|
| Status |
Public on Dec 11, 2013 |
| Title |
Sample_A3 |
| Sample type |
SRA |
| |
|
| Source name |
Exponentially growing
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF-7
cell type: breast cancer
|
| Growth protocol |
MCF-7 cells were either maintained in Dulbecco’s modified Eagle medium (DMEM) supplemented with 10% FBS, antibiotics (100U/ml penicillin, 100mg/ml streptomycin, 250ng/ml Amfotericin-B), 50µg/ml G418 (standard growth conditions) or hormone deprived (starvation). Starvation was performed by culturing in DMEM w/o phenol red and 5% Dextran Coated Charcoal stripped serum (DCC-FBS) for 5 days, as described earlier.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from MCF-7 wt using the standard RNA Extraction method with TRI Reagent (Sigma) method. 7.5μg of total RNA was used in a library preparation according to the Illumina TruSeq small RNA sample preparation protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Basecalls was performed using CASAVA version 1.8
Adapter sequence was removed using PERL script named "Adapter_trim.pl" downloaded from miRTools and held in iMir package.
To predict novel miRNAs iMir uses miRDeep2, while miRAnalyzer version 0.3 was used for the identification of known miRNAs.
Differential expression analisys of known miRNAs was done using DESEQ 1.0.6 package from R Bioconductor setting a p-value ≤ 0.05 and a fold-change ≤-1.5 and ≥1.5
Target prediction was performed using Target Scan and microRNA.org.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files represent known mature miRNAs. They were generated using miRAnalyzer version 0.3 and then filtered for readcount cut-off ≥5.
|
| |
|
| Submission date |
Sep 05, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Maria Rosaria De Filippo |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Salerno
|
| Street address |
Via Allende 1
|
| City |
Baronissi |
| ZIP/Postal code |
84081 |
| Country |
Italy |
| |
|
| Platform ID |
GPL10999 |
| Series (1) |
| GSE40617 |
iMir: An integrated pipeline for high-throughput miRNA-Seq data analysis |
|
| Relations |
| SRA |
SRX183071 |
| BioSample |
SAMN01162135 |
