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Series GSE71035 Query DataSets for GSE71035
Status Public on Jul 17, 2015
Title Integrative analyses of human reprogramming reveal dynamic nature of induced pluripotency [shRNA]
Organism Homo sapiens
Experiment type Other
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.
Overall design We infected hiF-T cells in biological replicate with a shRNA library (2,900 shRNA targeting 370 distinct epigenetic regulators). This library is a sub-pool of the human 45K shRNA pool (Luo et al., 2008) distributed by the Broad Institute Genomic Perturbations Platform and the RNAi Consortium (TRC). The plasmid for shRNA expression under the control of the constitutive U6 snRNA promoter was the lentiviral vector pLKO.1. shRNA pool production and infection conditions were performed as previously described (Luo et al., 2008). 24h hours after infection as well as at 15 days of repgrogramming, we extracted the genomic DNA and detrmined the abundance of distinct shRNAs based on their representation in the genomic DNA.
Contributor(s) Cacchiarelli D, Trapnell C, J. Ziller M, Ho Sui SJ
Citation(s) 26186193
Submission date Jul 17, 2015
Last update date May 15, 2019
Contact name Shannan J Ho Sui
Organization name Harvard T.H. han Scholol of Public Health
Department Biostatistics
Street address 655 Huntington Ave, Building 2, Rm 437A
City Boston
State/province Massachusetts
ZIP/Postal code 02115
Country USA
Platforms (1)
GPL15520 Illumina MiSeq (Homo sapiens)
Samples (4)
GSM1825831 shRNA_hiF-T_Rep1
GSM1825832 shRNA_hiF-T_Rep2
GSM1825833 15dd_DOX_shRNA_plus_Rep2
This SubSeries is part of SuperSeries:
GSE62777 Integrative analyses of human reprogramming reveal dynamic nature of induced pluripotency
BioProject PRJNA290154
SRA SRP061265

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Supplementary file Size Download File type/resource
GSE71035_shRNA_pool.counts.txt.gz 53.0 Kb (ftp)(http) TXT
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