Table 3 Positive control RNA seq data sets were analysed by RINS for presence of viral transcripts.

From: No association between HPV positive breast cancer and expression of human papilloma viral transcripts

Reference

Sample

Library

Platform

Read

Virus

Viral reads

Total reads

ppm

SRR540252

HeLa

Poly A

N.A

Paired

HPV18

21407

8000000

2675

SRR702400

HeLa

rRNA

GAII

Single

HPV18

26378

21000000

1256

SRR629571

HeLa

N.A

HiSeq

Paired

HPV18

44405

15000000

2960

SRR073726

Prostate

Poly A

N.A

Single

HPV18

25755

13000000

1981

SRR069060

Akata

N.A

GAII

Single

HHV4

34696

26000000

949

SRR497704

CD4 T-cells

N.A

GAII

Single

HIV

64478

23000000

2803

UNCID-1487840

HNSCC

Poly A

HiSeq

Paired

HPV16

3470

182000000

19

UNCID-1488824

HNSCC – normal adjacent

Poly A

Hiseq

Paired

n.d

0

169000000

0

UNCID-1494200

HNSCC

Poly A

HiSeq

Paired

HPV33

29131

112000000

260

UNCID-1489199

HNSCC – normal adjacent

Poly A

HiSeq

Paired

n.d

0

157000000

0

  1. Reference describes the accession identification used for data download from NCBI (SRR) or TCGA (UNCID). Poly A is a library prepared from poly A isolated mRNA, rRNA is a library prepared from rRNA depleted library. Sample describes the cell line or sample type used in the analysis, where HNSCC is head and neck squamous cell carcinoma. GAII is Illumina Genome Analyzer II, HiSeq refers to HiSeq 1000, 2000 or 2500 platforms. HPV is human papilloma virus, HHV is human herpes virus 4, HIV is human immunodeficiency virus. Total reads are total number of next generation sequencing reads, Viral reads are number of viral reads aligning to viral sequence. N.A is not available, n.d. is not detected, ppm is read proportion per million.
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