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Sample GSM6600330

Query DataSets for GSM6600330

Status

Public on Jul 05, 2023

Title

T218, Tumor Sample 17

Sample type

SRA

Source name

Subcutaneous

Organism

Canis lupus familiaris

Characteristics

tissue: Subcutaneous
breed: Mix
disease: Soft tissue sarcoma
Sex: Female

Extracted molecule

total RNA

Extraction protocol

TRIzol (Invitrogen), was used to extract total RNA from 29 primary tumors. The RNA samples were cleaned using RNeasy cleanup (Qiagen), respectively. RNA was quantified on a NanoDrop Microvolume Spectrophotometer and quality was assessed by Bioanalyzer (Agilent).
The total RNA extracted from 29 samples were processed using Universal Plus™ mRNA-Seq library preparation kit with NuQuant® (product number: 0520-A01), following manufacturer's protocol, and the resulting cDNA library was sequenced on Illumina NovaSeq6000 to generate

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NovaSeq 6000

Data processing

150 bp reads, Illumina raw reads were trimmed to remove adaptor and low-quality sequences (phred score <20) using Trimmomatic.
Trimmed sequence reads were mapped to CanFam3.1 genome using STAR aligner with default settings.
Read count extraction was done using HTSeq-Count tool and normalized using DESeq2.
Assembly: CanFam3.1
Supplementary files format and content: comma-separated csv file include raw count values for each tumor samples
Supplementary files format and content: comma-separated csv file include DESeq2 normalized counts for each tumor samples

Submission date

Sep 25, 2022

Last update date

Jul 05, 2023

Contact name

Sunetra Das

E-mail(s)

sdas@colostate.edu

Organization name

Colorado State University

Department

Clinical Sciences