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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | ILLUMINA | HiSeq 2000 | 2 × 75 | CD19 (1 × 1) | yes | 5.36E + 08 | 2.87E + 08 | 0.27 | 1494 |  | Donor_2 | |
ENCODE/SUNY Albany | 2016 | 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 |  |  |