Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA119359 | ENA |
REPOSITORIES: ENA
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Project description:Analysis of IgM+CD27+ B cells in individuals with hepatitis C virus (HCV)-associated mixed cryoglobulinemia (MC). We have previously shown that HCV+MC+ individuals have clonal expansions of IgM+ memory B cells. This study aims to characterize differentially expressed genes in peripheral IgM+CD27+ B cells in HCV RNA+MC+ individuals, compared to HCV RNA+MC- subjects and HCV RNA- healthy controls. IgM+ B cells were isolated form donor PBMCs by immunomagnetic negative selection, and the CD27+ subset was further purified by positive selection. 2ng RNA was isolated from cells and amplified using the Nugen WT-Ovation Amplification Kit. cDNA was synthesized, biotin labeled, and hybridized to Illumina human v2 microarrays. Data were collected and analyzed with Illumina Genome Studio. Raw data were normalized by transforming measurements less than 0.01 to 0.01, normalizing per chip to the 50th percentile, and normalizing per gene to the median. Normalized data were then filtered to remove genes with control signals <170. Genes that were significantly upregulated in HCV RNA+MC+ vs HCV RNA+MC- subjects' IgM+CD27+ B cells were identified using a Welch t-test with p-calue cutoff 0.05 and Benjamini-Hochberg false discovery rate of 0.05. The resulting gene list was then filtered for genes showing >2-fold differential expression.
2009-10-01 | GSE18084 | GEO
Project description:Analysis of IgM+CD27+ B cells in individuals with hepatitis C virus (HCV)-associated mixed cryoglobulinemia (MC). We have previously shown that HCV+MC+ individuals have clonal expansions of IgM+ memory B cells. This study aims to characterize differentially expressed genes in peripheral IgM+CD27+ B cells in HCV RNA+MC+ individuals, compared to HCV RNA+MC- subjects and HCV RNA- healthy controls. IgM+ B cells were isolated form donor PBMCs by immunomagnetic negative selection, and the CD27+ subset was further purified by positive selection. 2ng RNA was isolated from cells and amplified using the Nugen WT-Ovation Amplification Kit. cDNA was synthesized, biotin labeled, and hybridized to Illumina human v2 microarrays. Data was collected in BeadStudio and exported to GeneSpring for analysis. Raw data were normalized by transforming measurements less than 0.01 to 0.01, normalizing per chip to the 50th percentile, and normalizing per gene to the median. Normalized data were then filtered to remove genes with control signals <170. Genes that were significantly upregulated in HCV RNA+MC+ vs HCV RNA+MC- subjects' IgM+CD27+ B cells were identified using a Welch t-test with p-calue cutoff 0.05 and Benjamini-Hochberg false discovery rate of 0.05. The resulting gene list was then filtered for genes showing >2-fold differential expression. 4 HCV Ab-, 6 HCV AB+/HCV RNA-, 12 HCV RNA+/IgM MC-, and 11 HCV RNA+/IgM MC+ samples analyzed. The supplementary file 'GSE18084_non-normalized_data.txt' contains non-normalized data for Samples GSM452094-GSM452126. This file was obtained from the GeneSpring platform.
2010-06-25 | E-GEOD-18084 | biostudies-arrayexpress
Project description:Cytosolic lipid droplets (LDs) are vital to Hepatitis C Virus (HCV) infection as the putative sites of virion assembly. To identify novel regulators of HCV particle production, we performed quantitative LD proteome analysis. Huh7.5 cells were labeled by stable isotope labeling with heavy amino acids in cell culture (SILAC) and subsequently infected with an HCV Jc1 reporter virus. After selection for HCV-infected cells, equal amounts of HCV-infected and uninfected control cells were mixed, LDs were isolated and analyzed by LC-ESI-MS/MS.
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Project description:Antibodies produced by B cells aid in recognition and clearance of pathogens and is the cornerstone of vaccination strategies. Humans produce nine different antibody isotypes and their effector functions differ according to the type of antigen and route of exposure. Phenotypic variation between isotype-swithched B cell subsets is expected but not studied in detail. To obtain a molecular definition of isotype-defined B cell identity, we performed proteomics and transcriptomics on isotype-defined populations of human naive and memory B cells (MBCs): CD27-IgM+IgD+, CD27+CD38lo/-IgM+IgD+, CD27+CD38lo/-IgM+IgD-, and IgA1, IgA2, IgG1, IgG2, IgG3, and IgG4 MBCs (CD27+CD38lo/-Ig+). Combined proteome and transcriptome analysis revealed that mRNA and protein expression profiles segregate separate isotype-defined B cell subsets according to their differentiation status. mRNA and protein expression levels correlated reasonably well for many genes. IgG4+ MBCs were most distinct from naive B cells. Besides a distinct expression profile of cytokine and Fc receptors, we identified a high expression of IgE-coding mRNA in IgG4-switched B cells. SDR16C5 was identified as uniquely upregulated in IgG4-switched B cells.
2026-03-12 | PXD060953 | Pride
Project description:Gene expression profiling of immortalized human mesenchymal stem cells with hTERT/E6/E7 transfected MSCs. hTERT may change gene expression in MSCs. Goal was to determine the gene expressions of immortalized MSCs.
2010-09-25 | GSE24338 | GEO
Project description: Not available
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Project description:Transcriptionnal analysis of pathogenic IgM Memory B cells stimulated or not with CpG from 3 differents HCV related Cryoglobulinemia.
2019-07-11 | GSE114357 | GEO
Project description:RNA extracted at 240min. Samples are rRNA depleted. Expression measurement of Homo sapiens genes.
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Project description:Transcriptional profiling of human mesenchymal stem cells comparing normoxic MSCs cells with hypoxic MSCs cells. Hypoxia may inhibit senescence of MSCs during expansion. Goal was to determine the effects of hypoxia on global MSCs gene expression.
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