Supplemental Figure 1.

Supplemental Figure 1.Frozen whole-mount H&E section, without a cover slip, just prior to LCM dissection and just after dissection are on the left. An image of the dissected area on the cap is on the right.

Supplemental Figure 2.aRNA analysis before and after fragmentation: examples of aRNA profiles from NE (1-2), TE (2-4), NS (5-6) and TS (7-8) samples before (A) and after (B) fragmentation.

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A.

B.

Supplemental Figure 3 a.Signal Distribution of GeneChip hybridizations from Patient 1-5 samples: Log2 transformed signal intensities for each patient sample. NE=Nontumor epithelia, TE=tumor epithelia, NS=nontumor associated stromal, TS=tumor associated stromal.

Signal intensity distribution of individualhybridizations for patient 1

NE

pa

tie

nt

1a

NE

pa

tie

nt

1b

TE

pa

tie

nt

1a

TE

pa

tie

nt

1b

NS

pa

tie

nt

1a

NS

pa

tie

nt

1b

TS

pa

tie

nt

1a

TS

pa

tie

nt

1b

-5.0

-2.5

0.0

2.5

5.0

7.5

10.0

12.5

15.0

17.5

log

2(in

ten

sity

)

Signal intensity distribution of individualhybridizations for patient 2

NE

pa

tie

nt

2a

NE

pa

tie

nt

2b

TE

pa

tie

nt

2a

TE

pa

tie

nt

2b

NS

pa

tie

nt

2a

NS

pa

tie

nt

2b

TS

pa

tie

nt

2a

TS

pa

tie

nt

2b

-5.0

-2.5

0.0

2.5

5.0

7.5

10.0

12.5

15.0

17.5

log

2(in

ten

sity

)

Signal intensity distribution of individualhybridizations for patient 3

NE

pa

tie

nt

3a

NE

pa

tie

nt

3b

TE

pa

tie

nt

3a

TE

pa

tie

nt

3b

NS

pa

tie

nt

3a

NS

pa

tie

nt

3b

TS

pa

tie

nt

3a

TS

pa

tie

nt

3b

-5.0

-2.5

0.0

2.5

5.0

7.5

10.0

12.5

15.0

17.5

log

2(in

ten

sity

)

Signal intensity distribution of individualhybridizations for patient 4

NE

pa

tie

nt

4a

NE

pa

tie

nt

4b

TE

pa

tie

nt

4a

TE

pa

tie

nt

4b

NS

pa

tie

nt

4a

NS

pa

tie

nt

4b

TS

pa

tie

nt

4a

TS

pa

tie

nt

4b

-5.0

-2.5

0.0

2.5

5.0

7.5

10.0

12.5

15.0

17.5

log

2(in

ten

sity

)

Signal intensity distribution of individualhybridizations for patient 5

NE

pa

tie

nt

5a

NE

pa

tie

nt

5b

TE

pa

tie

nt

5a

TE

pa

tie

nt

5b

NS

pa

tie

nt

5a

NS

pa

tie

nt

5b

TS

pa

tie

nt

5a

TS

pa

tie

nt

5b

-5.0

-2.5

0.0

2.5

5.0

7.5

10.0

12.5

15.0

17.5

log

2(in

ten

sity

)

Supplemental Figure 3b. Red: Targets/genes present in both.Blue: Targets/genes absent or present in either, or marginal or present in either.Yellow: Targets/genes absent in both, or marginal in both, or absent or marginal in either.