Supplemental data sets for Raudabaugh et al., Where are they hiding? Testing the body snatchers hypothesis in pyrophilous fungi
Dataset Description |
The data set contains Supplemental data sets for the Manuscript entitled "Where are they hiding? Testing the body snatchers hypothesis in pyrophilous fungi." Environmental sampling: Amplification of nuclear DNA regions (ITS1 and ITS2) were completed using the Fluidigm Access Array and the resulting amplicons were sequenced on an Illumina MiSeq v2 platform runs using rapid 2 × 250 nt paired-end reads. Illumina sequencing run amplicons that were size selected into <500nt and >500nt sub-pools, then remixed together <500nt: >500nt by nM concentration in a 1x:3x proportion. All amplification and sequencing steps were performed at the Roy J. Carver Biotechnology Center at the University of Illinois Urbana-Champaign. ITS1 region primers consisted of ITS1F (5'-CTTGGTCATTTAGAGGAAGTAA-'3) and ITS2 (5'-GCTGCGTTCTTCATCGATGC-'3).
Supplemental files 1 through 5 contain the raw data files.
Supplemental 6 and 7 contain the resulting QIIME 1.9.1. OTU tables along with UNITE, NCBI, and CONSTAX taxonomic assignments in addition to the representative OTU sequence. Numeric samples within the OTU tables correspond to the following:
If a sample number is not present within the OTU table; either no sequences were obtained or no sequences passed the quality filtering step in QIIME. Supplemental 8 contains the Summary of unique species per location.
|
Subject |
Life Sciences |
License |
CC0 |
Funder |
U.S. National Science Foundation (NSF)-Grant:DEB 1733750; DEB 1733854 |
Corresponding Creator |
Andrew Miller |
Downloaded |
2151 times |
| Version | DOI | Comment | Publication Date |
|---|---|---|---|
| 1 | 10.13012/B2IDB-1530363_V1 | 2019-06-12 |
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| RelatedMaterial | create: {"material_type"=>"Article", "availability"=>nil, "link"=>"https://doi.org/10.1016/j.funeco.2019.100870", "uri"=>"10.1016/j.funeco.2019.100870", "uri_type"=>"DOI", "citation"=>"Raudabaugh, D.B., Matheny, P.B., Hughes, K.W., Iturriaga, T.,Sargent, M., Miller, A.N. (2020). Where are they hiding? Testing the body snatchers hypothesis in pyrophilous fungi. Fungal Ecology, Volume 43, February 2020, Article number 100870. doi: https://doi.org/10.1016/j.funeco.2019.100870", "dataset_id"=>972, "selected_type"=>"Article", "datacite_list"=>"IsSupplementTo"} | 2019-10-30T19:38:12Z |
| Dataset | update: {"title"=>["Supplemental data sets for Raudabaugh et al., Where are they hiding? Testing the body snatcher hypothesis in pyrophilous fungi", "Supplemental data sets for Raudabaugh et al., Where are they hiding? Testing the body snatchers hypothesis in pyrophilous fungi"], "description"=>["The data set contains Supplemental data sets for the Manuscript entitled \"Where are they hiding? Testing the body snatcher hypothesis in pyrophilous fungi.\"\r\n\r\nEnvironmental sampling: Amplification of nuclear DNA regions (ITS1 and ITS2) were completed using the Fluidigm Access Array and the resulting amplicons were sequenced on an Illumina MiSeq v2 platform runs using rapid 2 × 250 nt paired-end reads. Illumina sequencing run amplicons that were size selected into <500nt and >500nt sub-pools, then remixed together <500nt: >500nt by nM concentration in a 1x:3x proportion. All amplification and sequencing steps were performed at the Roy J. Carver Biotechnology Center at the University of Illinois Urbana-Champaign.\r\n\r\nITS1 region primers consisted of ITS1F (5'-CTTGGTCATTTAGAGGAAGTAA-'3) and ITS2 (5'-GCTGCGTTCTTCATCGATGC-'3).\r\nITS2 region primers consisted of fITS7 (5'-GTGARTCATCGAATCTTTG-'3) and ITS4 (5'-TCCTCCGCTTATTGATATGC-'3).\r\n\r\nSupplemental files 1 through 5 contain the raw data files.\r\nSupplemental 1 is the ITS1 Illumina MiSeq forward reads and Supplemental 2 is the corresponding index files. \r\nSupplemental 3 is the ITS2 Illumina MiSeq forward reads and Supplemental 4 is the corresponding index files.\r\nSupplemental 5 is the map file needed to process the forward reads and index files in QIIME.\r\n\r\n\r\nSupplemental 6 and 7 contain the resulting QIIME 1.9.1. OTU tables along with UNITE, NCBI, and CONSTAX taxonomic assignments in addition to the representative OTU sequence.\r\n\r\nNumeric samples within the OTU tables correspond to the following:\r\n1\tBrachythecium sp.\r\n2\tUsnea cornuta\r\n3\tDicranum sp.\r\n4\tLeucodon julaceus\r\n5\tLobaria quercizans\r\n6\tRhizomnium sp.\r\n7\tDicranum sp.\r\n8\tThuidium delicatulum\r\n9\tMyelochroa aurulenta\r\n10\tAtrichum angustatum\r\n11\tDicranum sp.\r\n12\tHypnum sp.\r\n13\tAtrichum angustatum\r\n14\tHypnum sp.\r\n15\tThuidium delicatulum\r\n16\tLeucobryum sp.\r\n17\tPolytrichum commune\r\n18\tAtrichum angustatum\r\n19\tAtrichum angustatum\r\n20\tAtrichum crispulum\r\n21\tBryaceae\r\n22\tLeucobryum sp.\r\n23\tConocephalum conicum\r\n24\tClimacium americanum\r\n25\tAtrichum angustatum\r\n26\tHuperzia serrata\r\n27\tPolytrichum commune\r\n28\tDiphasiastrum sp.\r\n29\tAnomodon attenuatus\r\n30\tBryoandersonia sp.\r\n31\tPolytrichum commune\r\n32\tThuidium delicatulum\r\n33\tBrachythecium sp.\r\n34\tLeucobryum glaucum\r\n35\tBryoandersonia sp.\r\n36\tAnomodon attenuatus\r\n37\tPohlia sp.\r\n38\tCinclidium sp.\r\n39\tHylocomium splendens\r\n40\tPolytrichum commune\r\n41\tnegative control\r\n42\tSoil\r\n43\tSoil\r\n44\tSoil\r\n45\tSoil\r\n46\tSoil\r\n47\tSoil\r\n\r\nIf a sample number is not present within the OTU table; either no sequences were obtained or no sequences passed the quality filtering step in QIIME. \r\n\r\nSupplemental 8 contains the Summary of unique species per location.\r\n ", "The data set contains Supplemental data sets for the Manuscript entitled \"Where are they hiding? Testing the body snatchers hypothesis in pyrophilous fungi.\"\r\n\r\nEnvironmental sampling: Amplification of nuclear DNA regions (ITS1 and ITS2) were completed using the Fluidigm Access Array and the resulting amplicons were sequenced on an Illumina MiSeq v2 platform runs using rapid 2 × 250 nt paired-end reads. Illumina sequencing run amplicons that were size selected into <500nt and >500nt sub-pools, then remixed together <500nt: >500nt by nM concentration in a 1x:3x proportion. All amplification and sequencing steps were performed at the Roy J. Carver Biotechnology Center at the University of Illinois Urbana-Champaign.\r\n\r\nITS1 region primers consisted of ITS1F (5'-CTTGGTCATTTAGAGGAAGTAA-'3) and ITS2 (5'-GCTGCGTTCTTCATCGATGC-'3).\r\nITS2 region primers consisted of fITS7 (5'-GTGARTCATCGAATCTTTG-'3) and ITS4 (5'-TCCTCCGCTTATTGATATGC-'3).\r\n\r\nSupplemental files 1 through 5 contain the raw data files.\r\nSupplemental 1 is the ITS1 Illumina MiSeq forward reads and Supplemental 2 is the corresponding index files. \r\nSupplemental 3 is the ITS2 Illumina MiSeq forward reads and Supplemental 4 is the corresponding index files.\r\nSupplemental 5 is the map file needed to process the forward reads and index files in QIIME.\r\n\r\n\r\nSupplemental 6 and 7 contain the resulting QIIME 1.9.1. OTU tables along with UNITE, NCBI, and CONSTAX taxonomic assignments in addition to the representative OTU sequence.\r\n\r\nNumeric samples within the OTU tables correspond to the following:\r\n1\tBrachythecium sp.\r\n2\tUsnea cornuta\r\n3\tDicranum sp.\r\n4\tLeucodon julaceus\r\n5\tLobaria quercizans\r\n6\tRhizomnium sp.\r\n7\tDicranum sp.\r\n8\tThuidium delicatulum\r\n9\tMyelochroa aurulenta\r\n10\tAtrichum angustatum\r\n11\tDicranum sp.\r\n12\tHypnum sp.\r\n13\tAtrichum angustatum\r\n14\tHypnum sp.\r\n15\tThuidium delicatulum\r\n16\tLeucobryum sp.\r\n17\tPolytrichum commune\r\n18\tAtrichum angustatum\r\n19\tAtrichum angustatum\r\n20\tAtrichum crispulum\r\n21\tBryaceae\r\n22\tLeucobryum sp.\r\n23\tConocephalum conicum\r\n24\tClimacium americanum\r\n25\tAtrichum angustatum\r\n26\tHuperzia serrata\r\n27\tPolytrichum commune\r\n28\tDiphasiastrum sp.\r\n29\tAnomodon attenuatus\r\n30\tBryoandersonia sp.\r\n31\tPolytrichum commune\r\n32\tThuidium delicatulum\r\n33\tBrachythecium sp.\r\n34\tLeucobryum glaucum\r\n35\tBryoandersonia sp.\r\n36\tAnomodon attenuatus\r\n37\tPohlia sp.\r\n38\tCinclidium sp.\r\n39\tHylocomium splendens\r\n40\tPolytrichum commune\r\n41\tnegative control\r\n42\tSoil\r\n43\tSoil\r\n44\tSoil\r\n45\tSoil\r\n46\tSoil\r\n47\tSoil\r\n\r\nIf a sample number is not present within the OTU table; either no sequences were obtained or no sequences passed the quality filtering step in QIIME. \r\n\r\nSupplemental 8 contains the Summary of unique species per location.\r\n "]} | 2019-06-27T20:17:58Z |