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Transcriptomic analysis of Brm-/- hematopoietic stem and progenitor cells (LSK)

ABSTRACT: Transcriptomic analysis of Brm-/- hematopoietic stem and progenitor cells (LSK)

PROVIDER: PRJNA760773 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR15719779_1.fastq.gz	Fastqsanger.gz
	SRR15719779_2.fastq.gz	Fastqsanger.gz
	SRR15719780_1.fastq.gz	Fastqsanger.gz
	SRR15719780_2.fastq.gz	Fastqsanger.gz
	SRR15719781_1.fastq.gz	Fastqsanger.gz

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Transcriptomic analysis of Brm-/- hematopoietic stem and progenitor cells (LSK)

Project description:Little is known of hematopoietic stem (HSC) and progenitor (HPC) cell self-renewal. The role of Brahma (BRM), a chromatin remodeler, in HSC/HPC function is unknown. Bone marrow (BM) from Brm-/- mice manifested increased numbers of long- and short-term HSCs, GMPs, and increased numbers and cycling of functional HPCs. Brm-/- HSC/HPC show demonstrated functional differences compared to wildtype HSC/HPC in vivo and ex vivo, due in part to increased intracellular valine in lineage negative BM. To determine changes in gene programs associated with loss of BRM, we performed RNA sequencing on Brm-/- LSK cells. Brm-/- LSK exhibited upregulated interferon response/cell cycle gene programs, suggesting important extrinsic effects on primitive HSC/HPC from more mature HPC due to the absence of BRM.

2021-11-08 | GSE183430 | GEO

LSK immunophenotype hematopoietic stem cells after irradiation at day points in 3 weeks

Project description:In this study, we aimed to investigate the differentiation dynamics of LSK (Lin-Sca1+c-Kit+) cells following radiation injury. LSK cells, which are a critical component of the hematopoietic stem and progenitor cell population, play a vital role in the regeneration and repair of the hematopoietic system after damage. By utilizing these cells, we sought to understand the mechanisms underlying their response to radiation, focusing on their capacity for self-renewal and differentiation into various blood cell lineages.

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Single-cell RNA Sequencing Facilitates Quantitative Analysis of Fbxw11 overexpressed hematopoietic stem/progenitor cells

Project description:We compared the transcriptomic changes in hematopoietic stem/progenitor cells (LSK) when Fbxw11 overexpressed. In order to study the function of Fbxw11 in hematopoietic stem/progenitor cells.

2022-06-15 | GSE160643 | GEO

Single cell RNA_Seq in aging of hematopoietic stem and progenitor cells

Project description:Here, we use single-cell RNA-Seq to examine variation between individual hematopoietic stem and progenitor cells from two mouse strains (C57BL/6 and DBA/2) as they age. We prepared libraries from long-term (LT-HSCs) (LSK CD150+CD48-), short-term hematopoietic stem cells (ST-HSCs) (LSK CD150-CD48-) and multipotent progenitors (MPPs) (LSK CD150+CD48+) from young (2-3 months) and old mice (22 months for C57BL/6 and 20 months for DBA/2). Population controls for each cell type and age were isolated by sorting processed in parallel.

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Genome wide chromatin accessibility of Helios null hematopoietic stem and progenitor cells

Project description:This experiment aimed to determine Helios contribution in chromatin accessibility in hematopoietic stem and progenitor cells. Thus, we examined the change in chromatin accessibility in purified hematopoietic stem cells (LSK, Lin-Sca1+ckit+) from 10 weeks old WT and Helios deficient mice using the ATAC-seq approach. We found that Helios null LSK an affected Open Chromatin Region (OCR) landscape, overall in the proximity of genes regulating platelets functions.

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Ageing-associated proteome and acetylome of hematopoietic progenitor cells

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LSK immunophenotype hematopoietic stem cells in Dapp1 knockout mice

Project description:To investigate the impact of perturbing key differentiation driver genes on hematopoietic stem cell fate decision, we employed a Dapp1 gene knockout approach. This allowed us to observe changes in the subpopulations of hematopoietic stem cells at the LSK level in mice. Additionally, we assessed alterations in their fate decision and lineage differentiation tendencies

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Transcriptional profiling of Cebpa knock-in mutant LSK hematopoietic stem cells

Project description:Gene expression of LSK (lin-Sca-Kit+) hematopoietic stem cells from wild type mice was compared with LSK from Cebpa knock-in mutant mice (K/K, K/L, and L/L mutants). Fetal liver cells for each genotype were competitively transplanted into irradiant recipients. Donor-derived LSK cells were isolated by FACS sorting of recipient bone marrow. 3 biological replicates of each were generated and expression profiles were determined by hybridization to Affymetrix Moe430_2 arrays.

2009-11-03 | E-TABM-695 | biostudies-arrayexpress

The neurotransmitter receptor Gabbr1 regulates proliferation and function of hematopoietic stem and progenitor cells

Project description:To better understand molecular phenotypes of Gabbr1 null mutant hematopoietic stem and progenitor cells (HSPCs), we sorted and pooled ~12,000 HSPCs (LSK population) from WT or Gabbr1 null P15 bone marrow for bulk RNA-seq analysis.

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MLL regulated genes in LSK/CD48- hematopoietic stem cells

Project description:The histone methyltransferase mixed lineage leukemia (MLL) is essential to maintain hematopoietic stem cells and is a leukemia protooncogene. Although Hox genes are well-characterized targets of MLL and MLL fusion oncoproteins, the range of Mll-regulated genes in normal hematopoietic cells remains unknown. Here we identify and characterize part of the Mll-transcriptional network in hematopoietic stem cells with an integrated approach by using conditional loss-of-function models, genomewide expression analyses, chromatin immunoprecipitation, and functional rescue assays. The Mll-dependent transcriptional network extends well beyond the previously appreciated Hox targets, is comprised of many characterized regulators of self-renewal, and contains target genes that are both dependent and independent of the MLL cofactor, Menin. Interestingly, Prdm16 emerged as a target gene that is uniquely effective at partially rescuing Mll-deficient hematopoietic stem and progenitor cells. This work highlights the tissue-specific nature of regulatory networks under the control of MLL/Trithorax family members and provides insight into the distinctions between the participation of MLL in normal hematopoiesis and in leukemia. We used microarrays to determine the gene expression profiles of HSCs upon conditional deletion of Mll. LSK/CD48- HSCs were sorted from 5 pI:pC injected MllF/F control mice or 5 pI:pC injected Mx1-cre;MllF/F mice 6 days after the initial injection. Total RNA was purified from 1,500 to 10,000 sorted cells, amplified, labeled, fragmented and hybridized to GeneChip Mouse Genome 430 2.0 arrays from Affymetrix.

2013-05-24 | E-GEOD-47205 | biostudies-arrayexpress

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