Ontology highlight
ABSTRACT:
PROVIDER: PRJNA898579 | ENA |
REPOSITORIES: ENA
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Project description:We performed ATAC-sequencing in LSK cells (Lin(neg)/c-Kit(+)/Sca-1(+)) from shRNA mice carrying an shRNA for either Renilla or Stag2. ATAC-sequencing control (Renilla) and Stag2 knockdown cells.
2015-09-16 | E-GEOD-72367 | biostudies-arrayexpress
Project description:We performed ATAC-sequencing in LSK cells (Lin(neg)/c-Kit(+)/Sca-1(+)) from shRNA mice carrying an shRNA for either Renilla or Stag2.
2015-09-16 | GSE72367 | GEO
Project description:Hematopoietic conditional knockout (cKO) of Phf6 in a mouse retroviral-HoxA9 AML model led to increased transplantability and accumulation of a c-Kit+ Ly6C- population that we termed the 'Leukemia Initiating Cell-Enriched' (LIC-e) population. We performed bulk ATAC-Seq on the LIC-e population sort purified 4 days after transduction of Ctrl (Vav-Cre/+, Phf6 +/Y) or cKO (Vav-Cre/+, Phf6 flox/Y) marrow retrovirally transduced with HoxA9.
2023-12-15 | GSE249110 | GEO
Project description:We show that meteorin (Metrn) from hypoxic macrophages restrains hematopoietic stem cells (HSCs) proliferation and mobilization. In macrophages specific Metrn knockout mice, reactive oxygen species levels in HSCs were upregulated through activating phospholipase C signaling. Macrophage specific knockout mice for Metrn (Metrn-fl/fl*LysM-Cre) were generated. Transcriptome profiling (RNA-Seq) and differential gene expression analysis of bone marrow LSK (lin- sca-1+ c-kit+) cells from Metrn-fl/fl*LysM-Cre (Metrn-cKO) and Metrn-fl/fl mice was performed. Metrn cKO mice showed a regulatory role for HSPCs by macrophages.
2023-08-04 | GSE198825 | GEO
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.
2022-04-27 | GSE180025 | GEO
Project description:Global gene expression changes induced by Setbp1 and Setbp1(D/N) in purified mouse hematopoietic stem and progenitor cells were characterized by RNA-seq analysis; ChIP-seq studies to identify cooperation between SETBP1/SETBP1(D/N) and MLL1 in regulating gene transcription in hematopoietic stem and progenitor cells.
2021-12-17 | GSE167301 | GEO
Project description:To detect the role of OP9 stromal cells in our optimized 3D self-assembling peptide induction system followed by the OP9 coculture system. First, we used RNA-seq to analyze mouse pluripotent stem cells derived total cells at day5 between the 3D+OP9 and 3D+0.1% group in our hematopoietic differentiation system. In addition, to further evaluate hematopoietic transcriptome differences between Lin-Sca-1+c-kit+CD201+ cells and Lin-Sca-1+c-kit+CD201- cells, we used RNA-seq to analyze mouse pluripotent stem cells derived Lin-Sca-1+c-kit+CD201+ and Lin-Sca-1+c-kit+CD201- cells at day5 in our 3D+OP9 hematopoietic differentiation system.Meanwhile,we used the mouse embryonic stem cell(mESC) as negative control and bone marrow derived Lin-Sca-1+c-kit+CD201+ and fetal liver derived Lin-Sca-1+c-kit+CD201+ as positive control.
2021-06-28 | GSE175563 | GEO
Project description:Purpose: To gain more mechanistic insights into the effects of SDHB deletion on T cells, we performed ATAC seq in activated WT and SDHB cKO T cells. Methods: 5x104 cells per experiment were first washed with RSB buffer and gently permeabilized with RSB lysis buffer on ice. Cells were suspended in 50 uL of tagmentation master mix prepared from Illumina Tagment DNA TDE1 Enzyme and Buffer Kit components (#20034197), and transposition was performed for 30 minutes at 37°C. Tagmented DNA fragments were isolated using Qiagen MinElute PCR Purification columns prior to library amplification. ATAC-seq libraries were amplified with barcoded Nextera primers for 14 cycles, and excess primers were removed by size selection with AMPure XP beads. Libraries were sequenced on the HiSeq4000 platform running in PEx150bp mode. Results: ATAC-seq revealed distinctive patterns of DNA accessibility that are associated with genomic loci of genes involved in T cell activation and inflammation in activated WT and SDHB cKO CD4 T cells Conclusions: DNA accessibility that is associated with genomic loci of inflammatory genes and transcription factors that regulate inflammatory genes in CD4 T cells
2022-03-08 | GSE184742 | GEO