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Sample GSM6850244 Query DataSets for GSM6850244
Status Public on Jun 08, 2023
Title RB39050
Sample type SRA
 
Source name Peptide affinity captured plasma extracellular RNA
Organism Homo sapiens
Characteristics condition: PDAC
Extracted molecule total RNA
Extraction protocol miRVana miRNA isolation kit
CleanTag Small RNA library prep kit
 
Library strategy ncRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Ion Torrent Proton
 
Data processing Raw reads from sRNAseq were processed with the Torrent Suite Software (v5.4.0), which runs the Torrent Mapping Alignment Program (TMAP).
Fastq's adapters removal and quality trimming with TrimGalore (v 0.6.5).
Alignment was performed using STAR (version 2.7.0f) to the human genome GRCh38 version
Reads Counts performed using Derfinder (version 1.18.9) in R(v3.4.1)
Counts normalized with TMM and differential expression analysis was performed using the Bioconductor package edgeR (v3.18.1)
Assembly: Human genome GRCh38
Supplementary files format and content: Raw reads counts in a csv (or tsv) format
 
Submission date Dec 16, 2022
Last update date Jun 08, 2023
Contact name Eric P Allain
E-mail(s) eric.allain@vitalitenb.ca
Phone 5068697347
Organization name Vitalité Health Network
Department Medical Genetics
Lab Bioinformatics
Street address 330 University ave
City Moncton
State/province New Brunswick
ZIP/Postal code E1C 2Z3
Country Canada
 
Platform ID GPL17303
Series (1)
GSE221185 Small RNA sequencing analysis of peptide-affinity isolated plasma extracellular vesicles distinguishes pancreatic cancer patients from non-affected individuals
Relations
BioSample SAMN32277937
SRA SRX18737546

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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