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Real- time quantiative PCR analysis of HSC derived from sleep deprived mice

ABSTRACT: HSC were derived from mice sleep deprived for 4 hours and compared to mice that slept for 4 hours during the same circadian time. 5 mice were pooled for each sample and bones from femur, tibia and spine were crushed and stained to lineage deplete and enrich for ckit+, sca-1+,Flk-,CD150+, CD34-

ORGANISM(S): Mus musculus Rattus norvegicus

PROVIDER: GSE48144 | GEO | 2013/12/11

SECONDARY ACCESSION(S): PRJNA208998

REPOSITORIES: GEO

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Real- time quantiative PCR analysis of HSC derived from sleep deprived mice

Project description:HSC were derived from mice sleep deprived for 4 hours and compared to mice that slept for 4 hours during the same circadian time. 5 mice were pooled for each sample and bones from femur, tibia and spine were crushed and stained to lineage deplete and enrich for ckit+, sca-1+,Flk-,CD150+, CD34- qpcr miRNA profiling from approximately 50ng total RNA extracted from HSC FACS sorted into Trizol.

2013-12-11 | E-GEOD-48144 | biostudies-arrayexpress

Differential expression of Hdc-GFP+/hi HSC VS Hdc-GFP-/lo hematopoetic stem cells (HSCs) from bone marrow.

Project description:Bone marrow Hdc-GFPhi and Hdc-GFPlo HSPC (SLAM-LSK, Lin-c-kit+Sca-1+CD150+CD48-) HSCs were isolated from mouse femur and tibia from histidine decarboxylase (Hdc) green fluorescent protein (Hdc-GFP) mice. Hdc-GFPhi HSC and Hdc-GFPlo HSC cells were sorted by combinations of GFP and the cell surface markers of HSC. total RNA was isolated from sorted 2,500 HSPCs using ARCTURUS PicoPure RNA isolation kit (Life Technologies). cDNA was amplified and libraries were constructed by using SMARTer Ultra Low Input RNA kit (Clontech Laboratories) and Nextera XT DNA Library Preparation kit (Illumina) according to manufacturer’s instructions respectively. Sequencing was performed on the Illumina HiSeq2000 platform.

2019-11-20 | GSE90787 | GEO

Expression data from growth plate cartilage of control and immobilized embryonic chickens

Project description:Affymetrix Chicken Gene 1.0 ST Array (ChiGene-1_1-st) profiles were generated from growth plate cartilage derived from the distal femur and proximal tibia of embryonic chickens at three developmental stages (day 12, 13 and 15) corresponding to stages prior to and immediately after the acqusition of mechano-responsive cartilage growth in the femur but not tibia (which does not respond to mechanical stimuli until later stages). Additionally, array profiles were generated from growth plate cartilage from the distal femur and proximal tibia of E15 chicks which were pharmacologically immobilized by decamethonium bromide treatment, which reduces longitudinal growth of the femur only at this stage.

2016-12-31 | GSE77412 | GEO

Transcriptional profiling of long bone skeletal stem cells and vertebral counterparts

Project description:To identify specific markers for vertebral skeletal stem cells (vSSCs), we isolated vSSC candidates and lbSSCs by FACS from p10 mice long bone (tibia and femur) and vertebrae.

2023-05-05 | GSE230852 | GEO

Functionally distinct subsets of lineage-biased multipotent progenitors control blood production in normal and regenerative conditions

Project description:To identify the molecular characterisitics of parallel lineage-biased MPP populations arising from hematopoietic stem cells (HSC) we conducted genome-wide analyses of hematopoietic stem, progenitor and mature myeloid cell populations using Affymetrix Gene ST1.0 arrays. Microarray analysis of 3-5 biological replicates of the indicated hematopoietic populations, isolated by FACS sorting from C57BL/6 mouse BM. Immunophenotypic definitions: Long-term HSC (HSCLT) (Lin-/cKit+/Sca1+/Flk2-/CD48-/CD150+); Short-term HSC (HSCST) (Lin-/cKit+/Sca1+/Flk2-/CD48-/CD150-); MPP2 (Lin-/cKit+/Sca1+/Flk2-/CD48+/CD150+); MPP3 (Lin-/cKit+/Sca1+/Flk2-/CD48+/CD150-); MPP4 (Lin-/cKit+/Sca1+/Flk2+); CMP (Lin-/cKit+/Fc?R-/CD34+); GMP (Lin-/cKit+/Fc?R+/CD34+); Pre-granulocyte (PreGr) (Mac1+/Gr1int); Granulocyte (Gr) (Mac1+/Gr1hi). HSC and GMP samples listed here were also used as controls for our related microarray study GSE48893.

2015-05-05 | E-GEOD-68529 | biostudies-arrayexpress

Proliferation-dependent alterations of the DNA methylation landscape underlie hematopoietic stem cell aging

Project description:Gene Expression profiling of HSCs isolated at different stages of ontogeny to address correlation between gene expression and changes in DNA methylation Gene expression profiling of hematopoietic stem cells isolated from e14.5 fetal liver (lineage- ckit+ sca1+CD150+ CD48- Mac1+), 3 month old mice (lineage- ckit+ sca1+ CD34- Flk2-) and 25 month old mice (lineage- ckit+ sca1+ CD34- Flk2-)

2013-02-14 | E-GEOD-43729 | biostudies-arrayexpress

RNA-seq profiling of HSC, MPPs and HPC-1s from Phf6-deleted and Phf6-intact mice

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.

2019-02-20 | GSE126316 | GEO

RNA profiling in mouse haemopoiesis

Project description:RNA profiling of mouse haemopoetic lineages RNA profiling of mouse haemopoetic lineages. For the isolation and sequencing of ouse granulocyte nuclei, bone marrow from C57BL/6J was harvested from the femur, tibia and spine using a mortar and pestle in PBS supplemented with 2% (v/v) FCS and mature granulocytes purified by flow cytometry as described previously. Purification was validated by reanalysis by flow cytometry and May-GrM-CM-<nwald Giemsa staining. Nuclear purification was carried out using the PARIS kit (Ambion). RNA was extracted from the nuclear fraction using Trizol before deep sequencing. Deep sequencing was performed by GeneWorks (Adelaide, Australia) on the Illumina GAII according to the manufacturer's instructions. For more details, see Supplementary Methods at the NSMB website. Additional files and resources can be found at http://matticklab.com/index.php?title=NuclearTinyRNAs

2010-07-01 | E-GEOD-20683 | biostudies-arrayexpress

WT and inv(16)/KITD816Y granulocyte macrophage progenitor (GMP) cells [mouse]

Project description:WT GMPs (Lin- IL7R- Sca1- ckit+ FcgRhiCD34+) and inv(16)/KITD816Y GMPs (Lin- Sca1- ckit+ CD41- FcgR+ CD150-) were FACS sorted as described in material and methods from supplementary data (Estruch M et al 2020)

2020-11-09 | GSE150158 | GEO

Profiling the transcriptome of the adult mouse skeleton: RNA-seq of osteocytes from tibiae, femora, humeri and calvariae

Project description:In this experiment we define the transcriptome of the adult mouse skeleton by performing total-RNA transcriptome-sequencing on osteocytes, the critical regulatory cells in bone. Osteocytes from 16 week-old male mice (n=8) were isolated for 4 bone types across the skeleton: the tibia, femur, humerus, and calvaria. All other soft tissues including marrow were removed from samples before sequencing.

2020-12-16 | E-MTAB-5532 | biostudies-arrayexpress

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