi and ATlo oHSC subsets.

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Project description:Maintenance of tissue-specific immunity is important for immunological fitness, but its establishment have been difficult to assess in humans. Here, we investigated reconstitution of the human uterine immune system by studying women undergoing uterus solid organ transplantation (UTx) or hematopoietic stem cell transplantation (HSCT). Through single-cell identification based on SNPs and disparate HLA expression using single-cell RNA sequencing or high-parameter flow cytometry, donor vs recipient cell origin was determined, and features of these cells were studied. Endometrial immune cell reconstitution occurred after both UTx and HSCT, at the transcriptomic, phenotypic, and spatial level. This occurred despite tacrolimus-induced calcineurin-mediated NFAT pathway inhibition, which affected de novo induction of tissue-residency features in vitro. Intriguingly, after HSCT, immune cells of male origin could reconstitute the endometrium. Collectively, our results proved insights into tissue immune system persistence and reconstitution capabilities in an organ undergoing continuous regeneration.

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