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Table 1 Summary of RNAseq dataset parameters for each study

From: Confounding factors in profiling of locus-specific human endogenous retrovirus (HERV) transcript signatures in primary T cells using multi-study-derived datasets

Study

year of data deposition

link to bioproject

platform

instrument

seqmode (bp)

cell type (no. donor x replicates)

matched donor samples

input reads (mean ± SD)

filtered reads (mean ± SD)

% HERV reads of filtered reads (mean ± SD)

no exp. HERVs (mean ± SD)

note

donor_number

Tan et al.

2020

https://www.ncbi.nlm.nih.gov/bioproject/PRJNA605014

ILLUMINA

NextSeq500

1 × 75

CD4 (3 × 3)

no

3.81E + 07 ± 2.19E + 07

2.11E + 07 ± 1.26E + 07

0.21 ± 0.02

597 ± 100.78

water

 

DFG

2020

https://www.ncbi.nlm.nih.gov/bioproject/PRJNA642003

ILLUMINA

Hiseq2500

1 × 50

CD4 (2 × 1) / CD8 (2 × 1)

yes

2.80E + 07 ± 2.01E + 07

1.71E + 07 ± 1.05E + 07

0.25 ± 0.01

811.75 ± 33.36

umbilical cord blood

Donor_9/10

Lopusna et al.

2021

https://www.ncbi.nlm.nih.gov/bioproject/PRJNA646366

ILLUMINA

NovaSeq 6000

2 × 150

CD4 (2 × 1) / CD8 (2 × 1)

no

1.35E + 08 ± 8.13E + 07

5.84E + 07 ± 3.08E + 07

0.31 ± 0.01

1033.25 ± 127.70

  

Linsley et al.

2014

https://www.ncbi.nlm.nih.gov/bioproject/PRJNA258216

ILLUMINA

HiScanSQ

2 × 50

CD4 (4 × 1) / CD8 (4 × 1)

yes

3.80E + 07 ± 6.87E + 06

1.82E + 07 ± 2.53E + 06

0.22 ± 0.01

500.63 ± 28.35

 

Donor_5/6/7/8

White et al.

2018

https://www.ncbi.nlm.nih.gov/bioproject/PRJNA396949

ILLUMINA

HiSeq 2000

2 × 50

CD4 (4 × 1)

no

2.06E + 08 ± 1.22E + 07

9.72E + 07 ± 7.20E + 06

0.23 ± 0.01

1094.75 ± 96.13

DMSO

 

University of Washington Human Reference Epigenome Mapping Project (UWashington.HREMP)

2013

https://www.ncbi.nlm.nih.gov/gds/200018927

ILLUMINA

HiSeq 2000

2 × 75

CD4 (2 × 1) / CD8 (2 × 1)

yes

3.96E + 08 ± 1.20E + 08

2.15E + 08 ± 5.49E + 07

0.31 ± 0.02

1705.75 ± 440.47

 

Donor_1/2

Bediaga et al.

2021

https://www.ncbi.nlm.nih.gov/bioproject/PRJNA521046

ILLUMINA

NextSeq500

2 × 80

CD4 (2 × 1) / CD8 (2 × 1)

yes

1.36E + 08 ± 7.00E + 07

8.27E + 07 ± 4.21E + 07

0.28 ± 0.01

1013.25 ± 147.22

 

Donor_3/4

University of Washington Human Reference Epigenome Mapping Project (UWashington.HREMP)

2012

https://www.ncbi.nlm.nih.gov/gds/200018927

ILLUMINA

HiSeq 2000

2 × 75

CD34 (1 × 1)

no

5.35E + 08

2.42E + 08

0.35

1340

cord blood

 

University of Washington Human Reference Epigenome Mapping Project (UWashington.HREMP)

2013

https://www.ncbi.nlm.nih.gov/gds/200018927

ILLUMINA

HiSeq 2000

2 × 75

CD19 (1 × 1)

yes

5.36E + 08

2.87E + 08

0.27

1494

 

Donor_2

ENCODE/SUNY Albany

2016

https://www.ncbi.nlm.nih.gov/bioproject/PRJNA30709

ILLUMINA

Genome Analyzer IIx

2 × 75

Keratinocytes (1 × 3)

no

2.84E + 08 ± 2.88E + 06

1.44E + 08 ± 4.16E + 06

0.17 ± 0.02

1085.67 ± 135.24

  

CSHL

2011

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM758566

ILLUMINA

Genome Analyzer IIx

2 × 75

H1-hESC (1 × 1)

no

1.62E + 08

8.37E + 07

1.82

1786

  

Caltech

2012

https://trace.ncbi.nlm.nih.gov/Traces/?view=study&acc=SRP014320

ILLUMINA

Genome Analyzer

1 × (1x75), 2 × (2x75)

H1-hESC (3 × 1)

no

1.91E + 08 ± 1.45E + 08

7.01E + 07 ± 6.22E + 07

1.94 ± 0.52

1543.33 ± 349.81

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