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Developmental Cell, Volume 38
Supplemental Information
Spatiotemporal Reconstruction of the Human
Blastocyst by Single-Cell Gene-Expression Analysis
Informs Induction of Naive Pluripotency
Jens Durruthy-Durruthy, Mark Wossidlo, Sunil Pai, Yusuke Takahashi, GugeneKang, Larsson Omberg, Bertha Chen, Hiromitsu Nakauchi, Renee ReijoPera, and Vittorio Sebastiano
Supplementary Information
Spatiotemporal reconstruction of the human blastocyst by single-cell gene
expression analysis informs induction of naive pluripotency
Authors
Jens Durruthy-Durruthy1,2,†, Mark Wossidlo1,2,3†, Sunil Pai1, Yusuke Takahashi2,3
Gugene Kang1, Larsson Omberg3, Bertha Chen1, Hiromitsu Nakauchi2,3 Renee Reijo Pera4, Vittorio Sebastiano1,2,*.
†contributed equally
*correspondence
Affiliations
1Department of Obstetrics and Gynecology, Stanford University, Stanford, CA
94305. 2Institute for Stem Cell Biology & Regenerative Medicine, Stanford University,
Stanford, CA 94305. 3Department of Genetics, Institute for Stem Cell Biology & Regenerative
Medicine, Stanford University, Stanford, CA 94305 3Sage Bionetworks, Seattle, WA 98109 4Department of Cell Biology and Neuroscience, Montana State University,
Bozeman, MT 59717
Inventory of Supplementary Materials:
Figure S1, related to Fig. 1. Quality control of single-cell gene expression analysis on different human blastocyst-stage development.
Figure S2, related to Fig. 2. Three-dimensional PCA to reconstruct the ICM of human blastocysts. Figure S3, related to Fig. 2. Three-dimensional reconstruction of the
trophectoderm (TE) of human blastocysts. Figure S4, related to Fig. 3. Three-dimensional PCA predicts “salt and steak”
model for NANOG and GATA4 expression. Figure S5, related to Fig. 4 and Fig. 5. Single-cell gene expression analysis in
NANOG-/GATA4- cells of the human blastocyst. Figure S6, related to Fig. 6. MCRS1, TET1 and THAP11 induce naive
pluripotency in human embryonic stem cells. Figure S7, related to Fig. 7. Global gene expression and functional analysis of
MTTH-overexpressed hESCs. Table S1, related to Fig. 1 and Fig S1. Assays used in this study.
Table S2, related to Fig. 1. Data matrix of normalized Ct values. Movie S1, related to Fig. 3. GATA4+ (blue) and NANOG+ (orange) cells in three-
dimensional PCA plot in ICM of early human blastocysts. Movie S2, related to Figure 3. Rotation of z-stack of immunostained human
embryo (NANOG in red, GATA4 in white). Movie S3, related to Figure 3. GATA4+ (blue) and NANOG+ (orange) cells in
three-dimensional PCA plot in ICM of late human blastocysts. Movie S4, related to Figure 7. Rotation of z-stack of immunostained mouse embryo injected with naive human stem cells (green: Cdx2, white: Oct4, red:
NANOG [human specific]) Movie S5, related to Figure 7. Rotation of z-stack of immunostained mouse
embryo injected with naive human stem cells (green: Cdx2, white: Oct4, red: NANOG [human specific]). Example 2.
Supplementary Experimental Procedures
Supplementary References
Supplemental Figure legends S1-S7
Fig. S1, related to Fig. 1. Quality control of single-cell gene expression
analysis on different human blastocyst-stage development.
(A) Representative brightfield images of an early and late human blastocyst with
Gardner expansion grading (Gardner et al). Scale bar = 50 µm.
(B) Table summarizing number of blastocysts used in this study for gene
expression analysis.
(C) Representative example of dilution series for all 96 assays. Ct values were
plotted as a function of dilution factors (1:2) on a log-scale. Linear regression
analysis depicted with red line. 7 assays with R2 < 0.97 were excluded, thus
leaving 89 assays.
(D) Distribution histogram of calculated primer efficiencies for 89 DELTAgene
assays estimated from the slopes of standard curve plots. The average
efficiency is 90.51% with standard deviation of 20.38.
(E) Q-Q plot with experimental estimated efficiencies (y-axis) and the values
expected for a normal distribution with mean efficiency = 0.09051 and standard
deviation = 0.2038 (x-axis). The red line indicates the values expected for a
normal distribution (y = x). Efficiency values that were derived from plots with 3
points in the standard curve are depicted in blue. Values derived from plots with
> 3 points in the standard curve are depicted in black.
(F) Principal component analysis (PCA) on gene expression analysis of single
cells collected from late blastocysts. Two independent C1 chips were run
highlighting low chip-to-chip variance.
(G) Correlation analysis of mean Ct values generated 91 cells of two dynamic
IFC arrays (single cells of two independent experiments). Genes that were
detected in at least 20% of 91 cells per dynamic IFC array are considered.
Outliers are shown in blue. Assays in blue (total of 5) were excluded from
subsequent analysis due to non-correlative pattern among arrays leaving 89
assays that are listed in Table S1.
(H) Hierarchical cluster analysis represented as a dendrogram identifies three
distinct subpopulations in the combined analysis of all blastocyts.
(I) PCA on 241 single cells colored and encircled according to their blastocyst
origin. Subpopulations are color-coded.
(J) PC projections of 84 genes, showing the contribution of each gene to the
first two PCs. Genes highlighted in orange are key markers of all three lineages.
(K) Microscopic view of a representative small and big cell captured by the C1
chip representing likely inner cell mass (ICM)- and trophectoderm (TE)-like cells.
(L) Correlation between cell size and identified subpopulations indicate that cells
of subpopulation 1 are bigger compared to subpopulation 2 and 3.
(M-N) Hierarchical cluster analysis represented as a dendrogram identifies two
and three distinct subpopulations in early and late blastocysts, respectively.
Fig. S2, related to Fig. 2. Three-dimensional PCA to reconstruct the ICM of
human blastocysts.
(A) Gene expression analysis of epiblast markers for cells projected onto the
first three PCs and projected onto a sphere. XY-view facilitates to locate each
cell on sphere. Cells in grey represent undetectable gene expression.
Expression values for cells that were defined as epiblast and PE, respectively,
were combined and plotted as bar plots with +SEM shown.
(B) Gene expression analysis of PE-marker CXCR4. See (A) for details.
(C-E) Gene expression analysis of selected chromatin remodeling markers (C)
and ICM-specific retroviral-derived long noncoding RNAs (D-E). See (A) for
details.
Fig. S3, related to Fig. 2. Three-dimensional reconstruction of the
trophectoderm (TE) of human blastocysts.
(A) PCA on single cells collected from all blastocysts. Highlighted in red are cells
that were defined as TE (n = 45) that were subject to subsequent 3D PC
analysis.
(B) First 3 principal components of TE cells projected in 3D space and projected
onto a sphere in the 3D space. View from the XY axes (PC1 and PC2) with single
cells projected onto the sphere.
(C) Grouping of single cells based on k-means and specific asymmetrical
expression on the sphere.
(D) Cells of the TE are defined as mural and polar origin and color-coded
accordingly on the 3D sphere. View from the XY axes of color-coded cells
projected onto the sphere.
(E) Gene expression analysis of TE markers for cells projected onto the first
three PCs and projected onto a sphere. XY-view facilitates to locate each cell on
sphere. Cells in grey represent undetectable gene expression. Expression values
for cells that were defined as mural and polar, respectively, were combined and
plotted as bar plots with +SEM shown.
(F) Gene expression analysis of epiblast markers. See (E) for details.
(G) Representative immunostaining of CDX2 (green) and NANOG (red) in a
human blastocyst indicates asymmetric CDX2 distribution. N=26 human
blastocysts, scale bar = 60 µm.
Fig. S4, related to Fig. 3. Three-dimensional PCA predicts “salt and steak”
model for NANOG and GATA4 expression.
(A) Normalized expression of GATA4 and GATA6 in early (n = 24 and 11,
respectively) and late human cells of the ICM (n = 28 and 23, respectively) with
+SEM shown.
(B-C) NANOG and GATA4 expression analysis of single cells in early and late
ICMs.
(D) Spatial distribution analysis of NANOG and/or GATA4 positive cells in early
and late ICM along PC1-PC3.
(E) Represenative immunostainings of GATA4 (grey) and NANOG (red) in two
early human blastocysts validates 3D modeling using PCA. N=16 human
Blastocysts, scale bar = 50 µm.
(F) NANOG+ and GATA4+ cells presented in one sphere (3D PCA) of an early
ICM.
(G) PCA on 29 single cells of NANOG-/GATA4- cells in early blastocysts.
(H) PC projections of the 84 genes, showing the contribution of each gene to the
first two PCs. Genes highlighted in color indicate driving key markers for
population separation in (E).
(I) NANOG+ and GATA4+ cells presented in one sphere (3D PCA) of a late ICM.
(J) PCA on 84 single cells of NANOG-/GATA4- cells in late blastocysts.
(K) PC projections of the 84 genes, showing the contribution of each gene to the
first two PCs. Genes highlighted in color indicate driving key markers for
population separation in (H).
Fig. S5, related to Fig. 4 and Fig. 5. Single-cell gene expression analysis in
NANOG-/GATA4- cells of the human blastocyst.
(A) Normalized and scaled gene expression changes over time (along PC1) of
epiblast-markers and pluripotent-specific HPATs during epiblast differentiation.
Data points are plotted via third order polynomial curve fitting.
(B) Normalized and scaled gene expression changes over time (along PC2) of
epiblast-markers and pluripotent-specific HPATs during PE differentiation. Data
points are plotted via third order polynomial curve fitting.
(C) Normalized TEAD4 expression.
(D-E) Gene expression analysis of epiblast and PE markers. Cells are plotted
along PC1 (x-axis) and a pseudo vector (y-axis) to highlight lineage
specification. Curve presents gene expression changes of single cells that are
ranked along PC1. Expression values were scaled and curves fit with the
LOWESS method (Prism 6).
(F-I) Gene expression analysis of selected genes for cells projected onto the first
2 PCs. Four different expression patterns are shown.
(J) Bayesian network analysis of pluripotency specific markers in cells of early
blastocyst.
(K) Bayesian network analysis of pluripotency specific markers in cells of late
blastocyst.
Fig. S6, related to Fig. 6. MCRS1, TET1 and THAP11 induce naive
pluripotency in human embryonic stem cells.
(A) Representative immunostaining of MCRS1 (red), THAP11 (green) and OCT4
(white) in human blastocysts. N = 8 human blastocysts, scale bar = 50 µm.
(B) Single cell gene expression analysis of three overexpression vectors
transfected into hESCs (48h post-transfection). GFP overexpression vector used
as negative control. +SEM are shown.
(C-D) Fraction of OCT4-reporter (GFP) positive cells in hESCs transiently
overexpressed with different factor combinations in feeder-free, non-naïve
culture conditions.
(E) Representative image of OCT4-reporter positive hESCs
(F) Fluorescence activity of OCT4-reporter line after overexpression of novel
genes.
(G) Box-and-whisker plots comparing naive gene marker expression of naive
versus primed hESCs. Expression is combined from single-cell data. Significant
upregulation of naive markers in M+T+TH transfected hESCs 48 hours later.
+SEM shown.
(H) Box-and-whisker plots showing no differences between naive versus primed
hESCs in non-naive pluripotency markers and house keeping genes. +SEM
shown.
(I) Immunostaining of TFCPL21 (green) in hESCs transfected with MCRS1,
THAP11 and TET1 with MOCK control.
(J) Intensity and distribution of H3K9me3. Single cells were selected at random
and intensity and distribution of staining were analyzed by Image J. Primed
hESCs in conventional culture medium. MTTH overexpressed hESCs in 5i/L/A
medium. Scale bar = 10 µm.
Fig. S7, related to Fig. 7. Global gene expression and functional analysis of
MTTH-overexpressed hESCs.
(A) Heatmap and hierarchical clustering of primed and naive hESCs after
microarray analysis.
(B-C) Gene Ontology (GO) and pathway analysis.
(D) Validation of expression of candidate genes identified in microarray assay.
Supplemental Tables legends S1-S2 (as Excel)
Table S1, related to Fig. 1 and Fig. S1. – Assays used in this study.
Table S2, related to Fig. 1. – Data matrix of normalized Ct values.
Supplemental Movie legends S1-S5
Movie S1, related to Fig. 3. GATA4+ (blue) and NANOG+ (orange) cells in three-
dimensional PCA plot in ICM of early human blastocysts.
Movie S2, related to Fig. 3. Rotation of z-stack of immunostained human
embryo (NANOG in red, GATA4 in white).
Movie S3, related to Fig. 3. GATA4+ (blue) and NANOG+ (orange) cells in three-
dimensional PCA plot in ICM of late human blastocysts.
Movie S4, related to Fig. 7. Rotation of z-stack of immunostained mouse
embryo injected with naive human stem cells (green: Cdx2, white: Oct4, red:
NANOG [human specific])
Movie S5, related to Fig. 7. Rotation of z-stack of immunostained mouse
embryo injected with naive human stem cells (green: Cdx2, white: Oct4, red:
NANOG [human specific]). Example 2.
Supplemental Experimental Procedures
Assay performance validation
Primers were designed intron-spanned to avoid amplification of possible
contaminating genomic DNA. Each primer pair was tested prior use for single-
cell gene expression analysis for efficiency, sensitivity and specificity as well as
to determine the expected melting temperature (Tm) for the specific amplicon for
each assay as previously described (Durruthy-Durruthy et al., 2016).
Determine limit of detection (LOD) value
Because of the lognormal distribution described by Bengtsson et al. (Bengtsson
et al., 2005) and others, single-cell data are best viewed as expression level
above detection limit on a log scale. For qPCR data we determine the log base 2
and defined Log2Ex with Log2Ex = LOD Ct – Ct raw [of gene]. We used bulk RNA
and the dilution series of generated cDNA samples to calculate LOD Ct as
follows: mean Ct and standard deviations for each assay (6 replicates) were
calculated for all serial dilutions. Average Ct values with SD > 1 determined the
threshold that was assigned to the limit of detection for each assay. We finally
calculated the median of all LOD Ct values across all assays to determine a
universal LOD Ct score of 27, which was used throughout this study.
Quality assessment and normalization of single-cell expression values
Melting curves were analyzed and false positive signals excluded. Chip to chip
variation was assessed with 2 IFCs (2 rounds of late blastocysts) to identify
assays that significantly change across different IFC chips. We excluded 7
assays for subsequent analysis since they did not correlate within an acceptable
range between the three 2 IFCs and did not pass quality assessment. Then, raw
Ct values were converted to expression levels using Log2Ex = LOD Ct – Ct raw
[of gene] with LOD Ct = 27. Values with Log2Ex < 0 were excluded. Genes
expressed in fewer than 5 % of single cells were eliminated as well. Single cells
with Log2Ex lower than 3x SD of an assay across all cells were labeled apoptotic
and were excluded. 134 cells were removed from further analysis due to failed
quality assessment, resulting in 241 cells. We normalized such that each cell has
the same median Log2Ex value across all genes detected in that cell. This
ensured that the normalization factor included data from all genes in the study.
For this study we generated a high quality data matrix of 241 genes across 89
assays resulting in 21,449 single cell expression values that was used for data
analysis (Table S2).
Data analysis
We used R (version 3.1.2, Matlab (version 8.4.0) and GraphPad Prism 6 for all
multivariate single-cell data analysis, statistical computing and graphic
visualizations.
Source and procurement of human embryos
Supernumerary human blastocysts from successful (in vitro fertilized) IVF cycles,
donated for basic research, were obtained with written informed consent from
the Stanford University RENEW Biobank. De-identification was performed
according to the Stanford University Institutional Review Board approved
protocol #10466 entitled ‘The RENEW Biobank’ and the molecular analysis of
the embryos was in compliance with institutional regulations.
Chimera formation
Chimeric embryos were generated by microinjection of H9-MTTH pluripotent
stem cells into eight-cell or morula-stage embryos. BDF1 mouse embryos were
collected in M2 medium (EMD Millipore) at eight-cell or morula stage. Embryos
were cultured in KSOM (EMD Millipore) for several hours for eight-cell/morula
stage injection. Cells for injection were accutased into single cells and
suspended in culture medium (either 2i/LIF+dox or W8). Ten cells were injected
into the subzonal space of each individual embryo by using a piezo-driven
micro-manipulator (Primetech) under the microscope. After injection, embryos
underwent follow-up culture in KSOM (supplemented with 2i/LIF+dox) for 48
hours.
Immunofluorescence on human preimplantation embryos and embryonic
stem cells
For immunostaining of early and late stage human blastocysts, the zona
pellucida was removed by Acidic Tyrode’s solution (Millipore) and embryos were
fixed in 4% PFA in PBS for 20 min at 4⁰ C. After permeabilization in 0.2% Triton-
X, 0.1% BSA in PBS for 10 min at RT blastocysts were blocked overnight in
0.1% BSA in PBS at 4⁰ C. Embryos were then incubated with primary antibodies
in blocking solution for 3-4 h at RT at following conditions: 1:200 OCT4 (goat,
Santa Cruz), 1:100 NANOG (rabbit, ReproCell), 1:200 CDX2 (mouse, Abcam),
1:200 GATA4 (goat, abcam), 1:250 MCRS1 (rabbit, Santa Cruz), 1:500 THAP11
(mouse, Abcam) and 1:1000 NUMA (human specific antibody, Abcam) . After
several washes in blocking solution at RT blastocysts were incubated with
secondary antibodies using 488-, 568- or 647 Alexa Fluor conjugates
(Invitrogen) at 1:500 dilution for 1-2 h at RT. Following several washes in
blocking solution embryos were stained with DAPI for 10 min.
For immunostaining of human primed and MTTH-overexpressed embryonic
stem cells, cells were fixed in 4% PFA in PBS for 20 min at RT on a silanized
slide. After permeabilization in 0.2% Triton-X, 0.1% BSA in PBS for 15 min at
RT, cells were blocked overnight in 0.1% BSA in PBS at 4⁰ C. Primary antibody
staining in blocking solution was done using 1:500 H3K9me3 (rabbit, Actif Motif)
for 2h at RT. After several washes in blocking solution at RT secondary antibody
staining with 1:500 Alexa Fluor 568 (Invitrogen) was done 1h at RT. Following
several washes in blocking solution cells were stained with DAPI for 5 min.
Images were acquired using a Zeiss LSM510 Meta inverted laser scanning
confocal microscope and computations of z-stack images were processed as
described previously (Wossidlo et al., 2011).
hES cell culture and induction of naive pluripotency in vitro
Conventional (primed) human iPSC lines C1 (Whitehead Institute Center for
Human Stem Cell Research, Cambridge, MA) (Hockemeyer et al., 2008) were
maintained on mitomycin C inactivated MEF feeder layers and passaged
mechanically using a drawn Pasteur pipette or enzymatically by treatment for
20 min with 1 mg/ml Collagenase type IV (GIBCO) followed by sequential
sedimentation steps in human ESC medium (hESM) to remove single cells. C1
hESCs were cultured in hESM—DMEM/F12 (Invitrogen) supplemented with 15%
FBS (Hyclone), 5% KSR (Invitrogen), 1 mM glutamine (Invitrogen), 1%
nonessential amino acids (Invitrogen), penicillin-streptomycin (Invitrogen),
0.1 mM β -mercaptoethanol (Sigma), and 4 ng/ml FGF2 (R&D systems). Human
ESC line H1 and derived iPSC lines were maintained in feeder-free conditions
and cultured in basal mTeSR1 medium (STEMCELL Technologies)
supplemented with 5x mTeSR1 supplement (STEMCELL Technologies). Cells
were maintained in culture by daily media change and enzymatically passaged
at 1:2 to 1:5 dilutions with pre-warmed Accutase (Innovative Cell Technologies).
Differentiated cells were removed and/or cleaned under a laminar flow
dissection hood. All cultures were maintained at 37°C, 5 % CO2 and 4 % O2.
For conversion of preexisting primed human ESCs, se seeded 2 x 105
trypsinized single cells on a MEF feeder layer in hESC medium supplemented
with ROCK inhibitor Y-27632 (Stemgent, 10 μM). Two days later, medium was
switched to 5i/L/A naïve hESC medium. Dome-shaped naive colonies appeared
within 10 days and could be picked or expanded polyclonally using 3–5 min
treatment with Accutase (GIBCO) on an MEF feeder layer. Naive human
pluripotent cells were derived and maintained in serum-free N2B27-based
media supplemented with 5i/L/A. Medium was generated as described
(Theunissen et al., 2014).
For transient expression experiments we transfected primed hESCs with 3 μg of
circular MCRS1, TET1 and THAP11 constitutive expression plasmids. Two days
later, medium was switched to 2i/L conditions (Takashima et al., 2014). At day 4,
cells were retransfected (nucleofection), and on day 7 cells were assayed for
gene expression and reporter activity. Naive human ESCs were cultured on
mitomycin C-inactivated MEF feeder cells and were passaged every 5–7 days
by a brief PBS wash followed by single-cell dissociation using 3–5 min treatment
with Accutase (GIBCO) and centrifugation in fibroblast medium (DMEM
[Invitrogen] supplemented with 10% FBS [Hyclone], 1 mM glutamine
[Invitrogen], 1% nonessential amino acids [Invitrogen], penicillin-streptomycin
[Invitrogen], and 0.1 mM β -mercaptoethanol). For continues passaging (up to
passage 4), cells were retransfected prior replating. For cells cultured in 5i/L/A
conditions (Theunissen et al., 2014) no transfection was necessary.
For making stable transfectants piggyBac (PB) vectors (2 μg) carrying
doxycycline-inducible NANOG, TET1 and THAP11 were co-transfected with an
rtTA expression construct (2 μg) and pBase helper plasmid (4 μg) using the
Neon Transfection System. Two days later, G418 was applied (100 μg/ml). Cells
were selected for 2 weeks. Transfectants were dissociated with trypsin and
replated in the presence of Rho-associated kinase inhibitor (ROCKi) (Y-27632,
Calbiochem) prior to addition of DOX (1 μM) on day 1 on feeders. On day 2,
medium was changed to W8 or 2i/LIF and DOX. Medium was changed daily.
Cells were split every 5–7 days after dissociation with Accutase (Life
Technologies). After 4-7 days cells transitioned into naïve-like colonies and were
maintained on MEF feeders.
Flow cytometry
To assess the proportion of OCT4-∆PE-GFP+ human ESCs, a single cell
suspension was filtered, washed once in PBS and respuspended in PBS + 5 %
FBS prior fluorescence-activated cell sorting (FACS) analysis.
Microarray analysis. Total mRNA was isolated from H9-hESCs using the RNeasy kit (Qiagen). The
quality of the total RNA was confirmed using an Agilent 2100 Bioanalyzer.
Samples were sent to the Pan Facility at Stanford University for further
processing. Biotinylated cRNA was prepared according to the standard
Affymetrix protocol from 6 μg of total RNA (GeneChip Whole-Transcript Sense
Target-Labeling Assay, 701880 Rev.5, Affymetrix). The samples were then
hybridized to the Human Gene 2.0 ST array. Probe arrays were washed and
scanned with the Hewlett-Packard GeneArray Scanner G2500A. Raw data files
were created by Command Console, the Affymetrix operating software program.
The Affymetrix Expression Console Program was used to examine the
Affymetrix Gene Array quality control factors for all samples in a project. Data
can be found on ArrayExpress (E-MTAB-4567). Global scaling was used as the
normalization method (RMA). Data were processed using Bioconductor
packages in R.
Statistical Analysis
For single-cell analysis, individual cells were considered as biological replicates
(n = 241). Calculated primer efficiencies revealed a normal distribution
determined by the Shapiro-Wilk test. For normal distributed data we used the
two-tailed Student’s t-test for significance calculations. Nonparametric
statistical approaches were applied for data not following a normal distribution.
Specifically, we chose the Kurskal-Wallis test for independent and unequal sized
sample calculations. Statistical significance was set to p < 0.05 for gene
expression analysis (n > 3). Only Bayesian network connections with p < 0.05
are shown. Correlation analysis revealed only significant correlations with p <
0.05. Resulting values (for each experiment) were subject to two-tailed Student’s
t-test. Error bars represent SEM in all statistical significance tests. The tightness
of clusters was assessed using a Levene’s test for equality of variance.
Supplemental References
Bengtsson, M., Stahlberg, A., Rorsman, P., and Kubista, M. (2005). Gene expression profiling in single cells from the pancreatic islets of Langerhans reveals lognormal distribution of mRNA levels. Genome Res 15, 1388-1392.
Durruthy-Durruthy, J., Sebastiano, V., Wossidlo, M., Cepeda, D., Cui, J., Grow, E.J., Davila, J., Mall, M., Wong, W.H., Wysocka, J., et al. (2016). The primate-specific noncoding RNA HPAT5 regulates pluripotency during human preimplantation development and nuclear reprogramming. Nature genetics 48, 44-52.
Hockemeyer, D., Soldner, F., Cook, E.G., Gao, Q., Mitalipova, M., and Jaenisch, R. (2008). A drug-inducible system for direct reprogramming of human somatic cells to pluripotency. Cell stem cell 3, 346-353.
Takashima, Y., Guo, G., Loos, R., Nichols, J., Ficz, G., Krueger, F., Oxley, D., Santos, F., Clarke, J., Mansfield, W., et al. (2014). Resetting transcription factor control circuitry toward ground-state pluripotency in human. Cell 158, 1254-1269.
Theunissen, T.W., Powell, B.E., Wang, H., Mitalipova, M., Faddah, D.A., Reddy, J., Fan, Z.P., Maetzel, D., Ganz, K., Shi, L., et al. (2014). Systematic identification of culture conditions for induction and maintenance of naive human pluripotency. Cell stem cell 15, 471-487.
Wossidlo, M., Nakamura, T., Lepikhov, K., Marques, C.J., Zakhartchenko, V., Boiani, M., Arand, J., Nakano, T., Reik, W., and Walter, J. (2011). 5-Hydroxymethylcytosine in the mammalian zygote is linked with epigenetic reprogramming. Nature communications 2, 241.
-10 0 10 20 30
-50
510
15
PC1
PC2
0 50 100
Subpopulation 3
Subpopulation 2
Subpopulation 1
% of captured cells in C1
Big cellSmall cell
P < 0.0001
A C D
E F f
K
G
Supplemental Figure 1
5
10
15
-5 0 5 10 15
Chi
p 1
[nor
mal
ized
Ct]
Chip 2 [normalized Ct]
R2 = 0.67531/slope = 0.9734
WNT2B
CGA
HLA-G HPAT11
ELF5
Chip 1 - 6 dpf embryosChip 2 - 6 dpf embryos
LSmall cell
Big cell
n = 153 cells
# of pooled blastocysts Exp. grad. # of C1 chips Single cells
8798
1 - 31 - 34 - 64 - 6
1111
53358271
TOTAL: 32 4 241
~ 8-10 µm
~ 4-7 µm
15
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-5
PC2
3020100-10PC1
B
60 80 100 120 1400
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Estimated efficiency
Num
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f ass
ays
Mean efficiency: 90.51%Standard dev.: 20.38
-4 -3 -2 -1 015
20
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1:2 dilution series - log10 [template]
Raw
Ct v
alue
PDGFRa
-3 -2 -1 0 1 2 3
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Efficiency expected from normal distribution - z(j)
Estim
ated
effi
cien
cy
Q-Q plot
Early blastocyst Late blastocyst
Expansion grading 2 Expansion grading 6
67 68 82 72 73 47 48 45 49 52 53 55 51 56 78 79 84 76 77 63 64 66 80 83 74 81 86 87 85 88 65 69 75 70 71 41 39 35 42 61 62 46 58 54 60 57 50 59 36 40 29 32 43 24 37 31 33 26 28 25 23 30 27 34 38 44 1 4 2 3 5 6 7 8 9 12 10 11 22 20 21 19 13 18 14 15 16 17 105
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Cluster Dendrogram
hclust (*, "ward")distance
Hei
ght
3 17 21 19 20 11 18 14 15 12 13 10 4 7 1 5 8 9 16 2 6 85 86 79 81 83 84 65 66 63 64 67 72 68 73 69 70 76 71 77 74 78 82 87 51 44 47 38 52 42 46 56 57 55 58 59 60 61 62 88 53 80 24 34 29 41 45 50 31 37 49 43 48 27 35 25 30 36 22 23 54 28 32 40 26 33 39 75
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050
060
0
Cluster Dendrogram
hclust (*, "ward")distance
Hei
ght
M N
PC1
-10 -5 0 5 10 15 20 25 30 35
PC2
-10
-5
0
5
10
15
20
25
Epiblast-like
Trophectoderm-like
PE-likeSubpopulation 1 Subpopulation 2 Subpopulation 3
55 56 57 58 59 54 72 79 8084 82 83 74 81 77 78 75 7666 73 67 70 64 63 61 62 68 71 69 60 65 23 26 24 25 27
28 29 30 31 34 32 339 22
130
118
124
111
131
116
123 97 102
109 99 108
234
231
224
235 85 90 94
101
106
115
10498 105
114
100
113
170
236
184
227
208
217
187
189
103
110
126
117
128
185
183
207
141
228
237
188
222
120
125
172
173
171
174
226
233
206
214
176
177
178
179
197
229
238
209
186
219
133
161
142
143164
175
144
145
146
150
132
134
136
137
159
160
157
158
140
165
147
138
139
148
149
163
153
154
156
151
152
135
155
162
167
168
166
169
180
196
190
195 88 89 86 87 91 107 92 112 93 95 127
119
129 96 218
122
202
203
210
198
211
221
230
220
223
239
181
213
193
200
191
205 5 62 8 12 3 4 13 14 18 217 11 16 1 10 46 50 121 52 42 48 37
225
232 43 45 38 40 35 41 36 39 44 47 51 194
201
182
192
204
215
199
212
216 17 20 240
241 49 5315 19
0200
400
600
800
1000
Cluster Dendrogram
hclust (*, "ward")
Height
n = 45 n = 133 n = 63
n = 241 cells1000
800
600
400
200
0
Hei
ght
Loading PC1-0.05 0 0.05 0.1 0.15 0.2 0.25 0.3
Load
ing
PC2
-0.3
-0.2
-0.1
0
0.1
0.2
0.3
0.4
TEAD4
TROP2
CDX2
LIN28A
SALL4
TDGF1
GRB2
GATA4
n = 84 genes
H I J
Supplemental Figure 2
10.5
0-0.5
-1-1-0.5
00.5
-1
-0.5
0
0.5
1
1
10.5
0-0.5
-1-1-0.5
00.5
-1
-0.5
0
0.5
1
1
10.5
0-0.5
-1-1-0.5
00.5
-1
-0.5
0
0.5
1
1
10.5
0-0.5
-1-1-0.5
00.5
-1
-0.5
0
0.5
1
1
10.5
0-0.5
-1-1-0.5
00.5
-1
-0.5
0
0.5
1
1
10.5
0-0.5
-1-1-0.5
00.5
-1
-0.5
0
0.5
1
1
10.5
0-0.5
-1-1-0.5
00.5
-1
-0.5
0
0.5
1
1
10.5
0-0.5
-1-1-0.5
00.5
-1
-0.5
0
0.5
1
1
-1
-0.8
-0.6
-0.4
-0.2
0
0.2
0.4
0.6
0.8
1
-1-0.500.51
-1
-0.8
-0.6
-0.4
-0.2
0
0.2
0.4
0.6
0.8
1
-1-0.500.51
-1
-0.8
-0.6
-0.4
-0.2
0
0.2
0.4
0.6
0.8
1
-1-0.500.51
-1
-0.8
-0.6
-0.4
-0.2
0
0.2
0.4
0.6
0.8
1
-1-0.500.51
-1
-0.8
-0.6
-0.4
-0.2
0
0.2
0.4
0.6
0.8
1
-1-0.500.51
-1
-0.8
-0.6
-0.4
-0.2
0
0.2
0.4
0.6
0.8
1
-1-0.500.51
-1
-0.8
-0.6
-0.4
-0.2
0
0.2
0.4
0.6
0.8
1
-1-0.500.51-1
-0.8
-0.6
-0.4
-0.2
0
0.2
0.4
0.6
0.8
1
-1-0.500.51
PE
Epiblast
0
1
2
3
Nor
mal
ized
exp
ress
ion P = 0.0025
PE
Epiblast
0
1
2
3
Nor
mal
ized
exp
ress
ion P < 0.0001
PE
Epiblast
0.0
0.5
1.0
1.5
2.0
2.5
Nor
mal
ized
exp
ress
ion P < 0.0001
PE
Epiblast
0.0
0.5
1.0
1.5
2.0
Nor
mal
ized
exp
ress
ion P = 0.2113
PE
Epiblast
0.0
0.5
1.0
1.5
2.0
Nor
mal
ized
exp
ress
ion P < 0.0001
PE
Epiblast
0
1
2
3
4N
orm
aliz
ed e
xpre
ssio
n P = 0.0436
PE
Epiblast
0.0
0.1
0.2
0.3
Nor
mal
ized
exp
ress
ion
PE
Epiblast
0
1
2
3
4
Nor
mal
ized
exp
ress
ion P = 0.0001
MCRS1
THAP11
TET1
HPAT2
HPAT3
HPAT5
HPAT15 HPAT4E
PC1 PC2
PC2
PC1
PC1 PC2
PC2
PC1
PC1 PC2
PC2
PC1
PC1 PC2
PC2
PC1
PC1 PC2
PC2
PC1
PC1 PC2
PC2
PC1
PC1 PC2
PC2
PC1PC1 PC2
PC2
PC1
PC3
PC3
PC3
PC3
PC3
PC3
PC3
PC3
-1-0.500.51-1
-0.8
-0.6
1
0.8
0.6
0.4
0.2
0
-0.2
-0.4
3
3.5
4
4.5
5
5.5
6
6.5
7
7.5
8
high
low
-1
-0.8
-0.6
-0.4
-0.2
0
0.2
0.4
0.6
0.8
1
-1-0.500.51
10.5
0-0.5
-1-1-0.5
00.5
1
0.5
0
-0.5
-11
10.5
0-0.5
-1-1-0.5
00.5
1
0.5
0
-0.5
-11
10.5
0-0.5
-1-1-0.5
00.5
1
0.5
0
-0.5
-11
-1
-0.8
-0.6
-0.4
-0.2
0
0.2
0.4
0.6
0.8
1
-1-0.500.51
-1
-0.8
-0.6
-0.4
-0.2
0
0.2
0.4
0.6
0.8
1
-1-0.500.51
PE
Epiblast
0.0
0.5
1.0
1.5
2.0
2.5
Nor
mal
ized
exp
ress
ion
PE
Epiblast
0
1
2
3
4
Nor
mal
ized
exp
ress
ionTFCP2L1
KLF5
CXCR4B
PC1PC2
PC2
PC1
PC1PC2
PC2
PC1
PC1PC2
PE
Epiblast
0.0
0.5
1.0
1.5
2.0
Nor
mal
ized
exp
ress
ion
PC3
PC3
PC3
PC2
PC1
10.5
0-0.5
-1-1-0.5
00.5
1
0.5
0
-0.5
-11 -1
-0.8
-0.6
-0.4
-0.2
0
0.2
0.4
0.6
0.8
1
-1-0.500.51
PE
Epiblast
0.0
0.2
0.4
0.6
Nor
mal
ized
exp
ress
ionPOU5F1
PC1PC2
PC2
PC1
PC3
A
C D
Supplemental Figure 3
-1
-0.8
-0.6
-0.4
-0.2
0
0.2
0.4
0.6
0.8
1
-1-0.500.511
0.50
-0.5-1-1
-0.50
0.5
-1
-0.5
0
0.5
1
1
-1
-0.8
-0.6
-0.4
-0.2
0
0.2
0.4
0.6
0.8
1
-1-0.500.51
10.5
0-0.5
-1-1-0.5
00.5
1
0.5
0
-0.5
-11
10.5
0-0.5
-1-1-0.5
00.5
1
0.5
0
-0.5
-11
10.5
0-0.5
-1-1-0.5
00.5
1
0.5
0
-0.5
-11 -1
-0.8
-0.6
-0.4
-0.2
0
0.2
0.4
0.6
0.8
1
-1-0.500.51
-1
-0.8
-0.6
-0.4
-0.2
0
0.2
0.4
0.6
0.8
1
-1-0.500.51
-1
-0.8
-0.6
-0.4
-0.2
0
0.2
0.4
0.6
0.8
1
-1-0.500.51
PC1-10 -5 0 5 10 15 20 25 30 35
PC2
-10
-5
0
5
10
15
20
25
Cluster 1presumptive
“Mural”
A
E
10.5
0-0.5
-1-1-0.5
00.5
1
0.5
0
-0.5
-11
Trophectoderm (n=45)
10.5
0-0.5
-1-1-0.5
00.5
1
0.5
0
-0.5
-11
10.5
0-0.5
-1-1-0.5
00.5
1
0.5
0
-0.5
-11
10.5
0-0.5
-1-1-0.5
00.5
1
0.5
0
-0.5
-11
-1
-0.8
-0.6
-0.4
-0.2
0
0.2
0.4
0.6
0.8
1
-1-0.500.51
-1
-0.8
-0.6
-0.4
-0.2
0
0.2
0.4
0.6
0.8
1
-1-0.500.51
-1
-0.8
-0.6
-0.4
-0.2
0
0.2
0.4
0.6
0.8
1
-1-0.500.51
PolarMural
0
2
4
6
8
Nor
mal
ized
exp
ress
ion P = 0.0006
PolarMural
0
2
4
6
8
10
Nor
mal
ized
exp
ress
ion P = 0.0023
PolarMural
0
2
4
6
8
Nor
mal
ized
exp
ress
ion P < 0.0001
PolarMural
0
1
2
3
Nor
mal
ized
exp
ress
ion P = 0.006
PolarMural
-0.3
-0.2
-0.1
0.0
0.1
0.2
0.3
Nor
mal
ized
exp
ress
ion P = 0.0158
PolarMural
-0.5
0.0
0.5
1.0
1.5N
orm
aliz
ed e
xpre
ssio
n P < 0.0001
XY-view
F
C
CDX2
TEAD4
TROP2
POU5F1
UTF1
ZFP42
PC1PC2
PC2
PC1
PC1PC2
PC2
PC1
PC1PC2
PC2
PC1
PC1PC2
PC2
PC1
PC1PC2
PC2
PC1PC1
PC2
PC1PC2
PC2
PC1
PC1PC2
PC2
PC1
X Y
Z
X Y
Z
PC3
PC3
-10 0 10 20 30PC1
20
10
0
-10
PC2
PC3
PC3
PC3
PC3
PC3
PC3
PC2
PC1
DAPI CDX2 Merge (-DNA)
Bla
stoc
yst
NANOGG
-1-0.500.51-1
-0.8
-0.6
1
0.8
0.6
0.4
0.2
0
-0.2
-0.4
3
3.5
4
4.5
5
5.5
6
6.5
7
7.5
8
high
low
3020
100
-10-20-20
-100
10
20
15
10
5
0
-5
-10
PC1PC2
PC3
Cluster 2presumptive
“Polar”
B
16 17 18 19 20 15 33 40 41 45 43 44 35 42 38 39 36 37 27 34 28 31 25 24 22 23 29 32 30 21 26 3 6 4 5 7 8 9 10 11 14 12 13 1 2
020
4060
8010
0
Cluster Dendrogram
hclust (*, "ward")distance
Hei
ght
D
3D PCA
3D PCA on sphere
2D PCA on sphere
3D PCA on sphere 2D PCA on sphere
Cluster 1 Cluster 2
DAPI CDX2 Merge (-DNA)
Bla
stoc
yst
NANOG
10.5
0-0.5
-1-1-0.5
00.5
-1
-0.5
0
0.5
1
1
10.5
0-0.5
-1-1-0.5
00.5
1
0.5
0
-0.5
-11
Supplemental Figure 4
1 3 5 7 9 11 13 15 17 19 21 23 25 27 29 31 33 35 37 39 41 43 45 47 49 51 53 55 57 59 61 63 65 670
2
4
6
8
single cells
Nor
mal
ized
exp
ress
ion
1 3 5 7 9 11 13 15 17 19 21 23 25 27 29 31 33 35 37 39 41 43 45 47 49 51 53 55 57 59 61 630
2
4
6
8
single cells
Nor
mal
ized
exp
ress
ion
1 3 5 7 9 11 13 15 17 19 21 23 25 27 29 31 33 35 37 39 41 43 45 47 49 51 53 55 57 59 61 63 650
2
4
6
8
single cells
Nor
mal
ized
exp
ress
ion
B C
PC1-5 0 5 10
PC2
-6
-4
-2
0
2
4
6
8
10
PC1-10 -5 0 5 10 15 20 25
PC2
-15
-10
-5
0
5
10
2D PCA - Early ICMNANOG-/GATA4- cells
n = 84 cells
n = 29 cells
PC1PC2
3D PCA on sphere - Early ICM
PC1PC2
PC3
2D PCA - Late ICMNANOG-/GATA4- cells
3D PCA on sphere - Late ICM
PC3
Loading PC1-0.4 -0.2 0 0.2 0.4 0.6
Load
ing
PC2
-0.3
-0.2
-0.1
0
0.1
0.2
0.3
0.4
0.5
0.6
EZH2
HPAT5
GATA6FGFR2
HPAT3HPAT8
HPAT15
n = 84 genesTHAP11
E-CADHERIN
LIN28A
Loading PC1-0.1 0 0.1 0.2 0.3
Load
ing
PC2
-0.4
-0.3
-0.2
-0.1
0
0.1
0.2
0.3
0.4DNMT1
FN1
JARID2TET2CXCR4
HPAT5LIN28A
TET1MCRS1
YAP
TFCP2L1
SALL4
GATA6E-CADHERIN
DNMT3B
P300
TEAD4
BPTF1
n = 84 genes
HPAT21
Primitive endoderm Epiblast
F G H
I J K
DAPI NANOG GATA4 Zoom (-DNA)
Early
em
bryo
D
PC projections - Early ICMNANOG-/GATA4- cells
PC projections - Late ICMNANOG-/GATA4- cells
Early ICM Late ICM
GATA4+NANOG+
low/no detection
GATA4+NANOG+
GATA4
GATA60.0
0.5
1.0
1.5N
orm
aliz
ed e
xpre
ssio
nEarly ICM
GATA4
GATA60.0
0.5
1.0
1.5Late ICM
Nor
mal
ized
exp
ress
ion
A
E
NANOG GATA4 NANOG GATA4 NANOG GATA4
PC1
PC2
PC3
PC1
PC2
PC3
NANOGGATA4 NANOG GATA4 NANOG
GATA4 NANOG GATA4NANOGGATA4 NANOG GATA4
Early ICM Late ICM
DAPI NANOG GATA4 Zoom (-DNA)
Early
em
bryo
0 20 40 60 80 1000.0
0.5
1.0
PC1
0 20 40 60 80 1000.0
0.5
1.0
PC1
0 20 40 60 80 1000.0
0.5
1.0
PC1
0 20 40 60 80 1000.0
0.5
1.0
PC1
0 20 40 60 80 1000.0
0.5
1.0
PC1
0 20 40 60 80 1000.0
0.5
1.0
PC1
0 20 40 60 80 1000.0
0.5
1.0
PC1
0 20 40 60 80 1000.0
0.5
1.0
PC1
0 20 40 60 80 1000.0
0.5
1.0
PC1
0 20 40 60 80 1000.0
0.5
1.0
PC1
0 20 40 60 80 1000.0
0.5
1.0
PC1
0 20 40 60 80 1000.0
0.5
1.0
PC1
0 20 40 60 80 1000.0
0.5
1.0
PC1
0 20 40 60 80 1000.0
0.5
1.0
PC1
0 20 40 60 80 1000.0
0.5
1.0
PC1
0 20 40 60 80 1000.0
0.5
1.0
PC1
0 20 40 60 80 1000.0
0.5
1.0
PC1
0 20 40 60 80 1000.0
0.5
1.0
PC1
-10 -5 0 5 10 15 20 25-15
-10
-5
0
5
10
15
-10 -5 0 5 10 15 20 25-15
-10
-5
0
5
10
15
-10 -5 0 5 10 15 20 25-15
-10
-5
0
5
10
15DNMT1 TET2GRB7
-10 -5 0 5 10 15 20 25-15
-10
-5
0
5
10
15
-10 -5 0 5 10 15 20 25-15
-10
-5
0
5
10
15
-10 -5 0 5 10 15 20 25-15
-10
-5
0
5
10
15MBD3 HPAT5HPAT2
-10 -5 0 5 10 15 20 25-15
-10
-5
0
5
10
15
-10 -5 0 5 10 15 20 25-15
-10
-5
0
5
10
15
-10 -5 0 5 10 15 20 25-15
-10
-5
0
5
10
15
-10 -5 0 5 10 15 20 25-15
-10
-5
0
5
10
15
-10 -5 0 5 10 15 20 25-15
-10
-5
0
5
10
15
-10 -5 0 5 10 15 20 25-15
-10
-5
0
5
10
15
-10 -5 0 5 10 15 20 25-15
-10
-5
0
5
10
15
-10 -5 0 5 10 15 20 25-15
-10
-5
0
5
10
15
-10 -5 0 5 10 15 20 25-15
-10
-5
0
5
10
15
-10 -5 0 5 10 15 20 25-15
-10
-5
0
5
10
15
-10 -5 0 5 10 15 20 25-15
-10
-5
0
5
10
15
-10 -5 0 5 10 15 20 25-15
-10
-5
0
5
10
15
P300 CD9BPTF
JARID2
YAP
FN1
DNMT3B LAMC1E-CADHERIN
TAF1
LMNB1
TEAD4
DE
F
G
H
I
SOX2
POU5F1
TERTTDGF1
HPAT23
LIN28A
HPAT3
TFCP2L1HPAT20
HPAT2
HPAT1
THAP11
NANOG
HPAT5
DPPA3
TET1
HPAT23
POU5F1
SOX2
HPAT15HPAT2
MCRS1
HPAT4
THAP11
TFCP2L1
LINC_ROR
HPAT7
HPAT1
ZFP42
NANOG
DNMT3B
HPAT3
HPAT5
UTF1
J
K
Lineage 1 Lineage 2
Lineage 1 Lineage 2
ZFP4
2SA
LL4
POU
5F1
LIN
28A
SOX1
7PD
GFR
AG
RB
2G
ATA
6C
XCR
4
Single cells along PC1
Nor
mal
ized
exp
ress
ion
PC1
PC2
PC1
PC1
PC1
PC2
PC2
PC2
-10 0 10 20
10
0
-10
-10 0 10 20
10
0
-10
-10 0 10 20
10
0
-10
-10 0 10 20
10
0
-10
-10 0 10 20
10
0
-10
-10 0 10 20
10
0
-10
-10 0 10 20
10
0
-10
-10 0 10 20
10
0
-10
-10 0 10 20
10
0
-10
-10 0 10 20
10
0
-10
-10 0 10 20
10
0
-10
-10 0 10 20
10
0
-10
-10 0 10 20
10
0
-10
-10 0 10 20
10
0
-10
-10 0 10 20
10
0
-10
-10 0 10 20
10
0
-10
-10 0 10 20
10
0
-10
-10 0 10 20
10
0
-10
Early human ICM
Late human ICM
-1-0.500.51-1
-0.8
-0.6
1
0.8
0.6
0.4
0.2
0
-0.2
-0.4
3
3.5
4
4.5
5
5.5
6
6.5
7
7.5
8
high
low
Supplemental Figure 5
0 5 10 15 20 25
0
5
10
Single cells along PC1
Nor
mal
ized
exp
ress
ion
TFCP2L1NANOG
HPAT5
HPAT2HPAT3
0 20 40 60 80
0
5
10
Single cells along PC2
Nor
mal
ized
exp
ress
ion
NANOGTFCP2L1
HPAT5
HPAT2HPAT3
Epiblast pathway
PE pathway
A
B
0 5 10NANOG-/GATA4-
NANOG+ or GATA4+ *
n = 113n = 85
Normalized TEAD4 expression
C
Supplemental Figure 6
MOCK
TFC
P2L1
M+T+TH
DA
PI
A B D
I
MCRS1-OEGFP
02468
10
Rel
ativ
e ex
pres
sion ****
MCRS1
TET1-OEGFP
0.0
0.5
1.0
1.5
Rel
ativ
e ex
pres
sion
*
TET1
THAP11-O
EGFP
0
2
4
6
8
Rel
ativ
e ex
pres
sion
*
THAP11
C
DA
PIM
CR
S1TH
AP1
1O
CT4
Hu. Blast.
MC
RS1
[M]
TET1
[T]
THA
P11
[TH
]
M+T
+TH
NA
NO
G0
1
2
3
4
5
GFP
pos
itive
cel
ls [%
]
OCT4-ΔPE
E
MTTH overexpressedPrimed hESCs
0.00 0.05 0.10 0.15 0.20 0.25
Distance
Gre
y Va
lue
300
200
100
0.00 0.05 0.10 0.15 0.20 0.25
Distance
Gre
y Va
lue
300
200
100
0.00 0.05 0.10 0.15 0.20
Distance
Gre
y Va
lue
300
200
100
0.00 0.05 0.10 0.15 0.20
Distance
Gre
y Va
lue
300
200
100
H3K9me3 DAPI H3K9me3 DAPI
J
Phase OCT4-ΔPE
MC
RS1
TET1
THA
P11
M+T
+TH
NA
NO
G
F G
0
5
10
15
Nor
mal
ized
exp
ress
ion
of n
aive
plu
ripot
ency
mar
kers
******** ** ****
****
***
NANOG UTF1 DPPA3 REST TFCP2L1 KLF5
0
5
10
15
20
Nor
mal
ized
exp
ress
ion
of
prim
ed p
lurip
oten
cy/H
K m
arke
rs
n.s.
DNMT3B
n.s.
n.s.
n.s.
TDGF1 POU5F1 PRDM14
n.s.
RPLP0
H
M+T+TH transfected:non-transfected:
non-transfectedM+T+TH transfected
n = 90 single cellsn = 92 single cells
M+T
M+T
H
T+TH
M+T
+TH
Con
trol
0
1
2
3
4
5
GFP
pos
itive
cel
ls [%
]
Supplemental Figure 7
Upregulated in H9-MTTH (+2i/LIF, DOX)Downregulated in H9-MTTH (+2i/LIF, DOX)
0 2 4 6ephrin receptor bidirectional signaling axis
hippo signaling pathwayneural Crest Differentiation
extracellular matrix associated proteinsaxon guidance
Wnt signaling pathwaycell-Cell communication
regulation of nuclear SMAD2/3 signalingTGF Beta Signaling Pathway
cell-cell junction organizationcell junction organization
-Log(p-Value)
Pathway analysis
0 5 10 15neurogenesis
generation of neuronsbrain development
pattern specification processcentral nervous system development
tissue morphogenesisepithelium development
regulation of cell proliferationtissue development
regulation of multicellular organismal development
-Log(p-Value)
GO Biological Processes
.CEL
2.C
EL
3.C
EL
2.C
EL
.CEL
3.C
EL
361136816323760140818813457108175188206203226168164581259291243478430607541574562578549550554555552553632593577592585507512413420391393252411274250268329560533537551498470539582542535422476402438386408389257248280326372337293265249279283260467362612557606597437325416518570261310275383427398480457466487401341256264273317369308400385154169160982082111041301221842162141961071956766125176194192205167158114691412292303421370150227217222212135741331435582372341529421519982218124186187143173220138115171209443223326392518228105102688462711218710618117418223120217816315191157146291713242371221193056507220023321920415516696951291281261271311031771111471371171181621791562381902351831985102115415949273876446163891591422362012211721611492238511080113123139132283140486465737946545345170153207232929986931122391361912242401891851931452101651162091971017522518014410014812011983554252514790971097778634626622639623631637638636643615629628619621613543522497532514516482445473376356254245267301270281431461414458449451394418387399350423388319300316286358272441392442419390403436287324374359302334297314299288309558517595571561559591564567548563598596594572579583486491452489496506536519534523521520525504481515453492479508513455434432290277262343351266367404377345320361352242397331429378327357295285456421382447395348332364271276303282284640610609618627633625635642641624630620617603608611604616614600605601602599566573547538545575568468444426530511460469454342253322304241269371384335366246278244347339312433428381465509495488472485502501499500580569584590556544529524526540546565576589588586587474462477435446355365405338307396294311353333370375373247315346292354409415379494483528493464471527531505510503475484440439450425463490459448306349323443406424368330336407417410412363344360340328313296289380321298263251258255305318
−3 −2 −1 0 1 2 3Column Z−Score
Color Key
MTTH + Dox
MTTH - Dox
0.00
0.05
0.10
0.15
0.20
NANOG
Rel
ativ
e ex
pres
sion
MTTH + Dox
MTTH - Dox
0.0
0.5
1.0
1.5
ZFP42
Rel
ativ
e ex
pres
sion
MTTH + Dox
MTTH - Dox
0.000
0.005
0.010
0.015
0.020
GDF3
Rel
ativ
e ex
pres
sion
MTTH + Dox
MTTH - Dox
0.0
0.2
0.4
0.6
0.8
LINC-ROR
Rel
ativ
e ex
pres
sion
MTTH + Dox
MTTH - Dox
0.0
0.1
0.2
0.3
0.4
PRDM14
Rel
ativ
e ex
pres
sion
W8 media2i/LIF media
H9_
prim
ed_2
H9_
prim
ed_1
H9_
prim
ed_3
H9_
naiv
e_1
H9_
naiv
e_2
H9_
naiv
e_3
A B
C
D
