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Table 1 Quality and quantity of extracted DNA, PCR amplicon, and HTS-read and amplicon sequence variant (ASV) count per sediment sample

From: Sediment-associated microbial community profiling: sample pre-processing through sequential membrane filtration for 16S rRNA amplicon sequencing

Site Code Filter Type Extracted DNAa Amplicon Library Read Processing Taxonomic Assignment
qPCR (nM)b DNA Assayc
ng/ul A260/A280 A260/A230 Size (bp) Band Raw Reads Quality Filtered Denoised Non-Chimeric Reads w/ Tax. ID ASVs w/ Tax ID
A ANP NP 307.1 1.40 0.46 4.88 410 1 1,166,991 560,891 456,284 446,586 424,397 461
A02 0.22 479.7 1.37 0.61 14.16 409 2 305,045 171,106 154,579 147,490 143,019 436
A05 5 110.1 1.43 0.50 45.97 408 1 73,962 40,433 32,181 31,458 30,146 183
A10 10 619.2 1.45 0.37 56.53 413 1 260,341 148,596 112,796 105,220 96,643 633
B BNP NP 625.5 1.45 0.30 56.79 413 1 446,984 135,890 87,857 86,948 85,109 75
B02 0.22 397.9 1.61 0.75 27.33 414 1 79,771 29,699 22,339 22,153 20,745 104
B05 5 44.3 2.53 0.06 8.34 415 1 146,808 101,535 86,288 82,169 77,590 465
B10 10 35.8 3.08 0.04 17.38 415 1 182,665 135,387 125,620 112,804 105,066 1,071
C CNP NP 107.1 1.67 0.13 1.44 396 1 790,386 381,687 285,719 275,483 113,715 426
C02 0.22 2.3 1.86 0.09 76.9 412 2 112,123 61,001 54,375 50,476 46,631 295
C05 5 5.1 1.03 0.17 43.23 411 3 23,323 14,327 12,515 10,757 9,582 141
C10 10 7.6 5.10 0.03 4.40 388 2 217,176 138,449 97,116 94,199 89,877 460
Total 3,805,575 1,919,001 1,527,669 1,465,743 1,242,520 2,875
  1. aInitial quantification and quality assessment of extracted DNA via NanoDrop Spectrophotometer
  2. bAmplicon library quantification via Kappa Illumina Library Quantification Kit
  3. cDNA Assay for fragment size quantification and quality via Agilent 2100 BioAnalyzer High Sensitivity DNA Kit. "NP" stands for non-processed sediment samples; "10" for the pre-filter (10 μm), "5" for the mid-filter (5 μm), and "0.22" for the collection filter (0.22 μm)