{"owner": "ArrayExpress Uploader", "pop_total": 0, "id": 5019, "factors": [{"GSE9169GSM231608": {"growth condition": "retinoic acid", "time": 0, "compound": "LY294002"}}, {"GSE9169GSM231609": {"growth condition": "retinoic acid", "time": 6, "compound": "LY294002"}}, {"GSE9169GSM231610": {"growth condition": "retinoic acid", "time": 1, "compound": "LY294002"}}, {"GSE9169GSM231611": {"growth condition": "retinoic acid", "time": 2, "compound": "LY294002"}}, {"GSE9169GSM231612": {"growth condition": "retinoic acid", "time": 3, "compound": "LY294002"}}, {"GSE9169GSM231613": {"growth condition": "retinoic acid", "time": 5, "compound": "LY294002"}}, {"GSE9169GSM231608": {"growth condition": "retinoic acid", "time": 0, "compound": "LY294002"}}, {"GSE9169GSM231609": {"growth condition": "retinoic acid", "time": 6, "compound": "LY294002"}}, {"GSE9169GSM231610": {"growth condition": "retinoic acid", "time": 1, "compound": "LY294002"}}, {"GSE9169GSM231611": {"growth condition": "retinoic acid", "time": 2, "compound": "LY294002"}}, {"GSE9169GSM231612": {"growth condition": "retinoic acid", "time": 3, "compound": "LY294002"}}, {"GSE9169GSM231613": {"growth condition": "retinoic acid", "time": 5, "compound": "LY294002"}}, {"GSE9169GSM231620": {"growth condition": "retinoic acid", "time": 0, "compound": "none"}}, {"GSE9169GSM231621": {"growth condition": "retinoic acid", "time": 6, "compound": "none"}}, {"GSE9169GSM231622": {"growth condition": "retinoic acid", "time": 1, "compound": "none"}}, {"GSE9169GSM231623": {"growth condition": "retinoic acid", "time": 2, "compound": "none"}}, {"GSE9169GSM231624": {"growth condition": "retinoic acid", "time": 3, "compound": "none"}}, {"GSE9169GSM231625": {"growth condition": "retinoic acid", "time": 5, "compound": "none"}}, {"GSE9169GSM231620": {"growth condition": "retinoic acid", "time": 0, "compound": "none"}}, {"GSE9169GSM231621": {"growth condition": "retinoic acid", "time": 6, "compound": "none"}}, {"GSE9169GSM231622": {"growth condition": "retinoic acid", "time": 1, "compound": "none"}}, {"GSE9169GSM231623": {"growth condition": "retinoic acid", "time": 2, "compound": "none"}}, {"GSE9169GSM231624": {"growth condition": "retinoic acid", "time": 3, "compound": "none"}}, {"GSE9169GSM231625": {"growth condition": "retinoic acid", "time": 5, "compound": "none"}}, {"GSE9169GSM231608": {"growth condition": "retinoic acid", "time": 0, "compound": "LY294002"}}, {"GSE9169GSM231609": {"growth condition": "retinoic acid", "time": 6, "compound": "LY294002"}}, {"GSE9169GSM231610": {"growth condition": "retinoic acid", "time": 1, "compound": "LY294002"}}, {"GSE9169GSM231611": {"growth condition": "retinoic acid", "time": 2, "compound": "LY294002"}}, {"GSE9169GSM231612": {"growth condition": "retinoic acid", "time": 3, "compound": "LY294002"}}, {"GSE9169GSM231613": {"growth condition": "retinoic acid", "time": 5, "compound": "LY294002"}}, {"GSE9169GSM231608": {"growth condition": "retinoic acid", "time": 0, "compound": "LY294002"}}, {"GSE9169GSM231609": {"growth condition": "retinoic acid", "time": 6, "compound": "LY294002"}}, {"GSE9169GSM231610": {"growth condition": "retinoic acid", "time": 1, "compound": "LY294002"}}, {"GSE9169GSM231611": {"growth condition": "retinoic acid", "time": 2, "compound": "LY294002"}}, {"GSE9169GSM231612": {"growth condition": "retinoic acid", "time": 3, "compound": "LY294002"}}, {"GSE9169GSM231613": {"growth condition": "retinoic acid", "time": 5, "compound": "LY294002"}}, {"GSE9169GSM231620": {"growth condition": "retinoic acid", "time": 0, "compound": "none"}}, {"GSE9169GSM231621": {"growth condition": "retinoic acid", "time": 6, "compound": "none"}}, {"GSE9169GSM231622": {"growth condition": "retinoic acid", "time": 1, "compound": "none"}}, {"GSE9169GSM231623": {"growth condition": "retinoic acid", "time": 2, "compound": "none"}}, {"GSE9169GSM231624": {"growth condition": "retinoic acid", "time": 3, "compound": "none"}}, {"GSE9169GSM231625": {"growth condition": "retinoic acid", "time": 5, "compound": "none"}}, {"GSE9169GSM231650": {"growth condition": "brain-derived neurotrophic factor", "time": 6, "compound": "none"}}, {"GSE9169GSM231651": {"growth condition": "brain-derived neurotrophic factor", "time": 1, "compound": "none"}}, {"GSE9169GSM231652": {"growth condition": "brain-derived neurotrophic factor", "time": 2, "compound": "none"}}, {"GSE9169GSM231653": {"growth condition": "brain-derived neurotrophic factor", "time": 3, "compound": "none"}}, {"GSE9169GSM231620": {"growth condition": "retinoic acid", "time": 0, "compound": "none"}}, {"GSE9169GSM231621": {"growth condition": "retinoic acid", "time": 6, "compound": "none"}}, {"GSE9169GSM231622": {"growth condition": "retinoic acid", "time": 1, "compound": "none"}}, {"GSE9169GSM231623": {"growth condition": "retinoic acid", "time": 2, "compound": "none"}}, {"GSE9169GSM231624": {"growth condition": "retinoic acid", "time": 3, "compound": "none"}}, {"GSE9169GSM231625": {"growth condition": "retinoic acid", "time": 5, "compound": "none"}}, {"GSE9169GSM231650": {"growth condition": "brain-derived neurotrophic factor", "time": 6, "compound": "none"}}, {"GSE9169GSM231651": {"growth condition": "brain-derived neurotrophic factor", "time": 1, "compound": "none"}}, {"GSE9169GSM231652": {"growth condition": "brain-derived neurotrophic factor", "time": 2, "compound": "none"}}, {"GSE9169GSM231653": {"growth condition": "brain-derived neurotrophic factor", "time": 3, "compound": "none"}}, {"GSE9169GSM231620": {"growth condition": "retinoic acid", "time": 0, "compound": "none"}}, {"GSE9169GSM231621": {"growth condition": "retinoic acid", "time": 6, "compound": "none"}}, {"GSE9169GSM231622": {"growth condition": "retinoic acid", "time": 1, "compound": "none"}}, {"GSE9169GSM231623": {"growth condition": "retinoic acid", "time": 2, "compound": "none"}}, {"GSE9169GSM231624": {"growth condition": "retinoic acid", "time": 3, "compound": "none"}}, {"GSE9169GSM231625": {"growth condition": "retinoic acid", "time": 5, "compound": "none"}}, {"GSE9169GSM231650": {"growth condition": "brain-derived neurotrophic factor", "time": 6, "compound": "none"}}, {"GSE9169GSM231651": {"growth condition": "brain-derived neurotrophic factor", "time": 1, "compound": "none"}}, {"GSE9169GSM231652": {"growth condition": "brain-derived neurotrophic factor", "time": 2, "compound": "none"}}, {"GSE9169GSM231653": {"growth condition": "brain-derived neurotrophic factor", "time": 3, "compound": "none"}}, {"GSE9169GSM231620": {"growth condition": "retinoic acid", "time": 0, "compound": "none"}}, {"GSE9169GSM231621": {"growth condition": "retinoic acid", "time": 6, "compound": "none"}}, {"GSE9169GSM231622": {"growth condition": "retinoic acid", "time": 1, "compound": "none"}}, {"GSE9169GSM231623": {"growth condition": "retinoic acid", "time": 2, "compound": "none"}}, {"GSE9169GSM231624": {"growth condition": "retinoic acid", "time": 3, "compound": "none"}}, {"GSE9169GSM231625": {"growth condition": "retinoic acid", "time": 5, "compound": "none"}}, {"GSE9169GSM231650": {"growth condition": "brain-derived neurotrophic factor", "time": 6, "compound": "none"}}, {"GSE9169GSM231651": {"growth condition": "brain-derived neurotrophic factor", "time": 1, "compound": "none"}}, {"GSE9169GSM231652": {"growth condition": "brain-derived neurotrophic factor", "time": 2, "compound": "none"}}, {"GSE9169GSM231653": {"growth condition": "brain-derived neurotrophic factor", "time": 3, "compound": "none"}}, {"GSE9169GSM231620": {"growth condition": "retinoic acid", "time": 0, "compound": "none"}}, {"GSE9169GSM231621": {"growth condition": "retinoic acid", "time": 6, "compound": "none"}}, {"GSE9169GSM231622": {"growth condition": "retinoic acid", "time": 1, "compound": "none"}}, {"GSE9169GSM231623": {"growth condition": "retinoic acid", "time": 2, "compound": "none"}}, {"GSE9169GSM231624": {"growth condition": "retinoic acid", "time": 3, "compound": "none"}}, {"GSE9169GSM231625": {"growth condition": "retinoic acid", "time": 5, "compound": "none"}}, {"GSE9169GSM231650": {"growth condition": "brain-derived neurotrophic factor", "time": 6, "compound": "none"}}, {"GSE9169GSM231651": {"growth condition": "brain-derived neurotrophic factor", "time": 1, "compound": "none"}}, {"GSE9169GSM231652": {"growth condition": "brain-derived neurotrophic factor", "time": 2, "compound": "none"}}, {"GSE9169GSM231653": {"growth condition": "brain-derived neurotrophic factor", "time": 3, "compound": "none"}}], "ownerprofile_id": "arrayexpress_sid", "platform": 4, "summary_wrapped": "Background: SH-SY5Y cells exhibit a neuronal phenotype when treated with all-trans retinoic acid (RA), but the molecular mechanism of...", "pubmed_id": 18957096, "geo_gse_id": "E-GEOD-9169", "owner_profile": "/profile/8773/arrayexpressuploader", "factor_count": 3, "sample_count": 86, "tags": ["amino acid", "brain", "cell", "gene cluster", "laminin", "phosphatidylinositol", "serum"], "lastmodified": "Dec.12, 2014", "is_default": false, "geo_gds_id": "", "slug": "transcription-profiling-by-array-of-human-neurob-2", "geo_id_plat": "E-GEOD-9169_A-AFFY-44", "name": "Transcription profiling by array of human neuroblastoma cells after growth with retinoic acid or brain-derived neurotrophic factor and treatment with LY294002", "created": "Sep.22, 2014", "summary": "Background: SH-SY5Y cells exhibit a neuronal phenotype when treated with all-trans retinoic acid (RA), but the molecular mechanism of activation in the signaling pathway mediated by phosphatidylinositol 3-kinase (PI3K) is not sufficiently understood. To shed new light on the mechanism, we comprehensively compared the gene expression profiles between SK-N-SH cells and two subtypes of SH-SY5Y cells (SH-SY5Y-A and SH-SY5Y-E), each of which showed a different phenotype during RA-mediated differentiation. Results: SH-SY5Y-A cells differentiated in the presence of RA, whereas RA-treated SH-SY5Y-E cells required additional treatment with brain-derived neurotrophic factor (BDNF) for full differentiation. In combination with perturbation using a PI3K inhibitor, LY294002, we identified 386 genes and categorized them into two clusters dependent on the PI3K signaling pathway during RA-mediated differentiation in SH-SY5Y-A cells. Transcriptional regulation of the gene cluster was greatly reduced in SK-N-SH cells or partially impaired in SH-SY5Y-E cells in coincidence with a defect in the neuronal phenotype of these cell lines. Additional stimulation with BDNF induced a set of neural genes which were down-regulated in RA-treated SH-SY5Y-E cells but were abundant in the differentiated SH-SY5Y-A cells. Conclusions: We identified the gene clusters controlled by PI3K- and TRKB-mediated signaling pathways during differentiation in two subtypes of SH-SY5Y cells. TRKB-mediated bypass pathway compensates for the impaired neural functions generated by defects in several signaling pathways including PI3K in SH-SY5Y-E cells. The expression profiling data are useful for further studies to elucidate the signal transduction-transcriptional network including PI3K and/or TRKB. Experiment Overall Design: Human neuroblastomas, SK-N-SH (HTB-11) and SH-SY5Y-A cells (CRL-2266) were obtained from the American Type Culture Collection (ATCC). We also obtained SH-SY5Y-E cells (EC94030304) from the European Collection of Cell Cultures (ECACC). Tissue culture cells were maintained in D-MEM/F12 1:1 mixture supplemented with 15% FBS (Fetal Bovine Serum) and 1% NEAA (Non-essential amino acid) in a 5% CO2 humidified incubator at 37oC. The culture medium was changed twice a week. For the RA-inducible experiment, random culture cells from two clone subtypes of SH-SY5Y and SK-N-SH were seeded in laminin coated culture dishes (BioCoat Laminin Cellware; BD Biosciences, Billerica, MA, USA) for 1 day and then transferred to a medium containing 10 \u03bcM of RA in the presence or the absence of LY294002 (10\u03bcM) for five days. For BDNF-induced sequential differentiation of the SH-SY5Y-E strain, cells were washed with D-MEM/F12 twice after five days in the presence of RA and then incubated with 50 ng/ml of BDNF in D-MEM/F12 without serum for three days.", "source": "http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-9169", "species": "human", "sample_source": "http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-9169/samples/"}