|
| Status |
Public on Jun 08, 2023 |
| Title |
RB38502 |
| 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 |
SAMN32277945 |
| SRA |
SRX18737538 |
