|
| Status |
Public on Feb 06, 2018 |
| Title |
HD_MCF7_siCTR_Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
HD_MCF7_siCTR
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF-7
cell type: breast cancer cell line
transfected with: siCTR
|
| Treatment protocol |
MCF-7 cells were grown 4 days in this media before being transfected with siRNAs using Lipofectamine2000 (Life Technologies), according to the reverse transfection protocol. Stealth RNAi™ siRNAs from Invitrogen were used to target ERα mRNA (ESR1HSS103376, ESR1HSS103377, ESR1HSS176619); stealth RNAi™ siRNA Negative Control medium GC was used as a control (siCTR).
|
| Growth protocol |
MCF-7 were growth in hormone-depleted (HD) media obtained from phenol red-free DMEM supplemented with 5% charcoal-dextran-treated serum.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
The starting RNA-seq datasets were obtained from libraries generated with the TruSeq stranded library preparation kit (Illumina) using as input material polyA(+) RNA fraction.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
siRNA_CTRL_1
Sample_siRNA_CTRL_A
|
| Data processing |
Raw RNA-Seq reads were aligned using using TopHat v2. Gencode v24 was used as reference set of gene annotations and hg38 as referenge genomic sequence.
Read count was performed using featureCounts algorithm in default settings and read count tables were normalized with DESeq2 package.
Differentially expression between siCTR and siERα-treated MCF-7 was performed using DESeq2 in default settings.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include the normalized read counts for each sample
|
| |
|
| Submission date |
Jan 03, 2018 |
| Last update date |
Feb 06, 2018 |
| Contact name |
Giulio Ferrero |
| Organization name |
University of Turin
|
| Department |
Dept. Clinical and Biological Sciences
|
| Street address |
Regione Gonzole, 10
|
| City |
Orbassano |
| State/province |
TO |
| ZIP/Postal code |
10043 |
| Country |
Italy |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE108693 |
Luminal lncRNAs Regulation by ERα-controlled Enhancers in a Ligand-independent Manner in Breast Cancer Cells |
|
| Relations |
| BioSample |
SAMN08287201 |
| SRA |
SRX3527676 |
