Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Population RNA Seq of long-term HSCs isolated from mice after myocardial infarction (day 2 post infarct) or sham surgery and at-RA treatment or DMSO control treatment

ABSTRACT: Study of the effects of at-RA treatment on the transcriptome of murine Long-Term Hematopoietic Stem Cells (LT-HSCs) in the context of myocardial infarction (MI). MI was induced in female C57BL/6J mice aged 6 to approximately 12 weeks through permanent occlusion of the left anterior descending artery (LAD). Mice were intraperitoneally injected on the 1st and 2nd day after MI surgery with either 30 mg/kg body weight at-RA (Sigma-Aldrich; MI+at-RA condition), or with the corresponding amount of DMSO in phosphate-buffered saline (PBS) (MI+vehicle condition). Two days after MI, LT-HSCs (Lin-negative, Sca1-positive, c-Kit-positive, CD150-positive, CD48-negative, CD34-negative) were isolated from the bone marrow, sorted, and analyzed for their transcriptome profiles. This study aimed to understand how at-RA treatment influences gene expression in LT-HSCs following MI.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Mus musculus

SUBMITTER:

PROVIDER: E-MTAB-13506 | biostudies-arrayexpress |

SECONDARY ACCESSION(S): E-MTAB-13509

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Single-cell RNA sequencing of bone marrow cells and spleen isolated from mice after sham surgery or myocardial infarction, followed by treatments (vehicle/4-oxo-RA)

Project description:Study of the impact of 4-oxo-RA on LSK (bone marrow and spleen) cell characteristics post-myocardial infarction in C57BL/6J mice. Myocardial infarction was induced in female C57BL/6J mice (aged 6 to approximately 12 weeks) through LAD occlusion. Post-surgery, mice were intraperitoneally injected with 30 mg/kg 4-oxo-RA (MI+4-oxo-RA) or the equivalent DMSO in PBS (MI+vehicle) on the 1st and 2nd days after MI. Three days post-MI, mice were euthanized. ScRNA-seq was performed on 25k LSK cells (Lin-, Sca1+, c-Kit+) that were facs sorted.

2025-02-06 | E-MTAB-13510 | biostudies-arrayexpress

Single-cell RNA sequencing of bone marrow cells isolated from RarB KO mice after sham surgery or myocardial infarction, followed by treatments (vehicle/4-oxo-RA)

Project description:Study of the impact of 4-oxo-RA on LSK cell characteristics post-myocardial infarction in RarB KO mice. Myocardial infarction was induced in female RarB KO mice aged 6 to 12 weeks by LAD occlusion. On the 1st and 2nd post-MI days, mice were intraperitoneally injected with 30 mg/kg 4-oxo-RA (MI+4-oxo-RA) or DMSO in PBS (MI+vehicle). Three days post-MI, mice were euthanized. ScRNA-seq was performed on 25k LSK cells (Lin-, Sca1+, c-Kit+) that were facs sorted.

2025-02-06 | E-MTAB-13511 | biostudies-arrayexpress

Gene profiling of HSCs in C57BL/6 TEL-SYK BM versus control

Project description:The aim of the study was to analyse gene expression differences in LT and ST HSCs in BM of TEL-SYK transplanted versus control C57BL/6mice

2014-12-31 | E-MTAB-2240 | biostudies-arrayexpress

Single-cell RNA sequencing of mouse myeloid cardiac tdTomato+ and tdTomato- cells (Fgd5-CreERT2) post-myocardial infarction upon DMSO and 4-oxo-RA treatment.

Project description:This lineage tracing experiment focused on studying the transcriptome of cardiac myeloid cells derived from BM HSCs post-MI. We performed Left coronary artery ligation (LAD) in a tamoxifen-inducible in vivo HSC-lineage tracing mouse model which allows HSC-progeny lineage tracing via Tomato expression (Fgd5-CreERT2 tdTomato; PMID: 30561324). This was followed by a 2-day treatment with either vehicle (DMSO) or 4-oxo-RA. On day 3 post-MI, hearts were extracted, and tdTomato-positive and tdTomato-negative myeloid cells (CD11b+) were isolated from the myocardium. scRNA-seq was performed.

2025-02-06 | E-MTAB-13580 | biostudies-arrayexpress

Immediate response of hematopoietic stem cells to low doses of Î³-irradiation

Project description:Analysis of highly purified long-term hematopoietic stem cells (LT-HSCs) 2 hours after irradiation at 0Gy, 0.02Gy and 2.5Gy. Results provide insight into the molecular mechanisms underlying LT-HSCs immediate response to low doses of Î³-irradiation compared to high doses. Three samples were analyzed and correlated with the control group (0Gy).

2016-02-26 | E-GEOD-66374 | biostudies-arrayexpress

RNA-seq of long-term hematopoietic stem cells and myeloid progenitors of control mice or mice conditionally deficient for Trp53 or Elp3 or both genes in the hematopoietic system

Project description:Aim of the experiment was to compare the gene expression responses of long-term hematopoietic stem cells (HSCs) and myeloid-restricted progenitors (MyPs) to the hematopoietic cell-restricted deletion of the catalytic subunit Elp3 of the Elongator complex. Since Elp3 deletion resulted in activation of the p53 pathway, we also studied the transcriptome of MyPs deficient for Trp53 or for both Elp3 and Trp53. The Elp3fl/fl strain was generated in house and first described in (DOI: 10.1084/jem.20142288). The Trp53 strain was first described in (DOI: 10.1101/gad.14.8.994) and was purchased from the Jackson Laboratory. Littermates of 8-12 weeks old were used in all experiments.

2020-12-10 | E-MTAB-6992 | biostudies-arrayexpress

Next Generation Sequencing of long-term hematopoietic cells (LT-HSCs) with or without mutations in JAK2 and Ezh2

Project description:Comparison of mRNA expression profiles of LT-HSCs with or without mutations in JAK2 and Ezh2 by RNA sequencing. LT-HSC mRNA was extracted from six different transgenic mice (SclCre, SclCre;Ezh2+/-, SclCre;Ezh2-/-, SclCre; JAK2V617F, SclCre; JAK2V617F;Ezh2+/-, SclCre; JAK2V617F;Ezh2-/-) 10 weeks after tamoxifen injection. Our study represents the first detailed analysis of mRNA expression profile of LT-HSC with or without mutations in JAK2 and Ezh2 , with biologic replicates, generated by RNA-seq technology. Our results revealed that mRNA expression profile of LT-HSC with different genotype showed specific gene expression patterns, which allows to do biological comprehensive and quantitative analysis for hematopoiesis. LT-HSCs mRNA profiles six different transgenic mice (SclCre, SclCre;Ezh2+/-, SclCre;Ezh2-/-, SclCre; JAK2V617F, SclCre; JAK2V617F;Ezh2+/-, SclCre; JAK2V617F;Ezh2-/-) were generated by deep sequencing.

2016-06-24 | E-GEOD-82073 | biostudies-arrayexpress

RNA-seq comparison of bone marrow stem cells isolated from two genotypes WT and Ppm1dT/+

Project description:Ppm1d T/+ mice exhibit altered BM composition. The aim is to determine the molecular mechanisms possibly responsible for this alterations in sorted long-term hematopoietic stem cells isolated from bone marrow. Long-term HSCs (LT-HSCs sorted from 12-week-old WT and Ppm1DT/+ mice. The Ppm1dT/+ HSC transcriptome shows enrichment of MYC, mTOR compared to WT.

2023-12-31 | E-MTAB-13090 | biostudies-arrayexpress

Imprinting Affy

Project description:Murine long-term hematopoietic stem cells (HSCs), short-term HSCs and multipotent progenitor cells (MPPs) were isolated from bone marrow and expression profiled on Affy chips. The behavior of maternal-specific imprinting genes, particularly in the H19-Igf2 locus, was focused on, to see if any might be involved in maintaining quiescence of long-term stem cells.

2013-08-12 | E-MTAB-1644 | biostudies-arrayexpress

Long-term effects of low doses of Î³-irradiation on hematopoietic stem cells

Project description:Analysis of highly purified long-term hematopoietic stem cells (LT-HSCs) irradiated at 0Gy, 0.02Gy, 0.1Gy and 0.5Gy six months after transplantation. Results provide insight into the molecular mechanisms underlying multiple aspects of LT-HSCs premature ageing after low doses of Î³-irradiation (0.02Gy). Four samples were analyzed and correlated with the control group (0Gy).

2016-02-26 | E-GEOD-66375 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data