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Development of a Focused Microarray to Assess Human Embryonic Stem Cell Differentiation

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Raj K. Puri, MD, PhD

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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

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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)

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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.

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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.

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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.

 

Updated May 20, 2005
 
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