|
| Status |
Public on Feb 21, 2014 |
| Title |
MCF-7 C3 |
| Sample type |
SRA |
| |
|
| Source name |
MCF-7_osteopontin-c
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF-7
tissue source: mammary gland
cell type: epithelial cells
transfected with: osteopontin-c
|
| Growth protocol |
To assess the osteopontin splice variant-induced protection from cell death or cell cycle arrest through deadhesion, we plated cells on 0.4 mg/mm2 poly-HEMA for 2 days. We then harvested them for gene expression analysis by RNASeq or metabonomic analysis by NMR.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
mRNA was extracted by TirReagent
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1000 |
| |
|
| Description |
Sample 9
|
| Data processing |
bcl files were demultiplexed and converted to fastq files using bcl2fastq in Casava 1.8
fastq seqences were aligned to mm10 using Tophat
number of reads was calculated for each Entrez gene
differential expression analysis was performed using Deseq
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited raw counts with genes in rows and samples in columns
|
| |
|
| Submission date |
Feb 20, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Mario Medvedovic |
| Organization name |
University of Cincinnati
|
| Department |
Department of Environmental Health
|
| Lab |
Laboratory for Statistical Genomics and Systems Biology
|
| Street address |
3223 Eden Av. ML 56
|
| City |
Cincinnati |
| State/province |
OH |
| ZIP/Postal code |
45267-0056 |
| Country |
USA |
| |
|
| Platform ID |
GPL15433 |
| Series (1) |
| GSE55193 |
Energy Metabolism during Anchorage-Independence |
|
| Relations |
| BioSample |
SAMN02646663 |
| SRA |
SRX474496 |
