Additional file 2: Table S2. of Cancer associated fibroblasts (CAFs) are activated in cutaneous basal cell carcinoma and in the peritumoural skin

The list contains the 65 genes coding for extracellular matrix components or enzymes involved in matrix metabolism that were found upregulated in BCC. (DOCX 18 kb

Additional file 1: Table S1. of Cancer associated fibroblasts (CAFs) are activated in cutaneous basal cell carcinoma and in the peritumoural skin

The number of reads in the mRNA sequencing analysis and the following reads that were actually mapped. Whereas approximately 97% of all reads mapped to the human genome, duplicate reads constituted a significant fraction leaving only around 48 million unique reads. (DOCX 33 kb

Sequencing required to reach threshold coverage of viral target genomes.

<p>Sequencing required to reach threshold coverage of viral target genomes.</p

Quantity of virus in complex control sample material.

<p>HIV-1; Human Immunodeficiency Virus type-1, HPV-18; Human papillomavirus type 18, HAdV; Human Adenovirus C, EV; Enterovirus B Coxsackievirus B3, MeV; Measles virus, aRNA; armored RNA.</p><p>Quantity of virus in complex control sample material.</p

Expected and observed proportion of reads in DNA shotgun libraries.

<p>* Proportions expressed in ppm.</p><p>Expected and observed proportion of reads in DNA shotgun libraries.</p

Rarefaction analysis showing the covered proportion of the EV genome as a function of the total number of sequence reads from each sample for RNA shotgun sequencing.

<p>Numbers provided for each sample are given as copies/μl in the test sample.</p

Overview of the experimental design.

<p>Fractions of each sample, consisting of varying viral material spiked into human PBMCs were subjected to shotgun sequencing of DNA or RNA. On other fractions virion enrichment procedures including centrifugation, filtration and nuclease treatment were performed prior to library preparation (DNA or RNA) and sequencing.</p

Expected and observed proportion of reads in RNA shotgun libraries.

<p>ND: None detected.</p><p>* Proportions expressed in ppm.</p><p>^# Value defined by the observed.</p><p>Expected and observed proportion of reads in RNA shotgun libraries.</p

Fold increase in of the proportion of HAdV (A) or EV (B) sequences in virion-enriched libraries as compared to non-enriched shotgun sequenced libraries.

<p>Proportions are calculated as the number of viral reads relative to the total number of assigned reads.</p

Rarefaction analysis showing the covered proportion of the (A) HAdV genome, (B) the HPV-18 genome, (C) the HI-1 genome, and (D) the MeV plasmid, as a function of the total number of sequence reads from each sample for DNA shotgun sequencing.

<p>Numbers provided for each sample are given as copies/μl in the test sample.</p