Investigation of epigenetic features of human B cells
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE326191 | GEO | 2026/05/14
REPOSITORIES: GEO
Similar Datasets
Project description:This dataset was generated as part of a multi-omics study aimed at investigating human B cells development. The study included bulk and single cell epigenetic methodologies coupled with single cell transcriptomics and proteomics. Data included in this submission were generated using the 10x Chromium Single Cell Multiome ATAC + Gene Expression method to allow simultaneous investigation of epigenetic and transcriptomic features in sorted B cells from human blood. The study demonstrated the emergence of epigenetic differences in B cell subsets at early stages of development that drive divergent developmental paths. Epigenetic features established at early stages are retained in distinct mature cell subpopulations, where they are coupled with transcription of accessible genomic regions. Identified features are retained after cell migration in secondary lymphoid organs.
2026-05-14 | GSE322590 | GEO
Project description:This dataset was generated as part of a multi-omics study aimed at investigating human B cells development. The study included bulk and single cell epigenetic methodologies coupled with single cell transcriptomics and proteomics. Data included in this submission were generated using the 10x Genomics single-cell RNA, V(D)J Sequencing and Protein feature barcoding method on sorted B cells from adult human blood. The study demonstrated the emergence of epigenetic differences in B cell subsets at early stages of development that drive divergent developmental paths. Epigenetic features established at early stages are retained in distinct mature cell subpopulations, where they are coupled with transcription of accessible genomic regions. Identified features are retained after cell migration in secondary lymphoid organs.
2026-05-14 | GSE321688 | GEO
Project description:This study aimed to characterize the whey proteome of colostrum, transitional milk, and mature milk from Murciano-Granadina goats, and to evaluate the use of transitional milk as a substitute for colostrum in feeding neonatal kids. Proteomic analysis identified a total of 1,385 proteins, with 736 in colostrum, 668 in transitional milk, and 625 in mature milk. Colostrum and transitional milk displayed a high degree of similarity between colostrum and transitional milk, particularly in proteins related to immune response and inflammation. In contrast, mature milk showed a shift toward proteins involved in metabolic and transport functions. To evaluate the practical application of transitional milk, newborn goat kids were fed either frozen colostrum (following standard farm protocol), freeze-dried colostrum, or freeze-dried transitional milk. All feeding strategies were well tolerated, with no adverse health effects, and resulted in similar growth performance. At 48 hours of life, serum IgG concentrations were 13.95 mg/mL in kids fed frozen colostrum, 17.36 mg/mL in those fed freeze-dried colostrum and 11.65 mg/mL in those fed freeze-dried transitional milk. Notably, kids fed freeze-dried transitional milk achieved satisfactory immunoglobulin levels, supporting its potential for passive immune transfer. These results highlight the biological value of transitional milk and support its use as a colostrum substitute in intensive farming systems, particularly when maternal colostrum is unavailable or insufficient. Furthermore, freeze-drying effectively preserved its functional properties, enabling convenient storage, handling, and administration. Overall, the successful use and preservation of transitional milk represent a sustainable approach to improving colostrum management, reducing waste, and increasing the efficiency of kid rearing in dairy goat production, in line with circular economy principles.
2026-04-29 | PXD068261 | Pride
Project description:Human milk fat globules, by enveloping cell contents during their secretion into milk, are a rich source of mammary cell RNA. Here, we pair this non-invasive mRNA source with RNA sequencing technology to probe the milk fat layer transcriptome during three stages of lactation: colostral, transitional, and mature milk production. We find that transcriptional profiles cluster not by postpartum day, but by milk Na:K ratio, indicating that women sampled during the same postpartum time frame could be at markedly different stages of gene expression. Each stage of lactation is characterized by a dynamic range (105-fold) in transcript abundances not previously observed with microarray technology. We discovered that transcripts for isoferritins and cathepsins are strikingly abundant during colostrum production, highlighting the potential importance of these proteins for neonatal health. Two transcripts, encoding M-NM-2-casein (CSN2) and a-lactalbumin (LALBA), make up 45% of the total pool of mRNA in mature lactation. Genes significantly expressed across all stages of lactation are associated with making, modifying, transporting, and packaging milk proteins. Stage-specific transcripts are associated with immune defense during the colostral stage, up-regulation of the machinery needed for milk protein synthesis during the transitional stage, and the production of lipids during mature lactation. We observed strong modulation of key genes involved in lactose synthesis and insulin signaling. In particular, PTPRF may serve as a biomarker linking insulin resistance with insufficient milk supply. This study provides the methodology and reference data set to enable future targeted research on the physiological contributors to sub-optimal lactation in humans. Milk fat mRNA profiles were generated from Day 2 and mature milk samples obtained from lactating mothers
2013-07-22 | E-GEOD-45669 | biostudies-arrayexpress
Project description:RNA-sequencing of the human milk fat layer during colostrum, transitional, and mature stages of lactation
| PRJNA195585 | ENA
Project description:Human milk fat globules, by enveloping cell contents during their secretion into milk, are a rich source of mammary cell RNA. Here, we pair this non-invasive mRNA source with RNA sequencing technology to probe the milk fat layer transcriptome during three stages of lactation: colostral, transitional, and mature milk production. We find that transcriptional profiles cluster not by postpartum day, but by milk Na:K ratio, indicating that women sampled during the same postpartum time frame could be at markedly different stages of gene expression. Each stage of lactation is characterized by a dynamic range (105-fold) in transcript abundances not previously observed with microarray technology. We discovered that transcripts for isoferritins and cathepsins are strikingly abundant during colostrum production, highlighting the potential importance of these proteins for neonatal health. Two transcripts, encoding β-casein (CSN2) and a-lactalbumin (LALBA), make up 45% of the total pool of mRNA in mature lactation. Genes significantly expressed across all stages of lactation are associated with making, modifying, transporting, and packaging milk proteins. Stage-specific transcripts are associated with immune defense during the colostral stage, up-regulation of the machinery needed for milk protein synthesis during the transitional stage, and the production of lipids during mature lactation. We observed strong modulation of key genes involved in lactose synthesis and insulin signaling. In particular, PTPRF may serve as a biomarker linking insulin resistance with insufficient milk supply. This study provides the methodology and reference data set to enable future targeted research on the physiological contributors to sub-optimal lactation in humans.
2013-07-22 | GSE45669 | GEO
Project description:miRNA profiling has been performed on normal mature B cells at different stages of differentiation (naive, germinal center and memory). The main goal is to identify miRNA signatures associated with differentiation stages of normal B cells. Keywords: miRNA, normal mature B cells Cells were isolated by magnetic cell sorting from tonsil tissues obtained from pediatric donors. Each phenotype is represented by 6 samples, each isolated from a different donor. The experiment does not include technical replicates.
2010-05-16 | E-GEOD-15144 | biostudies-arrayexpress
Project description:Single-cell sequencing methodologies such as scRNA-seq and scATAC-seq have become widespread and effective tools to interrogate tissue composition. Increasingly, variant callers are being applied to these methodologies to resolve the genetic heterogeneity of a sample, especially in the case of detecting the clonal architecture of a tumor. Typically, traditional bulk DNA variant callers are applied to the pooled reads of a single-cell library to detect candidate mutations. Recently, multiple studies have applied such callers on reads from individual cells, with some citing the ability to detect rare variants with higher sensitivity. Many studies apply these two approaches to the Chromium (10x Genomics) scRNA-seq and scATAC-seq methodologies. However, Chromium-based libraries may offer additional challenges to variant calling compared to existing single-cell methodologies, raising questions for the validity of variants obtained from such a workflow. To determine the merits and challenges of various variant-calling approaches on Chromium scRNA-seq and scATAC-seq libraries, we use sample libraries with matched bulk whole-genome-sequencing to evaluate the performance of callers. We review caller performance, finding that bulk callers applied on pooled reads significantly outperform individual-cell approaches. We also evaluate variants unique to scRNA-seq and scATAC-seq methodologies, finding patterns of noise but also potential capture of RNA-editing events. Finally, we review the notion that variant calling at the single-cell level can detect rare somatic variants, providing empirical results that suggest resolving such variants is infeasible in single-cell Chromium libraries.
2024-08-05 | GSE213503 | GEO
Project description:Single-cell sequencing methodologies such as scRNA-seq and scATAC-seq have become widespread and effective tools to interrogate tissue composition. Increasingly, variant callers are being applied to these methodologies to resolve the genetic heterogeneity of a sample, especially in the case of detecting the clonal architecture of a tumor. Typically, traditional bulk DNA variant callers are applied to the pooled reads of a single-cell library to detect candidate mutations. Recently, multiple studies have applied such callers on reads from individual cells, with some citing the ability to detect rare variants with higher sensitivity. Many studies apply these two approaches to the Chromium (10x Genomics) scRNA-seq and scATAC-seq methodologies. However, Chromium-based libraries may offer additional challenges to variant calling compared to existing single-cell methodologies, raising questions for the validity of variants obtained from such a workflow. To determine the merits and challenges of various variant-calling approaches on Chromium scRNA-seq and scATAC-seq libraries, we use sample libraries with matched bulk whole-genome-sequencing to evaluate the performance of callers. We review caller performance, finding that bulk callers applied on pooled reads significantly outperform individual-cell approaches. We also evaluate variants unique to scRNA-seq and scATAC-seq methodologies, finding patterns of noise but also potential capture of RNA-editing events. Finally, we review the notion that variant calling at the single-cell level can detect rare somatic variants, providing empirical results that suggest resolving such variants is infeasible in single-cell Chromium libraries.
2024-08-05 | GSE213338 | GEO
Project description:In our manuscript, we describe novel methodologies for bidirectional DNA methylation editing at targeted genomic loci through homologous recombination (HR) in human pluripotent stem cells. In order to gain insights on the applicability of these methodologies towards modeling epigenetic alterations, as well as for the development of platforms for cell transplantation upon epigenetic correction.
2017-12-01 | GSE63938 | GEO