ZOE 2.0 microbiome
Public Deposited- Last modified date
- May 20, 2022
- Creator
- Divaris, Kimon
- Roach, Jeff
- Azcarate-Peril, M. Andrea
- Ribeiro, Apoena
- Cho, Hunyong
- Wu, Di
- Abstract
- Derived microbiome data (i.e., microbiome taxonomy from metagenomics and metatranscriptomics, pathways, and targeted metatranscriptomics data for 4 top species) and traits from the ZOE 2.0 and ZOE pilot studies.
- Methodology
- Sequencing of supragingival biofilm in the ZOE 2.0 and ZOE pilot studies (i.e., DNAseq and RNAseq.) was done with Illumina HiSeq 4000 (2x150). After QC and trimming of adapter reads with Trim Galore, the resulting paired-end reads were classified with Kraken2 and Bracken and all reads identified as ‘host’ were eliminated. Paired-end reads were joined with vsearch. Estimates of taxonomic composition, gene family, path abundance, and path coverage were produced from the remaining reads using Kracken2/Bracken and a custom database including human, fungal, bacterial, and the expanded Human Oral Microbiome Database (eHOMD) genomes. Additionally, targeted metatranscriptomics/gene expression analyses for the four “top species” that were tested experimentally. Reads classified by Kraken2 as belonging to each of the four top species and any strain thereof were extracted by species, individually by bacterial species aligned to the relevant reference transcriptome with STAR, and subsequently quantified via Salmon.
- Date of publication
- May 20, 2022
- DOI
- Kind of data
- Other
- Resource type
- Dataset
- License
- CC0 1.0 Universal
- Language
- English
Relations
Items
| Thumbnail | Title | Date Uploaded | Visibility | Actions |
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data.outcome.ZOE2_main_20200606.xlsx | 2022-05-20 | Public | Download |
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data.outcome.ZOE2_pilot_20200527.xlsx | 2022-05-20 | Public | Download |
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data_dictionary.xlsx | 2022-05-20 | Public | Download |
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CDR_ZOEmicro_20220521.zip | 2022-05-23 | Public | Download |