|
| Status |
Public on Nov 02, 2017 |
| Title |
NAF+LO(22RV1)-1 |
| Sample type |
SRA |
| |
|
| Source name |
normal associated human prostatic fibroblasts treated with large oncosomes
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: fibroblasts from surgical explants of patients diagnosed with benign prostatic hyperplasia
tissue: prostate
|
| Treatment protocol |
serum starved fibroblasts were exposed for 6h to vehiclle or 20ug/ml of cancer cell derived large oncosomes
|
| Growth protocol |
fibroblasts were maintained in culture in 10% FBS supplemented DMEM medium
|
| Extracted molecule |
total RNA |
| Extraction protocol |
samples were collected in Trizol and total RNA was extracted using the RNeasy Mini Kit (Qiagen). RNA concentration and quality were tested respectively with Nanodrop 8000 (Thermo Scientific) and 2100 Bioanalyzer (Agilent)
1 μg of total RNA per sample was used for library construction with the Illumina TruSeq stranded mRNA library preparation kit. Briefly streptavidin-coated magnetic beads were employed for poly-A mRNA selection and cDNA was synthesized from enriched and fragmented RNA using reverse transcriptase (Super-Script II, Invitrogen) and random primers. After conversion into double stranded DNA and PCR amplification the products were enriched for library preparation and purified using Agencourt AMPure XP beads (Beckman Coulter Genomics).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Raw reads obtained from RNA-Seq were aligned to the custom human GRCh38 transcriptome reference (http://www.gencodegenes.org) using Bowtie (version 1.1.1)65 and RSEM (version 1.2.20)66 with default parameters.
Expression counts for each gene, fragments per kilobase of transcript per million (FPKM), in all samples were normalized by the sequencing depth.
Genome_build: GRCh38
Supplementary_files_format_and_content: FPKM
|
| |
|
| Submission date |
Oct 03, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Sungyong You |
| Organization name |
Cedars-Sinai Medical Center
|
| Street address |
8700 Beverly Blvd
|
| City |
Los Angeles |
| ZIP/Postal code |
90048 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE87563 |
RNAseq of normal associate fibroblasts after treatment with large oncosomes from prostate cancer cells |
|
| Relations |
| BioSample |
SAMN05859551 |
| SRA |
SRX2207934 |
