1. RNA sequencing atopic dermatitis transcriptome profiling provides insights into novel disease mechanisms with potential therapeutic implications 
Mayte Suárez-Fariñas, PhD, Benjamin Ungar, BA, Joel Correa da Rosa, PhD, David A. Ewald, MSc, Mariya Rozenblit, BA, Juana Gonzalez, PhD, Hui Xu, MSc, Xiuzhong Zheng, MSc, Xiangyu Peng, MSc, Yeriel D. Estrada, MSc, Stacey R. Dillon, PhD, James G. Krueger, MD, PhD, Emma Guttman-Yassky, MD, PhD 
Journal of Allergy and Clinical Immunology 
Volume 135, Issue 5, Pages (May 2015)
DOI: /j.jaci
Copyright © 2015 American Academy of Allergy, Asthma & Immunology Terms and Conditions

2. Fig 1
Exprs, Absolute expression levels measured in units of log2 counts per minute for RNA-seq and GCRMA–derived log2(expression) for microarrays. Low expressions are color coded as orange, and high expressions as yellow.
Journal of Allergy and Clinical Immunology  , DOI: ( /j.jaci )
Copyright © 2015 American Academy of Allergy, Asthma & Immunology Terms and Conditions

3. Fig 2
AD transcriptome identified by using microarray and RNA-seq. A and B, Venn diagram showing upregulated (red) and downregulated (blue) DEGs by using ensembl_ID (Fig 2, A) and unique genes with known identifiers (Fig 2, B). The outer section of DEGs determined by using only RNA-seq is a subset of DEGs not on the microarray. C, Scatterplot comparison of measured expression levels of all DEGs by using each technology (log2FCH). The y value and blue line are the linear regression fit; r and ρ values are Pearson and Spearman correlation coefficients, respectively. D, The intraclass correlation coefficient for agreement (ICA) and Pearson (r) and Spearman (ρ) correlation coefficients for DEGs by tercile of expression, as measured by using RNA-seq and microarrays. E, Ingenuity Pathway Analysis of DEGs found by using RNA-seq only, with DEGs in the TREM-1 signaling pathway.
Journal of Allergy and Clinical Immunology  , DOI: ( /j.jaci )
Copyright © 2015 American Academy of Allergy, Asthma & Immunology Terms and Conditions

4. Fig 3
FCH estimation and bias. A and B, Scatterplots of estimated FCHs of lesional (LS) versus nonlesional (NL) skin in RT-PCR versus microarray (Fig 3, A) and RNA-seq (Fig 3, B). C and D, FCH bias (relative to RT-PCR) as a function of average expression in microarrays (Fig 3, C) and RNA-seq (Fig 3, D). The y value and blue line are the linear regression fit; r is the Pearson and ρ is the Spearman correlation coefficient. E, FCH agreement of microarrays and RNA-seq with RT-PCR among all 34 preselected genes and among the 19 (70%) genes with the highest expression. ICA, Intraclass correlation coefficient for agreement. F, Box plots (means; boxes, 25% to 75%; ± whiskers, 95%) showing that each platform tends to underestimate FCHs compared with RT-PCR. Point diameters are proportional to average expression.
Journal of Allergy and Clinical Immunology  , DOI: ( /j.jaci )
Copyright © 2015 American Academy of Allergy, Asthma & Immunology Terms and Conditions

5. Fig 4
TREM-1 pathway identified by using RNA-seq. A, Immunohistochemical staining of TREM-1 and CCL2 in lesional (LS) and nonlesional (NL) samples at baseline and after 12 weeks of CsA, showing increased baseline lesional expression, with significant reduction after CsA. B, Bar graph of cell counts showing significantly more cells expressing TREM-1 (n = 18) and CCL2 (n = 12) in lesional skin and significantly reduced counts after CsA. C, Bar graphs (means ± SEMs) showing significantly increased TREM-1, CCL2, CCL3, and TLR2 mRNA expression in baseline lesional skin, with significant reductions after CsA (n = 20 for each). D, Box plot (means ± SEMs) showing significantly increased soluble TREM-1 (sTREM1) levels in patients with serum from patients with AD (n = 20) compared with that from 8 healthy control subjects. *P < .05, **P < .01, and ***P < .001.
Journal of Allergy and Clinical Immunology  , DOI: ( /j.jaci )
Copyright © 2015 American Academy of Allergy, Asthma & Immunology Terms and Conditions

6. Fig 5
IL-36 RT-PCR. Comparison of IL-36A (A), IL-36G (B), IL-36RN (C), and IL-36B (D) mRNA expression by using RT-PCR in lesional (LS) versus nonlesional (NL) AD skin and lesional versus nonlesional psoriasis (PSO) skin (n = 18 for AD and n = 10 for psoriasis). *P < .05, **P < .01, and ***P < .001.
Journal of Allergy and Clinical Immunology  , DOI: ( /j.jaci )
Copyright © 2015 American Academy of Allergy, Asthma & Immunology Terms and Conditions

7. Fig 6
Box plots for gene characteristics for DEG subsets by using microarray and RNA-seq. A, Expression measured by using microarray. B, Expression measured by using RNA-seq. C, Distance to the 3′ end. D, Coverage. E, GC content grouped by upregulated and downregulated DEGs. F, Gene length grouped by upregulated and downregulated DEGs. *P < .05, **P < .01, and ***P < Microarray only and RNA-seq only are DEGs only found by using one platform, respectively. Both indicates DEGs found by using both platforms, and None indicates genes not found to be DEGs.
Journal of Allergy and Clinical Immunology  , DOI: ( /j.jaci )
Copyright © 2015 American Academy of Allergy, Asthma & Immunology Terms and Conditions