Project description:Analysis of gene expression and alternate splicing effects of retinoic acid treatment on gestational day 15 rat fetal testes in whole testis culture Retinoic acid exposure in cultured fetal testis has previously been demonstrated to have significant effects on the histology of the fetal testis in multiple species, as well as to alter the meiotic states of germ cells. However, previous experiments have not analyzed the mechanisms by which retinoic acid exposure leads to altered tubulogenesis and loss of seminiferous cord structure. This experiment demonstrated that retinoic acid exposure activated signaling pathways that promote the ovary development program and oppose normal testis development in mid-gestational rat fetal testes. Overall design: Testes were isolated from rats on gestational day 15. A paired design was used in which a single testis from each of six rat fetuses was cultured in 10^-6 M all-trans retinoic acid (ATRA), while the contralateral testis was cultured in vehicle (DMSO) media. After 24 h culture, total RNA was isolated, and gene expression and alternate splicing were analyzed using the Affymetrix Clariom D Rat assay.
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 Overall design: 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
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
Project description:Gene expression profiles of promyelocytic NB4 cells treated with all-trans retinoic acid (ATRA, 1 microM) during short periods of time (1h30 and 3h) were performed and compared to untreated cells (vehicule control, 0,02% ethanol).
Project description:The acute promyelocytic leukemia-derived cell line, NB4, was grown at 37°C in 5% CO2 in an RPMI medium supplemented with 2 mM L-glutamine and 10% decomplemented fetal calf serum. Cells were cultured for 48 h with or without 1 μM All-trans retinoic acid (ATRA). Duplicates of 3 independent experiments were analyzed.
Project description:Pyrydopyrazine A2 induced in vitro the differentiation of leukemic cells (HoxA9-Meis1) into macrophages, we decided to perform a transcriptomic study in order to analyze the GM-CSF pathway regulation. We therefore compared effect with A2 to cells treated with Retinoic acid and D3 Vitamin, a combination known to induce also differentiation of leukemic cells. HoxA9-Meis1 murine AML cells were treated in vitro during 24h, with Pyrydopyrazine( A2) at 3.4μM or a combination of all-trans Retinoic Acid (RA) and 1α-hydroxy-D3 Vitamin (D3V), 10μM each. Gene expression signature was compared to untreated control. One sample was tested for each condition
Project description:To identifiy stage-dependent genes in Sertoli cells, we performed expression microarray analysis of the adult whole testes, cultured primary Sertoli cells, Sertoli cells directly isolated from wild-type and Nanos3 (germ-less) testes,seminiferous tubules at stages I-III, IV-VI, VII-VIII and IX-XII. Next to examine the relationship between stage-dependent gene expression change and retinoic acid signaling, we performed expression microarray analysis of the cultured primary Sertoli cells treated with retinoic acid and stage-specific seminiferous tubules injected with lentivirus containing Venus or dominat negative form of RARa, a dominant receptor for retinoic acid in Sertoli cells. Biological duplicates were examined at each sample
Project description:The morphologic changes of neuroepithelial cells, and their interactions with surrounding cells, are fundamental to primary neurulation and are a function of several timed signaling gradients. Retinoic acid administration at fetal day E10 induces neural tube defects in 84.2% of rat pups. Negative selection using A2B5 and E-NCAM has been validated for isolation of neuroepithelial cells for culture. Here we report the isolation and analysis of the fundamental actors in primary neurulation by flow cytometry with CD147 positive selection followed by whole transcriptome analysis of this purified population via microarray enhanced with the ERCC RNA internal controls. Comparison of the gene expression in Retinoic acid exposed versus wild-type isolates shows excellent correspondence to known neural tube defect genes. Analysis of transcription factor binding sites in regulatory regions of differentially expressed genes, implicates a binding site “cross-roads” where improper signaling through a multitude of pathways could potentially elicit neural tube defects. Overall design: Six samples total, three replicates each, of pooled biological replicates. ERCC ExFold mix 1 added to CTR ERCC ExFold mix 2 added to RA.
Project description:Identification of the role of retinoic acid on the activation of the dHSCs Overall design: Mouse HSCs were cultured in the presence of DMSO (control) or all trans retinoic acid (ATRA)
Project description:This SuperSeries is composed of the following subset Series: GSE34672: Inhibition of the LSD1 (KDM1A) demethylase reactivates the all-trans-retinoic acid differentiation pathway in acute myeloid leukemia [Illumina HumanHT-12 gene expression array] GSE34725: Inhibition of the LSD1 (KDM1A) demethylase reactivates the all-trans-retinoic acid differentiation pathway in acute myeloid leukemia [ChIP-Seq] Refer to individual Series