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Sample GSM3104682 Query DataSets for GSM3104682
Status Public on Feb 12, 2019
Title V-RAS rep2
Sample type SRA
Source name fibroblast tumor
Organism Mus musculus
Characteristics tissue: fibroblast tumors
genotype: control
Growth protocol Early passage wild-type Mouse Embryo Fibroblasts (MEF) were immortalized with shp53, then retrovirally transduced with a SIX1 expression vector and the corresponding empty vector, and finally infected with a vector expressing Ha-RASV12. Transformed fibroblasts with or without SIX1 overexpression (SIX1-RAS or V-RAS respectively) were injected subcutaneously in athymic nude (Foxn1nu/Foxn1nu) mice. Fourteen days after the injection (or when the tumors reached the maximum allowed size) the mice were euthanized and the tumors were excised, weighed and processed for RNA extraction. Total RNA from three tumors of each genotype was used for RNASeq analysis.
Extracted molecule total RNA
Extraction protocol Tumors were removed, flash frozen on dry ice, and RNA was prepared using Trizol reagent. 1 ug of total RNA was used for construction of sequencing libraries.
PolyA+ fraction was purified and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments using Illumina's TruSeq Stranded Library Prep Kit. Adapter-ligated library was completed by PCR with Illumina PE primers.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
Data processing Image analysis, per-cycle basecalling and quality score assignment was performed with Illumina Real Time Analysis software
Illumina BCL files were converted to bam format with Illumina2bam
Sequencing reads were aligned to the transcriptome with Tophat, and alignment data were quantitated with HTSeq
Differential gene expression analysis was performed with DESeq
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Tab-delimited text file includes non-normalized read counts calculated with HTSeq and RPM (reads per million) for each sample.
Submission date Apr 19, 2018
Last update date Mar 15, 2022
Contact name Ignacio Palmero
Organization name CSIC
Street address Arturo Duperier, 4.
City Madrid
State/province Madrid
ZIP/Postal code 28029
Country Spain
Platform ID GPL17021
Series (1)
GSE113385 Gene expression profiling in mouse fibroblast tumors with overexpression of the homeoprotein SIX1
BioSample SAMN08956259
SRA SRX3972596

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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