|
| Status |
Public on Nov 22, 2021 |
| Title |
non inflamed sample S17 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: notInflamed
surgery: first
patient: 10
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 a healthy gut portion of patient 10 affected by Crohn's disease
S17
|
| 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 |
SAMN17025373 |
| SRA |
SRX9649149 |
