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Table 1 RNA-sequencing data and mapping statistics

From: Human endogenous retroviruses sustain complex and cooperative regulation of gene-containing loci and unannotated megabase-sized regions

ENCODE/CSHL datasets

Positions

SF

wgEncodeCshlLongRnaSeqHelas3CellLongnonpolyaFastqRd1Rep2.fastq

392

2.11

wgEncodeCshlLongRnaSeqHelas3CellLongnonpolyaFastqRd2Rep2.fastq

wgEncodeCshlLongRnaSeqHepg2CellLongnonpolyaFastqRd1Rep1.fastq

295

1.26

wgEncodeCshlLongRnaSeqHepg2CellLongnonpolyaFastqRd2Rep1.fastq

wgEncodeCshlLongRnaSeqK562CellLongnonpolyaFastqRd1Rep1.fastq

294

2.17

wgEncodeCshlLongRnaSeqK562CellLongnonpolyaFastqRd2Rep1.fastq

wgEncodeCshlLongRnaSeqMcf7CellLongnonpolyaFastqRd1Rep1.fastq

140

0.76

wgEncodeCshlLongRnaSeqMcf7CellLongnonpolyaFastqRd2Rep1.fastq

wgEncodeCshlLongRnaSeqGm12878CellLongnonpolyaFastqRd1Rep1.fastq

416

1.44

wgEncodeCshlLongRnaSeqGm12878CellLongnonpolyaFastqRd2Rep1.fastq

wgEncodeCshlLongRnaSeqHuvecCellLongnonpolyaFastqRd1Rep1.fastq

267

1.40

wgEncodeCshlLongRnaSeqHuvecellLongnonpolyaFastqRd2Rep1.fastq

wgEncodeCshlLongRnaSeqH1hescCellLongnonpolyaFastqRd1Rep1.fastq

355

1.91

wgEncodeCshlLongRnaSeqH1hescCellLongnonpolyaFastqRd2Rep1.fastq

wgEncodeCshlLongRnaSeqHsmmCellLongnonpolyaFastqRd1Rep1.fastq

16

0.49

wgEncodeCshlLongRnaSeqHsmmCellLongnonpolyaFastqRd2Rep1.fastq

wgEncodeCshlLongRnaSeqHmecCellLongnonpolyaFastqRd1Rep1.fastq

5

0.24

wgEncodeCshlLongRnaSeqHmecCellLongnonpolyaFastqRd2Rep1.fastq

wgEncodeCshlLongRnaSeqNhekCellLongnonpolyaFastqRd1Rep1.fastq

202

1.53

wgEncodeCshlLongRnaSeqNhekCellLongnonpolyaFastqRd2Rep1.fastq

wgEncodeCshlLongRnaSeqNhlfCellLongnonpolyaFastqRd1Rep1.fastq

18

0.39

wgEncodeCshlLongRnaSeqNhlfCellLongnonpolyaFastqRd2Rep1.fastq

  1. The table lists paired-end RNA-seq datasets from ENCODE/CSHL that were used to map positions of chimeric transcription. The scale factor (SF) which indicates the relative sequencing depth of each library was computed using Cufflinks [55].
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Retrovirology

ISSN: 1742-4690

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