{"owner": "ArrayExpress Uploader", "ownerprofile_id": "arrayexpress_sid", "species": "human", "factors": [{"GSE16962GSM424768": {}}, {"GSE16962GSM424769": {}}, {"GSE16962GSM424770": {}}, {"GSE16962GSM424765": {}}, {"GSE16962GSM424766": {}}, {"GSE16962GSM424767": {}}, {"GSE16962GSM424762": {}}, {"GSE16962GSM424763": {}}, {"GSE16962GSM424764": {}}, {"GSE16962GSM424759": {}}, {"GSE16962GSM424760": {}}, {"GSE16962GSM424761": {}}], "id": 3342, "pop_total": 0, "platform": 4, "summary_wrapped": "MicroRNAs (miRNAs) are small non-protein-coding RNAs that are incorporated into the RNA-induced silencing complex (RISC) and inhibit gene...", "geo_gse_id": "E-GEOD-16962", "owner_profile": "/profile/8773/arrayexpressuploader", "factor_count": 0, "sample_count": 12, "tags": ["amino acid", "capillary", "cell", "endothelial cell", "membrane", "protein", "tyrosine"], "lastmodified": "Dec.12, 2014", "is_default": false, "geo_id_plat": "E-GEOD-16962_A-AFFY-44", "slug": "transcription-profiling-of-human-umbilical-vein-ce", "geo_gds_id": "", "name": "Transcription profiling of human umbilical vein cells under/over expressing mir-210", "created": "Sep.12, 2014", "summary": "MicroRNAs (miRNAs) are small non-protein-coding RNAs that are incorporated into the RNA-induced silencing complex (RISC) and inhibit gene expression by regulating the stability and/or the translational efficiency of target mRNAs. Previously, we demonstrated that miR-210 is a key player of endothelial cell (EC) response to hypoxia, modulating EC survival, migration and ability to form capillary like-structures. Moreover, the receptor tyrosine kinase ligand Ephrin-A3 was identified as one functionally relevant target. Since each miRNA regulates hundreds of mRNAs, different approaches were combined to identify new miR-210 targets: a Using target prediction software, 32 new miR-210 potential targets were identified. b The proteomic profiling of miR-210 over-expressing ECs identified 11 proteins that were specifically inhibited by miR-210, either directly or indirectly. c Affymetrix based gene expression profiles identified 51 genes that were both down-modulated by miR-210 over-expression and de-repressed when miR-210 was blocked. Surprisingly, only few genes identified either by proteomics or transcriptomics were recognized as miR-210 targets by target prediction algorithms. However, a low-stringency pairing research revealed enrichment for miR-210 putative binding sites, raising the possibility that these genes were targeted via non-canonical recognition sequences. To clarify this issue, miR-210-loaded RISC was purified by immuno-precipitation along with its mRNA targets. The presence of Ephrin-A3 mRNA in the complex validated this approach. We found that 32 potential targets were indeed enriched in miR-210-loaded RISC, and thus can be considered as genuine miR-210 targets. In keeping with this conclusion, we were able to further validate a sub-set of them by 3\u2019UTR-reporter assays. Gene ontology analysis of the targets confirmed the known miR-210 activity in differentiation and cell cycle regulation, highlighting new functions such as involvement in RNA processing, DNA binding, development, membrane trafficking and amino acid catabolism.  In conclusion, we validated a multidisciplinary approach for miRNAs target identification and indicated novel molecular mechanisms underpinning miR-210 role in EC response to hypoxia. Experiment Overall Design: Gene expression modifications induced by both miR-210 over-expression and blockade were evaluated. In order to identify new direct and indirect miR-210 targets, transcripts repressed by miR-210 over-expression and up-regulated by miR-210 inhibition (and vice versa) were selected.", "source": "http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-16962", "sample_source": "http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-16962/samples/"}