|
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 |