Table 4. Detailed information for example projects presented to validate our approach.
Summarized information for all example projects used to demonstrate Taggimatrix. The “Method” column refers to methods in Table 3; the “Pool name” column applies only to projects in which individual samples were pooled prior to the final pooling proportionate to targeted read number; the “Samples in pool” column cites the number of samples (including replicates) pooled together before final pooling for sequencing; the “Target reads” column cites the approximate number of reads per pool (i.e., not per individual sample) we targeted when pooling samples with other libraries. Note that these data were generated on many independent MiSeq runs.
| # | Organism | Project Goal | Target Loci | Library type | Method | Pool name | Samples in pool |
Target reads | Actual reads | Summary |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | Kissing bug | Diet analysis | cyt-b | iTru | 1 | N/A | 1 | 100k (<1%) |
916k | Identified five vertebrate sources of blood meals. |
| 2 | Fungal Community | Fungal identification | Full-ITS1 (standard & “flipped”) |
iTru | 2 | Homokaryon | 48 | 400k (2.7%) |
515k | Identified the primary fungal OTU from each culture |
| Het. multispore | 48 | 400k (2.7%) |
619k | |||||||
| Het. tissue | 47 | 400k (2.7%) |
444k | |||||||
| Full-ITS2 (standard & “flipped”) | iTru | 2 | Homokaryon | 48 | 400k (2.7%) |
268k | ||||
| Het. multispore | 48 | 400k (2.7%) |
310k | |||||||
| Het. tissue | 47 | 400k (2.7%) |
257k | |||||||
| Incomplete-ITS1&ITS2 (standard & “flipped”) |
iTru | 2 | Homokaryon | 48 | 400k (2.7%) |
460k | ||||
| Het. multispore | 48 | 400k (2.7%) |
579k | |||||||
| Het. tissue | 47 | 400k (2.7%) |
514k | |||||||
| 3 | Salamander | Environmental DNA | 12S | iTru | 4 & 5 | Reference samples | 7 | 10k (<1%) |
8k | Detected 6/7 species of salamander expected in community |
| eDNA samples | 30 | 12M (48%) |
4.4M | |||||||
| 4 | Human | Methylation |
p21-TSS SIE-1 |
iTru | 4 | N/A | 1 | 40k (0.3%) |
121k | Compared methylation patterns between cell types |
| 5 | Peromyscus | Microbiome | 16S | iTru | 5 | Ash Basin | 44 | 1.5M (6%) |
3.8M | Detected 90,862 bacterial OTUs |
| Pond B | 35 | 1.5M (6%) |
2.8M | |||||||
| Tim’s Branch | 48 | 1.5M (6%) |
0.7M | |||||||
| Upper Three Runs | 44 | 1.5M (6%) |
2.9M | |||||||
| 6 | Wisteria | Population genetics | nr824 nr997 trnL; trnL/F nad4 cyt-b |
iNext | 5 | N/A | 1 | 150k (1.3%) |
79k | Demonstrated mixed ancestry and no population structure in an introduced population |