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Transcript profiling of Lin-Sca-1+c-Kit+ (LSK) cells from mice reconstituted with wild type and necdin null fetal liver cells following a sublethal dose of irradiation (6,5 Gy)

ABSTRACT: 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

ORGANISM(S): Mus musculus

PROVIDER: GSE39153 | GEO | 2012/09/05

SECONDARY ACCESSION(S): PRJNA170112

REPOSITORIES: GEO

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Transcript profiling of Lin-Sca-1+c-Kit+ (LSK) cells from mice reconstituted with wild type and necdin null fetal liver cells following a sublethal dose of irradiation (6,5 Gy)

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

2012-09-05 | E-GEOD-39153 | biostudies-arrayexpress

Expression data from small intestinal Lin-c-Kit+Sca-1- cells and Lin-c-Kit-Sca-1- cells.

2012-09-15 | GSE40882 | GEO

Expression data from small intestinal Lin-c-Kit+Sca-1- cells and Lin-c-Kit-Sca-1- cells.

Project description:Small intestinal innate lymphoid cells (ILCs) are known to regulate intestinal epithelial cell homeostasis and to help prevent pathogenic bacterial infections, by producing IL-22. However, other functions of these cells and the lineal relationship between ILCs and lymphoid or myeloid cells have not been clear. We performed a global gene expression analysis to examine which genes are highly expressed by small intestinal ILCs (Lin-c-Kit+Sca-1- cells) compared with non-ILCs (Lin-c-Kit-Sca-1- cells). To examine the gene expression profiles of ILCs within the small intestinal lamina propria (LP), we isolated Lingeage (Lin)-c-Kit+Sca-1- cells [consisting of NKp46+ ILC22 (Lin-c-Kit+Sca-1-NKp46+ cells) and LTi-like ILC (Lin-c-Kit+Sca-1-CD4+ cells)] as the ILC population, and Lin-c-Kit-Sca-1- cells as the non-ILC population, from the small intestinal LP of 8 week-old mice by FACS, then compared the gene expression profiles between these two populations by microarray analysis.

2012-09-15 | E-GEOD-40882 | biostudies-arrayexpress

Expression data from Bone marrow and Fetal liver Lineage-c-Kit+Sca-1+ (LSK) cells

Project description:Loss of polycomb-group gene Ezh2 causes activation of fetal gene signature in adult mouse bone marrow (BM) hematopoietic stem and progenitor cells (HSPCs). Ezh2 directly represses fetal-specific let-7 target genes, including Lin28, thereby cooperates with let-7 microRNAs in silencing fetal gene signature in BM HSPCs. We purified Lineage-Sca-1+c-Kit+ (LSK) HSPCs from E14.5 FL and adult BM and subjected them to microarray analysis.

2015-08-27 | E-GEOD-69760 | biostudies-arrayexpress

Gene expression data from lineage negative c-kit positive sca-1 positive hematopoietic stem cells (LSK, Lin-Sca-1+c-kit+) isolated from Jak2VF/+ vector and Jak2VF/+ Hmga2 mice

Project description:The JAK2V617F mutation has been detected in ~50% cases of MF. Elevated expression of high mobility group AT hook 2 (HMGA2) also has been frequently observed in patients with MF. Interestingly, upregulation of HMGA2 expression has been found in association with the JAK2V617F mutation in significant cases of MF. However, the contribution of HMGA2 in the pathogenesis of MF remains elusive. To determine the effects of concurrent expression of HMGA2 and JAK2V617F mutation in hematopoiesis, we transduced bone marrow cells from Jak2V617F knock-in mice with lentivirus expressing Hmga2 and performed bone marrow transplantation. In order to assess the effects of Hmga2 overexpression on gene expression, we performed RNA sequencing analysis for the LSK from Jak2VF/+ vector and Jak2VF/+ Hmga2mice.

2017-08-01 | GSE99485 | GEO

H3K27me3 ChIP-sequencing on LSK (Lin-Sca-1+c-kit+) cells isolated from control, MxCre Jak2VF/+ and MxCre Jak2VF/+ EZH2-/- mice

Project description:Inactivating EZH2 mutations have been associated with myelofibrosis (MF). Moreover, EZH2 mutations co-exist with the JAK2V617F mutation in a significant cases of MF. To determine the effects of concomitant loss of EZH2 and JAK2V617F mutation in hematopoiesis, we generated Ezh2-deficient Jak2V617F-expressing mice. To identify the Ezh2 target genes that are regulated by H3K27me3 in MF, we performed H3K27me3 ChIP-sequencing in sorted LSK cells from control, MxCre;Jak2VF/+ and MxCre;Jak2VF/+ EZH2-/- mice.

2016-04-19 | GSE79319 | GEO

Single cell RNA sequencing of LSK (lineage negative, Sca-1+, c-Kit+) cells isolated by fluorescence-activated cell sorting from the bone marrow of control young C57Bl/6Jax mice

Project description:Hematopoietic stem cells (HSCs) and different multipotent progenitor populations (MPPs) contained in the Lin- Sca-1+ c-Kit+ (LSK) compartment have previously been identified using diverse surface marker panels. However, a comprehensive and complete characterization of the complete LSK compartment is lacking to date. Here, we present a single cell RNA sequencing of LSK cells that was used to establish trajectories within the HSPC compartment. A related bulk 3’-seq study of HSCs and MPP1-4 cells was also conducted, available in the ArrayExpress database under accession number E-MTAB-7391. Another related 3’-seq study of MPP5 population is available in the ArrayExpress database under accession number E-MTAB-9135.

2021-05-13 | E-MTAB-9208 | biostudies-arrayexpress

Gene expression data of Lsd1fl/fl and Lsd1fl/fl Mx1Cre CD150+ CD48- lin- c-Kit+ Sca-1+ LT-HSCs

Project description:We discovered that mice that lack Lsd1 in hematopoietic cells were exhibited increased frequencies of CD150+ CD48- lin- c-Kit+ Sca-1+ LT-HSCs, but completely lacked the lin- c-Kit+ Sca-1- myeloid progenitor compartment. To determine the genes altered by Lsd1-loss, CD150+ CD48- lin- c-Kit+ Sca-1+ LT-HSCs from Lsd1fl/fl and Lsd1fl/fl Mx1Cre mice were FACS-purified to be analyzed by gene expression profiling.

2013-06-25 | GSE40284 | GEO

Mx-Cre mediated deletion of SRF in murine hematopoietic LSK (Lin-Sca1+c-Kit+) cells

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

2010-08-12 | GSE23556 | GEO

Whole-genome bisulfite-seq (WGBS) on Lin-Sca1+Kit+ (LSK) bone marrow cells from wild-type C57BL/6J mice

Project description:Hematopoietic stem cells (HSC) are heterogeneous in their ability to durably reconstitute the blood system. Epigenome surveys along the hematopoietic hierarchy and within the HSC compartment have revealed distinct epigenomic states associated with functionally defined hematopoietic cell types. However, the degree to which epigenomic states vary within functionally defined hematopoietic populations is still largely unknown. To address this question we performed single-cell genome-wide DNA methylation profiling of linage negative Sca+cKit+ (LSK) and EPCR+CD45+CD48-CD150+ (ESLAM) hematopoietic stem cell populations purified from adult mouse bone marrow. For this we developed a bisulfite based whole genome protocol suitable for use on single index sorted mammalian cells. Analysis of the resulting data from 148 single cells revealed that the methylomes of single HSCs show characteristics consistent with those defined from bulk populations. Comparing methylation states across single HSCs revealed a significant reduction in CpG state adjacency compared to bulk estimates and that on average 13% of CpGs exist in the opposite methylation state between any two cells within both surface marker defined HSC containing populations. Utilizing a novel analytical approach designed to address missing data inherent in single cell assays we identified an epigenetically distinct subpopulation of cells present in both the LSK and ESLAM populations. Enrichment analysis of genes associated with this distinct epigenetic state revealed pathways consistent with hematopoietic stem cell function, and integration with single-cell RNA-seq data defined putative surface proteins that mark this population, including the previously identified hematopoietic marker, NRXN1.

2017-12-31 | GSE95697 | GEO

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