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Series GSE62772 Query DataSets for GSE62772
Status Public on Jul 16, 2015
Title Integrative analyses of human reprogramming reveal dynamic nature of induced pluripotency [mRNA-Seq]
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
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 mRNA sequencing of primary and secondary fibroblasts with reference BJ (supplementary file fibroblasts), reprogramming intermendiates from untreated hiF-T reprogramming (supplementary file reprogramming), or selective time points upon LSD1 inhibitor treatment (supplementary file LSD1i). RNA samples used for mRNA sequencing are the same used for smallRNA sequencing.
Contributor(s) Cacchiarelli D, Trapnell C, Ziller MJ, Ho Sui S
Citation(s) 26186193
Submission date Oct 28, 2014
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 (2)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (81)
GSM1533212 2dd_DOX_minus_Rep1_mRNA
GSM1533213 2dd_DOX_minus_Rep2_mRNA
GSM1533214 2dd_DOX_plus_Rep1_mRNA
This SubSeries is part of SuperSeries:
GSE62777 Integrative analyses of human reprogramming reveal dynamic nature of induced pluripotency
BioProject PRJNA265099
SRA SRP049340

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Supplementary file Size Download File type/resource
GSE62772_all_genes_LSD1i.fpkm_tracking.csv.gz 1.7 Mb (ftp)(http) CSV
GSE62772_all_genes_fibroblasts.fpkm_tracking.csv.gz 1.6 Mb (ftp)(http) CSV
GSE62772_all_genes_reprogramming.fpkm_tracking.csv.gz 2.2 Mb (ftp)(http) CSV
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