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Sample GSM6171895 Query DataSets for GSM6171895
Status Public on Jun 29, 2022
Title Bacteriota of stool from patient CH41
Sample type SRA
 
Source name Stool
Organism Homo sapiens
Characteristics condition: EGPA
Sex: F
major_organ_involvement: 1
digestives_symptoms: 0
anca: 0
severe_eosinophilia: 0
immunosuppression: 1
active_disease: 1
Growth protocol Sample were stored at -80°C
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 CH41
Data processing from raw to demultiplexed fastq files please contact IGA Technology Services (Udine, Italy)
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
qiime demux summarize --i-data trimmed-seqs.qza --o-visualization demux.qzv
qiime dada2 denoise-paired --i-demultiplexed-seqs trimmed-seqs.qza --p-trim-left-f 5 --p-trim-left-r 0 --p-trunc-len-f 227 --p-trunc-len-r 220 --o-table table.qza --o-representative-sequences rep-seqs.qza --o-denoising-stats denoising-stats.qza --p-n-threads 12
qiime dada2 denoise-paired --i-demultiplexed-seqs trimmed-seqs.qza --p-trim-left-f 0 --p-trim-left-r 0 --p-trunc-len-f 232 --p-trunc-len-r 211 --o-table table.qza --o-representative-sequences rep-seqs.qza --o-denoising-stats denoising-stats.qza
qiime feature-classifier classify-consensus-vsearch --i-query rep-seqs.qza --i-reference-reads silva-138-99-seqs.qza --i-reference-taxonomy silva-138-99-tax.qza --p-perc-identity 0.99 --p-threads 12 --o-classification assigned_taxa.qza –verbose
Library strategy: amplicon sequencing
 
Submission date May 20, 2022
Last update date Jun 29, 2022
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)
GSE203432 Exploring the microbiota pecularity in stool and biopsies of Eosinophilic Granulomatosis with Polyangiitis (EGPA) patients
Relations
BioSample SAMN28561557
SRA SRX15391322

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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