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Sample GSM4801423

Query DataSets for GSM4801423

Status

Public on Sep 25, 2020

Title

Osx-Cre;NT3 #18

Sample type

SRA

Source name

spontaneous trunk tumor

Organism

Mus musculus

Characteristics

tissue: spontaneous trunk tumor
Sex: female
tumor latency (days): 168

Treatment protocol

none

Growth protocol

spontaneous NT3-Tg driven tumor model

Extracted molecule

total RNA

Extraction protocol

Tumors were excised to remove any gross overlaying tissue, and either stored at -20C in RNAlater (R0901; Sigma, USA) or flash frozen in liquid nitrogen, and stored at -80C. Frozen tumors were pulverized in liquid nitrogen using a Mikro Dismembrator (Mikro‐Dismembrator S; B. Braun Biotech International, Melsungen, Germany), resuspended in TRIzol (15596026; Invitrogen, Carlsbad, CA, USA), and stored at –80°C. Total RNA was isolated using a Direct‐zol kit per the manufacturer’s instructions (R2072; Zymo Research, Irvine, CA, USA).
mRNA version 2 library prep kit (Illumina)

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2500

Data processing

Base calling was performed with the Illumina bcl2fastq
QC was performed on the FASTQ files using RSeQC software (http://rseqc.sourceforge.net/)
The paired end reads were aligned by TopHat 2.0.6
Gene counts were generated using HTseq (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include Raw counts and FPKM values for each gene per sample

Submission date

Sep 24, 2020

Last update date

Sep 25, 2020

Contact name

Asha Nair

E-mail(s)

nair.asha@mayo.edu

Organization name

Mayo Clinic

Street address

200 1ST ST SW