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High throughput single cell long-read sequencing analyses of same-cell genotypes and phenotypes in human tumors.

ABSTRACT: High throughput single cell long-read sequencing analyses of same-cell genotypes and phenotypes in human tumors.

PROVIDER: PRJNA878505 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR21492154_1.fastq.gz	Fastqsanger.gz
	SRR21492155_1.fastq.gz	Fastqsanger.gz
	SRR21492156_1.fastq.gz	Fastqsanger.gz
	SRR21492157_1.fastq.gz	Fastqsanger.gz
	SRR21492158_1.fastq.gz	Fastqsanger.gz

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High throughput single cell long-read sequencing analyses of same-cell genotypes and phenotypes in human tumors.

Project description:Single cell Nanopore sequencing of full-length RNAs (scNanoRNAseq) is transforming single cell multi-omics analysis, however it is computationally challenged and relying on paralleled short-read sequencing to curate errors. We developed scNanoGPS to calculate same-cell genotypes-phenotypes from scNanoRNAseq data and eliminate dependance on short-reads guidance. To test its accuracy, robustness and applications, we analyzed 6 single nuclei transcriptomes composited of 4 frozen tumors and 2 cancer cell lines. Our results showed that scNanoGPS accurately deconvoluted raw long-reads into single-cells and single-molecules without short-reads guidance and calculated same-cell gene expressions, isoforms, and mutations and copy numbers simultaneously for thousands of cells. In a kidney tumor, we can identify cell-type-specific alternatively spliced genes enriched in important tumorigenic pathways, in addition to expression levels. Further, we detected transcriptome-wide mutations of each cell-type, enabling direct cell-lineage (genotype) and cell-fate (phenotype) alignment to investigate tumor progression. Together, scNanoGPS addresses major computational challenges and largely simplifies experimental workflow of scNanoRNAseq.

2023-06-03 | GSE212945 | GEO

High throughput single cell long-read sequencing analyses of same-cell genotypes and phenotypes in human tumors.

Project description:Single-cell nanopore sequencing of full-length mRNAs transforms single-cell multi-omics studies. However, challenges include high sequencing errors and dependence on short-reads and/or barcode whitelists. To address these, we develop scNanoGPS to calculate same-cell genotypes (mutations) and phenotypes (gene/isoform expressions) without short-read nor whitelist guidance. We apply scNanoGPS onto 23,587 long-read transcriptomes from 4 tumors and 2 cell-lines. Standalone, scNanoGPS deconvolutes error-prone long-reads into single-cells and single-molecules, and simultaneously accesses both phenotypes and genotypes of individual cells. Our analyses reveal that tumor and stroma/immune cells express distinct combination of isoforms (DCIs). In a kidney tumor, we identify 924 DCI genes involved in cell-type-specific functions such as PDE10A in tumor cells and CCL3 in lymphocytes. Transcriptome-wide mutation analyses identify many cell-type-specific mutations including VEGFA mutations in tumor cells and HLA-A mutations in immune cells, highlighting the critical roles of different mutant populations in tumors. Together, scNanoGPS facilitates applications of single-cell long-read sequencing technologies.

| S-EPMC10336110 | biostudies-literature

Single-cell sequencing reveals the relationship between phenotypes and genotypes of Klinefelter syndrome

Project description:Single-cell sequencing reveals the relationship between phenotypes and genotypes of Klinefelter syndrome

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Distinct transcriptional profiles in the different phenotypes of neurofibroma from the same neurofibromatosis 1 subject

Project description:Background: Neurofibromatosis 1 (NF1) is one of the most common hereditary neurocutaneous disorders. Among clinical phenotypes of NF1, cutaneous neurofibroma (cNF) and plexiform neurofibroma (pNF) display distinct clinical manifestations and pNF should be carefully followed up due to its potential for malignant transformation. However, the detailed distinct features of pNF compared to the other phenotypes in NF1 remains unclear. Objective: To elucidate whether transcriptional features are altered between cNF and pNF within the same patient. Methods: Single-cell RNA-sequencing was performed on the isolated cNF and pNF cells from the same patient. Immunohistochemical analysis was conducted on 6 cNF and 5 pNF specimens from different subjects. Results: cNF and pNF have different microenvironment and distinct transcriptional profiles. Schwann cells with robust metabolic capacity and fibroblasts with cancer-associated fibroblast-like phenotype are enriched in pNF, while CD8 T cells with tissue residency markers are endowed in cNF. The density of CD8 T cells is histologically augmented in cNF. Conclusion: cNF and pNF, the different NF phenotypes in NF1, are transcriptionally distinct in terms of various involved cell types including immune cells.

2023-09-30 | GSE218493 | GEO

Comparative physiological and proteomic signatures reveal contrasting stay green and senescence phenotypes in drought tolerant and susceptible pearl millet and wheat genotypes

Project description:The marker- and genome-based development of drought resistant and high yield cereal crops is the most pressing activity in a constantly more stress- and harmful environment for plant productivity. Genome-based assisted breeding is only capable to cover 30-40 % of phenotypic variance according to the most recent GWAS studies. There are many processes which are not predictable by genome information, especially protein translation and activity which is crucial for phenotypic responses and survival of the plants under severe stresses. Therefore, we present comparative proteomic and physiological analysis under drought stress in two of the most important staple food crops pearl millet and wheat thereby representing C4 and C3 plants. Here, we have selected contrasting genotypes, and performed a large-scale comparative analysis from the molecular to the phenotypic level under drought stress. We were able to establish molecular-physiological phenotypes for: 1. Stay green protein signature in contrasting pearl millet genotypes which is highly correlated to the physiological data, in the submitted manuscript. 2. No clear indication of stay green proteome signatures in contrasting wheat genotypes but instead differential senescence proteome signatures not capable to cope with similar drought stress. These mechanisms are decisive for drought resistance and yield/grain filling under stress conditions and for the first time these physiological phenotypes (seed yield, root growth, and photosynthesis) are directly linked to the molecular proteomic phenotype. We think these results are of broad importance for the scientific community. This study demonstrates the enormous molecular and phenotypic plasticity because the selected genotypes represent the extreme points of stress adaptation and yield protection.

2021-02-15 | PXD021446 | Pride

Comparative Transcriptome Analysis of Two Rice Genotypes with Varying Tolerance to Salt Stress

Project description:The goals of this study were to compare the transcriptome of two rice genotypes under salt stress by RNA-Seq. We performed differential gene expression analysis by comparing samples of same genotypes in control and stress conditions and different genotypes in the same condition.

2024-04-15 | GSE210952 | GEO

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Project description:Same lang Raw sequence reads

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Distinct transcriptional profiles in the different phenotypes of neurofibroma from the same neurofibromatosis 1 subject

Project description:Distinct transcriptional profiles in the different phenotypes of neurofibroma from the same neurofibromatosis 1 subject

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Genotypes

Project description:Genotypes

2021-01-11 | OEX00011366 | NODE

Macrophage programming rewires cancer‑cell phenotypes

Project description:Macrophage programming rewires cancer‑cell phenotypes