|
| Status |
Public on May 03, 2023 |
| Title |
Microbiota of Stool from patient SYN_12 PRE treatment [SF12] |
| Sample type |
SRA |
| |
|
| Source name |
Stool
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Stool
patient id: SYN_12
treatment time: PRE
treatment type: Placebo
condition: Obese
age: 67
gender: F
smoker: No
|
| Treatment protocol |
NA
|
| Growth protocol |
NA
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using the DNeasy PowerSoil Pro Kit (Qiagen, Hilden, Germany)
Illumina 16S Metagenomic Sequencing Library Preparation protocol ( see https://emea.support.illumina.com)
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
16s rRNA v3-v4 sequencing of human Stool
|
| Data processing |
library strategy: 16s rRNA v3-v4 paired-end (2x300) amplicon sequencing
demultiplexing: from raw to demultiplexed fastq files please contact IGA Technology Services (Udine, Italy)
primer check and trimming: qiime cutadapt trim-paired --i-demultiplexed-sequences demux-paired-end.qza --p-front-f CCTACGGGNGGCWGCAG --p-front-r GACTACNVGGGTWTCTAATCC --p-cores 7 --o-trimmed-sequences trimmed-seqs.qza --p-discard-untrimmed --p-minimum-length 100 --verbose >Log_di_cutadapt.txt
quality check: qiime demux summarize --i-data trimmed-seqs.qza --o-visualization demux.qzv
quality trimming, pair merging and ASV table creation: qiime dada2 denoise-paired --i-demultiplexed-seqs trimmed-seqs.qza --p-trim-left-f 0 --p-trim-left-r 0 --p-trunc-len-f 264 --p-trunc-len-r 179 --o-table table.qza --o-representative-sequences rep-seqs.qza --o-denoising-stats denoising-stats.qza --p-n-threads 7
taxonomic assignment: qiime feature-classifier classify-sklearn --i-classifier SILVA_138_V3V4_BayesClassifier.qza --i-reads rep-seqs.qza --o-classification taxonomy.qza
further analyses: R software (see the relative script publicly available at github.com/LeandroD94)
Assembly: NA
Supplementary files format and content: feature_table.csv: CSV text file containing the abundance table
Supplementary files format and content: taxonomy.tsv: TSV text file containing the complete taxonomic classification of the reference sequence
Supplementary files format and content: dna-sequences.fasta: txt file containing the ASV names and sequences
|
| |
|
| Submission date |
Jan 12, 2023 |
| Last update date |
May 03, 2023 |
| Contact name |
Matteo Ramazzotti |
| E-mail(s) |
matteo.ramazzotti@unifi.it
|
| Organization name |
University of Florence
|
| Department |
Experimental and Clinical Biomedical Sciences
|
| Street address |
viale Morgagni 50
|
| City |
Firenze |
| ZIP/Postal code |
50134 |
| Country |
Italy |
| |
|
| Platform ID |
GPL15520 |
| Series (1) |
| GSE222755 |
Survey of microbiota composition differences between obese subjects before and after Lactiplantibacillus plantarum probiotic treatment |
|
| Relations |
| BioSample |
SAMN32717688 |
| SRA |
SRX19017716 |
