| Series | GSE69292 |
| Title | Integrative analyses of human reprogramming reveal dynamic nature of induced pluripotency [smartseq2] |
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| Year | 2015 |
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| Country | USA |
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| Article | Mikkelsen TS,Lander ES,Meissner A,Daley GQ,Rinn JL,Doench J,Gifford CA,Akopian V,Wu Z,Ho Sui SJ,Zhang X,Ratanasirintrawoot S,Smith ZD,Donaghey J,Karnik R,Cesana M,Soumillon M,Ziller MJ,Trapnell C,Cacchiarelli D.Integrative Analyses of Human Reprogramming Reveal Dynamic Nature of Induced Pluripotency.Cell.2015 Jul 16 |
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| PMID | 26186193 |
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| Bio Project | SubSeries of: GSE62777 |
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| Sra | BioProject: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA285094 |
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| Overall Desgin | single cell RNA-seq profiles from 52 unfractionated hiF-T cells after 10 days of reprogramming |
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| Summary | Induced pluripotency is a promising avenue for disease modeling and therapy, but the molecular principles underlying this process, particularly in human cells, remain poorly understood due to donor-to-donor variability and intercellular heterogeneity. Here we constructed and characterized a clonal, inducible human reprogramming system that provides a reliable source of cells at any stage of the process. This system enabled integrative transcriptional and epigenomic analysis across the human reprogramming timeline at high resolution. We observed distinct waves of gene network activation, including the ordered re-activation of broad developmental regulators followed by early embryonic patterning genes and culminating in the emergence of a signature reminiscent of pre-implantation stages. Moreover, complementary functional analyses allowed us to identify and validate novel regulators of the reprogramming process. Altogether, this study sheds light on the molecular underpinnings of induced pluripotency in human cells and provides a robust cell platform for further studies. |
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| Experimental Protocol | The single-cell RNA-seq libraries were prepared from MEF-depleted hiF-T cells at day 10 of reprogramming directly sorted in lysis buffer at single cell using an ARIA facs sorter (BD).; Library preparation was performed using SMART-seq2 protocol with minor modifications (Trombetta et al., 2014) on 96 cells
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| Data processing | Data processing was performed using the Tuxedo RNAseq suite (Trapnell et al., 2012). 52 single cells displayed more than 50% alignment rate and 100,000 reads per sample and were therefore considered for further analysis.; Genome_build: hg19; Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample
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| Platform | GPL16791 |
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| Public On | Public on Jul 16 2015 |
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