E-MTAB-3825 - Genetic variability exceeds cell-type memory and determines iPSCs differentiation potential-implications for biobanking

Status
Submitted on 16 July 2013, released on 7 January 2016, last updated on 22 August 2016
Organism
Homo sapiens
Samples (48)
Array (1)
Protocols (6)
Description
Summary To address the issue of retention of somatic cell memory in iPSCs we compared gene expressions of genetically matched human iPSCs derived from fibroblasts and blood. We were using the all-in-one type footprint free SeVdp-iPS system, for generation of uniform iPSC lines Our results show that iPSC lines derived from the same donor are highly similar to each other. Overal design Total RNA was extracted from fibroblasts derived iPSC (N=8) and blood derived iPSC (N=10) as well as parental fibroblasts and peripheral blood mononuclear cells (N=4 different donors: T14; T42; T53; T55). Total RNA was also extracted from spontaneously differentiated Embryonic bodies derived from fibroblasts derived iPSC (N=4) and blood derived iPSC (N=4) from four donors. RNA from control human embryonic stem cell lines (H9, and FES22) was used as control. Samples were run in two different batches (1 and 2).
Experiment types
transcription profiling by array, cell type comparison design
Contact
Citations
Genetic Variability Overrides the Impact of Parental Cell Type and Determines iPSC Differentiation Potential. Kyttälä A, Moraghebi R, Valensisi C, Kettunen J, Andrus C, Pasumarthy KK, Nakanishi M, Nishimura K, Ohtaka M, Weltner J, Van Handel B, Parkkonen O, Sinisalo J, Jalanko A, Hawkins RD, Woods NB, Otonkoski T, Trokovic R. :200-212 (2016), PMID:26777058
Genetic Variability Overrides the Impact of Parental Cell Type and Determines iPSC Differentiation Potential. Kyttälä A , Moraghebi R , Valensisi C , Kettunen J , Andrus C , Pasumarthy KK , Nakanishi M , Nishimura K , Ohtaka M , Weltner J , Van Handel B , Parkkonen O , Sinisalo J , Jalanko A , Hawkins RD , Woods NB , Otonkoski T , Trokovic R. Stem Cell Reports 6(2):200-212 (2016), PMID:26777058
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-MTAB-3825.idf.txt
Sample and data relationshipE-MTAB-3825.sdrf.txt
Raw data (1)E-MTAB-3825.raw.1.zip
Processed data (1)E-MTAB-3825.processed.1.zip
Array designA-MEXP-2072.adf.txt