|
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: 81 Sex: F condition: CRC crc site: Ascending colon crc sex: Adenocarcinoma, NOS tumor grading: G2 tumor stage: pT4aN2b
|
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
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|
|
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
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|
|
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 |
SAMN31456017 |
SRA |
SRX18027153 |