Project description:The study profiled the effect of Phf6 deletion on gene expression in hematopoietic stem cells (HSCs), multipotent progenitor cells (MPPs) and hematopoietic progenitor cells (HPC-1). Phf6lox/Y;Tie2-creTg/+ mice were prepared on a C57BL/6 background so that Phf6 deletion could be selectively mediated by Tie2-cre. Cell populations were sorted from bone marrow samples using standard surface markers (Lin–SCA1+cKIT+(LSK) CD150+ CD48– for HSCs, Lin–SCA1+cKIT+(LSK) CD150– CD48– for MPPs and Lin–SCA1+cKIT+(LSK) CD150- CD48+ for HPC-1 cells). Phf6 intact and Phf6-delected cells of all three types were profiled by paired-end RNA-seq using an Illumina NextSeq 500 sequencer. RNA-seq libraries were prepared from the HPC-1 samples used a standard Illumina TruSeq library protocol whereas the libraries for the HSC and MPP samples used a SMART-seq ultra low input kit for cDNA synthesis and amplification. Statistical analysis of the TruSeq and SMART-seq samples was undertaken separately.
Project description:Peripheral inflammation affects hematopoietic stem and progenitor cells (HSPCs) in the bone marrow and induce myeloid lineage skewing of the progenitor cells. In this study, we performed single cell ATAC-sequencing in LSK (Lin—Sca-1+cKit+ ) and GMP (Lin—c-Kit+Sca1—CD16/32+CD34+) cells to determine the impact of ligature-induced periodontitis (LIP) on the epigenomic profile of these BM cells.
Project description:Reduced representation bisulfite sequencing (RRBS) of hematopoeitic stem/progenitor cells and mature B-cells from wild-type mice and mice transiently expressing Bcl6 under control of the Sca1 promoter. CBAxC57BL/6J mice were engineered to transiently express a Bcl6 cDNA in hematopoeitic stem/progenitor cells under control of the Sca1 promoter and then delete the transgene by cre-mediated recombination upon expression of Cd79a (Sca1-BCL6?). Hematopoeitic stem/progentior cells (HSPC, Sca1+Lin-) from the bone marrow and mature B-cells (B220+) from the peripheral blood were isolated from these mice and wild-type CBAxC57BL/6J mice by fluorescence activated cell sorting. Cells from 6-9 mice were pooled, for a total of 4 experimental conditions. DNA was extracted for each condition and analyzed by reduced representation bisulfite sequencing.
Project description:Analysis of hematopoietic LSK(Lin-Sca1+c-Kit+) cells lacking the Serum response factor (SRF) gene. Results provide insight into the role of SRF in regulating genetic programs important for hematopoietic stem cell development Comparison of the gene expression profile between murine Lin-Sca1+c-Kit+ cells from Mx-Cre C57BL/6 Srf WT (3) and C57BL/6 Srf KO (3). Cells were sorted by flow cytometry and RNA was harvested and hybridized to Affymetrix MOE430A.
Project description:The study was a comparison of gene expression using RNA-seq. We analyzed the stem and progenitor cells from WT and Vav-cre+ Tet2fl/fl Flt3-ITD (T2F3) mice. We isolated stem cells LSK (lin- sca+ kit+) and granulocyte-macrophage progenitors GMP (lin- sca- kit+ fcgr+ cd34+) cells from bone marrow. Comparisons were made across genotypes WT vs. T2F3 and cell types LSK vs. GMP.
Project description:compare the gene expression profile between irradiated Lin-Sca-1+c-Kit+ (LSK) cells from mouse bone marrow reconstituted with wild type and necdin null fetal liver cells The Affymetrix oligonucleotide array was used for this analysis compare the gene expression profile betweenirradiated Lin-Sca-1+c-Kit+ (LSK) cells from mouse bone marrow reconstituted with wild type and necdin null fetal liver cells
Project description:Runx/Cbfb heterodimers play important roles in the development of hematopoietic cells in mouse embryos and adults. In order to identify genes that are regulated by Runx/Cbfb, we purified Lin– c-kit+ Sca1+ (LSK) cells and Lin– c-kit+ Sca1– CD16/32+ (GMP) cells from Vav1-iCre x Cbfb(F/F) and Vav1-iCre x Cbfb(F/+) mice and profiled gene expression using microarray.
Project description:The study was a comparison of gene expression using RNA-seq. We analyzed the stem and progenitor cells from WT and Vav-cre+ Tet2fl/fl Flt3-ITD (T2F3) mice. We isolated stem cells LSK (lin- sca+ kit+) and granulocyte-macrophage progenitors GMP (lin- sca- kit+ fcgr+ cd34+) cells from bone marrow. Comparisons were made across genotypes WT vs. T2F3 and cell types LSK vs. GMP. Comparison of WT and Tet2-/-Flt3ITD bone marrow stem and progenitor cells.
Project description:compare the gene expression profile between irradiated Lin-Sca-1+c-Kit+ (LSK) cells from mouse bone marrow reconstituted with wild type and necdin null fetal liver cells The Affymetrix oligonucleotide array was used for this analysis
Project description:Small RNA sequenicg was performed on mouse bone marrow GMPs (Lin-, cKit+, Sca1-, CD34+, CD16/32 hi) labeled by osteoblastic cell derived extracellular vesicles as indicated by GFP labeling. Cells were isolated by FACS sorting from the bone marrow of Ocn-GFPTopaz mice and total RNA was extracted using the miRNeasy micro kit from (Qiagen)
