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 human HSPCs (Lineage negative, CD38 negative, CD34 positive) of control patients or myocardial infarction patients and treated with at-RA/4-oxo-RA/DMSO for 72h in culture

ABSTRACT: Study of the transcriptomic changes in human HSPCs under the influence of at-RA and 4-oxo-RA. Human Hematopoietic Stem and Progenitor Cells (HSPCs)(Lineage negative, CD38 negative, CD34 positive cells) were isolated from sternal bone marrow of patients who had experienced myocardial infarction or from control patients. For in vitro cultivation, cells were treated with at-RA (2.5 μM final concentration), 4-oxo-RA (2.5 μM final concentration), or the respective volume of DMSO (control) for 72 hours. After incubation period, cells were harvested for RNA extraction.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Homo sapiens

SUBMITTER:

PROVIDER: E-MTAB-13508 | biostudies-arrayexpress |

SECONDARY ACCESSION(S): E-MTAB-13509

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Population RNA Seq of enriched human peripheral blood monocytes treated with at-RA/4-oxo-RA/DMSO for 24h in culture

Project description:Study of the effects of at-RA and 4-oxo-RA 72h treatment on the transcriptome of human peripheral blood monocytes from healthy individuals.

2025-02-06 | E-MTAB-14660 | biostudies-arrayexpress

Population RNA Seq of cardiac fibroblasts, cardiac endothelial cells, cardiac monocytes, cardiac macrophages - isolated from mice after at-RA treatment or 4-oxo-RA or DMSO control treatment (24h post injection)

Project description:Study of the gene expression patterns of specific cardiac cell populations, including monocytes (CD45+, CD11b+, F4/80-, LyC6+), endothelial cells (CD45-, CD31+), macrophages (CD45+, CD11b+, F4/80+, LyC6-), and fibroblasts (CD45-, GP38+), in response to at-RA and 4-oxo-RA treatments. Female C57BL/6J mice aged 12 weeks were intraperitoneally injected with 30 mg/kg body weight at-RA (Sigma-Aldrich), 30 mg/kg body weight 4-oxo-RA (Sigma-Aldrich), or an equivalent volume of DMSO in phosphate-buffered saline (PBS) as the vehicle control. After 24 hours of injection, the mice were euthanized for analysis.

2025-02-06 | E-MTAB-13505 | 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

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

Analysis of RA vs 4-oxo-RA gene expression regulation in Xenopus laevis

Project description:We analyzed anterior halves of NF stage 15 embryos that were treated with 10uM DMSO (control), or 1uM RA and 10uM 4-oxo-RA (experimental) for changes in gene expression induced by the two mophogens. RNA-sequencing revealed significant overlap in genes upregulated by both RA and 4-oxo-RA, and to a lesser extent, those downregulated by them. We report all Zic-1 targets described in accompanying manuscript to be regulated by both RA and 4-oxo-RA.

2022-03-09 | GSE180269 | GEO

3’RNA-seq of murine post-differentiation CD142− ASPCs treated with retinoic acid (RA)

Project description:To study the impact of retinoic acid treatment on the transcriptome of CD142− ASPCs, we performed bulk RNA-seq on CD142− ASPCs treated with different RA concentrations ranging between 0.01 to 100 μM, with 100 ng/ml of BSA (negative control), DMSO (negative control) or 100 ng/ml of EGF (positive control).

2021-06-26 | E-MTAB-10184 | biostudies-arrayexpress

Gene regulation by phosphomimetic Myc (MycD), cytosine arabinoside (AraC) and retinoic acid (RA)

Project description:We aimed to investigate whether the previously observed synergistic effects of AraC and RA in stimulating leukemia differentiation could be at least partially dependent on Pak2-mediated phosphorylation of Myc. Genome-wide analysis of NB4 cells treated with RA, AraC with RA, or MycD with RA revealed a significant 60% overlap between RA-target genes superactivated by AraC with RA, or MycD with RA, with respect to RA alone. NB4 cells infected with ER-tagged inducible empty vector (CTL), MycD or MycA were treated with 4-OHT (200 nM, 16 h) to induce MycD-ER and MycA-ER expression. CTL cells were either vehicle or AraC (25 μM) treated for 16 h. Short treatment of RA (10 nM, 4 h) was performed in CTL, AraC and MycD-expressing cells. Four biologically independent experiments were performed at each time.

2012-01-05 | E-GEOD-29213 | biostudies-arrayexpress

Analysis of RA vs 4-oxo-RA gene expression regulation in Xenopus laevis

Project description:Analysis of RA vs 4-oxo-RA gene expression regulation in Xenopus laevis

| PRJNA747290 | ENA

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

Tandem Mass Tag (TMT)-coupled LC-MS/MS in OA and RA patients synovial tissues

Project description:All the synovial tissue specimens for TMT relative quantitative proteomics and further experiments were obtained from the patients with RA or OA undergoing surgical joint replacement at the clinical of joint surgery (Xi'an Hong Hui Hospital, Xi'an Jiaotong University, China). The diagnosis of the patients were accorded to the criteria of the American College of Rheumatology (ACR) and European League Against Rheumatism (EULAR) in 2010.a quantitative proteomic profiling of synovial tissue obtained from RA and OA patients was carried out by using TMT labeling followed by high resolution mass spectrometry analysis. We have identified 4822 proteins out of which 510 proteins were found to be differentially expressed by ≥1.2 fold change in the synovial tissue from RA verses OA patients.

2021-12-30 | PXD027703 | Pride

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