|
| Status |
Public on Sep 20, 2023 |
| Title |
Microbiota of adrenal gland from subject H7 |
| Sample type |
SRA |
| |
|
| Source name |
Adrenal gland
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Adrenal gland
gender: F
age: 23
condition: Healthy
acc stage: Healthy
secretion: None
fastq id: ML25
sequencing batch: 2_o
|
| 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)
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
16s rRNA v3-v4 sequencing of human adrenal gland biopsy
|
| 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 7 --o-trimmed-sequences trimmed-seqs.qza --p-discard-untrimmed --p-minimum-length 100 --verbose
qiime demux summarize --i-data trimmed-seqs.qza --o-visualization demux.qzv
qiime dada2 denoise-paired --i-demultiplexed-seqs trimmed-seqs.qza --p-trim-left-f 0 --p-trim-left-r 0 --p-trunc-len-f 275 --p-trunc-len-r 168 --o-table table.qza --o-representative-sequences rep-seqs.qza --o-denoising-stats denoising-stats.qza --p-n-threads 7
bowtie2 -x ~/GRCh38_noalt_as -U filtered_dna-sequences.fasta -S bowtie2_SAM_output.txt -f -p 4
qiime feature-classifier classify-sklearn --i-classifier SILVA_138_V3V4_BayesClassifier.qza --i-reads filtered_dna-sequences.qza --o-classification taxonomy.qza
R software (see the relative script publicly available at github.com/LeandroD94)
Assembly: NA
Supplementary files format and content: filtered_dna-sequences.fasta: text containing every processed ASV code and sequence retained after off-target reads decontamination
Supplementary files format and content: feature_table.csv: CSV text file containing the abundance table (after off-target reads decontamination)
Supplementary files format and content: taxonomy.tsv: TSV text file containing the complete taxonomic classification of the reference sequences
Library strategy: paired-end (2x300) amplicon sequencing
|
| |
|
| Submission date |
Mar 28, 2023 |
| Last update date |
Sep 20, 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) |
| GSE228424 |
Comparing the adrenal gland microbiota composition between healthy subjects and patient with adrenal corticoma |
|
| Relations |
| BioSample |
SAMN33956802 |
| SRA |
SRX19800255 |
