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Sample GSM7706736 Query DataSets for GSM7706736
Status Public on Apr 17, 2024
Title Microbiota of Stool from subject RCC_3
Sample type SRA
 
Source name Stool
Organism Homo sapiens
Characteristics tissue: Stool
patient id: RCC_3
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 Stool
feature_abundance_table.tsv
FL5
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 SAMN36943993
SRA SRX21337124

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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