|
| Status |
Public on May 29, 2024 |
| Title |
Microbiota of stool from mice AD18 |
| Sample type |
SRA |
| |
|
| Source name |
Stool
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Stool
treatment: DSS
genotype: WT
|
| 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 mice stool
|
| Data processing |
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 –verbose
quality check qiime demux summarize --i-data trimmed-seqs.qza --o-visualization demux.qzv --p-n 500000
ASV generation qiime dada2 denoise-paired --i-demultiplexed-seqs trimmed-seqs.qza --p-trim-left-f 5 --p-trim-left-r 0 --p-trunc-len-f 274 --p-trunc-len-r 174 --o-table table.qza --o-representative-sequences rep-seqs.qza --o-denoising-stats denoising-stats.qza --p-n-threads 6
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: dna-sequences.fasta: text containing every processed ASV code and sequence
Supplementary files format and content: Feature_table.tsv: TSV 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
Library strategy: 16s rRNA-seq
|
| |
|
| Submission date |
Jan 12, 2024 |
| Last update date |
May 29, 2024 |
| 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 |
GPL16417 |
| Series (1) |
| GSE253108 |
DSS-colitis induced in young age accelerates the onset of cognitive defects in Tg2576 mice, a model of Alzheimer disease |
|
| Relations |
| BioSample |
SAMN39423095 |
| SRA |
SRX23203454 |
