Development of a Focused Microarray to Assess Human Embryonic Stem Cell Differentiation
Raj K. Puri, MD, PhD
Journal:
STEM CELLS and DEVELOPMENT, Volume 14, Issue 3, June, 2005
Authors:
Amy X. Yanga*, Josef Mejidoa*, Yongquan Luob, Xianmin Zengc, Catherine Schwartzb, Tianxia Wud, R. Scott Thiese, Bhaskar Bhattacharyaa, Jing Hana, Bill Freedc, Mahendra Rao b,f, Raj K. Puria
a Laboratory of Molecular Tumor Biology, Division of Cellular and Gene Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, MD 20892;
b Laboratory of Neurosciences, Gerontology Research Center, National Institute on Aging, Baltimore, MD 21224;
c Cellular Neurobiology Branch, National Institute on Drug Abuse, Baltimore, MD 21224;
d Biostatistics Core Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892;
e Geron Corporation, 230 Constitution Avenue, Menlo Park CA 94025;
f Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD 21218.
* Co-first authors
Supplementary Tables:
Table 1 - Genes selected for ESC focused array
Table 2 - Genes over-expressed in hESC BG01 compared to hURNA
Table 3 - Genes over-expressed in hESC BG02 compared to hURNA
Table 4 - Genes over-expressed in hEC NTERA-2 compared to hURNA
Supplementary Table S1
This table provides information on 755 oligonucleotides for the human stem cell focused array. Information is provided for oligonucleotide source, gene symbol, functional category, chromosome location, gene description, UniGene and GeneBank accessory number or transcript count numbers.
(PDF version)
Supplementary Table S2
This table lists over-expressed genes in hESC BG01 compared to hURNA. Data shown represent mean fold expression of genes in ES, EB and other category compared to hURNA. (PDF version)
Genes over-expressed in hESC BG01 compared to hURNAa |
Category |
Gene |
UniGene No. |
Fold |
SDb |
Gene |
UniGene No. |
Fold |
SDb |
ES |
CCNB1 |
Hs.23960 |
2.05 |
0.55 |
NME2 |
Hs.433416 |
2.86 |
0.58 |
CCT8 |
Hs.416211 |
1.63 |
0.34 |
NPM1 |
Hs.411098 |
8.09 |
2.35 |
CD24 |
Hs.375108 |
5.61 |
1.31 |
NS |
Hs.313544 |
1.69 |
0.59 |
CRABP2 |
Hs.183650 |
1.55 |
0.43 |
OK/SW-cl.56 |
Hs.356729 |
2.98 |
0.79 |
DNMT3B |
Hs.251673 |
5.52 |
1.91 |
PHF17 |
Hs.12420 |
1.53 |
0.36 |
EIF4A1 |
Hs.129673 |
2.11 |
0.68 |
POU5F1 |
Hs.249184 |
2.10 |
0.08 |
FABP5 |
Hs.408061 |
2.71 |
0.63 |
PSMA2 |
Hs.333786 |
1.64 |
0.34 |
GAL |
Hs.278959 |
12.67 |
4.71 |
RPL24 |
Hs.184582 |
3.19 |
0.78 |
GJA1 |
Hs.74471 |
5.62 |
1.42 |
RPL4 |
Hs.186350 |
2.04 |
0.41 |
HDAC2 |
Hs.3352 |
1.99 |
0.57 |
RPL6 |
Hs.528668 |
3.65 |
0.77 |
HMGA1 |
Hs.57301 |
4.85 |
1.56 |
RPL7 |
Hs.421257 |
2.73 |
0.54 |
HMGB2 |
Hs.434953 |
2.54 |
0.62 |
RPLP0 |
Hs.443796 |
2.57 |
0.33 |
HNRPAB |
Hs.81361 |
2.14 |
0.60 |
RPS24 |
Hs.356794 |
4.55 |
1.14 |
HSPA4 |
Hs.90093 |
1.60 |
0.48 |
SEMA6A |
Hs.443012 |
1.96 |
0.80 |
IDH1 |
Hs.11223 |
2.41 |
0.85 |
SEPHS1 |
Hs.124027 |
1.66 |
0.67 |
IFITM1 |
Hs.458414 |
3.18 |
1.00 |
SET |
Hs.436687 |
4.03 |
1.48 |
IMP-2 |
Hs.30299 |
1.45 |
0.38 |
SFRP2 |
Hs.31386 |
1.98 |
0.68 |
IMPDH2 |
Hs.75432 |
1.92 |
0.64 |
SNRPF |
Hs.105465 |
1.61 |
0.48 |
KPNA2 |
Hs.252712 |
1.86 |
0.30 |
TD-60 |
Hs.380857 |
1.56 |
0.47 |
LAPTM4B |
Hs.296398 |
2.63 |
0.90 |
TDGF1 |
Hs.385870 |
3.16 |
1.15 |
LDHB |
Hs.234489 |
2.35 |
0.39 |
ZNF43 |
Hs.419763 |
1.98 |
0.33 |
LEFTB |
Hs.278239 |
2.17 |
0.72 |
Clone RP3-447F3 |
|
3.85 |
0.68 |
LIN28 |
Hs.86154 |
8.74 |
3.47 |
Clone RP11-438F9 |
|
2.96 |
0.68 |
MAD2L2 |
Hs.19400 |
1.64 |
0.50 |
Clone RP3-334F4 |
|
1.86 |
0.47 |
NASP |
Hs.446206 |
3.78 |
1.14 |
Clone RP11-248N6 |
|
5.86 |
1.86 |
EB |
None |
|
|
|
|
|
|
|
Othersc |
ENO1 |
Hs.433455 |
1.74 |
0.19 |
MFAP2 |
Hs.389137 |
1.65 |
0.28 |
FKBP3 |
Hs.379557 |
1.77 |
0.62 |
MIF |
Hs.407995 |
2.12 |
0.92 |
GA17 |
Hs.44893 |
1.99 |
0.95 |
PHC1 |
Hs.305985 |
1.53 |
0.39 |
HSPA8 |
Hs.180414 |
1.55 |
0.39 |
TERF1 |
Hs.442707 |
1.53 |
0.22 |
HSPCA |
Hs.446579 |
1.92 |
0.56 |
XRCC5 |
Hs.257082 |
1.80 |
0.24 |
HSPCB |
Hs.74335 |
2.57 |
0.58 |
HERV-H protein mRNA |
|
5.05 |
1.49 |
HSPD1 |
Hs.79037 |
5.02 |
1.95 |
Clone 38C16 |
|
2.02 |
0.24 |
K-ALPHA-1 |
Hs.446608 |
1.59 |
0.14 |
Clone RP1-269M15 |
|
3.21 |
0.53 |
LDHA |
Hs.2795 |
3.65 |
0.64 |
Clone RP11-371L19 |
|
1.83 |
0.19 |
LIN28 |
Hs.86154 |
8.74 |
1.61 |
Clone RP5-1028D15 |
|
3.17 |
0.56 |
LOC402057 |
Hs.512525 |
3.51 |
0.69 |
Clone RP11-352D3 |
|
2.31 |
0.35 |
a Total RNA derived from BG01 ES cell line was labeled with Cy5 and huURNA with Cy3, respectively, and arrays were hybridized. Data shown represent means of gene expression ratios in BG01 compared to hURNA from triplicate spots.
b SD, standard deviation of means.
c LIN28, redundant to ES category.
Supplementary Table S3
This table lists over-expressed genes in hESC BG02 compared to hURNA. Data shown represent mean fold expression of genes in ES, EB and other category compared to hURNA. (PDF version)
Genes over-expressed in hESC BG02 compared to hURNAa |
Category |
Gene |
UniGene No. |
Ratio |
SDb |
Gene |
UniGene No. |
Ratio |
SDb |
ES |
AURKB |
Hs.442658 |
1.53 |
0.29 |
OK/SW-cl.56 |
Hs.356729 |
3.14 |
0.09 |
CCNB1 |
Hs.23960 |
1.79 |
0.20 |
PHF17 |
Hs.12420 |
1.72 |
0.48 |
|
|
|
|
PODXL |
Hs.16426 |
2.53 |
0.41 |
CD24 |
Hs.375108 |
3.88 |
0.08 |
POU5F1 |
Hs.249184 |
7.08 |
1.74 |
DNMT3B |
Hs.251673 |
3.17 |
0.26 |
PSIP2 |
|
1.60 |
0.19 |
EIF4A1 |
Hs.129673 |
2.23 |
0.12 |
PSMA2 |
Hs.333786 |
1.99 |
0.46 |
FABP5 |
Hs.408061 |
1.76 |
0.10 |
RPL24 |
Hs.184582 |
3.17 |
0.70 |
GAL |
Hs.278959 |
3.13 |
0.45 |
RPL4 |
Hs.186350 |
2.50 |
0.37 |
GJA1 |
Hs.74471 |
3.57 |
0.24 |
RPL6 |
Hs.528668 |
3.68 |
0.96 |
HDAC2 |
Hs.3352 |
1.67 |
0.32 |
RPL7 |
Hs.421257 |
4.16 |
0.73 |
HMGA1 |
Hs.57301 |
8.23 |
1.08 |
RPLP0 |
Hs.443796 |
2.04 |
0.69 |
HMGB2 |
Hs.434953 |
2.44 |
0.50 |
RPS24 |
Hs.356794 |
5.41 |
0.88 |
HNRPAB |
Hs.81361 |
2.12 |
0.40 |
|
|
|
|
HSPA4 |
Hs.90093 |
1.85 |
0.25 |
SET |
Hs.436687 |
2.14 |
0.19 |
IFITM1 |
Hs.458414 |
2.31 |
0.15 |
SFRP2 |
Hs.31386 |
1.77 |
0.08 |
IMPDH2 |
Hs.75432 |
1.91 |
0.25 |
SLC16A1 |
Hs.75231 |
1.86 |
0.39 |
KPNA2 |
Hs.252712 |
1.53 |
0.24 |
SNRPF |
Hs.105465 |
1.89 |
0.44 |
KRT18 |
Hs.406013 |
2.10 |
0.30 |
SSB |
Hs.309316 |
1.50 |
0.60 |
KRT8 |
Hs.356123 |
1.61 |
0.33 |
TD-60 |
Hs.380857 |
1.89 |
0.30 |
LAPTM4B |
Hs.296398 |
1.79 |
0.15 |
|
|
|
|
LDHB |
Hs.234489 |
2.46 |
0.37 |
ZNF117 |
Hs.250693 |
2.67 |
0.52 |
LEFTB |
Hs.278239 |
2.25 |
0.35 |
ZNF257 |
Hs.283900 |
2.46 |
0.35 |
LIN28 |
Hs.86154 |
3.67 |
0.50 |
ZNF43 |
Hs.419763 |
2.99 |
0.42 |
NASP |
Hs.446206 |
3.25 |
0.45 |
clone RP3-447F3 |
|
3.28 |
0.40 |
NBR2 |
Hs.375149 |
1.60 |
0.28 |
clone RP11-438F9 |
|
4.25 |
0.68 |
NME2 |
Hs.433416 |
2.57 |
0.40 |
clone RP3-334F4 |
|
2.71 |
0.56 |
NPM1 |
Hs.411098 |
7.07 |
1.34 |
clone RP11-248N6 |
|
4.49 |
0.75 |
EB |
None |
|
|
|
|
|
|
|
Othersc |
ENO1 |
Hs.433455 |
2.38 |
0.67 |
NPPB |
Hs.219140 |
1.70 |
0.47 |
FGFR1 |
Hs.533922 |
1.54 |
0.37 |
TMSB10 |
Hs.446574 |
1.50 |
0.52 |
GA17 |
Hs.44893 |
1.97 |
0.56 |
ZNF117 |
Hs.250693 |
3.66 |
1.44 |
HSPCA |
Hs.446579 |
1.51 |
0.36 |
Clone 391O22 |
|
2.85 |
0.84 |
HSPCB |
Hs.74335 |
2.40 |
0.74 |
HERV-H protein mRNA |
|
4.94 |
1.41 |
HSPD1 |
Hs.79037 |
4.24 |
1.36 |
Clone 167F1 |
|
1.93 |
0.47 |
K-ALPHA-1 |
Hs.446608 |
2.25 |
0.81 |
Clone 38C16 |
|
2.19 |
0.67 |
LDHA |
Hs.2795 |
1.95 |
0.70 |
beta-galactoside-binding lectin |
|
1.59 |
0.43 |
LIN28 |
Hs.86154 |
4.29 |
1.56 |
Clone RP1-269M15 |
|
2.52 |
1.00 |
LOC402057 |
Hs.512525 |
3.01 |
1.05 |
Clone RP11-371L19 |
|
2.64 |
0.82 |
LOC51685 |
|
2.08 |
0.70 |
Clone RP5-1028D15 |
|
3.11 |
1.06 |
MIF |
Hs.407995 |
2.28 |
0.57 |
Clone RP11-352D3 |
|
3.31 |
0.95 |
a Total RNA derived from BG02 ES cell line was labeled with Cy5 and hURNA with Cy3, respectively, and arrays were hybridized. Data shown represent means of gene expression ratios in BG01 compared to huURNA from triplicate spots.
b SD, standard deviation of means.
c LIN28 and ZNF117, redundant to ES category in BG02.
Supplementary Table S4
This table lists over-expressed genes in hEC NTERA-2 cell line compared to hURNA. Data shown represent mean fold expression of genes in ES, EB and other category compared to hURNA. (PDF version)
Genes over-expressed in hEC NTERA-2 compared to hURNAa |
Category |
Gene |
UniGene No. |
Ratio |
SDb |
Gene |
UniGene No. |
Ratio |
SDb |
ES |
AURKB |
Hs.442658 |
1.7 |
0.26 |
OK/SW-cl.56 |
Hs.356729 |
2.0 |
0.18 |
CCT8 |
Hs.416211 |
2.5 |
0.99 |
POU5F1 |
Hs.249184 |
4.6 |
0.00 |
CD24 |
Hs.375108 |
2.8 |
0.71 |
PSMA2 |
Hs.333786 |
4.2 |
0.93 |
CRABP2 |
Hs.183650 |
2.1 |
1.05 |
PTTG1 |
Hs.350966 |
1.5 |
0.00 |
GAL |
Hs.278959 |
3.0 |
0.94 |
RPL24 |
Hs.184582 |
3.3 |
0.05 |
GJA1 |
Hs.74471 |
2.7 |
0.68 |
RPL4 |
Hs.186350 |
3.3 |
0.16 |
HMGA1 |
Hs.57301 |
4.2 |
0.90 |
RPL6 |
Hs.528668 |
6.3 |
0.13 |
HMGB2 |
Hs.434953 |
2.9 |
0.54 |
RPL7 |
Hs.421257 |
2.9 |
0.09 |
HNRPAB |
Hs.81361 |
1.6 |
0.28 |
RPLP0 |
Hs.443796 |
3.2 |
0.22 |
HSPA4 |
Hs.90093 |
1.8 |
0.51 |
RPS24 |
Hs.356794 |
4.7 |
0.14 |
KRT18 |
Hs.406013 |
1.9 |
0.22 |
SET |
Hs.436687 |
1.9 |
0.00 |
KRT8 |
Hs.356123 |
2.9 |
0.79 |
SFRP2 |
Hs.31386 |
1.9 |
0.34 |
LAPTM4B |
Hs.296398 |
1.7 |
0.39 |
ZNF117 |
Hs.250693 |
1.7 |
0.45 |
LDHB |
Hs.234489 |
8.2 |
0.11 |
ZNF257 |
Hs.283900 |
2.8 |
0.59 |
LIN28 |
Hs.86154 |
14.1 |
4.21 |
ZNF43 |
Hs.419763 |
3.7 |
0.33 |
MGST1 |
Hs.389700 |
2.2 |
0.00 |
clone RP3-447F3 |
|
2.8 |
0.00 |
NASP |
Hs.446206 |
3.1 |
0.00 |
clone RP11-438F9 |
|
3.3 |
0.00 |
NBR2 |
Hs.375149 |
2.8 |
0.00 |
clone RP3-334F4 |
|
4.2 |
0.00 |
NME2 |
Hs.433416 |
2.1 |
0.00 |
clone RP11-248N6 |
|
3.6 |
0.00 |
NPM1 |
Hs.411098 |
2.9 |
0.00 |
|
|
|
|
EB |
None |
|
|
|
|
|
|
|
Others |
AURKB |
Hs.442658 |
1.7 |
0.12 |
LOC51685 |
|
3.1 |
0.13 |
CGI-94 |
Hs.111449 |
1.5 |
0.00 |
PHC1 |
Hs.305985 |
1.7 |
0.00 |
FGF5 |
Hs.37055 |
2.3 |
0.00 |
RPS4L |
Hs.447032 |
2.4 |
0.12 |
HSPA8 |
Hs.180414 |
2.6 |
0.15 |
TEBP |
Hs.355693 |
1.6 |
0.20 |
HSPC163 |
Hs.445890 |
1.6 |
0.00 |
ZNF117 |
Hs.250693 |
1.7 |
0.00 |
HSPCA |
Hs.446579 |
2.6 |
0.13 |
clone 38C16 |
|
3.8 |
0.00 |
HSPCB |
Hs.74335 |
1.9 |
0.07 |
clone RP1-269M15 |
|
4.4 |
0.18 |
HSPD1 |
Hs.79037 |
3.1 |
0.00 |
clone RP11-371L19 |
|
2.1 |
0.04 |
K-ALPHA-1 |
Hs.446608 |
1.8 |
0.00 |
clone RP5-1028D15 |
|
2.0 |
0.13 |
LIN28 |
Hs.86154 |
14.1 |
0.00 |
clone RP11-352D3 |
|
3.1 |
0.23 |
LOC402057 |
Hs.512525 |
4.6 |
0.34 |
|
|
|
|
a Total RNA derived from NTERA-2 cell line was labeled with Cy5 and huURNA with Cy3, and hybridized to focused array. Data shown represent means of the gene expression ratios of NTERA-2 to hURNA from triplicate spots.
b SD, standard deviation of means.
|