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. 2020 Jul 27;14(11):2748–2765. doi: 10.1038/s41396-020-0727-y

Table 1.

List of airway microbiome and host transcriptome datasets included in the meta-analysis.

Dataset Sample type PMID Sequencing reads per sample Country Platform Data type Samples
COPD Control
SRP102480 Sputum 29269441 54,100–355,368 UK Miseq V4 445 0
SRP102629 Sputum 29386298 37,359–155,862 UK Miseq V4 423 0
SRP073159 Sputum 29101284 10,636–220,475 UK Miseq V3–V4 134 0
SRP065072 Sputum 26917613 4231–31,326 UK 454 V3–V5 106 0
ERP108788 Sputum 31234826 9633–95,264 Spain Miseq V3–V4 95 0
Dyrad.5GC82 Sputum 28851370 10,210–150,821 Norway Miseq V3–V4 81 0
SRP066375 Sputum NA 13,866–159,955 Peru, Nepal, China, Bangladesh Miseq V4 74 107
SRP136124 Sputum 31170986 85,087–343,461 UK Miseq V4 52 16
ERP003401 Sputum 25253795 6406–14,573 Spain 454 V1–V2 31 0
ERP014054 Sputum NA 5566–15,687 UK 454 V6–V8 28 0
SRP124904 Sputum 29518088 24,172–106,899 USA Miseq V3–V4 26 0
SRP107187 Sputum 29579057 5859–12,506 Canada 454 V6–V8 14 0
SRP075523 Sputum 27428540 25,345–83,640 China Miseq V4 8 0
ERP010088 Sputum 26872143 5,291,496–100,983,368a UK Hiseq MetaG 8 10
ERP110331 Sputum NA 4,460,248–98,972,436a Germany NextSeq MetaG 8 0
GSE47460 Lung 27609773 NA USA Agilent HostT 219 108
GSE76925 Lung 28287180 NA USA Illuminab HostT 111 40
GSE57148 Lung 25834810 8,888,399–22,119,664 South Korea Hiseq HostT 98 91
GSE37147 Bronchial 23471465 NA Canada Affy HostT 87 82
GSE103174 Lung NA NA Spain Affy HostT 37 10
GSE73395 BAL 30141961 NA Germany, Italy, Belgium Affy HostT 29 28
GSE38974 Lung 21940491 NA USA Agilent HostT 23 9
GSE11906 Small airways 19852842 NA USA Affy HostT 20 72
GSE12472 Bronchial 20832896 NA Netherlands Agilent HostT 18 10
GSE37768 Lung NA NA Spain Affy HostT 18 9
GSE8581 Lung 18849563 NA USA Affy HostT 16 19
GSE106986 Lung NA NA Germany Agilent HostT 14 5
GSE86064 Large airways 29581847 12,623,264–24,609,574 USA Hiseq HostT 13 30
GSE13896 Alveolar macrophage 19635926 NA USA Affy HostT 12 24
GSE56341 Small airways 24298892 NA Canada Affy HostT 8 14
GSE11784 Small airways 21829517 NA USA Affy HostT 7 31
GSE119040 Lung NA NA Argentina Affy HostT 6 4
GSE16972 Alveolar macrophage 21430361 NA Hungary Affy HostT 5 5
GSE112260 Sputum 30074017 NA Poland Affy HostT 4 4

MetaG metagenome, HostT host transcriptome.

aThe number of non-human reads.

bIllumina Human HT-12 V4.0 microarray.