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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Feb 22, 2017 |
| Title |
Untreated_195 |
| Sample type |
SRA |
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| Source name |
Mammary gland tumor
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| Organism |
Mus musculus |
| Characteristics |
strain: p53R270HWAPCre mouse model
sequence sample id: 102392-49
tissue: mammary gland tumor
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| Treatment protocol |
Every other day these mice have been injected (subcutaneously) with either vehicle, insulin, glargine, X10 or IGF1 till tumor development.
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| Growth protocol |
8 week old female p53R270H/+WAPCre mice were obtained from an in house breeding project
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| Extracted molecule |
total RNA |
| Extraction protocol |
Once the tumors reached a size of 1 cm3 and 24 hours after their last injection the mice were sacrificed. Tumors and other tissues were isolated. ¼ of the tumor was stored in RNALater at 4 degrees Celsius for RNA isolation. A miRNA isolation kit was used to isolate and purify small and large RNA molecules in one fraction
The Ion Total RNA-Seq kit was used to process the samples. Samples were Poly-A selected prior to library preparation. This library preparation included the cDNA synthesis and purification steps with the Ion Total RNA-Seq kit v2 (Life Technologies, UK) according to manufacturer’s instructions. The Ion PI Template OT2 200 Kit v3 and Ion Sequencing 200 kit v3 (both, Life Technologies, UK) were used according to manufactures instructions for sequencing libraries on the PI chip
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
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| Data processing |
No additional trimming or filtering of reads was performed before processing. Raw data obtained in the .bam file format was converted to fastQ format.
Reads were aligned to mouse genome build GRCm38 - Ensembl using Tophat2 (Version 2.0.10).
Reads which could not be aligned using TopHat2 were aligned in an additional step, using Bowtie2 (Version 2-2.10) in the local, very sensitive mode.
Tophat2- and Bowtie2- aligned reads were merged into a single .bam file for each sample before further analysis
Gene expression was quantified using HTSeq-Count (Version 0.6.1), using the default options ( stranded = yes, mode = union).
Differential gene expression was analyzed for a. Insulin(n=10) versus untreated(n=10), b. Glargine(n=10) versus untreated(n=10), c. X10(n=10) versus untreated(n=10), d. IGF1(n=10) versus untreated(n=10)
differential expression analysis was performed using DESeq2 (Version1.2.10)
Coverage data for the 5 sample groups (Control and treatment) in the bigWig format
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file include RPKM values for each Sample
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| Submission date |
Feb 22, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Bas ter Braak |
| E-mail(s) |
basterbraak@gmail.com
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| Organization name |
Leiden University/LACDR
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| Department |
Toxicology
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| Street address |
Einsteinweg 55
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| City |
Leiden |
| State/province |
Zuid-Holland |
| ZIP/Postal code |
2333CC |
| Country |
Netherlands |
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| Platform ID |
GPL18635 |
| Series (1) |
| GSE78156 |
Next generation sequencing reveals increased glycolysis and biomass production rate in mammary gland tumors of mice chronically exposed to insulin analogue |
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| Relations |
| BioSample |
SAMN04506082 |
| SRA |
SRX1596261 |
| 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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