|
| Status |
Public on Dec 28, 2023 |
| Title |
Skin of a patient affected by diffuse (anti Scl70/RNA Pol III) sclerodermia [C_21_D] |
| Sample type |
SRA |
| |
|
| Source name |
skin
|
| Organism |
human skin metagenome |
| Characteristics |
sample: C_21_D
disease type: diffuse
patientid: 21
|
| Growth protocol |
Stool, skin and saliva samples were collected and stored at -80°C
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA extraction with DNeasy PowerLyzer PowerSoil 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 |
16S V3-V4 sequencing of skin from patient 21 affected by diffuse systemic sclerosis
|
| Data processing |
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 5
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 merging: micca merge -i *.hiqual.fastq -o merged.fastq -f fastq
OTU table creation by clustering: micca 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/2022sclero)
Library strategy: paired-end amplicon sequencing
|
| |
|
| Submission date |
Apr 08, 2022 |
| Last update date |
Dec 28, 2023 |
| 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 |
GPL32156 |
| Series (1) |
| GSE200486 |
16S V3-V4 -based microbial profiling of stool, skin and saliva samples of patients affected by systemic sclerosis (SSc) |
|
| Relations |
| BioSample |
SAMN27478836 |
| SRA |
SRX14787057 |
