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Sample GSM2068302 Query DataSets for GSM2068302
Status Public on Feb 22, 2017
Title glargine_78
Sample type SRA
 
Source name Mammary gland tumor
Organism Mus musculus
Characteristics strain: p53R270HWAPCre mouse model
sequence sample id: 102392-20
tissue: mammary gland tumor
Treatment protocol Every other day these mice have been injected (subcutaneously) with either vehicle, insulin, glargine, X10 or IGF1 till tumor development.
Growth protocol 8 week old female p53R270H/+WAPCre mice were obtained from an in house breeding project
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
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Ion Torrent Proton
 
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
 
Submission date Feb 22, 2016
Last update date May 15, 2019
Contact name Bas ter Braak
E-mail(s) basterbraak@gmail.com
Organization name Leiden University/LACDR
Department Toxicology
Street address Einsteinweg 55
City Leiden
State/province Zuid-Holland
ZIP/Postal code 2333CC
Country Netherlands
 
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
Relations
BioSample SAMN04506068
SRA SRX1596232

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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