<i>APOBEC3B</i> mRNA expression differences between primary breast tumors and paired metastases.

<p><i>(A) APOBEC3B</i> mRNA expression in primary breast tumors versus paired loco-regional and distant metastases. <i>(B) APOBEC3B</i> mRNA expression in primary breast tumors versus paired metastases, subdivided per location of metastasis (ovary (N = 4); liver (N = 6); bone (N = 4); brain (N = 14); lung (N = 5) and gastro-intestinal tract (N = 3). <i>(C) APOBEC3B</i> mRNA expression in <i>ESR1</i>-positive primary breast tumors versus paired distant and loco-regional metastases. <i>(D) APOBEC3B</i> mRNA expression in <i>ESR1</i>-negative primary breast tumors versus paired distant and loco-regional metastases. P-values obtained by paired Wilcoxon Signed Ranks test (2-tailed).</p

Association of <i>APOBEC3B</i> mRNA in matched primary tumors and their metastasis according metastatic site.

<p>Association of <i>APOBEC3B</i> mRNA in matched primary tumors and their metastasis according metastatic site.</p

Association of <i>APOBEC3B</i> mRNA expression with clinicopathological characteristics of the primary tumor.

<p>Association of <i>APOBEC3B</i> mRNA expression with clinicopathological characteristics of the primary tumor.</p

<i>ESR1</i> conversions from primary tumor to metastasis specified by site of metastasis.

<p><i>ESR1</i> conversions from primary tumor to metastasis specified by site of metastasis.</p

GRPR and SSTR2 mRNA levels in primary BC (PBC) and corresponding metastases (BCM).

<p>Significant differences are indicated by *.</p

Iulomorphid millipedes (Diplopoda, Spirostreptida, Iulomorphidae) of Tasmania, Australia

Volume: 652Start Page: 1End Page: 3

In vitro autoradiography of primary BC and corresponding regional lymph node metastases.

<p>A. Hematoxylin and eosin (H&E) staining and autoradiography results after incubating cells with the GRPR radioligand, ¹¹¹In-JMV4168, and the SSTR2 radioligand, ¹¹¹In-DOTA-Tyr³-octreotate. B+D. Correlation of quantified autoradiography results (% AD) with mRNA expression of fresh frozen (FF) tissue. C+E. Correlation of mRNA expression of FF and formalin fixed paraffin embedded (FFPE) tissue of the same tumor.</p

Association of receptor mRNA expression with <i>ESR1</i> and <i>ERBB2</i> status in BC metastases.

<p>Association of receptor mRNA expression with <i>ESR1</i> and <i>ERBB2</i> status in BC metastases.</p

Integrative Analysis of Genomics and Proteomics Data on Clinical Breast Cancer Tissue Specimens Extracted with Acid Guanidinium Thiocyanate–Phenol–Chloroform

Acid guanidinium thiocyanate, phenol, and chloroform extraction (AGPC) is a commonly used procedure to extract RNA from fresh frozen tissues and cell lines. In addition, DNA and proteins can be recovered, which makes AGPC an attractive source for integrative analysis on tissues of which little material is available, such as clinical specimens. Despite this potential, AGPC has only scarcely been used for proteomic analysis, mainly due to difficulties in extracting proteins. We have used a quantitative mass spectrometry method to show that proteins can readily be recovered from AGPC extracted tissues with high recovery and repeatability, which allows this method to be used for global proteomic profiling. Protein expression data for a selected number of clinically relevant markers, of which transcript and protein levels are known to be correlated, were in agreement with genomic and transcriptomic data obtained from the same AGPC lysate. Furthermore, global proteomic profiling successfully discriminated breast tumor tissues according to their clinical subtype. Lastly, a reference gene set of differentially expressed transcripts was strongly enriched in the differentially abundant proteins in our cohort. AGPC lysates are therefore well suited for comparative protein and integrative analyses

Additional file 7: of Gene length corrected trimmed mean of M-values (GeTMM) processing of RNA-seq data performs similarly in intersample analyses while improving intrasample comparisons

Comparison correlation coefficients by method. Boxplots show correlation coefficient of 30 genes, comparing 4 methods to RT-qPCR generated data. P-values are derived from the Mann-Whitney test. (PDF 3492 kb