|
| Status |
Public on Oct 15, 2023 |
| Title |
Microbiota of Stool from patient HPV+10 |
| Sample type |
SRA |
| |
|
| Source name |
Stool
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Stool
patient id: HPV+10
time: 83
Sex: F
condition: CRC+HPV
crc site: Descending colon
crc sex: Adenocarcinoma, NOS
tumor grading: G3
tumor stage: pT3N2b
|
| 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 |
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
|
| Data processing |
from raw to demultiplexed fastq files please contact IGA Technology Services (Udine, Italy)
qiime cutadapt trim-paired --i-demultiplexed-sequences demux-paired-end.qza --p-front-f CCTACGGGNGGCWGCAG --p-front-r GACTACNVGGGTWTCTAATCC --p-cores 8 --o-trimmed-sequences trimmed-seqs.qza --p-discard-untrimmed --verbose >Log_di_cutadapt.txt
qiime demux summarize --i-data trimmed-seqs.qza --o-visualization demux.qzv --p-n 500000
qiime dada2 denoise-paired --i-demultiplexed-seqs trimmed-seqs.qza --p-trim-left-f 0 --p-trim-left-r 0 --p-trunc-len-f 261 --p-trunc-len-r 198 --o-table table.qza --o-representative-sequences rep-seqs.qza --o-denoising-stats denoising-stats.qza --p-n-threads 8
qiime feature-classifier classify-sklearn --i-classifier SILVA_138_V3V4_BayesClassifier.qza --i-reads rep-seqs.qza --o-classification taxonomy.qza
R software (see the relative script publicly available at github.com/LeandroD94)
Assembly: NA
Supplementary files format and content: rep_sequences.fasta: representative ASV sequences in fasta fomat (sequence names correspond to row names of the feature_table.tsv file)
Supplementary files format and content: feature_table.tsv: TSV text file containing the abundance table
Supplementary files format and content: taxonomy.tsv: TSV text file containing the complete taxonomic classification of the reference sequence
|
| |
|
| Submission date |
Oct 26, 2022 |
| Last update date |
Oct 15, 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) |
| GSE216589 |
Comparing the microbiota composition between HPV positive and negative patients with CRC |
|
| Relations |
| BioSample |
SAMN31456027 |
| SRA |
SRX18027143 |
