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B lymphocyte activation induces DNA methylation reprogramming and establishes a common epigenetic signature in memory B and plasma cell compartments [DNA methylation profiling]

ABSTRACT: DNA methylation profiling of human B cell populations representing a developmental series before and after immune activation. The B cells are derived from inflamed tonsils. The B cells were already activated in vivo in patients, therefore there was no need to stimulate the B cells after isolation. Gene expression profiling was also performed from the same samples.

ORGANISM(S): Homo sapiens

PROVIDER: GSE24918 | GEO | 2013/08/13

SECONDARY ACCESSION(S): PRJNA133397

REPOSITORIES: GEO

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B lymphocyte activation induces DNA methylation reprogramming and establishes a common epigenetic signature in memory B and plasma cell compartments [DNA methylation profiling]

Project description:DNA methylation profiling of human B cell populations representing a developmental series before and after immune activation. The B cells are derived from inflamed tonsils. The B cells were already activated in vivo in patients, therefore there was no need to stimulate the B cells after isolation. Gene expression profiling was also performed from the same samples. Four B cell subsets: Naïve, germinal center B cells (GC), memory B cells, and plasma cells (PC) were purified by FACS ex vivo from tonsils of 8 human subjects. Methylated CpG island Recovery assay (MIRA) was utilized to enrich for methylated DNA fragments from each sample for microarray analysis. *** This Series reports DNA methylation profiling data. ***

2013-08-13 | E-GEOD-24918 | biostudies-arrayexpress

B lymphocyte activation induces DNA methylation reprogramming and establishes a common epigenetic signature in memory B and plasma cell compartments [gene expression profiling]

2013-08-13 | GSE24863 | GEO

B lymphocyte activation induces DNA methylation reprogramming and establishes a common epigenetic signature in memory B and plasma cell compartments [gene expression profiling]

Project description:DNA methylation profiling of human B cell populations representing a developmental series before and after immune activation. The B cells are derived from inflamed tonsils. The B cells were already activated in vivo in patients, therefore there was no need to stimulate the B cells after isolation. Gene expression profiling was also performed from the same samples. Four B cell subsets: Naïve, germinal center B cells (GC), memory B cells, and plasma cells (PC) were purified by FACS ex vivo from tonsils of 8 human subjects. Methylated CpG island Recovery assay (MIRA) was utilized to enrich for methylated DNA fragments from each sample for microarray analysis. RNA was copurified from the same cell samples for gene expression profiling on microarray. *** This Series reports gene expression profiling data. ***

2013-08-13 | E-GEOD-24863 | biostudies-arrayexpress

B lymphocyte activation induces DNA methylation reprogramming and establishes a common epigenetic signature in memory B and plasma cell compartments

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

2013-08-13 | E-GEOD-24919 | biostudies-arrayexpress

B lymphocyte activation induces DNA methylation reprogramming and establishes a common epigenetic signature in memory B and plasma cell compartments

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

2013-08-13 | GSE24919 | GEO

Expression data from CXCR4pos (centroblast) and CXCR4neg (centrocyte) Human Germinal Center B cells

Project description:Functional discrimination between normal centroblast and centrocyte obtained from human inflamed tonsils after cell sorting. We used microarrays to detail the segregation between these two B cell subsets

2009-06-04 | GSE15271 | GEO

DNA Methyltransferase 1 and DNA Methylation Patterning Contribute to Germinal Center B-Cell Differentiation

Project description:We performed DNA methylation (HELP) and gene expression profiling in 17 samples of purified Germinal center B cells (GCBs) and Naive B cells (NBC). We performed supervised analysis using HELP data and defined DNA methylation signature differentiting 2 subgroups of B cvells. Study included purification of human B cells form reactive tonsils, DNA purification and DNA methylation analysis using HELP assay.

2011-08-31 | E-GEOD-31671 | biostudies-arrayexpress

DNA methylation signatures follow preformed chromatin compartments in cardiac myocytes.

Project description: Not available

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Cross-tissue transcriptomic analysis of human secondary lymphoid organ residing ILC3 reveals a default quiescent state in the absence of inflammation

Project description:A cross tissue transcriptional comparison of human ILC3 isolated from non-inflamed lymph nodes (LN) and spleens, inflamed tonsils and the peripheral blood (PB). Using uniform gating and high-purity cell-sorting, ILC3 were sorted as Lineage(CD3,CD19,CD34,CD14,CD94)-CD45intCD127+CRTH2-CD117+. From LN, spleen, tonsils and PB, NKp44- ILC3 were isolated and, in addition, NKp44+ ILC3 were sorted from spleen and tonsils. RNA quality was measured on a RNA 6000 Pico Kit (Agilent Technologies) using a 2100 Bioanalyzer (Agilent Technologies). 100 pg high-quality RNA was isolated and cDNA was generated using the SMART-Seq (v3) Ultra Low Input RNA Kit (Clontech) with 15 cycles of amplification. Amplified and Covaris-fragmented cDNA was quality-checked on a High Sensitivity DNA chip (Agilent Technologies) and further processed according the TruSeq Nano DNA Library Preparation Kit (Illumina). Data was processed as follows: SMARTer adapters were trimmed with cutadapt and the resulting sequences were aligned to the human RefSeq transcriptome using 14 TopHat2 (Kim et al., 2013). Normalization and quantification was performed using Cufflinks (Trapnell et al., 2012). FPKM counts were determined per gene with HTSeq-count. Raw data has been deposited at the European Genome-Phenome Archive (www.ebi.ac.uk/ega) under accession EGAS00001002636.

2017-07-31 | E-MTAB-5909 | biostudies-arrayexpress

ena-DATASET-ErasmusMC-hema-04-09-2017-16:01:04:637-36 - samples

Project description:Rna sequencing of purified human group 3 innate lymphoid cells from non-reactive lymph nodes and spleen, inflamed tonsils and peripheral blood.

| EGAD00001003704 | EGA

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