|
| Status |
Public on Jan 10, 2025 |
| Title |
NC, C10 |
| Sample type |
SRA |
| |
|
| Source name |
fecal matter (not tissue)
|
| Organism |
human feces metagenome |
| Characteristics |
tissue: fecal matter (not tissue)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Stool DNA extraction was performed according to the manufacturer’s protocol using a QiAamp DNA Stool Mini Kit (Qiagen). The extracted DNA was stored in 1X ATE buffer (10 mM Tris-Cl pH 8.3, 0.1 mM EDTA, and 0.04% NaN3) at -20°C for subsequent 16S rRNA-targeted sequencing.
PCR was performed using the forward primer 5′- TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG CCT ACG GGN GGC WGC AG-3′ and reverse primer 5′- GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GGA CTA CHV GGG TAT CTA ATC C-3′ for the V3–V4 region of the 16S rRNA gene. Amplicons generated from each sample (~ 330 bp) were purified using AMPure XP magnetic beads (Beckman Coulter).
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
Library name: C10_S84
|
| Data processing |
After demultiplexing the 16S sequence reads based on sample-specific indices, primer sequences were trimmed using Cutadapt v.1.15. The trimmed reads were then processed using the DADA2 R package v.1.18.0 to construct amplicon sequence variants (ASVs). This was achieved using the filterAndTrim function with the standard parameters (maxN = 0, truncQ = 2, and maxEE = 2). Possible chimeric reads were removed using the remote Bimera Denovo function of DADA2. Taxonomic assignment of each amplicon sequence variant (ASV) was performed by similarity searching against the Greengene v13.8 database with a threshold of 97% similarity. The rarefied feature table was then converted into the linear discriminant analysis effect size (LEfSe) format using tools available on Galaxy Hutlab (http://huttenhower.sph.harvard.edu/galaxy/) and MicrobiomeAnalyst (https://www.microbiomeanalyst.ca/MicrobiomeAnalyst/home.xhtml).
Supplementary files format and content: Excel, Phylum-, Genus- and Species-Level Taxonomy Tables
Library strategy: 16S rRNA-seq
|
| |
|
| Submission date |
Jan 06, 2025 |
| Last update date |
Jan 10, 2025 |
| Contact name |
Kuang-Den Chen |
| E-mail(s) |
dennis8857@gmail.com
|
| Organization name |
Kaohsiung Chang Gung Memorial Hospital
|
| Department |
Translational Research Center in Biomedical Sicences
|
| Lab |
Liver transplantation lab
|
| Street address |
123, Ta-Pei Rd., Niao-Sung Dist.
|
| City |
Kaohsiung |
| ZIP/Postal code |
83342 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL29470 |
| Series (1) |
| GSE285935 |
Eggerthella lenta Down Regulated Flavone and Flaconol Biosynthesis Promoted Kawasaki Disease |
|
| Relations |
| BioSample |
SAMN46106744 |
| SRA |
SRX27260011 |
