Table 1 List of datasets used on Cont-ID
From: Cont-ID: detection of sample cross-contamination in viral metagenomic data
Batch_ID | NB of samples | Host type | Extraction Method | Extraction kit | Library kit | Sequencing | Data link | Publication |
|---|---|---|---|---|---|---|---|---|
A (1) | 27 | Plant (Musa) | Total RNA extraction | RNeasy Plus Mini Kit (Qiagen, Venlo, Netherlands) | Stranded Total RNA library Prep Human/Mouse/Rat illumine CA, United States) & Ribo-Zero™ Plant Leaf Kit (illumine CA, United States) | Illumina NextSeq 500 2X150 | BioProject: PRJNA777477 samples starting with (1-XXX) | Wei et al., 2022 https://doi.org/10.1094/PHYTOFR-03-22-0030-FI |
B (2) | 20 | Plant (Musa) | Total RNA extraction | RNeasy Plus Mini Kit (Qiagen, Venlo, Netherlands) | Stranded Total RNA library Prep Human/Mouse/Rat illumine CA, United States) & Ribo-Zero™ Plant Leaf Kit (illumine CA, United States) | Illumina NextSeq 500 2X150 | BioProject: PRJNA777477 samples starting with (2-XXX) | Wei et al., 2022 https://doi.org/10.1094/PHYTOFR-03-22-0030-FI |
C (3) | 27 | Plant (Musa) | Total RNA extraction | RNeasy Plus Mini Kit (Qiagen, Venlo, Netherlands) | Stranded Total RNA library Prep Human/Mouse/Rat illumine CA, United States) & Ribo-Zero™ Plant Leaf Kit (illumine CA, United States) & TruSeq® Stranded Total RNA Library Prep Plant (illumine CA, United States) | Illumina NextSeq 500 2X150 | BioProject: PRJNA777477 samples starting with (3-XXX) | Wei et al., 2022 https://doi.org/10.1094/PHYTOFR-03-22-0030-FI |
D (5) | 25 | Plant (Musa) | Total RNA extraction | RNeasy Plus Mini Kit (Qiagen, Venlo, Netherlands) | TruSeq® Stranded Total RNA Library Prep Plant (illumine CA, United States) | Illumina NovaSeq 6000 2X150 | BioProject: PRJNA777477 samples starting with (5-XXX) | Wei et al., 2022 https://doi.org/10.1094/PHYTOFR-03-22-0030-FI |
E (6 sRNA) | 31 | Plant (Musa) | Total RNA extraction | RNeasy Plus Mini Kit (Qiagen, Venlo, Netherlands) | SMARTer smRNA-Seq Kit (Clonetech) | Illumina NovaSeq 6000 2X150 | BioProject: PRJNA777477 samples starting with (1sR-XXXX) | Wei et al., 2022 https://doi.org/10.1094/PHYTOFR-03-22-0030-FI |
F (5 dsRNA) | 9 | Plant (Musa) | Double stranded RNA | see article (Armelle Marais) | NEBNext Ultra II DNA library prep kit (New England BioLabs, US) | Illumina NovaSeq 6000 2X150 | BioProject: PRJNA777477 samples starting with (5ds-XXX) | Method: Marais et al., 2018 https://doi.org/10.1007/978-1-4939-7683-6_4 |
G (Queensland university of technology) | 5 | Plant (mix) | Total nucleic acid | Maxwell® Rapid Sample Concentrator instrument using SimplyRNA Tissue kit (AS1340, Promega) | TruSeq Stranded Total RNA | Illumina NovaSeq 6000 2X150 | BioProject: PRJNA752836 | Gauthier et al., 2022 https://doi.org/10.3390/BIOLOGY11020263 |
H | 49 | Human | Total nucleic acid + amplification | NucliSENS EasyMAG platform (bioMérieux, Marcy l’Etoile, France) | Nextera XT (Illumina, San Diego, CA, USA) | Illumina NextSeq 500 2X150 | bioproject: PRJNA494633 | Bal et al., 2018 https://doi.org/10.1186/S12879-018-3446-5 |
I | 25 | Human | Total nucleic acid | MagNAPure 96 DNA and Viral NA Small Volume Kit (Roche Diagnostics, Almere, the Netherlands) | EBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA) | Illumina HiSeq 4000 and NextSeq 500 depth: 10 million 2X150 | bioproject: PRJNA560243 | Boheemen et al., 2020 https://doi.org/10.1016/J.JMOLDX.2019.10.007 |
J | 55 | Human | Total nucleic acid | TRlzol LS reagent (Invitrogen, USA) | SMARTer® Stranded Total RNA-Seq Kit v2—Pico Input Mammalian (Takara Bio, USA) and the Trio RNA-Seq kit (NuGEN Technologies, USA) | Illumina HiSeq 2X150 | bioproject: PRJNA540900 | Li et al., 2020 https://doi.org/10.1038/s41598-020-60992-6 |