Skip to main content

Table 2 Summary of sequencing results for the MCL cell linesa

From: Characterising a human endogenous retrovirus(HERV)-derived tumour-associated antigen: enriched RNA-Seq analysis of HERV-K(HML-2) in mantle cell lymphoma cell lines

Cell line

JVM2

G519

REC1

Sequencing method

Ion Torrent

(short-read)

MinION (long-read)

Ion Torrent

(short-read)

Enrichment

No

Yes Growth 1

Yes Growth 2

Yes Growth 3

Yes

Yes

Yes

Total reads after QC

3,255,142

2,749,743

2,672,868

3,508,762

218,872

2,839,730

3,073,933

Total reads assigned to HML-2 (%)

113b

(0.003%)

155,700 (5.6%)

232,687

(8.7%)

101,495

(2.9%)

14,147 (6.9%)

113,807

(4.0%)

28,014

(0.91%)

Percentage reads from Env-encoding provirusesc

N/A

5.3%

15.9%

12.8%

20.8%

17.2%

2.3%

  1. aRaw Ion Torrent run reports are shown in Additional file 3
  2. bAfter excluding the probably artifactual 52 hits to provirus 9q34.3 (see Additional file 2)
  3. cPercentage of reads mapping to Env-encoding proviruses was calculated after normalisation via conversion to RPKM values (Reads Per Kilobase of transcript per Million mapped reads)