Wong et al Supplementary Material Supplementary Figures and Legends Supplementary Figure 1. Related to Figure 2 Supplementary Figure 2. Related to Figure 2 Supplementary Figure 3. Related to Figure 3 Supplementary Figure 4. Related to Figure 4 Supplementary Figure 5. Related to Figure 5 Supplementary Figure 6. Related to Figure 5 Supplementary Figure 7. Related to Figure 5 Supplementary Figure 8. Related to Figure 6 Supplementary Table 1. Related to Figure 1 Supplementary Table 2. Related to Figure 1 Supplementary Table 3. Related to Figure 2 Supplementary Table 4. Related to Figure 5 Supplementary Table 5. Related to Figure 5 Supplementary Materials and Methods
22
Embed
Supplementary Material Supplementary Figures and Legendsgenesdev.cshlp.org/content/suppl/2013/03/19/27.6.670.DC1/Supp_M… · Supplementary Material Supplementary Figures and Legends
This document is posted to help you gain knowledge. Please leave a comment to let me know what you think about it! Share it to your friends and learn new things together.
Transcript
Wong et al Supplementary Material
Supplementary Figures and Legends
Supplementary Figure 1. Related to Figure 2
Supplementary Figure 2. Related to Figure 2
Supplementary Figure 3. Related to Figure 3
Supplementary Figure 4. Related to Figure 4
Supplementary Figure 5. Related to Figure 5
Supplementary Figure 6. Related to Figure 5
Supplementary Figure 7. Related to Figure 5
Supplementary Figure 8. Related to Figure 6!
Supplementary Table 1. Related to Figure 1
Supplementary Table 2. Related to Figure 1
Supplementary Table 3. Related to Figure 2
Supplementary Table 4. Related to Figure 5
Supplementary Table 5. Related to Figure 5
Supplementary Materials and Methods
Supplementary Figure 1. CD34 expression in Class A and Class B
carcinomas Immunofluorescence using an antibody against CD34 (bar =
100µm). Red indicates CD34; blue indicates nucleus (DAPI). Class A carcinomas
are depicted on the top row; Class B carcinomas are depicted on the bottom row.
Supplementary Figure 2. Class B carcinomas have a very similar molecular
profile to “claudin-low” breast cancers Unsupervised hierarchical clustering of
skin carcinoma gene expression levels using a published gene signature for
“claudin low” breast cancers (Prat et al., 2010). Red indicates higher expression;
green indicates lower expression.
Supplementary Figure 3. Validation of ErbB2 and Lrig1 array expression
results by immunostaining on mouse skin carcinoma sections (A, B) IHC
using an antibody against ErbB2 (bar = 100µm). (C, D) Immunofluorescence
using an antibody against Lrig1 (bar = 100µm). Red indicates Lrig1; blue
indicates nucleus (DAPI). Class A carcinomas are depicted on the left; Class B
carcinomas are depicted on the right.
Supplementary Figure 4. Gene expression of p15 and p19/Arf in skin
carcinomas (A) qRT-PCR for p15 in Class A and Class B carcinomas. (B) qRT-
PCR for p19/Arf in Class A and Class B carcinomas. Error bars represent
standard deviation from three replicate measurements.
Supplementary Figure 5. Expression of inflammatory markers in skin
carcinomas Heatmap of expression levels of inflammatory markers in Class A
and Class B carcinomas using data from our previously published study (Quigley
et al., 2011). Red indicates higher expression; blue indicates lower expression.
Supplementary Figure 6. Gene copy number of p16/p19 and p15 in skin
carcinomas from Hras WT and Hras -/- mice (A) Gene copy number analysis
of p16/p19 (top row) and p15 (bottom row) on SCCs and spindle cell carcinomas
from FVB Hras WT mice treated with TPA for 5 weeks, 10 weeks and 20 weeks.
(B) Gene copy number analysis of p16 (top row) and p15 (bottom row) on SCCs
and spindle cell carcinomas from FVB Hras -/- mice treated with TPA for 10
weeks and 20 weeks. Amplifications of the gene are marked with blue, deletions
with red, and two copies with white boxes.
Supplementary Figure 7. Histological and immunophenotypic features of
skin carcinomas from Hras null mice (A) Hras null mice developed both Class
A (squamous) and Class B (spindle) skin carcinomas. (B) IHC using antibodies
against E-cadherin and Vimentin. Class A carcinomas are depicted on the top
row; Class B carcinomas on the bottom row (bar = 200µm).
Supplementary Figure 8. Comparison of the p16 gene expression levels in
normal skin, papillomas, Class A and Class B carcinomas Box plots for p16
gene expression levels as determined by microarray. The Y-axis shows log2
expression. The horizontal line indicates estimated level of background
expression.
Supplementary Table 1. Snai1 is positively correlated with many genes
known to be involved in invasion and the EMT Table was generated by
calculating Spearman Rank Correlation between Log2 gene expression of Snai1
(Snail) and all other genes using the 60 carcinomas, reporting those where r ! +/-
0.8. Positive values of Fold change indicate higher expression in Class A than
Class B carcinomas. To calculate fold change, where DIFF = mean(values in
Class A)-mean(values in Class B), fold-change = 2^DIFF if DIFF>0 and -1*(2^(-