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StudyID metadata raw-data-url-forward-read raw-data-url-reverse-read raw-data-url-index-read qiita-id study-type target-gene human-readable-description
mock-1 https://github.com/caporaso-lab/mockrobiota/tree/master/data/mock-1/sample-metadata.tsv https://s3-us-west-2.amazonaws.com/mockrobiota/latest/mock-1/mock-forward-read.fastq.gz NA https://s3-us-west-2.amazonaws.com/mockrobiota/latest/mock-1/mock-index-read.fastq.gz 1687 marker-gene 16S A mock community composed of 48 bacteria represented in equal abundances in three replicate samples. These are the same community members present in mock-2, which consists of the same mock community samples analyzed on a separate Illumina MiSeq run. This was generated by Dr. Sathish Subramanian at Washington University, St. Louis, in 2012.
mock-2 https://github.com/caporaso-lab/mockrobiota/tree/master/data/mock-2/sample-metadata.tsv https://s3-us-west-2.amazonaws.com/mockrobiota/latest/mock-2/mock-forward-read.fastq.gz https://s3-us-west-2.amazonaws.com/mockrobiota/latest/mock-2/mock-reverse-read.fastq.gz https://s3-us-west-2.amazonaws.com/mockrobiota/latest/mock-2/mock-index-read.fastq.gz 1688 marker-gene 16S A mock community composed of 48 bacteria represented in equal abundances in three replicate samples. These are the same community members present in mock-1, which consists of the same mock community samples analyzed on a separate Illumina HiSeq run. This was generated by Dr. Sathish Subramanian at Washington University, St. Louis, in 2012.
mock-3 https://github.com/caporaso-lab/mockrobiota/tree/master/data/mock-3/sample-metadata.tsv https://s3-us-west-2.amazonaws.com/mockrobiota/latest/mock-3/mock-forward-read.fastq.gz https://s3-us-west-2.amazonaws.com/mockrobiota/latest/mock-3/mock-reverse-read.fastq.gz https://s3-us-west-2.amazonaws.com/mockrobiota/latest/mock-3/mock-index-read.fastq.gz 1685 marker-gene 16S A mock community composed of 21 bacterial strains represented in equal abundances in two replicate samples, and the same strains represented in uneven abundances in two replicate samples. These are the same community members present in mock-4 and mock-5, which consists of the same mock community samples analyzed on separate Illumina sequencing runs. This was generated by Dr. Dirk Gevers at Broad Institute in 2012.
mock-4 https://github.com/caporaso-lab/mockrobiota/tree/master/data/mock-4/sample-metadata.tsv https://s3-us-west-2.amazonaws.com/mockrobiota/latest/mock-4/mock-forward-read.fastq.gz https://s3-us-west-2.amazonaws.com/mockrobiota/latest/mock-4/mock-reverse-read.fastq.gz https://s3-us-west-2.amazonaws.com/mockrobiota/latest/mock-4/mock-index-read.fastq.gz 1686 marker-gene 16S A mock community composed of 21 bacterial strains represented in equal abundances in two replicate samples, and the same strains represented in uneven abundances in two replicate samples. These are the same community members present in mock-3 and mock-5, which consists of the same mock community samples analyzed on separate Illumina sequencing runs. This was generated by Dr. Dirk Gevers at Broad Institute in 2012.
mock-5 https://github.com/caporaso-lab/mockrobiota/tree/master/data/mock-5/sample-metadata.tsv https://s3-us-west-2.amazonaws.com/mockrobiota/latest/mock-5/mock-forward-read.fastq.gz https://s3-us-west-2.amazonaws.com/mockrobiota/latest/mock-5/mock-reverse-read.fastq.gz https://s3-us-west-2.amazonaws.com/mockrobiota/latest/mock-5/mock-index-read.fastq.gz 1972 marker-gene 16S A mock community composed of 21 bacterial strains represented in equal abundances in two replicate samples, and the same strains represented in uneven abundances in two replicate samples. These are the same community members present in mock-3 and mock-4, which consist of the same mock community samples analyzed on separate Illumina sequencing runs. This was generated by Dr. Dirk Gevers at Broad Institute in 2012.
mock-6 https://github.com/caporaso-lab/mockrobiota/tree/master/data/mock-6/sample-metadata.tsv https://s3-us-west-2.amazonaws.com/mockrobiota/latest/mock-6/mock-forward-read.fastq.gz NA https://s3-us-west-2.amazonaws.com/mockrobiota/latest/mock-6/mock-index-read.fastq.gz 721+722 marker-gene 16S A mock community composed of 67 bacteria represented in equal abundances in three replicate samples. These are the same community members present in [mock-7](../mock-7/) and [mock-8](../mock-8/), which consist of the same mock community samples analyzed on different Illumina sequencing runs. The mock community samples were generated by Dr. Peter Turnbaugh at Harvard in 2010, and sequenced by Illumina, Inc. in San Diego, CA, in 2010.
mock-7 https://github.com/caporaso-lab/mockrobiota/tree/master/data/mock-7/sample-metadata.tsv https://s3-us-west-2.amazonaws.com/mockrobiota/latest/mock-7/mock-forward-read.fastq.gz https://s3-us-west-2.amazonaws.com/mockrobiota/latest/mock-7/mock-reverse-read.fastq.gz https://s3-us-west-2.amazonaws.com/mockrobiota/latest/mock-7/mock-index-read.fastq.gz NA marker-gene 16S A mock community composed of 67 bacteria represented in equal abundances in three replicate samples. These are the same community members present in [mock-8](../mock-8), which consists of the same mock community samples analyzed on different Illumina sequencing runs. This was generated by Dr. Peter Turnbaugh at Harvard in 2012.
mock-8 https://github.com/caporaso-lab/mockrobiota/tree/master/data/mock-8/sample-metadata.tsv https://s3-us-west-2.amazonaws.com/mockrobiota/latest/mock-8/mock-forward-read.fastq.gz https://s3-us-west-2.amazonaws.com/mockrobiota/latest/mock-8/mock-reverse-read.fastq.gz https://s3-us-west-2.amazonaws.com/mockrobiota/latest/mock-8/mock-index-read.fastq.gz 1973 marker-gene 16S A mock community composed of 67 bacteria represented in equal abundances in three replicate samples. These are the same community members present in [mock-7](../mock-7), which consists of the same mock community samples analyzed on different Illumina sequencing runs. This was generated by Dr. Peter Turnbaugh at Harvard in 2012.
mock-9 https://github.com/caporaso-lab/mockrobiota/tree/master/data/mock-9/sample-metadata.tsv https://s3-us-west-2.amazonaws.com/mockrobiota/latest/mock-9/mock-forward-read.fastq.gz https://s3-us-west-2.amazonaws.com/mockrobiota/latest/mock-9/mock-reverse-read.fastq.gz https://s3-us-west-2.amazonaws.com/mockrobiota/latest/mock-9/mock-index-read.fastq.gz 1974 marker-gene ITS A mock community composed of 16 fungal strains (12 species) represented in equal abundances in three replicate samples. These are the same community members present in [mock-10](../mock-10/), which is the same mock community samples analyzed on a separate Illumina HiSeq run. This was generated by Dr. Benjamin Wolfe at Harvard University, in 2012.
mock-10 https://github.com/caporaso-lab/mockrobiota/tree/master/data/mock-10/sample-metadata.tsv https://s3-us-west-2.amazonaws.com/mockrobiota/latest/mock-10/mock-forward-read.fastq.gz NA https://s3-us-west-2.amazonaws.com/mockrobiota/latest/mock-10/mock-index-read.fastq.gz 1975 marker-gene ITS A mock community composed of 16 fungal strains (12 species) represented in equal abundances in three replicate samples. These are the same community members present in [mock-9](../mock-9/), which is the same mock community samples analyzed on a separate Illumina HiSeq run. This was generated by Dr. Benjamin Wolfe at Harvard University, in 2012.
mock-11 https://github.com/caporaso-lab/mockrobiota/tree/master/data/mock-11/sample-metadata.tsv https://s3-us-west-2.amazonaws.com/mockrobiota/latest/mock-11/mock-forward-read.fastq.gz NA https://s3-us-west-2.amazonaws.com/mockrobiota/latest/mock-11/mock-index-read.fastq.gz 10808 marker-gene 18S A mock community composed of 11 fungal strains plus human DNA, represented in equal abundances in a single sample. This was generated by the Broad Institute in 2011, and the sequencing data was contributed by Dr. Laura Parfrey at University of Colorado, Boulder, in 2012.
mock-12 https://github.com/caporaso-lab/mockrobiota/tree/master/data/mock-12/sample-metadata.tsv https://s3-us-west-2.amazonaws.com/mockrobiota/latest/mock-12/mock-forward-read.fastq.gz https://s3-us-west-2.amazonaws.com/mockrobiota/latest/mock-12/mock-reverse-read.fastq.gz NA NA marker-gene 16S Composed of 27 bacterial strains amplified with 515f/806r primers. Intended to include more closely related taxa than the other mock communities, the members of which were chosen in part for their well-separated 16S rRNA gene sequences. These strains are all distinguishable over the sequenced region of the 16S rRNA gene, but some pairs of strains differ by as little as one nucleotide. Generated by Benjamin Callahan at Stanford University in 2015.
mock-13 https://github.com/caporaso-lab/mockrobiota/tree/master/data/mock-13/sample-metadata.tsv https://s3-us-west-2.amazonaws.com/mockrobiota/latest/mock-13/mock-forward-read.fastq.gz https://s3-us-west-2.amazonaws.com/mockrobiota/latest/mock-13/mock-reverse-read.fastq.gz NA NA marker-gene 16S Mock community generated by Kozich et al. dual indexing V4 HMP mock, composed of even amounts of purified genomic DNA from 21 bacterial strains.
mock-14 https://github.com/caporaso-lab/mockrobiota/tree/master/data/mock-14/sample-metadata.tsv https://s3-us-west-2.amazonaws.com/mockrobiota/latest/mock-14/mock-forward-read.fastq.gz https://s3-us-west-2.amazonaws.com/mockrobiota/latest/mock-14/mock-reverse-read.fastq.gz NA NA marker-gene 16S Mock community generated by Kozich et al. dual indexing V4 HMP mock, composed of even amounts of purified genomic DNA from 21 bacterial strains.
mock-15 https://github.com/caporaso-lab/mockrobiota/tree/master/data/mock-15/sample-metadata.tsv https://s3-us-west-2.amazonaws.com/mockrobiota/latest/mock-15/mock-forward-read.fastq.gz https://s3-us-west-2.amazonaws.com/mockrobiota/latest/mock-15/mock-reverse-read.fastq.gz NA NA marker-gene 16S Mock community generated by Kozich et al. dual indexing V4 HMP mock, composed of even amounts of purified genomic DNA from 21 bacterial strains.
mock-16 https://github.com/caporaso-lab/mockrobiota/tree/master/data/mock-16/sample-metadata.tsv https://s3-us-west-2.amazonaws.com/mockrobiota/latest/mock-16/mock-forward-read.fastq.gz https://s3-us-west-2.amazonaws.com/mockrobiota/latest/mock-16/mock-reverse-read.fastq.gz NA NA marker-gene 16S Mock community generated by Melanie Schirmer at University of Glasgow in 2015. Composed of even amounts of purified genomic DNA from 49 bacteria and 10 archaea.
mock-17 https://github.com/caporaso-lab/mockrobiota/tree/master/data/mock-17/sample-metadata.tsv https://s3-us-west-2.amazonaws.com/mockrobiota/latest/mock-17/mock-forward-read.fastq.gz https://s3-us-west-2.amazonaws.com/mockrobiota/latest/mock-17/mock-reverse-read.fastq.gz NA NA metagenome NA Mock metagenome community generated by Kozich et al. dual indexing V4 HMP mock, composed of even amounts of purified genomic DNA from 21 bacterial strains.
mock-18 https://github.com/caporaso-lab/mockrobiota/tree/master/data/mock-18/sample-metadata.tsv https://s3-us-west-2.amazonaws.com/mockrobiota/latest/mock-18/mock-forward-read.fastq.gz https://s3-us-west-2.amazonaws.com/mockrobiota/latest/mock-18/mock-reverse-read.fastq.gz NA NA marker-gene 16S Mock community generated by Tourlousse et al., composed of an even mixture of cloned 16S rRNA genes in pUC19 plasmid vector from 15 bacterial strains.
mock-19 https://github.com/caporaso-lab/mockrobiota/tree/master/data/mock-19/sample-metadata.tsv https://s3-us-west-2.amazonaws.com/mockrobiota/latest/mock-19/mock-forward-read.fastq.gz https://s3-us-west-2.amazonaws.com/mockrobiota/latest/mock-19/mock-reverse-read.fastq.gz NA NA marker-gene 16S Mock community generated by Tourlousse et al., composed of an even mixture of cloned 16S rRNA genes in pUC19 plasmid vector from 15 bacterial strains and 12 synthetic spike-in standards.
mock-20 https://github.com/caporaso-lab/mockrobiota/tree/master/data/mock-20/sample-metadata.tsv https://s3-us-west-2.amazonaws.com/mockrobiota/latest/mock-20/mock-forward-read.fastq.gz https://s3-us-west-2.amazonaws.com/mockrobiota/latest/mock-20/mock-reverse-read.fastq.gz NA NA marker-gene 16S Mock community generated by Gohl et al., composed of even amounts of purified genomic DNA from 20 bacterial strains.
mock-21 https://github.com/caporaso-lab/mockrobiota/tree/master/data/mock-21/sample-metadata.tsv https://s3-us-west-2.amazonaws.com/mockrobiota/latest/mock-21/mock-forward-read.fastq.gz https://s3-us-west-2.amazonaws.com/mockrobiota/latest/mock-21/mock-reverse-read.fastq.gz NA NA marker-gene 16S Mock community generated by Gohl et al., composed of uneven (staggered) amounts of purified genomic DNA from 20 bacterial strains.
mock-22 https://github.com/caporaso-lab/mockrobiota/tree/master/data/mock-22/sample-metadata.tsv https://s3-us-west-2.amazonaws.com/mockrobiota/latest/mock-22/mock-forward-read.fastq.gz https://s3-us-west-2.amazonaws.com/mockrobiota/latest/mock-22/mock-reverse-read.fastq.gz NA NA marker-gene 16S Mock community generated by Gohl et al., composed of even amounts of purified genomic DNA from 20 bacterial strains.
mock-23 https://github.com/caporaso-lab/mockrobiota/tree/master/data/mock-23/sample-metadata.tsv https://s3-us-west-2.amazonaws.com/mockrobiota/latest/mock-23/mock-forward-read.fastq.gz https://s3-us-west-2.amazonaws.com/mockrobiota/latest/mock-23/mock-reverse-read.fastq.gz NA NA marker-gene 16S Mock community generated by Gohl et al., composed of uneven (staggered) amounts of purified genomic DNA from 20 bacterial strains.
mock-24 https://github.com/caporaso-lab/mockrobiota/tree/master/data/mock-24/sample-metadata.tsv https://s3-us-west-2.amazonaws.com/mockrobiota/latest/mock-24/mock-forward-read.fastq.gz https://s3-us-west-2.amazonaws.com/mockrobiota/latest/mock-24/mock-reverse-read.fastq.gz NA NA marker-gene ITS A mock community composed of 8 fungal species represented in uneven abundances. These are the same community members present in [mock-25](../mock-25/), but at different relative abundances. This was generated by Dr. Lee Taylor at UNM, in 2016.
mock-25 https://github.com/caporaso-lab/mockrobiota/tree/master/data/mock-25/sample-metadata.tsv https://s3-us-west-2.amazonaws.com/mockrobiota/latest/mock-25/mock-forward-read.fastq.gz https://s3-us-west-2.amazonaws.com/mockrobiota/latest/mock-25/mock-reverse-read.fastq.gz NA NA marker-gene ITS A mock community composed of 8 fungal species represented in uneven abundances. These are the same community members present in [mock-24](../mock-24/), but at different relative abundances. This was generated by Dr. Lee Taylor at UNM, in 2016.
mock-26 https://github.com/caporaso-lab/mockrobiota/tree/master/data/mock-26/sample-metadata.tsv https://s3-us-west-2.amazonaws.com/mockrobiota/latest/mock-26/mock-forward-read.fastq.gz NA https://s3-us-west-2.amazonaws.com/mockrobiota/latest/mock-26/mock-index-read.fastq.gz NA marker-gene ITS A mock community composed of ITS amplicons from 11 fungal species mixed at both even and uneven abundances in replicate samples, and 11 samples containing a single species. Compiled by Dr. Bjorn Lindahl, Swedish University of Agricultural Sciences, Uppsala, in 2012.
mock-27 https://github.com/caporaso-lab/mockrobiota/tree/master/data/mock-27/sample-metadata.tsv https://s3-us-west-2.amazonaws.com/mockrobiota/latest/mock-27/mock-forward-read.fastq.gz https://s3-us-west-2.amazonaws.com/mockrobiota/latest/mock-27/mock-reverse-read.fastq.gz NA NA marker-gene nifH This mock community was comprised of DNA from the following six diazotrophic isolates: Anabaena torulosa (Carm.) Lagerh. (Cyanobacteria) Algae Collection Vienna (ASW 01028), Desulfosporosinus acidophilus strain SJ4T (DSM22704) (Firmicutes) (Alazard et al., 2010), Kosakonia sacchari (Gammaproteobacteria) (in house strain, 99.89% sequence identical (1105 bp) to K. sacchari SP1T (Chen et al., 2014)), Mesorhizobium loti strain R7A (Alphaproteobacteria) (Kelly et al., 2014), Nostoc microscopicum Vaucher (Cyanobacteria) Algae Collection Vienna (ASW 01020), and Telmatospirillum siberiense 26-4b1T (Alphaproteobacteria) (Hausmann et al., in press). DNA was extracted using Qiagen DNeasy Blood and Tissue Kit (Qiagen) according to the manufacturer’s instructions except that 200 µl of culture was first transferred to Lysing Matrix A tube and cells were disrupted using bead beating (30 s at 4 m s-1; FastPrep-24, MP Biomedicals) after adding PBS and AL buffers. DNA was then used for PCR amplification of the nifH gene using primers Ueda19-R6 as described above. PCR products were cloned using TOPO TA Cloning Kit (Thermo Fisher Scientific). One clone containing nifH gene fragment from each strain was used for colony PCR amplification using primers M13, flanking the insert region. The identity of all isolates were confirmed using Sanger sequencing. The taxonomic affiliation and sequences of these isolates appear in taxonomy.tsv and expected-sequences.fasta. The taxonomy is based on the SILVA taxonomic classification, but the given nifH sequences cannot be used for classification using SILVA, since SILVA is an rRNA-gene database. phylogenetic_clusters_CART.tsv details the phylogenetic clustering of the isolates, which was done using [nifH-CART](https://wwwzehr.pmc.ucsc.edu/CART_model_public/).
mock-28 https://github.com/caporaso-lab/mockrobiota/tree/master/data/mock-28/sample-metadata.tsv https://s3-us-west-2.amazonaws.com/mockrobiota/latest/mock-28/mock-forward-read.fastq.gz https://s3-us-west-2.amazonaws.com/mockrobiota/latest/mock-28/mock-reverse-read.fastq.gz NA NA marker-gene nifH This mock community was comprised of DNA from the following six diazotrophic isolates: Anabaena torulosa (Carm.) Lagerh. (Cyanobacteria) Algae Collection Vienna (ASW 01028), Desulfosporosinus acidophilus strain SJ4T (DSM22704) (Firmicutes) (Alazard et al., 2010), Kosakonia sacchari (Gammaproteobacteria) (in house strain, 99.89% sequence identical (1105 bp) to K. sacchari SP1T (Chen et al., 2014)), Mesorhizobium loti strain R7A (Alphaproteobacteria) (Kelly et al., 2014), Nostoc microscopicum Vaucher (Cyanobacteria) Algae Collection Vienna (ASW 01020), and Telmatospirillum siberiense 26-4b1T (Alphaproteobacteria) (Hausmann et al., in press). DNA was extracted using Qiagen DNeasy Blood and Tissue Kit (Qiagen) according to the manufacturer’s instructions except that 200 µl of culture was first transferred to Lysing Matrix A tube and cells were disrupted using bead beating (30 s at 4 m s-1; FastPrep-24, MP Biomedicals) after adding PBS and AL buffers. DNA was then used for PCR amplification of the nifH gene using primers Ueda19-R6 as described above. PCR products were cloned using TOPO TA Cloning Kit (Thermo Fisher Scientific). One clone containing nifH gene fragment from each strain was used for colony PCR amplification using primers M13, flanking the insert region.The identity of all isolates were confirmed using Sanger sequencing. The taxonomic affiliation and sequences of these isolates appear in taxonomy.tsv and expected-sequences.fasta. The taxonomy is based on the SILVA taxonomic classification, but the given nifH sequences cannot be used for classification using SILVA, since SILVA is an rRNA-gene database. phylogenetic_clusters_CART.tsv details the phylogenetic clustering of the isolates, which was done using [nifH-CART](https://wwwzehr.pmc.ucsc.edu/CART_model_public/).
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