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Sample GSM8069021 Query DataSets for GSM8069021
Status Public on May 07, 2024
Title Artificial sample
Sample type SRA
 
Source name In silico
Organism synthetic construct
Characteristics tissue: In silico
disease state: Sample control
Extracted molecule total RNA
Extraction protocol The concentration and quality of the RNA pools was measured using Bioanalyzer 2100 instrument (Agilent Technologies, Santa Clara, CA, USA) before library preparation at CD Genomics (Shirley, New York, NY, USA). After normalization, rRNA was depleted from the total RNA sample using the Ribo-Zero rRNA removal kit (Illumina, San Diego, CA, USA) and followed by purification and fragmentation steps.
Strand-specific cDNA synthesis was performed, the 3′ ends were adenylated, and adaptors were ligated. The resulting libraries were subjected to standard quality control and normalization processes. Paired-end sequencing was performed with Illumina HiSeq X Ten (Illumina, San Diego, CA, USA), and an average of 40–50 × 10^6 reads were obtained per sample.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
Description ARTIFICIAL
Homo sapiens, Cutibacterium acnes, Dietzia maris, Bifidobacterium bifidum, Lactobacillus acidophilus, Bacteroides fragilis, Roseburia intestinalis, Stenotrophomonas maltophilia, Sphingomonas paucimobilis, Taylorella equigenitalis, Kinneretia asaccharophila, Aspergillus chevalieri, Malassezia restricta, Saccharomyces cerevisiae, Plenodomus lingam, Alternaria alternata, Burzaovirus, Elvirus, Lentivirus, Nickievirus, Lymphocryptovirus
Data processing Reads from samples were mapped to human references twice. A first map was performed using GRCh38 (Ensembl version 109) using nf-core/rnaseq v3.12.0 module, with STAR v2.7.9a as mapper. Unmapped reads were again mapped, this time using bowtie2 v2.4.5 with --very-sensitive argument and CHM13 genome version.
Unmapped reads are then mapped using different profilers: kaiju, kraken2, krakenuniq and centrifuge. For each profiler, specific available databases were downloaded or constructed consisting, at least of human, archaeal, bacterial, viral and fungal genomes. After individual profiling was performed, taxpasta v0.3.0 was used to standardise the outputs of each profiler into a common format. Taxa lineages were cut at the genus level.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited file with raw counts per sample
 
Submission date Feb 08, 2024
Last update date May 07, 2024
Contact name Alex Martínez Ascensión
E-mail(s) alexmascension@gmail.com
Organization name Biogipuzkoa HRI
Street address P/ Doctor Begiristain
City Donostia
State/province Gipuzkoa
ZIP/Postal code 20014
Country Spain
 
Platform ID GPL26697
Series (1)
GSE255317 Study of microbial species in extracellular vesicles of sclerosis multiple patients
Relations
BioSample SAMN39875251
SRA SRX23571134

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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