|
| Status |
Public on Jun 14, 2023 |
| Title |
Tumor sample of female patient 7 |
| Sample type |
SRA |
| |
|
| Source name |
breast
|
| Organism |
Homo sapiens |
| Characteristics |
individual: F07
tissue: breast
Sex: F
disease state: tumor
|
| Treatment protocol |
NA
|
| Growth protocol |
NA
|
| 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)
paired-end (2x300) amplicon sequencing
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
FT07
|
| Data processing |
[demultiplexing} from raw data 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
[reads merging} micca merge -i *.hiqual.fastq -o merged.fastq -f fastq
[abundance table creation} 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 and figure production} R phyloseq package (see https://github.com/matteoramazzotti/papers/tree/main/2022breast)
Supplementary files format and content: otutable.txt, taxa.txt, otus.fasta
|
| |
|
| Submission date |
Sep 08, 2022 |
| Last update date |
Jun 14, 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 |
GPL15520 |
| Series (1) |
| GSE212891 |
Analysis of microbiota composition within breast tumor and healthy breast tissues in males and females |
|
| Relations |
| BioSample |
SAMN30724422 |
| SRA |
SRX17487024 |
