3ff3c74c-d0b2-4c2b-aa48-c534cd259731 - samples
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ABSTRACT:
PROVIDER: EGAD00001010906 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:Human data for chromatin accessibility (ATAC-Seq) in eight B-cell precursors: HSC, CLP, pro-B, pre-B, Immature B, Transitional B, Naive B CD5-, Naive B CD5+ cells
| EGAD00001010908 | EGA
Project description:Human data for chromatin accessibility (ATAC-Seq) in eight B-cell precursors: HSC, CLP, pro-B, pre-B, Immature B, Transitional B, Naive B CD5-, Naive B CD5+ cells
| EGAD00001010909 | EGA
Project description:We generated paired transcriptomic (RNA-Seq) and chromatin accessibility (ATAC-Seq) profiles from 8 immune cell populations representing the early lymphoid hematopoietic differentiation stages along the B cell lineage: HSC, CLP, pro-B, pre-B, Immature B, Transitional B, Naive B CD5-, Naive B CD5+. Cell populations were isolated from healthy adult human bone marrow precursors and peripheral blood (n=13) following a predefined sorting strategy. For each donor, a subset of different cell type populations was obtained.
Additionally, to explore the continuous dynamic of RNA and ATAC, we generated a single-cell sample of human CD34+ B cell precursors.
| EGAS00001007296 | EGA
Project description:We have characterized several stages of normal human B cell development in adult bone marrow by gene expression profiling of hemopoietic stem cells, early B (E-B), pro-B, pre-B, and immature B cells, using RNA amplification and Lymphochip cDNA microarrays (n = 6). Hierarchical clustering of 758 differentially expressed genes clearly separated the five populations. We used gene sets to investigate the functional assignment of the differentially expressed genes. Genes involved in VDJ recombination as well as B lineage-associated transcription factors (TCF3 (E2A), EBF, BCL11A, and PAX5) were turned on in E-B cells, before acquisition of CD19. Several transcription factors with unknown roles in B lymphoid cells demonstrated interesting expression patterns, including ZCCHC7 and ZHX2. Compared with hemopoietic stem cells and pro-B cells, E-B cells had increased expression of 18 genes, and these included IGJ, IL1RAP, BCL2, and CD62L. In addition, E-B cells expressed T/NK lineage and myeloid-associated genes including CD2, NOTCH1, CD99, PECAM1, TNFSF13B, and MPO. Expression of key genes was confirmed at the protein level by FACS analysis. Several of these Ags were heterogeneously expressed, providing a basis for further subdivision of E-B cells. Altogether, these results provide new information regarding expression of genes in early stages of human B cell development. Total RNA was extracted from HSC, E-B (CLP), pro-B, pre-B, and IM-B cell populations from human BM, 6 different donors from each population. Total RNA was also extracted from naive B cells, centroblasts, centrocytes or memoty B cells from tonsils, each population was pooled from 4 different donors). The total RNA was amplified, and hybridized to Lymphochip cDNA microarrays
2010-06-25 | E-GEOD-14714 | biostudies-arrayexpress
Project description:An optimized whole genome bisulfite sequencing protocol (µWGBS, Farlik et al. 2015 Cell Reports) was used to establish DNA methylation profiles of FACS-purified stem and progenitor cells types of the human blood lineage. Most cell types were sorted from the peripheral blood of three donors each (43 donors total) with eight pools of ten cells, two pools of 50 cells, and one pool of 1000 cells. Additionally, two cell types (HSC, MPP) were sorted from bone marrow, fetal liver, and cord blood; single-cell methylome sequencing (scWGBS, Farlik et al. 2015 Cell Reports) was done for selected cell types (HSC, MPP, CMP, GMP, CLP, MLP0); and gene expression profiling using the Smart-seq2 protocol (Picelli et al. 2013 Nature Methods) was done on all stem/progenitor cell types (HSC, MPP, CMP, MEP, GMP, CLP, MLP0, MLP1, MLP2, MLP3).
2016-11-06 | GSE87196 | GEO
Project description:An optimized whole genome bisulfite sequencing protocol (µWGBS, Farlik et al. 2015 Cell Reports) was used to establish DNA methylation profiles of FACS-purified stem and progenitor cells types of the human blood lineage. Most cell types were sorted from the peripheral blood of three donors each (43 donors total) with eight pools of ten cells, two pools of 50 cells, and one pool of 1000 cells. Additionally, two cell types (HSC, MPP) were sorted from bone marrow, fetal liver, and cord blood; single-cell methylome sequencing (scWGBS, Farlik et al. 2015 Cell Reports) was done for selected cell types (HSC, MPP, CMP, GMP, CLP, MLP0); and gene expression profiling using the Smart-seq2 protocol (Picelli et al. 2013 Nature Methods) was done on all stem/progenitor cell types (HSC, MPP, CMP, MEP, GMP, CLP, MLP0, MLP1, MLP2, MLP3).
2016-11-06 | GSE87195 | GEO
Project description:we analyzed the gene expression profile of newly produced transgenic bone marrow subpopulations and compared it to the expression patterns obtained from cells isolated from wild type mice at different stages of the hematopoietic differentiation process. These populations were enriched in HSC, CMP, CD41+ c-kit+ and CD41+ c-kit- populations for the myelo-megakaryocytic lineage; and for the B lymphoid lineage, the populations were enriched in CLP, Pro-B and mature B lymphocytes. To produce comparable profiles total bone marrow RNA was used as a common reference.
2010-06-05 | E-GEOD-1289 | biostudies-arrayexpress
Project description:Studies from mouse models show that differences in self-reactivity, as read-out by CD5 levels, identifies naïve T cell subsets with distinct functional properties during an immune response. Whether CD5 levels can also be used to parse functional biases in naive human CD4+ T cells is incompletely understood. Our study establishes CD5 as a reliable marker of T cell self-reactivity and functional heterogeneity in human CD4+ T cells.
2020-04-15 | GSE148662 | GEO
Project description:Bivalency has been postulated to be a ‘poised’ state from which removal of one or the other mark permits gene activation or repression. To determine whether gene expression changes accompanied resolution of bivalent genes, we first obtained the expression pattern of hematopoietic stem cells (HSC), lymphoid-primed multipotent progenitors (LMPP), common lymphoid progenitors (CLP) , early thymic precursors (ETP), double negative 2 (DN2) and double negative 3 (DN3) cells using Affymetrix arrays. Consistent with trends noted in earlier studies, K4+ genes were, on average, expressed at higher levels compared to K4+K27+ or K27+ genes in all subsets.
2018-12-31 | GSE43427 | GEO
Project description:we analyzed the gene expression profile of newly produced transgenic bone marrow subpopulations and compared it to the expression patterns obtained from cells isolated from wild type mice at different stages of the hematopoietic differentiation process. These populations were enriched in HSC, CMP, CD41+ c-kit+ and CD41+ c-kit- populations for the myelo-megakaryocytic lineage; and for the B lymphoid lineage, the populations were enriched in CLP, Pro-B and mature B lymphocytes. To produce comparable profiles total bone marrow RNA was used as a common reference. Keywords: repeat sample
2004-12-01 | GSE1289 | GEO