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Series GSE255317 Query DataSets for GSE255317
Status Public on May 07, 2024
Title Study of microbial species in extracellular vesicles of sclerosis multiple patients
Organisms Lactobacillus acidophilus; Homo sapiens; synthetic construct; Bifidobacterium animalis subsp. lactis
Experiment type Expression profiling by high throughput sequencing
Summary Extracellular vesicles (EVs) are released by most cell types and are implicated in several biological and pathological processes, including multiple sclerosis (MS). In this study we performed RNA sequencing to analyze the diversity of microorganisms by assignment of reads using different taxa profilers. To diminish the risk of false positive biases derived from sample handling, we performed a similar analysis on EVs derived from known cultured bacterial species, as well as artificially-generated samples. Overall, we detect a range of microbial species in MS and healthy control (HC) samples, that are not detected in control samples, as well as species with differential abundance between MS and HC samples. These results reveal the relevance of putative communication of microbial species using EVs as a communication vector.
 
Overall design Peripheral blood from 20 MS patients and 10 HC was collected by venipuncture in EDTA tubes and centrifuged to separate the plasma from the cellular fraction. Additionally, cultured samples of from L. acidophilus and B. lactis were also retrieved.
To isolate EVs, plasma aliquots were double-centrifuged to pellet EVs. The pellet was then resuspended with 100 µL of DPBS, and RNA was isolated using Trizol LS.
Lastly, samples were pooled to fulfil a minimum input of 2 ug of RNA. rRNA was depleted from the total RNA sample and cDNA libraries were built. Paired-end sequencing was performed with Illumina HiSeq X Ten with an average of 40–50 × 10^ reads obtained per sample.
 
Contributor(s) Ascensión AM, Iparraguirre L, Alberro A, Moles Alegre L, Otaegui D
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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
 
Platforms (4)
GPL20795 HiSeq X Ten (Homo sapiens)
GPL26697 HiSeq X Ten (synthetic construct)
GPL34171 HiSeq X Ten (Lactobacillus acidophilus)
Samples (15)
GSM8069007 Pool1 RRMS
GSM8069008 Pool2 RRMS
GSM8069009 Pool3 RRMS
Relations
BioProject PRJNA1074665

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE255317_salmon.merged.gene_counts.csv.gz 1.1 Mb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA

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