|
Status |
Public on Apr 17, 2024 |
Title |
Microbiota of Stool from subject HC_9 |
Sample type |
SRA |
|
|
Source name |
Stool
|
Organism |
Homo sapiens |
Characteristics |
tissue: Stool patient id: HC_9 condition: Healthy
|
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)
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|
|
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 EN47
|
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
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|
|
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 |
SAMN36944009 |
SRA |
SRX21337108 |