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Merge pull request #28 from dholab/proposals
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Adding proposal instructions and a new column to the line list
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@willvuyk
willvuyk authored May 23, 2024
2 parents b5b2fa8 + a847f63 commit 26cb662
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62 changes: 31 additions & 31 deletions DETECTION_RESULTS.tsv
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sample carton date_purchased date_expiration average_cycle_threshold average_copies_per_uL primer_asset_file probe_asset_file RNA_extraction_method positive_for_HPAI processing_plant_state SRA_bioproject SRA_accession contributors date_contributed
dholab_30081_01 dholab_carton_0001 2024-04-24 2024-05-08 NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE IA dholab 2024-05-14
dholab_30081_02 dholab_carton_0002 2024-04-24 2024-05-01 NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE IA dholab 2024-05-14
dholab_30081_03 dholab_carton_0003 2024-04-24 2024-06-05 NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE MN dholab 2024-05-14
dholab_30081_04 dholab_carton_0004 2024-04-24 2024-05-30 NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE MN dholab 2024-05-14
dholab_30081_05 dholab_carton_0005 2024-04-24 2024-06-20 32.435 19 AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" TRUE CO dholab 2024-05-14
dholab_30081_06 dholab_carton_0006 2024-04-24 2024-05-19 33.055 13 AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" TRUE CO dholab 2024-05-14
dholab_30081_07 dholab_carton_0007 2024-04-24 2024-05-08 NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE WI dholab 2024-05-14
dholab_30081_08 dholab_carton_0008 2024-04-24 2024-05-08 NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE WI dholab 2024-05-14
dholab_30081_09 dholab_carton_0009 2024-04-24 2024-05-02 NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE WI dholab 2024-05-14
dholab_30081_10 dholab_carton_0010 2024-04-24 2024-05-01 NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE IA dholab 2024-05-14
dholab_30081_11 dholab_carton_0011 2024-04-24 2024-05-01 NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE IA dholab 2024-05-14
dholab_30081_12 dholab_carton_0012 2024-04-24 2024-05-02 NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE WI dholab 2024-05-14
dholab_30081_13 dholab_carton_0013 2024-04-24 2024-05-07 NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE WI dholab 2024-05-14
dholab_30081_14 dholab_carton_0014 2024-04-24 NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE IA dholab 2024-05-14
dholab_30081_15 dholab_carton_0015 2024-04-26 NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE WI dholab 2024-05-14
dholab_30114_01 dholab_carton_0016 2024-05-02 2024-05-17 NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE VA dholab 2024-05-14
dholab_30114_02 dholab_carton_0017 2024-05-02 2024-06-06 NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE NY dholab 2024-05-14
dholab_30114_03 dholab_carton_0018 2024-05-02 2024-06-04 NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE OH dholab 2024-05-14
dholab_30114_04 dholab_carton_0019 2024-05-02 2024-06-17 33.52 10 AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" TRUE KY dholab 2024-05-14
dholab_30114_06 dholab_carton_0020 2024-05-02 2024-06-27 NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE CO dholab 2024-05-14
dholab_30114_07 dholab_carton_0021 2024-05-02 2024-06-04 31.17 46 AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" TRUE TX dholab 2024-05-14
dholab_30114_08 dholab_carton_0022 2024-05-02 2024-05-16 NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE UT dholab 2024-05-14
dholab_30114_09 dholab_carton_0023 2024-05-02 2024-05-30 NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE IN dholab 2024-05-14
dholab_30114_10 dholab_carton_0024 2024-05-02 2024-07-11 26.29 1145 AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" TRUE MI dholab 2024-05-14
dholab_30114_14 dholab_carton_0005 2024-04-24 2024-06-20 31.34 40 AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta 400ul sample added to MagMax wastewater ultra x96 isolation on Kingfisher Apex TRUE CO dholab 2024-05-14
dholab_30125_1 dholab_carton_0018 2024-05-02 2024-06-04 NA DHO_influenzaAsurveillance_primers.fasta DHO_influenzaAsurveillance_probe.fasta 400ul sample added to MagMax wastewater ultra x96 isolation on Kingfisher Apex FALSE OH dholab 2024-05-14
dholab_30125_2 dholab_carton_0018 2024-05-02 2024-06-04 NA DHO_influenzaAsurveillance_primers.fasta DHO_influenzaAsurveillance_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE OH dholab 2024-05-14
dholab_30125_3 dholab_carton_0019 2024-05-02 2024-06-17 28.97 468 DHO_influenzaAsurveillance_primers.fasta DHO_influenzaAsurveillance_probe.fasta 400ul sample added to MagMax wastewater ultra x96 isolation on Kingfisher Apex TRUE KY dholab 2024-05-14
dholab_30125_4 dholab_carton_0019 2024-05-02 2024-06-17 30.065 116 DHO_influenzaAsurveillance_primers.fasta DHO_influenzaAsurveillance_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" TRUE KY dholab 2024-05-14
dholab_30125_5 dholab_carton_0021 2024-05-02 2024-06-04 26.63 3500 DHO_influenzaAsurveillance_primers.fasta DHO_influenzaAsurveillance_probe.fasta 400ul sample added to MagMax wastewater ultra x96 isolation on Kingfisher Apex TRUE TX dholab 2024-05-14
sample carton date_purchased date_expiration assay average_cycle_threshold average_copies_per_uL primer_asset_file probe_asset_file RNA_extraction_method positive_for_HPAI processing_plant_state SRA_bioproject SRA_accession contributors date_contributed
dholab_30081_01 dholab_carton_0001 2024-04-24 2024-05-08 qPCR NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE IA dholab 2024-05-14
dholab_30081_02 dholab_carton_0002 2024-04-24 2024-05-01 qPCR NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE IA dholab 2024-05-14
dholab_30081_03 dholab_carton_0003 2024-04-24 2024-06-05 qPCR NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE MN dholab 2024-05-14
dholab_30081_04 dholab_carton_0004 2024-04-24 2024-05-30 qPCR NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE MN dholab 2024-05-14
dholab_30081_05 dholab_carton_0005 2024-04-24 2024-06-20 qPCR 32.435 19 AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" TRUE CO dholab 2024-05-14
dholab_30081_06 dholab_carton_0006 2024-04-24 2024-05-19 qPCR 33.055 13 AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" TRUE CO dholab 2024-05-14
dholab_30081_07 dholab_carton_0007 2024-04-24 2024-05-08 qPCR NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE WI dholab 2024-05-14
dholab_30081_08 dholab_carton_0008 2024-04-24 2024-05-08 qPCR NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE WI dholab 2024-05-14
dholab_30081_09 dholab_carton_0009 2024-04-24 2024-05-02 qPCR NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE WI dholab 2024-05-14
dholab_30081_10 dholab_carton_0010 2024-04-24 2024-05-01 qPCR NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE IA dholab 2024-05-14
dholab_30081_11 dholab_carton_0011 2024-04-24 2024-05-01 qPCR NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE IA dholab 2024-05-14
dholab_30081_12 dholab_carton_0012 2024-04-24 2024-05-02 qPCR NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE WI dholab 2024-05-14
dholab_30081_13 dholab_carton_0013 2024-04-24 2024-05-07 qPCR NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE WI dholab 2024-05-14
dholab_30081_14 dholab_carton_0014 2024-04-24 qPCR NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE IA dholab 2024-05-14
dholab_30081_15 dholab_carton_0015 2024-04-26 qPCR NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE WI dholab 2024-05-14
dholab_30114_01 dholab_carton_0016 2024-05-02 2024-05-17 qPCR NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE VA dholab 2024-05-14
dholab_30114_02 dholab_carton_0017 2024-05-02 2024-06-06 qPCR NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE NY dholab 2024-05-14
dholab_30114_03 dholab_carton_0018 2024-05-02 2024-06-04 qPCR NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE OH dholab 2024-05-14
dholab_30114_04 dholab_carton_0019 2024-05-02 2024-06-17 qPCR 33.52 10 AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" TRUE KY dholab 2024-05-14
dholab_30114_06 dholab_carton_0020 2024-05-02 2024-06-27 qPCR NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE CO dholab 2024-05-14
dholab_30114_07 dholab_carton_0021 2024-05-02 2024-06-04 qPCR 31.17 46 AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" TRUE TX dholab 2024-05-14
dholab_30114_08 dholab_carton_0022 2024-05-02 2024-05-16 qPCR NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE UT dholab 2024-05-14
dholab_30114_09 dholab_carton_0023 2024-05-02 2024-05-30 qPCR NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE IN dholab 2024-05-14
dholab_30114_10 dholab_carton_0024 2024-05-02 2024-07-11 qPCR 26.29 1145 AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" TRUE MI dholab 2024-05-14
dholab_30114_14 dholab_carton_0005 2024-04-24 2024-06-20 qPCR 31.34 40 AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta 400ul sample added to MagMax wastewater ultra x96 isolation on Kingfisher Apex TRUE CO dholab 2024-05-14
dholab_30125_1 dholab_carton_0018 2024-05-02 2024-06-04 qPCR NA DHO_influenzaAsurveillance_primers.fasta DHO_influenzaAsurveillance_probe.fasta 400ul sample added to MagMax wastewater ultra x96 isolation on Kingfisher Apex FALSE OH dholab 2024-05-14
dholab_30125_2 dholab_carton_0018 2024-05-02 2024-06-04 qPCR NA DHO_influenzaAsurveillance_primers.fasta DHO_influenzaAsurveillance_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE OH dholab 2024-05-14
dholab_30125_3 dholab_carton_0019 2024-05-02 2024-06-17 qPCR 28.97 468 DHO_influenzaAsurveillance_primers.fasta DHO_influenzaAsurveillance_probe.fasta 400ul sample added to MagMax wastewater ultra x96 isolation on Kingfisher Apex TRUE KY dholab 2024-05-14
dholab_30125_4 dholab_carton_0019 2024-05-02 2024-06-17 qPCR 30.065 116 DHO_influenzaAsurveillance_primers.fasta DHO_influenzaAsurveillance_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" TRUE KY dholab 2024-05-14
dholab_30125_5 dholab_carton_0021 2024-05-02 2024-06-04 qPCR 26.63 3500 DHO_influenzaAsurveillance_primers.fasta DHO_influenzaAsurveillance_probe.fasta 400ul sample added to MagMax wastewater ultra x96 isolation on Kingfisher Apex TRUE TX dholab 2024-05-14
2 changes: 1 addition & 1 deletion assets/positivity_tally.tsv
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Processing Plant State Negative Cartons Positive Cartons Total Cartons As of
Processing Plant State Negative Cartons Positive Cartons Total Cartons Latest Date Sampled
CO 1 2 3 2024-05-02
IA 5 0 5 2024-04-24
IN 1 0 1 2024-05-02
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2 changes: 1 addition & 1 deletion assets/proposal_template.tsv
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sample carton date_purchased date_expiration average_cycle_threshold average_copies_per_uL primer_asset_file probe_asset_file RNA_extraction_method positive_for_HPAI processing_plant_state SRA_bioproject SRA_accession contributors date_contributed
sample carton date_purchased date_expiration assay average_cycle_threshold average_copies_per_uL primer_asset_file probe_asset_file RNA_extraction_method positive_for_HPAI processing_plant_state SRA_bioproject SRA_accession contributors date_contributed
1 change: 1 addition & 0 deletions assets/still.schema
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Expand Up @@ -10,6 +10,7 @@ sample: is_string() && !is_empty() && !is_missing()
carton: is_string() || is_missing() || is_empty()
date_purchased: is_date() && is_date_format("[2020-02-10]")
date_expiration: is_date() || is_missing() || is_empty()
assay: any("qPCR", "dPCR", "other") || is_missing() || is_empty()
average_cycle_threshold: is_numeric() || is_empty() || is_missing()
average_copies_per_uL: is_numeric() || is_empty() || is_missing()
primer_asset_file: is('REDACTED') || is_string()
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