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RNA sequencing of CTOT19 transplantation patients, and single-cell RNA sequencing of PBMC with and without LILRB3-4SNPs pretransplant and posttransplant

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE252274 | GEO | 2024/12/26

REPOSITORIES: GEO

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Single-cell RNA sequencing of PBMC with and without LILRB3-4SNPs pretransplant and posttransplant

Project description:Single-cell RNA sequencing were conducted on PBMCs from patients with and without LILRB3-4SNPs risk allele to evaluate the potential effects of this SNP on cell level.

2024-12-26 | GSE252273 | GEO

RNA sequencing of CTOT19 transplantation patients, and single-cell RNA sequencing of PBMC with and without LILRB3-4SNPs pretransplant and posttransplant

Project description:RNA sequencing of CTOT19 transplantation patients, and single-cell RNA sequencing of PBMC with and without LILRB3-4SNPs pretransplant and posttransplant

| PRJNA1059051 | ENA

Single-cell RNA sequencing of PBMC with and without LILRB3-4SNPs pretransplant and posttransplant

Project description:Single-cell RNA sequencing of PBMC with and without LILRB3-4SNPs pretransplant and posttransplant

| PRJNA1059053 | ENA

PBMC fixation and processing for Chromium single-cell RNA sequencing.

Project description:BackgroundInterest in single-cell transcriptomic analysis is growing rapidly, especially for profiling rare or heterogeneous populations of cells. In almost all reported works investigators have used live cells, which introduces cell stress during preparation and hinders complex study designs. Recent studies have indicated that cells fixed by denaturing fixative can be used in single-cell sequencing, however they did not usually work with most types of primary cells including immune cells.MethodsThe methanol-fixation and new processing method was introduced to preserve human peripheral blood mononuclear cells (PBMCs) for single-cell RNA sequencing (scRNA-Seq) analysis on 10× Chromium platform.ResultsWhen methanol fixation protocol was broken up into three steps: fixation, storage and rehydration, we found that PBMC RNA was degraded during rehydration with PBS, not at cell fixation and up to 3-month storage steps. Resuspension but not rehydration in 3× saline sodium citrate (SSC) buffer instead of PBS preserved PBMC RNA integrity and prevented RNA leakage. Diluted SSC buffer did not interfere with full-length cDNA synthesis. The methanol-fixed PBMCs resuspended in 3× SSC were successfully implemented into 10× Chromium standard scRNA-seq workflows with no elevated low quality cells and cell doublets. The fixation process did not alter the single-cell transcriptional profiles and gene expression levels. Major subpopulations classified by marker genes could be identified in fixed PBMCs at a similar proportion as in live PBMCs. This new fixation processing protocol also worked in several other fixed primary cell types and cell lines as in live ones.ConclusionsWe expect that the methanol-based cell fixation procedure presented here will allow better and more effective batching schemes for a complex single cell experimental design with primary cells or tissues.

| S-EPMC6050658 | biostudies-literature

Utilizing single-cell RNA sequencing for analyzing the characteristics of PBMC in patients with Kawasaki disease.

Project description:BackgroundKawasaki disease (KD) is the main cause of acquired heart disease in children and can lead to coronary artery lesions. This present study was designed to analyze the characteristics of KD peripheral blood mononuclear cells (PBMC) through single-cell RNA sequencing (scRNA-seq) and to explore the potential molecular mechanism of KD.MethodsPBMC was collected from one healthy child and one KD patient, and was used to single-cell RNA sequencing for cell clusters identification and differently expressed gene (DEG) determination. GO function enrichment analysis of DEG in B cell and T cells were performed to explore the most active biological function in KD immune cells.ResultsTwelve cell clusters can be identified in two samples. Compared with healthy child, naive CD8+ T cell, T helper cell and B cell in KD child were decreased, mainly immune-related T cells, and natural killer T (NKT) cell were increased. Cell activation, lymphocyte activation and regulation of immune system process were 3 GO function shared by all four types of T cells and B cell.ConclusionsImmune cell disorder appears in the KD patient at single cell level by scRNA-seq.

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RNA sequencing of 20 whole blood with and without LILRB3-4SNPs 3 months after kidney transplantation

Project description:RNA sequencing were conducted on 20 transplant patients with (n=10) and without (n=10) LILRB3-4SNPs risk allele 3 months after kidney transplantation to evaluate the potential effects of this SNP on post-transplant blood.

2024-12-26 | GSE261408 | GEO

MYC-negative BL frequent in posttransplant patients

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2014-12-12 | E-GEOD-64086 | biostudies-arrayexpress

MYC-negative BL frequent in posttransplant patients

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

2014-12-12 | GSE64086 | GEO

Temporally integrated single cell RNA sequencing analysis of PBMC from experimental and natural primary human DENV-1 infections.

Project description:Dengue human infection studies present an opportunity to address many longstanding questions in the field of flavivirus biology. However, limited data are available on how the immunological and transcriptional response elicited by an attenuated challenge virus compares to that associated with a wild-type DENV infection. To determine the kinetic transcriptional signature associated with experimental primary DENV-1 infection and to assess how closely this profile correlates with the transcriptional signature accompanying natural primary DENV-1 infection, we utilized scRNAseq to analyze PBMC from individuals enrolled in a DENV-1 human challenge study and from individuals experiencing a natural primary DENV-1 infection. While both experimental and natural primary DENV-1 infection resulted in overlapping patterns of inflammatory gene upregulation, natural primary DENV-1 infection was accompanied with a more pronounced suppression in gene products associated with protein translation and mitochondrial function, principally in monocytes. This suggests that the immune response elicited by experimental and natural primary DENV infection are similar, but that natural primary DENV-1 infection has a more pronounced impact on basic cellular processes to induce a multi-layered anti-viral state.

| S-EPMC7875406 | biostudies-literature

Metabolic Serum Profiles for Patients Receiving Allogeneic Stem Cell Transplantation: The Pretransplant Profile Differs for Patients with and without Posttransplant Capillary Leak Syndrome.

Project description:Allogeneic stem cell transplantation is commonly used in the treatment of younger patients with severe hematological diseases, and endothelial cells seem to be important for the development of several posttransplant complications. Capillary leak syndrome is a common early posttransplant complication where endothelial cell dysfunction probably contributes to the pathogenesis. In the present study we investigated whether the pretreatment serum metabolic profile reflects a risk of posttransplant capillary leak syndrome. We investigated the pretransplant serum levels of 766 metabolites for 80 consecutive allotransplant recipients. Patients with later capillary leak syndrome showed increased pretherapy levels of metabolites associated with endothelial dysfunction (homocitrulline, adenosine) altered renal regulation of fluid and/or electrolyte balance (betaine, methoxytyramine, and taurine) and altered vascular function (cytidine, adenosine, and methoxytyramine). Additional bioinformatical analyses showed that capillary leak syndrome was also associated with altered purine/pyrimidine metabolism (i.e., metabolites involved in vascular regulation and endothelial functions), aminoglycosylation (possibly important for endothelial cell functions), and eicosanoid metabolism (also involved in vascular regulation). Our observations are consistent with the hypothesis that the pretransplant metabolic status can be a marker for posttransplant abnormal fluid and/or electrolyte balance.

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