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Sample GSM1679001 Query DataSets for GSM1679001
Status Public on Dec 08, 2016
Title TUBO, replicate #3
Sample type SRA
 
Source name Murine cell line
Organism Mus musculus
Characteristics source: Mouse breast cancer cell line derived from primary tomors of Balb-NeuT
Treatment protocol None
Growth protocol Cells were cultured in DMEM, 10% FCS mediume
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using TRIzol reagent (Life Technologies) following the manufacturer’s recommendations.
In short, an adenylated adapter was ligated to the 3’ end of the total RNA by a truncated T4 RNA Ligase 2, followed by the ligation of a 5’ RNA-adapter by T4 RNA Ligase 1 (NEB). After reverse-transcription using a specific primer, the cDNA was amplified by PCR. After gel-fractionation bands corresponding to miRNA inserts were cut out. PCR products from these bands were eluted in elution buffer, precipitated and dissolved in water. The quality of the libraries was assessed by qPCR and Bioanalyzer measurements.
 
Library strategy miRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina MiSeq
 
Description small RNA sequencing data
Data processing MiSeq analysis pipeline: MCS 2.4.1, RTA 1.18.54, MSR 2.4.60
Following data analysis was completely done using custom scripts:
3' adapter and not reliable parts of the reads were trimmed
Remaining read-sequences with at least 18 nt were mapped to murine miRNAs listed in miRBase (version 20). In this mapping no mismatches were allowed.
Annotated reads were normalized as RPM-values regarding the total number of annotated miRNA-reads
Calculation of additional statistical values for comparison of triplicate samples (mean RPM values, log2-foldchanges, p-values)
Genome_build: miRBase 20
Supplementary_files_format_and_content: tab-delimited TXT-file; trimmed read sequence followed by a tab and the number of reads
Supplementary_files_format_and_content: MS Excel-file; tab1: annotated normalized reads (mean RPM, CV), tab2: annotated log2-folds, p-values (t-test), FDR-adjusted p-values for MM3MG-Her2 vs. MM3MG comparison
 
Submission date May 08, 2015
Last update date May 15, 2019
Contact name Christoph Andreas Klein
Organization name University of Regensburg
Department Experimental Medicine and Therapy Research
Street address Franz-Josef-Strauß-Allee 11
City Regensburg
State/province Bavaria
ZIP/Postal code 93053
Country Germany
 
Platform ID GPL16417
Series (2)
GSE68682 Cell density, Her2 and progesterone signaling regulate dissemination of breast cancer cells [miRNA-Seq]
GSE68683 Cell density, Her2 and progesterone signaling regulate dissemination of breast cancer cells
Relations
BioSample SAMN03649099
SRA SRX1022060

Supplementary file Size Download File type/resource
GSM1679001_TUBO1_3.txt.gz 353.7 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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