Expression data from early B cell progenitors including CLP,ProB and PreB of Pax5 knockout and wild type C57Bl6 mice
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE39554 | GEO | 2012/07/23
SECONDARY ACCESSION(S): PRJNA171116
REPOSITORIES: GEO
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Project description:we have investigated molecular and functional properties in early B-lineage cells from Pax-5 deficient animals crossed to a B-lineage restricted reporter mouse. Gene expression analysis of ex vivo isolated progenitor cells revealed that Pax-5 deficiency has a minor impact on Bcell specification.By comparison of gene expression patterns in ex vivo isolated Pax-5 and Ebf-1 deficient progenitors, it was possible to identify a set of B-cell restricted genes dependent of Ebf-1 but not Pax-5, supporting the idea that B-cell specification and commitment is controlled by distinct regulatory networks. wt ?5 reporter+ and Pax5ko ?5reporter+ fetal liver from d15 embryos isolated and transplanted into sublethaly irradiated mice. After 4 weeks B220+?5+ cells were sorted out from the bone marrow of the mice and subjected to microarray analyses
2012-07-22 | E-GEOD-39554 | biostudies-arrayexpress
Project description:We have determined that sustained expression of EBF suppresses alternate lineage genes independently of Pax5. Keywords: Transcription factor EBF restricts alternate lineage options and promotes B cell fate commitment independently of Pax5.
2007-12-15 | GSE9878 | GEO
Project description:We have determined that sustained expression of EBF suppresses alternate lineage genes independently of Pax5. Experiment Overall Design: Pax5-/- pro-B cells transduced with control or EBF retrovirus. Transduced cells were FACS sorted based on GFP expression and total RNA was isolated. RNA isolated from control or EBF transduced cells was analyzed using the Affymetrix Rat 230A microarrays.
2008-06-16 | E-GEOD-9878 | biostudies-arrayexpress
Project description:Loss of one allele of Ebf1 impairs pre-B cell (B220+CD19+CD43low/negIgM-) expansion. In order to better understand the underlying cause of the reduced pre-B cell compartment in Ebf1+/- mice, we sorted pro-B (B220+CD19+CD43highIgM- ) as well as pre-B cells from Wt and Ebf1 heterozygote mutant mice and performed Affymetrix based microarray gene expression analysis. While the overall gene expression patterns as well as Pax5 expression in Wt and Ebf1 pro-B cells were similar, gene set enrichment (GSE) analysis of the microarray data suggested a reduced expression of cell division (p<0.001) and mitosis (p<0.001) genes in the Ebf1+/- pre-B cells as compared to their Wt counterparts. This in combination with rather normal expression of B-lineage genes in Ebf1+/- pre-B cells opens for the possibility that the phenotypic loss of pre-B cells in Ebf1+/- mice could be a result of reduced expansion of progenitors rather than by a differentiation block.
2013-10-18 | GSE51385 | GEO
Project description:Loss of one allele of Ebf1 impairs pre-B cell (B220+CD19+CD43low/negIgM-) expansion. In order to better understand the underlying cause of the reduced pre-B cell compartment in Ebf1+/- mice, we sorted pro-B (B220+CD19+CD43highIgM- ) as well as pre-B cells from Wt and Ebf1 heterozygote mutant mice and performed Affymetrix based microarray gene expression analysis. While the overall gene expression patterns as well as Pax5 expression in Wt and Ebf1 pro-B cells were similar, gene set enrichment (GSE) analysis of the microarray data suggested a reduced expression of cell division (p<0.001) and mitosis (p<0.001) genes in the Ebf1+/- pre-B cells as compared to their Wt counterparts. This in combination with rather normal expression of B-lineage genes in Ebf1+/- pre-B cells opens for the possibility that the phenotypic loss of pre-B cells in Ebf1+/- mice could be a result of reduced expansion of progenitors rather than by a differentiation block. RNA was extracted from 20,000 or 25000 purified adult bone marrow cells using the RNAeasy microkit. RNA was labeled and amplified by dual amplification and hybridized to Affymetrix microarray MOE430_2, according to AffymetrixTM GeneChip Expression Analysis Technical Manual. Probe level expression values were calculated using the RMA algorithm.
2013-10-18 | E-GEOD-51385 | biostudies-arrayexpress
Project description:In order to investigate how transcription factor dose impacts B-lymphocyte development, we generated mice carrying transheterozygous mutations in the Pax5 and Ebf1 genes. While combined reduction of Pax5 and Ebf1 dose had minimal impact on the development of the earliest CD19+ progenitors, these cells displayed an increased T-cell potential in vivo and in vitro. Alteration in lineage fate depended on a Notch1 mediated conversion process while no signs of de-differentiation could be detected. The differences in functional response to Notch signaling in Wt and Pax5+/-Ebf1+/- pro-B cells was reflected in the transcriptional response because even though cells of both genotypes responded by the generation of intracellular Notch1 and activation of a set of target genes, only the Pax5+/-Ebf1+/- pro-B cells down-regulated genes central for the preservation of stable B-cell identity. This report stresses the importance of transcription factor dose in lymphocyte development and suggests that Pax5 and Ebf1 collaborate to modulate the transcriptional response to Notch signaling after the generation of activated intracellular Notch1. This provides an insight to how transcription factors like Ebf1 and Pax5 preserve cellular identity during differentiation. EBF-1 ChIP-seq: Cultivated CD43+IgM- cells (ProB) cells from Wt, EBF-1 +/-, PAX-5 +/- and EBF-1 +/- PAX-5 +/- (TH) were assessed for EBF-1 binding by ChIP-seq. Replicate Ebf1 ChIP-seq runs on each genotype (Wt, TH, Ebf1+/- and Pax5+/-) and corresponding inputs were pooled into one dataset and analyzed as one combined sample per genotype. RNA-seq no treatment: Briefly, ProB-cells from C57BL/6J Ebf1+/-Pax5+/- (n=4), WT (n=4), Ebf1+/- (n=2) and Pax5+/- (n=2) were sorted and RNA extracted with Qiagen RNeasy Micro Kit. RNA was sent to UCLA Microarray Core for library preparation and were subsequently for 50 cycles of HiSeq 2000 SBS sequencing generating 20-30 million reads/sample. Data analysis was performed with Arraystar® (DNASTAR)). RNA-seq 1 day on OP9DL1 and OP9: In short, in vitro expanded ProB-cells from C57BL/6J Ebf1+/-Pax5+/- (n=4) and WT (n=4) were exposed either on OP9 or OP9-DL1 stromal cells for 24 hours and RNA extracted with Qiagen RNeasy Micro Kit. Due to low reads, two Wt and Ebf1+/-Pax5+/- were sequenced twice. Libraries were constructed using Nugen's Ovation Ultralow Library systems and were subsequently for 50 cycles of NextSeq500 sequencing generating 20-30 million reads/sample. Data analysis was performed with Arraystar® (DNASTAR)).
2015-05-27 | E-GEOD-69227 | biostudies-arrayexpress
Project description:Human lymphopoiesis is a dynamic life-long process that starts in utero at 6 weeks gestation; however developmental pathways defining fetal lymphopoiesis are largely unexplored. While the first committed B-progenitor in normal human bone marrow (BM) is a CD10+ve ProB-progenitor, the identification of a CD10-ve B-progenitor (Pre/ProB progenitor) in cord blood suggests there may be a second B-lymphoid development program in fetal life. Here, we provide a comprehensive analysis of the fetal B-cell developmental hierarchy and report the presence of both PreProB- and ProB-progenitors in fetal tissues and describe their ontogeny, molecular and functional characteristics. PreProB- and ProB-progenitors appear early in the first trimester in fetal liver, followed by a sustained second wave of B-progenitor development in fetal BM, where together they form >40% of the total HSC/progenitor pool. Unexpectedly, one-third of the B-progenitors (13±1% of lin-CD34+ cells) are CD10-ve PreProB-progenitors while, by contrast, PreProB-progenitors are virtually undetectable in adult BM. Single-cell transcriptomics and functional assays place PreProB- upstream of ProB-progenitors, identifying them as the first B-lymphoid restricted progenitor in human fetal life. Fetal BM PreProB- and ProB-progenitors both give rise solely to B-lineage cells yet they are transcriptionally distinct. PreProB- unlike ProB-progenitors, continue to express a number of key myeloid and stem cell genes and share some transcriptomic signatures with CD10-ve B-progenitor infant acute lymphoblastic leukemia blast cells. Our data identify PreProB-progenitors as the earliest B-lymphoid restricted progenitor in human fetal life, and suggest that this fetal-restricted committed B-progenitor might provide a permissive cellular context for prenatal B-progenitor leukemia initiation.
2019-08-06 | GSE122989 | GEO
Project description:In order to understand the developmental trajectories of early lymphocyte differentiation it is crucial to identify linage-restricted progenitors. It has become clear that the classical early lymphoid progenitor compartments in the bone marrow are molecularly and functionally heterogeneous which warrants further investigation to refine the marker combinations used to isolate these progenitors. Herein, an initial antibody screen revealed extensive surface marker heterogeneity amongst early lymphoid progenitors. This heterogeneity was resolved using single cell gene expression assays and single cell in vitro differentiation assays, identifying marker combinations that isolate functionally distinct populations. In addition, surface markers that could be used alone or in combination with classical targets to capture specific stages of B-cell development were identified in the screen. The data provides a greater resolution of the complexity of the lymphoid progenitor compartment within the bone marrow than has been understood to date and provides novel tools for the further identification of cell populations in B-lineage development.
2018-06-04 | GSE92464 | GEO
Project description:Mouse Bcell, upon ectopic expression of the transcription factor Cebpa for 18h, can be reprogrammed to iPS with extremely high efficiency. To understand the molecular control of this phenomena we performed multiple high throughtput functional genomic analysis. Transcriptomic by microarray in Bcell, Bcell+Cebpa18h, Bcell+Cebpa18h+OKSM1d, Bcell+Cebpa18h+OKSM2d, ES cells
2016-02-19 | E-GEOD-71213 | biostudies-arrayexpress
Project description:Mouse Bcell, upon ectopic expression of the transcription factor Cebpa for 18h, can be reprogrammed to iPS with extremely high efficiency. To understand the molecular control of this phenomena we performed multiple high throughtput functionnal genomic analysis. Chromatin accessibility by ATACseq in Bcell, Bcell+Cebpa18h, Bcell+Cebpa18h+OKSM1d, Bcell+Cebpa18h+OKSM2d, ES cells
2016-02-19 | E-GEOD-71214 | biostudies-arrayexpress