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| Status |
Public on Dec 08, 2016 |
| Title |
MM3MG, replicate #3 |
| Sample type |
SRA |
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| Source name |
Murine cell line
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| Organism |
Mus musculus |
| Characteristics |
source: MM3MG is a normal mammary epithelial cell line from BALB/c mouse strain
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| Treatment protocol |
None
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| Growth protocol |
Cells were cultured in DMEM, 10% FCS mediume
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| 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.
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina MiSeq |
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| Description |
small RNA sequencing data
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| 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
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| Submission date |
May 08, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Christoph Andreas Klein |
| Organization name |
University of Regensburg
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| Department |
Experimental Medicine and Therapy Research
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| Street address |
Franz-Josef-Strauß-Allee 11
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| City |
Regensburg |
| State/province |
Bavaria |
| ZIP/Postal code |
93053 |
| Country |
Germany |
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| 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 |
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| Relations |
| BioSample |
SAMN03649090 |
| SRA |
SRX1022051 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1678992_MM3MG_3.txt.gz |
193.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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