Transcriptome profiling of induced hair cells (iHCs) generated by combined expression of Gfi1, Pou4f3 and Atoh1 during embryonic stem cell differentiation.

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We found that combined activity of three transcription factors, Gfi1, Pou4f3, and Atoh1, can program ESC-derived progenitors towards HC fate with efficiencies of 55%-80%. These iHCs express several HC markers and exhibit polarized structures that are highly reminiscent of the mechanosensitive hair bundles, with many microvilli-like stereocilia. Here, we describe the experimental design, methodology, and data validation for the microarray analysis used to characterize the transcriptome profile of iHCs at different stages of their differentiation. This approach based on FACS sorting and microarray analysis revealed a highly similar iHC transcriptome to that of endogenous HCs in vivo. 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The data obtained in this study is availabl", "(induced HCs, iHCs) in vitro, starting from mouse embryonic stem cells (ESC). We found that co", "for use on Affymetrix (Santa Clara, CA, USA) Mouse Genome 2.1 ST Arrays Strip, by using the Amb"], "order_basis": "paper_text_order:359", "id": "assay:1"}, {"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["gn, methodology, and data validation for the microarray analysis used to characterize the transcript", "ion. This approach based on FACS sorting and microarray analysis revealed a highly similar iHC trans", "negative cell fraction was discarded for the microarray analysis. However, these nonfluorescent cell", "gh degree of purity of the iHC-sorted cells. 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T", "s confirmed the high degree of purity of the iHC-sorted cells. Microarray sample preparation"], "order_basis": "paper_text_order:1030", "id": "assay:4"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.69, "evidence": ["er unit into a new sterile flask. Cells were passaged every other day, at constant plating density"], "order_basis": "paper_text_order:2437", "id": "assay:5"}, {"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ls were used for quantitative-real time PCR (qPCR) analysis, to validate samples and to determ", "pulation in the Venus-positive fraction. The qPCR reaction was performed on 96-well plates (Mi", "nstruments used were Applied Biosystems 7500 Real-Time PCR or Applied Biosystems ViiA 7 Real-Time PCR.", "0 Real-Time PCR or Applied Biosystems ViiA 7 Real-Time PCR. The Real-Time PCR was carried out using iTa"], "order_basis": "paper_text_order:3435", "id": "assay:6"}]}