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Sample GSM4962785 Query DataSets for GSM4962785
Status Public on Nov 22, 2021
Title inflamed gut sample S28 from patient M
Sample type SRA
 
Source name 16S rDNA amplicons
Organism human gut metagenome
Characteristics tissue source: ileal mucosa
patient diagnosis: Crohn's disease
disease state: Inflamed
surgery: relapse
patient: 1
Sex: M
Treatment protocol isolation of 8 slices of 10 um from paraffin embedded gut tissue for each sample
Extracted molecule genomic DNA
Extraction protocol deparaffinatin with xylene followed by DNA extration with QIAamp DNA FFPE tissue kit (QIAGEN)
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 V3-V4 sequencing of a FFPE specimen from an inflamed gut portion of patient 1 affected by Crohn's disease
S28
Data processing Library strategy: 16S rDNA Metagenomic Sequencing
demultiplexing: from raw to demultiplexed fastq files please contact IGA Technology Services (Udine, Italy)
pair merging: micca mergepairs -i pair1.fastq -r pair2.fastq -o out.joined.fastq -l 30 -d 3
primer check and trimming: micca trim -i out.joined.fastq -o out.trimmed.fastq -w CCTACGGGNBGCWSCAG -r GACTACHVGGGTATCTAATCC -W -R -c
quality check: micca filter -i out.trimmed.fastq -o out.hiqual.fastq -e 0.5 -m 350 -f fastq
read mergingmicca merge -i *.hiqual.fastq -o merged.fastq -f fastq
OTU table creation by clusteringmicca otu -m denovo_greedy -i merged.fasta -o otudata -d 0.97 -c -t 20
taxonomic assignment (RDP)micca classify -m rdp -i otudata/otus.fasta -o otudata/taxa.txt
further analyses: R phyloseq package (see https://github.com/matteoramazzotti/papers/tree/main/2020crohn)
otu.fasta includes the longest sequence for each OTU that is the source for taxonomy assignment.
 
Submission date Dec 08, 2020
Last update date Nov 22, 2021
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 GPL29483
Series (1)
GSE162844 16S V3-V4 -based microbial profiling of matched healthy and inflamed ileal mucosa from patients affected by Crohn’s disease
Relations
BioSample SAMN17025372
SRA SRX9649150

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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