Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA244313 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:BMDMs were stimulated with ATRA and/or omentum culture supernatant and gene expression was determined by Illumina microarray
2014-05-02 | GSE56683 | GEO
Project description:BMDMs were stimulated with ATRA and/or omentum culture supernatant and gene expression was determined by Illumina microarray 8 BMDM Samples
2014-05-02 | E-GEOD-56683 | biostudies-arrayexpress
Project description:Expression profiling of U937 derived cell lines with induced expression of MN1or MN1-TEL in combination with all-trans retinoic acid (ATRA) Keywords: expression profiling Two similar experiments (A and B, biological duplicates) were performed. Hybridization includes dye swaps. See experimental_design.jpg (below) for detailed setup of the study. In short, different time points after induction of MN1 or MN1-TEL were compared to uninduced samples. The effects of all-trans retinoic acid (ATRA) were also investigated
2008-09-09 | E-GEOD-11441 | biostudies-arrayexpress
Project description:To recruit phagocytes, apoptotic cells characteristically release ATP, which functions as a “danger” signal. Here, we found that the culture supernatant of apoptotic cells activated the macrophages to express anti-inflammatory genes such as NR4A and Thbs1. A high level of AMP accumulated in the apoptotic cell supernatant in a Pannexin1-dependent manner. A nucleotidase inhibitor and A2a adenosine receptor antagonist inhibited the apoptotic supernatant-induced gene expression, suggesting AMP was metabolized to adenosine by an ecto-5’-nucleotidase expressed on macrophages, to activate the macrophage A2a adenosine receptor. Intraperitoneal injection of zymosan into AdoR A2a- or Panx1-deficient mice produced high, sustained levels of inflammatory mediators in the peritoneal lavage. These results indicated that AMP from apoptotic cells suppresses inflammation as a “calm down” signal. If apoptotic cells produce “danger” or “anti-danger” signal(s), we rationalized that such signals would activate gene expression in macrophages. To investigate this possibility, we examined the effect of the culture supernatant from apoptotic cells on macrophage gene expression by using microarrays. For mouse BMDMs, bone marrow cells from female C57BL/6J mice at 8 weeks of age were cultured for more than 7 days with DMEM containing 10% FCS supplemented with mouse M-CSF. We used adherent cells as BMDMs in the study. W3 cells, mouse T cell line expressing Fas, were treated with human Fas ligand at 37°C for 30 min to induce apoptosis. The cells were then washed and re-suspended at a concentration of 1 × 107 cells/ml with RPMI containing 1% FCS, and further incubated for 60 min at 37°C. Following Fas ligand treatment, more than 90% of the W3 cells were Annexin V positive, and only small percentage were positive for both Annexin V and propidium iodide (PI). The culture supernatant was collected from apoptotic W3 cells. Next, BMDMs were incubated with medium (BMDMs-Medium) or apoptotic W3 cell supernatant (BMDMs-Apoptotic cell supernatant) for 1 h. Total RNA was extracted from the cells and hybridized on Affymetrix microarrays.
2014-06-24 | E-GEOD-50883 | biostudies-arrayexpress
Project description:The differentiation of leukemia stem cells (LSCs) is generally regarded as a one-way alterative process to self-renewal. However, how differentiation impacts LSC stemness has largely been unexplored. Here we show that before reaching terminal differentiation (TD), apical LSCs of mouse acute promyelocytic leukemia passed through a partial differentiation (PD) stage, wherein the leukemia cells re-initiated leukemia via de-differentiation albeit at a reduced rate. Notably, while retinoic acid (RA) preferentially drove the transition of LSC to PD, monocytic Irf8 skewed PD cells to terminal maturation over de-differentiation and/or expansion. Remarkably, the combined use of RA and Irf8 induction depleted the total leukemogenic potential, which indicates that discrete stage- or lineage-specific mechanisms elaborate a step-wise LSC differentiation. We used microarrays to detail the global programme of gene expression indicating the molecular mechanisms unerlying the the process of LSC step-wise differentiation. Retroviral GFP-labled mouse APL cells (bone marrow sample) were repopulated in vivo through transplantation into syngenic recipients. At the proper time points, the GFP positive APL bone marrow cells were collected and sorted for UNSC, UNPD and UNTD samples through FACS. RA-PD and RA-TD cells were sorted from bone marrow tissue treated with ATRA (all trans retinoic acid) for 5 days. The freshly isolated samples were then lysed for RNA extration. Each sample had two biological replicates.
2014-05-01 | E-GEOD-46094 | biostudies-arrayexpress
Project description:Bone marrow was extracted from mice that are COP1-wt Rosa26-CreERT2 or COP1-floxed Rosa26-CreERT2 BMDMs were obtained by culturing bone marrow precursors in media containing 20% of supernatant from L929 cells. At day 4 of differentiation 4-OHT was added at 1uM to induce deletion of COP1 in BMDMs derived from COP1-floxed mice. At day 7 of differentiation, BMDMs were treated with 100 ng/ml of LPS or not. BMDMs were directly harvested in lysis buffer (from Qiagen RNeasy mini kit) at different time points (0h, 2.5h, 2.5h, 4h, 6h, 9h and 13h) following LPS stimulation. Three BMDMs preparations per group: G1: BMDMs from COP1-wt mice (expressing the wt allele of COP1) CRE positive. G2: BMDMs from COP1-floxed mice (expressing the floxed allele of COP1) CRE positive
2018-10-03 | GSE114762 | GEO
Project description:In order to determine P2X7R secretome we analyzed the proteins present in cell-free supernatants from wild-type (P2rx7+/+) or P2rx7-/- bone marrow-derived macrophages (BMDMs) polarized either to M1 or M2 and subsequently treated with ATP. BMDMs were primed with LPS (M1) or IL-4 (M2) for 4 hours and the proteins secreted during this step were extensively washed with PBS before ATP was added in fresh buffer. The complex mixture of proteins obtained in the macrophages supernatants after ATP stimulation were fractionated using one dimension gel electrophoresis and 10 bands were selected for LC-MS/MS analysis based in their presence in higher intensity in P2rx7+/+ supernatant compared with P2rx7-/- supernatant.
2016-03-11 | PXD001981 | Pride
Project description:Bone marrow-derived macrophages (BMDMs) are a key model system for studying macrophage biology in vitro. Commonly used methods to differentiate macrophages from bone marrow are treatment with either recombinant M-CSF or the supernatant of L929 cells, which secrete M-CSF. However, little is known about the composition of L929 conditioned media (CM) and how it affects BMDM phenotype. Here, we used quantitative mass spectrometry to characterise the kinetics of protein secretion from L929 cells over a two-week period. While M-CSF is very abundant in L929 CM, we identified several other immune-regulatory proteins at surprisingly high abundance. L929 CM induced a slightly pre-activated phenotype and the expression of a number of known innate immune proteins in macrophages. This resource will be valuable to all researchers using L929 CM for the differentiation of BMDMs.
2021-04-13 | PXD021026 | Pride
Project description:In acute promyelocytic leukemia (APL), differentiation therapy with all-trans retinoic acid (ATRA)
2009-10-06 | GSE18397 | GEO
Project description:All-trans retinoic acid (ATRA) has been shown to have anti-proliferative effects, particularly in the context of cancer. However, the effects of ATRA on gene and microRNA expression in solid tumors have not been investigated. In this study, we performed gene expression and microRNA analysis of the squamous cell carcinoma cell line, ME180, following treatment with 10 micromolar all-trans retinoic acid (ATRA) for 1, 3, and 6 hours. Results provide insight into the temporal regulation of genes and microRNAs by retinoids.
2014-08-01 | GSE54464 | GEO