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Table 1 Summary of the analyzed samples and datasets $

From: Inferring the expression variability of human transposable element-derived exons by linear model analysis of deep RNA sequencing data

Sample ID

Sample description

Platform

Mapped reads

Filtered reads

Resources

BT20

ER- breast cancer cell line

P/50

137897876

118362274

GEO: GSE27003; Sun et al., 2011 [35]

MDAMB231

ER- breast cancer cell line

P/50

96483262

80759008

Same as above

MDAMB468

ER- breast cancer cell line

P/50

123622490

104468212

Same as above

MCF7

ER + breast cancer cell line

P/50

129592066

107422464

Same as above

BT474

ER + breast cancer cell line

P/50

131597078

110877774

Same as above

T47D

ER + breast cancer cell line

P/50

119708904

99784684

Same as above

ZR751

ER + breast cancer cell line

P/50

107891488

90362316

Same as above

MCF10A

Normal breast cell line

P/50

125148556

108184998

Same as above

LNCaP

Prostate cancer cell line

S/35

38953595

27126677

GEO: GSE29155; Kim et al., 2011 [33]

PrEC

Normal prostate cell line

P/35

27825207

22366081

Same as above

LCL-1a

Lymphocyte cell lines

P/36,38

64168681

54301769

GEO: GSE25030; Montgomery et al., 2010 [34]

LCL-2

Lymphocyte cell lines

P/36,38

71571009

60017609

Same as above

OV-1-prb

Ovarian cancer cell line

P/42

75756477

69739708

SRA: ERP000710 [36]

OV-1-re

Ovarian cancer cell line

P/42

95813480

89853848

Same as above

OV-2-fi

Ovarian cancer cell line

P/42

90793509

84057374

Same as above

OV-2-se

Ovarian cancer cell line

P/42

100491160

93088808

Same as above

OV-3-pr

Ovarian cancer cell line

P/42

72611523

66647818

Same as above

OV-3-re

Ovarian cancer cell line

P/42

89393849

84067652

Same as above

prAd_1c

Prostate adenocarcinoma

S/33

32495059

23386861

GEO: GSE24283; Nacu et al., 2011 [9]

prAd_2

Prostate adenocarcinoma

S/33

34663805

24398162

Same as above

prAd_3

Prostate adenocarcinoma

S/33

66976637

48613865

Same as above

prNorm_1

Normal prostate tissue

S/50,75

37201269

30394802

Same as above

prNorm_2

Normal prostate tissue

S/50

37451643

30392995

Same as above

prNorm_3

Normal prostate tissue

S/33

33511439

25294452

Same as above

Brain

Brain tissue

S/50

48741218

42660318

Same as above

Liverd

Liver tissue

S/35

31258238

26253587

GEO: GSE17274; Blekhman et al., 2010 [32]

  1. $The letters and numbers in the third column represent sequencing types, single read (S) or paired-end reads (P), and read lengths, respectively. We excluded the non-primary hits when counting the mapped reads (fourth column). The numbers of unambiguously mapped reads are listed in the column of filtered reads.
  2. aLCL-1 and −2 are Coriell human lymphocyte lines NA12892 and NA19238.
  3. b-1, -2 and −3 indicate the IDs of the cell lines. –pr, -re, -fi, and –se indicate the clinical history. They represent “present”, “relapse”, “first relapse” and “second relapse”, respectively.
  4. c-1, -2 and −3 are the IDs of prostate adenocarcinoma (or normal prostate tissue) samples.
  5. dThe data sets of 12 liver samples (replicates) were combined before we mapped reads to the human genome and the computationally identified exon-exon junctions.