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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Feb 12, 2019 |
| Title |
V-RAS rep2 |
| Sample type |
SRA |
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| Source name |
fibroblast tumor
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| Organism |
Mus musculus |
| Characteristics |
tissue: fibroblast tumors
genotype: control
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| 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.
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| 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.
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| Submission date |
Apr 19, 2018 |
| Last update date |
Mar 15, 2022 |
| Contact name |
Ignacio Palmero |
| E-mail(s) |
ipalmero@iib.uam.es
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| Organization name |
CSIC
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| Street address |
Arturo Duperier, 4.
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| City |
Madrid |
| State/province |
Madrid |
| ZIP/Postal code |
28029 |
| Country |
Spain |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE113385 |
Gene expression profiling in mouse fibroblast tumors with overexpression of the homeoprotein SIX1 |
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| Relations |
| BioSample |
SAMN08956259 |
| SRA |
SRX3972596 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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