|
Status |
Public on Nov 22, 2021 |
Title |
non inflamed sample S16 from patient F |
Sample type |
SRA |
|
|
Source name |
16S rDNA amplicons
|
Organism |
human gut metagenome |
Characteristics |
tissue source: ileal mucosa patient diagnosis: Crohn's disease disease state: notInflamed surgery: first patient: 9 Sex: F
|
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 a healthy gut portion of patient 9 affected by Crohn's disease S16
|
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 |
SAMN17025374 |
SRA |
SRX9649148 |