Schwab et al.
MS2080491151562533--REVISED
Additional Tables
Table S1 Primers and Roche Universal Probe Library (UPL) FAM-labeled probes utilized in
quantitative real-time PCR assays.
Gene
Hif1a (genomic)
Hif1a (cDNA)
Vegf
Pgk1
Slc2a1 (Glut-1)
Prom1 (CD133)
Notch1
Notch2
Notch3
Notch4
Hey1
Hey2
Hes1
Hes2
Dll1
Jagged1
Jagged2
Snail1
Slug (Snail2)
Twist
Fibronectin (Fn1)
Ints3
cytokeratin 18
Forward Primer
tgagcttgctcatcagttgc
catgatggctccctttttca
aacgatgaagccctgagt
tacctgctggctggatgg
atggatcccagcagcaag
gaaggagcccagcttagagg
actatctcggcggcttttc
tgcctgtttgacaactttgagt
agctgggtcctgaggtgat
ggacctgcttgcaaccttc
catgaagagagctcacccaga
gtggggagcgagaacaatta
tgccagctgatataatggagaa
agctgcgcaagaacctaaag
gggacagaggggagaagatg
gaggcgtcctctgaaaaaca
tctgtgaggacctggtggat
gtctgcacgacctgtggaa
tgcaagatctgtggcaagg
agctacgccttctccgtct
cggagagagtgcccctacta
gtggctgttattgactctgcac
agatgacaccaacatcacaagg
Reverse Primer
tgagcctcataacagaagctttatc
gtcacctggttgctgcaata
aggtttgatccgcatgatct
cacagcctcggcatatttct
ccagtgttatagccgaactgc
ggtcattcactcaaagtaccatcc
ggcactcgttgatctcctct
gtggtctgcacagtatttgtcat
agacagagccggttgtcaat
ctcacagagcctcccttcc
cgccgaactcaagtttcc
gttgtcggtgaattggacct
ccatgataggctttgatgacttt
aacttcgaagagcgggaagt
cacaccctggcagacagat
acccaagccactgttaagaca
ggttcacagagatccatgtcc
caggagaatggcttctcacc
cagtgagggcaagagaaagg
tccttctctggaaacaatgaca
cgatattggtgaatcgcaga
caggttccccatcatcacat
cttccagaccttggacttcct
UPL ID
60
98
9
108
52
19
5
6
9
34
17
104
20
3
20
6
26
71
71
58
52
17
78
All assays were designed using the Roche Universal ProbeLibrary Assay Design Center
(http://qpcr.probefinder.com/organism.jsp).
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Schwab et al.
MS2080491151562533--REVISED
Table S2 Primary antibody source and dilution factors utilized in western blotting, immunohistochemistry (IHC), immunofluorescence (IF) and FACS.
Antibody
anti-mouse HIF-1
anti-mouse Lamin
A/C
antianti-mouse Ki67
anti-mouse
caspase3, active
anti-mouse CD133PE
anti-mouse CD133
anti-mouse ER
anti-mouse p63
anti-mouse keratin 14
anti-mouse keratin 5
anti-mouse keratin 8
anti-mouse CD24FITC
anti-mouse linage
panel-biotin
conjugated
anti-mouse CD31biotin conjugate
Secondary
1:50,000 anti-rabbit
HRP
1:50,000 anti-goat HRP
Source (Catalog #)
Novus Biologicals (NB100479, Lots E2 or M1)
Santa Cruz Biotechnology
(sc-6215)
Dilution
Purpose
1:5,000
western
1:1,000
western
Sigma-Aldrich (A5228)
Santa Cruz Biotechnology
(sc-7846)
1:5,000
western
1:50,000 anti-mouse
HRP
1:500
IHC
1:200; Vector Elite kit
R&D Systems (AF835)
1:750
1:100
1:200
IHC
FACS
IF
1:200; Vector Elite kit
eBiosciences (clone AC133)
N/A
1:500 AlexaFluor488 or
594
1:200; Vector Elite kit
Millipore (clone 13A4)
Santa Cruz Biotechnology
(sc-542)
Abcam (ab53039)
Covance (clone AF64)
Abcam (ab52635)
DSHB (Troma-1)
1:50
IF
1:10,000
1:20,000
1:750
1:100
1:20
IHC
IHC
IF
IF
IF
BD Biosciences (553261)
1:100
FACS
BD Pharmingen (559971)
1:100
FACS
N/A
SA-APC
(BD Pharmingen
554067)
BD Pharmingen (553371)
1:100
FACS
SA-APC
2
1:200; Vector Elite kit
1:500 AlexaFluor594
1:500 AlexaFluor594
1:500 AlexaFluor488
Schwab et al.
MS2080491151562533--REVISED
Table S3 Frequency of tumors in recipient mice at day 62 after limiting dilution transplantation.
_________________________________________________________________________________________
Day 62 Post-Transplant
Genotype of MTECs
Number
of cells
injected
HIF-1 WT
HIF-1 KO
Tumor-positive
Tumor-positive
Fisher’s exact test
100
50
25
10
92% (12/13)
88% (14/16)
70% (14/20)
78% (18/23)
50% (7/14)
19% (3/16)
15% (3/20)
9% (2/22)
N.S.
p= 0.0002
p= 0.0011
p< 0.0001
Estimated
TIC freq.
by ELDA
(95% C.I.)
HIF-1 WT
HIF-1 KO
Chi-square test
1/18
(1/13-1/26)
1/135
(1/84-1/217)
p= 3.96e-14
_________________________________________________________________________________________
A Fisher’s exact (Chi-square) test was utilized to compare significance of tumor-initiating
potential between WT and KO cells at each cell density (N.S., not significant). The estimated
TIC frequency at day 62 post-transplant was determined by ELDA software.
Table S4 Frequency of tumors in recipient mice at day 112 after limiting dilution transplantation.
_________________________________________________________________________________________
Day 112 post-transplant
Genotype of MTECs
Number
of cells
injected
HIF-1 WT
HIF-1 KO
Tumor-positive
Tumor-positive
Fisher’s exact test *
100
50
25
10
100% (13/13)
94% (15/16)
95% (19/20)
96% (22/23)
100% (14/14)
94% (15/16)
50% (10/20)
45% (10/22)
test not appropriate
N.S.
p= 0.0011
p< 0.0001
* ELDA analysis could not estimate TIC frequency with a 95% CI based on these data
_________________________________________________________________________________________
A Fisher’s exact (Chi-square) test was utilized to compare TIC potential between WT to KO cells
at each cell density. Data for the 10 and 25 cell input groups remain statistically significant,
whereas no significant differences (N.S.) were observed between WT and KO cells for the 50
cell input groups. The Chi-square test is no longer appropriate for the 100 cell input group, as all
recipient mice bearing WT or KO tumor cells had developed measurable tumors by day 112.
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MS2080491151562533--REVISED
Table S5 Summary of the percentage and total number of recipients bearing small tumors at
day 112 post-transplant.
GenotypeCell density
WT- 100
KO- 100
WT- 50
KO- 50
WT- 25
KO- 25
WT- 10
KO- 10
% tumor-positive
recipients with
tumor <250mm3
0% (0/13)
7% (1/14)
0% (0/15)
13.3% (2/15)
5.2% (1/19)
20% (2/10)
9% (2/22)
60% (6/10)
Table S6 Frequency of tumors in recipient mice at day 244 after limiting dilution transplantation.
_________________________________________________________________________
Day 244 Post-Transplant
Genotype of MTECs
Number
of cells
injected
HIF-1 WT
HIF-1 KO
Tumor-positive
Tumor-positive
Fisher’s exact test *
50
25
10
100% (16/16)
100% (20/20)
96% (22/23)
100% (16/16)
95% (19/20)
73% (16/22)
test not appropriate
N.S.
p< 0.047
* ELDA analysis could not estimate TIC frequency with a 95% CI based on these data
______________________________________________________________________
A Fisher’s exact test was utilized to compare significance of tumor-initiating potential between
WT to KO cells for the 10 and 25 cell input groups. The Chi-square test is no longer appropriate
for the 50 cell input group, as all recipient mice bearing WT or KO tumor cells had developed
measurable tumors by day 244.
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Schwab et al.
MS2080491151562533--REVISED
Table S7 Summary of the percentage and total number of recipients bearing small tumors at
day 244 post-transplant.
Genotype-Cell
density
WT- 50
KO- 50
WT- 25
KO- 25
WT- 10
KO- 10
% of tumor-positive
recipients with
tumors
< 250mm3
0% (0/16)
0% (0/16)
0% (0/20)
10.5% (2/19)
0% (0/22)
37.5% (6/16)
5