|
| Status |
Public on Apr 17, 2024 |
| Title |
Microbiota of Saliva from subject RCC_7 |
| Sample type |
SRA |
| |
|
| Source name |
Saliva
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Saliva
patient id: RCC_7
condition: RCC
|
| 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 Saliva
feature_abundance_table.tsv
FL14
|
| 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-adapter-f CCTACGGGNGGCWGCAG --p-adapter-r GACTACNVGGGTWTCTAATCC –o-trimmed-sequences trimmed-seqs.qza --p-discard-untrimmed --verbose
quality check: qiime demux summarize --i-data trimmed-seqs.qza --o-visualization demux.qzv
ASV generation: qiime dada2 denoise-paired --i-demultiplexed-seqs trimmed-seqs.qza --p-trim-left-f 0 --p-trim-left-r 0 --p-trunc-len-f 250 --p-trunc-len-r 204 --o-table table.qza --o-representative-sequences rep-seqs.qza --o-denoising-stats denoising-stats.qza --p-n-threads 8
host read decontamination: bowtie2 -x GRCh38_noalt_as -U dna-sequences.fasta --al eucar_contaminant_ASV.fasta -S bowtie2_SAM_output.txt -f -p 4 2> percentuals_aligned_bowtie2.txt
taxonomic assignment: qiime feature-classifier classify-sklearn --i-classifier SILVA_138_V3V4_BayesClassifier.qza --i-reads decontaminated_rep-seqs.qza --o-classification taxonomy.qza
further analyses: R software (see the relative script publicly available at github.com/LeandroD94)
Assembly: SILVA 138 (16S database)
Supplementary files format and content: dna-sequences.fasta: text containing every processed ASV code and sequence (already decontaminated through Bowtie2)
Supplementary files format and content: feature_abundance_table.tsv: TSV text file containing the abundance table
Library strategy: paired-end (2x300) amplicon sequencing
|
| |
|
| Submission date |
Aug 11, 2023 |
| Last update date |
Apr 17, 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 |
GPL15520 |
| Series (1) |
| GSE240646 |
First exploration of the altered microbial gut-lung axis in the pathogenesis of human refractory chronic cough |
|
| Relations |
| BioSample |
SAMN36944002 |
| SRA |
SRX21337115 |
