RNA- and ATAC-seq data of Wt, Ebf1-KO and Pax5-KO FL-ProB-cells.. Mus musculus

EBF1 and PAX5 are crucial factors for B-cell development. Knock down of either factor leads to an arrest in differentiation. RNA-seq data of WT, Ebf1-/- and Pax5-/- FL-ProB cells allowed for identification of activated and repressed target genes. ATAC-seq data of corresponding cell populations could connect gene activity and chromatin accessibility. This finding provided an explanation to the lineage instability observed in early B-cell progenitors. Taken together, the reported data provide an increased insight into mechanisms governing regulation of stage- and lineage specific transcription in early B-lymphocyte development. Overall design: ATAC-seq was performed on 80k cultured Fetal Liver ProB cells from Wt, Ebf1-/- or Pax5-/- mice to study changes in chromatin accessibility due to the loss of these proteins important for B-cell development. RNA seq was performed on cultured Fetal Liver ProB cells from Wt, Ebf1-/- or Pax5-/- mice to study changes in genes expression due to these genetic alterations. Data was aligned to mouse reference genome (mm10 /GRCm38)analysis and analyzed using the HOMER platform. ATAC and RNA-seq data was analyzed in relation to ChIP binding positions for Ebf1 and Pax5 on re-analyzed data retrieved from previously published ChIP-seq data deposited on GEO under: EBF1 (GSE69227) (Ungerback et al., 2015), PAX5 (GSE38046) (Revilla et al., 2012), or in relation to RNA seq data from CLP sub-fractions deposited under GSE92540 Please note that each processed data file was generated from multiple samples, as indicated in the corresponding sample description field.