Table 3:
Details of author-supplied processed data used to compare to DEE2 gene expression counts
| Species, GEO series | Contrast (control/case) | Spots | Author pipeline |
|---|---|---|---|
| A. thaliana, GSE53078 [36] | GSM1281703 | 15,143,653 | Genome: TAIR10 |
| GSM1281704 | 12,498,123 | Annotation version: Unknown | |
| GSM1281705 | 22,721,359 | Mapper: TopHat | |
| GSM1281706 | 17,255,612 | Counter: HTSeq | |
| C. elegans, GSE46344 [37] | GSM1128862 | 30,650,959 | Genome: WS220/ce10 |
| GSM1128863 | 47,245,721 | Annotation: Ensembl v66 | |
| GSM1128864 | 54,573,311 | Mapper: TopHat | |
| GSM1128868 | 49,315,179 | Counter: HTSeq | |
| GSM1128869 | 56,295,663 | ||
| GSM1128870 | 68,641,842 | ||
| D. melanogaster, GSE43180 [38] | GSM1057982 | 24,902,977 | Genome: dm3 |
| GSM1057983 | 36,434,276 | Annotation: Ensembl v64 | |
| GSM1057984 | 32,591,508 | Mapper: Tophat | |
| GSM1057985 | 35,375,654 | Counter: HTSeq | |
| D. rerio, GSE80768 [39] | GSM2136810 | 19,404,674 | Genome: Zv10 |
| GSM2136811 | 22,820,115 | Annotation: Ensembl (version unknown) | |
| GSM2136812 | 25,181,184 | Mapper: USeq and Novoalign | |
| GSM2136813 | 21,487,514 | Counter: USeq | |
| GSM2136814 | 24,831,643 | ||
| GSM2136815 | 22,664,352 | ||
| GSM2136816 | 22,629,782 | ||
| GSM2136817 | 21,842,104 | ||
| GSM2136818 | 20,601,291 | ||
| GSM2136819 | 18,183,746 | ||
| GSM2136820 | 21,007,467 | ||
| GSM2136821 | 20,992,396 | ||
| GSM2136822 | 24,708,106 | ||
| GSM2136823 | 21,105,462 | ||
| GSM2136824 | 28,069,482 | ||
| E. coli, GSE80251 [40] | GSM2122743 | 5,221,858 | Genome: E. coliK12 MG1655 |
| GSM2122744 | 6,503,454 | Annotation: GenBank NC_000913.3 | |
| GSM2122745 | 6,209,263 | Mapper: TMAP (map4) | |
| GSM2122746 | 6,391,549 | Counter: Bedtools | |
| GSM2122747 | 6,197,872 | ||
| GSM2122748 | 5,090,669 | ||
| H. sapiens, GSE63776 [41] | GSM1556982 | 30,007,994 | Genome: hg19 |
| GSM1556983 | 27,252,897 | Annotation: UCSC (version unknown) | |
| GSM1556984 | 42,212,497 | Mapper: Bowtie2 (after adapter clipping) | |
| GSM1556985 | 31,456,271 | Counter: HTSeq | |
| GSM1556986 | 31,569,339 | ||
| GSM1556987 | 37,477,777 | ||
| M. musculus, GSE59970 [42] | GSM1462883 | 32,015,112 | Genome: GRCm38.70/mm10 |
| GSM1462884 | 30,997,187 | Annotation: Ensembl v70 | |
| GSM1462885 | 32,612,584 | Mapper: Olego | |
| GSM1462886 | 31,485,760 | Counter: BedTools | |
| GSM1462887 | 30,207,461 | ||
| GSM1462888 | 31,028,501 | ||
| R. norvegicus, GSE65715 [43] | GSM1604049 | 42,296,446 | Genome: rn4 |
| GSM1604050 | 34,887,323 | Annotation: Ensembl (version unknown) | |
| GSM1604051 | 42,725,865 | Mapper: Tophat2 | |
| GSM1604052 | 28,210,194 | Counter: HTSeq | |
| GSM1604053 | 30,748,641 | ||
| GSM1604054 | 28,450,626 | ||
| S. cerevisiae, GSE76444 [44] | GSM2809655 | 35,869,614 | Genome: EF 4 |
| GSM2809656 | 37,425,737 | Annotation: Ensembl v72 | |
| GSM2809657 | 39,227,797 | Mapper: Bowtie | |
| GSM2809658 | 33,974,055 | Counter: HTSeq | |
| GSM2809659 | 33,339,067 | ||
| GSM2809660 | 37,546,069 |