Single-cell profiling identifies key pathways expressed by iPSCs cultured in different commercial media

Maciej Daniszewski, Quan Nguyen, Hun S. Chy, Vikrant Singh, Duncan E. Crombie, Tejal Kulkarni, Helena H. Liang, Priyadharshini Sivakumaran, Grace E. Lidgerwood, Damien Hernandez, Alison Conquest, Louise A. Rooney, Sophie Chevalier, Stacey B. Andersen, Anne Senabouth, James C. Vickers, David A. Mackey, Jamie E. Craig, Andrew L. Laslett, Alex W. Hewitt & 2 others Joseph E. Powell, Alice Pebay

Research output: Contribution to journalArticle

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Abstract

We assessed the pluripotency of human induced pluripotent stem cells (iPSCs) maintained on an automated platform using StemFlex and TeSR-E8 media. Analysis of transcriptome of single cells revealed similar expression of core pluripotency genes, as well as genes associated with naive and primed states of pluripotency. Analysis of individual cells from four samples consisting of two different iPSC lines each grown in the two culture media revealed a shared subpopulation structure with three main subpopulations different in pluripotency states. By implementing a machine learning approach, we estimated that most cells within each subpopulation are very similar between all four samples. The single-cell RNA sequencing analysis of iPSC lines grown in both media reports the molecular signature in StemFlex medium and how it compares to that observed in the TeSR-E8 medium.

Original languageEnglish
Pages (from-to)30-39
JournalIscience
Volume7
DOIs
Publication statusPublished - 28 Sep 2018

Cite this

Daniszewski, Maciej ; Quan Nguyen ; Chy, Hun S. ; Singh, Vikrant ; Crombie, Duncan E. ; Kulkarni, Tejal ; Liang, Helena H. ; Sivakumaran, Priyadharshini ; Lidgerwood, Grace E. ; Hernandez, Damien ; Conquest, Alison ; Rooney, Louise A. ; Chevalier, Sophie ; Andersen, Stacey B. ; Senabouth, Anne ; Vickers, James C. ; Mackey, David A. ; Craig, Jamie E. ; Laslett, Andrew L. ; Hewitt, Alex W. ; Powell, Joseph E. ; Pebay, Alice. / Single-cell profiling identifies key pathways expressed by iPSCs cultured in different commercial media. In: Iscience. 2018 ; Vol. 7. pp. 30-39.
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title = "Single-cell profiling identifies key pathways expressed by iPSCs cultured in different commercial media",
abstract = "We assessed the pluripotency of human induced pluripotent stem cells (iPSCs) maintained on an automated platform using StemFlex and TeSR-E8 media. Analysis of transcriptome of single cells revealed similar expression of core pluripotency genes, as well as genes associated with naive and primed states of pluripotency. Analysis of individual cells from four samples consisting of two different iPSC lines each grown in the two culture media revealed a shared subpopulation structure with three main subpopulations different in pluripotency states. By implementing a machine learning approach, we estimated that most cells within each subpopulation are very similar between all four samples. The single-cell RNA sequencing analysis of iPSC lines grown in both media reports the molecular signature in StemFlex medium and how it compares to that observed in the TeSR-E8 medium.",
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author = "Maciej Daniszewski and {Quan Nguyen} and Chy, {Hun S.} and Vikrant Singh and Crombie, {Duncan E.} and Tejal Kulkarni and Liang, {Helena H.} and Priyadharshini Sivakumaran and Lidgerwood, {Grace E.} and Damien Hernandez and Alison Conquest and Rooney, {Louise A.} and Sophie Chevalier and Andersen, {Stacey B.} and Anne Senabouth and Vickers, {James C.} and Mackey, {David A.} and Craig, {Jamie E.} and Laslett, {Andrew L.} and Hewitt, {Alex W.} and Powell, {Joseph E.} and Alice Pebay",
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Daniszewski, M, Quan Nguyen, Chy, HS, Singh, V, Crombie, DE, Kulkarni, T, Liang, HH, Sivakumaran, P, Lidgerwood, GE, Hernandez, D, Conquest, A, Rooney, LA, Chevalier, S, Andersen, SB, Senabouth, A, Vickers, JC, Mackey, DA, Craig, JE, Laslett, AL, Hewitt, AW, Powell, JE & Pebay, A 2018, 'Single-cell profiling identifies key pathways expressed by iPSCs cultured in different commercial media' Iscience, vol. 7, pp. 30-39. https://doi.org/10.1016/j.isci.2018.08.016

Single-cell profiling identifies key pathways expressed by iPSCs cultured in different commercial media. / Daniszewski, Maciej; Quan Nguyen; Chy, Hun S.; Singh, Vikrant; Crombie, Duncan E.; Kulkarni, Tejal; Liang, Helena H.; Sivakumaran, Priyadharshini; Lidgerwood, Grace E.; Hernandez, Damien; Conquest, Alison; Rooney, Louise A.; Chevalier, Sophie; Andersen, Stacey B.; Senabouth, Anne; Vickers, James C.; Mackey, David A.; Craig, Jamie E.; Laslett, Andrew L.; Hewitt, Alex W.; Powell, Joseph E.; Pebay, Alice.

In: Iscience, Vol. 7, 28.09.2018, p. 30-39.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Single-cell profiling identifies key pathways expressed by iPSCs cultured in different commercial media

AU - Daniszewski, Maciej

AU - Quan Nguyen, null

AU - Chy, Hun S.

AU - Singh, Vikrant

AU - Crombie, Duncan E.

AU - Kulkarni, Tejal

AU - Liang, Helena H.

AU - Sivakumaran, Priyadharshini

AU - Lidgerwood, Grace E.

AU - Hernandez, Damien

AU - Conquest, Alison

AU - Rooney, Louise A.

AU - Chevalier, Sophie

AU - Andersen, Stacey B.

AU - Senabouth, Anne

AU - Vickers, James C.

AU - Mackey, David A.

AU - Craig, Jamie E.

AU - Laslett, Andrew L.

AU - Hewitt, Alex W.

AU - Powell, Joseph E.

AU - Pebay, Alice

PY - 2018/9/28

Y1 - 2018/9/28

N2 - We assessed the pluripotency of human induced pluripotent stem cells (iPSCs) maintained on an automated platform using StemFlex and TeSR-E8 media. Analysis of transcriptome of single cells revealed similar expression of core pluripotency genes, as well as genes associated with naive and primed states of pluripotency. Analysis of individual cells from four samples consisting of two different iPSC lines each grown in the two culture media revealed a shared subpopulation structure with three main subpopulations different in pluripotency states. By implementing a machine learning approach, we estimated that most cells within each subpopulation are very similar between all four samples. The single-cell RNA sequencing analysis of iPSC lines grown in both media reports the molecular signature in StemFlex medium and how it compares to that observed in the TeSR-E8 medium.

AB - We assessed the pluripotency of human induced pluripotent stem cells (iPSCs) maintained on an automated platform using StemFlex and TeSR-E8 media. Analysis of transcriptome of single cells revealed similar expression of core pluripotency genes, as well as genes associated with naive and primed states of pluripotency. Analysis of individual cells from four samples consisting of two different iPSC lines each grown in the two culture media revealed a shared subpopulation structure with three main subpopulations different in pluripotency states. By implementing a machine learning approach, we estimated that most cells within each subpopulation are very similar between all four samples. The single-cell RNA sequencing analysis of iPSC lines grown in both media reports the molecular signature in StemFlex medium and how it compares to that observed in the TeSR-E8 medium.

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KW - COPY NUMBER VARIATION

KW - HIDDEN-MARKOV MODEL

KW - DERIVATION

KW - STATE

KW - LINES

KW - MAINTENANCE

KW - GROWTH

KW - NAIVE

KW - OCT4

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M3 - Article

VL - 7

SP - 30

EP - 39

JO - Iscience

JF - Iscience

SN - 2589-0042

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