|
| Status |
Public on Sep 03, 2021 |
| Title |
cells_OS-2_B |
| Sample type |
SRA |
| |
|
| Source name |
RNA from cells
|
| Organism |
Canis lupus familiaris |
| Characteristics |
source: Cell line OS-2
cell line: OS-2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Exosome enrichment was performed with ExoQuick reagent.
RNA was extracted with SeraMir ExoRNA Amp kit.
Library prep was performed with Clontech SMARTer Stranded Total RNA-seq Kit v2 - Pico Input Mammalian Kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
50bp paired-end sequencing RNAseq was performed on the Illumina HiSeq 2500.
Initial quality control analysis of RNA sequencing FASTQ data was performed using FastQC software (v0.11.5).
FASTQ data were trimmed with Trimmomatic (v0.33.0).
Kallisto (v0.43.0) was used for pseudoalignment and quantifying transcript abundance.
For alignment of sequencing reads to canine and murine genes, a kallisto index was built from a multi-sequence FASTA file containing both the canine (CanFam3.1) and murine (GRCm38.p5) genomes
Genome_build: CanFam3.1 and GRCm38.p5
|
| |
|
| Submission date |
Sep 01, 2021 |
| Last update date |
Sep 03, 2021 |
| Contact name |
Lauren Mills |
| E-mail(s) |
ljmills@umn.edu
|
| Phone |
6126241540
|
| Organization name |
University of Minnesota
|
| Department |
Department of Pediatrics
|
| Street address |
420 Delaware St SE
|
| City |
Minneapolis |
| State/province |
MN |
| ZIP/Postal code |
55455 |
| Country |
USA |
| |
|
| Platform ID |
GPL20988 |
| Series (2) |
| GSE183189 |
Development of an exosomal gene signature to detect residual disease in dogs with osteosarcoma using a novel xenograft platform and machine learning [canine data] |
| GSE183191 |
Development of an exosomal gene signature to detect residual disease in dogs with osteosarcoma using a novel xenograft platform and machine learning |
|
| Relations |
| BioSample |
SAMN21170525 |
| SRA |
SRX11983718 |
