TY - JOUR
T1 - KeyGenes, a Tool to Probe Tissue Differentiation Using a Human Fetal Transcriptional Atlas
AU - Roost, Matthias S.
AU - Van Iperen, Liesbeth
AU - Ariyurek, Yavuz
AU - Buermans, Henk P.
AU - Arindrarto, Wibowo
AU - Devalla, Harsha D.
AU - Passier, Robert
AU - Mummery, Christine L.
AU - Carlotti, Françoise
AU - De Koning, Eelco J.P.
AU - Van Zwet, Erik W.
AU - Goeman, Jelle J.
AU - Chuva De Sousa Lopes, Susana M.
N1 - Funding Information:
We thank H. Locher for help with the fetal dissection; M. Gomes Fernandes for the sex genotyping; G.M. de Roo for FACS of the NKX2.5:GFP cells; S.A.J de Zeeuw for bioinformatics support; and the Centre for Contraception, Abortion and Sexuality (CASA) in Leiden and the Hague for the collection of the human fetal material. S.M.C.d.S.L. is supported by the Netherlands Organisation for Scientific Research (NWO, ASPASIA 015.007.037) and the Interuniversity Attraction Poles (IAP, P7/07). M.S.R., C.L.M., and F.C. are supported by the Bontius Stichting (PANCREAS). E.J.P.d.K. is supported by Stichting DON.
Publisher Copyright:
© 2015 The Authors.
PY - 2015/6/9
Y1 - 2015/6/9
N2 - Differentiated derivatives of human pluripotent stem cells in culture are generally phenotypically immature compared to their adult counterparts. Their identity is often difficult to determine with certainty because little is known about their human fetal equivalents in vivo. Cellular identity and signaling pathways directing differentiation are usually determined by extrapolating information from either human adult tissue or model organisms, assuming conservation with humans. To resolve this, we generated a collection of human fetal transcriptional profiles at different developmental stages. Moreover, we developed an algorithm, KeyGenes, which uses this dataset to quantify the extent to which next-generation sequencing or microarray data resemble specific cell or tissue types in the human fetus. Using KeyGenes combined with the human fetal atlas, we identified multiple cell and tissue samples unambiguously on a limited set of features. We thus provide a flexible and expandable platform to monitor and evaluate the efficiency of differentiation in vitro.
AB - Differentiated derivatives of human pluripotent stem cells in culture are generally phenotypically immature compared to their adult counterparts. Their identity is often difficult to determine with certainty because little is known about their human fetal equivalents in vivo. Cellular identity and signaling pathways directing differentiation are usually determined by extrapolating information from either human adult tissue or model organisms, assuming conservation with humans. To resolve this, we generated a collection of human fetal transcriptional profiles at different developmental stages. Moreover, we developed an algorithm, KeyGenes, which uses this dataset to quantify the extent to which next-generation sequencing or microarray data resemble specific cell or tissue types in the human fetus. Using KeyGenes combined with the human fetal atlas, we identified multiple cell and tissue samples unambiguously on a limited set of features. We thus provide a flexible and expandable platform to monitor and evaluate the efficiency of differentiation in vitro.
UR - http://www.scopus.com/inward/record.url?scp=84930931809&partnerID=8YFLogxK
U2 - 10.1016/j.stemcr.2015.05.002
DO - 10.1016/j.stemcr.2015.05.002
M3 - Article
C2 - 26028532
AN - SCOPUS:84930931809
SN - 2213-6711
VL - 4
SP - 1112
EP - 1124
JO - Stem cell reports
JF - Stem cell reports
IS - 6
ER -