|
| Status |
Public on Dec 07, 2016 |
| Title |
control 8h rep2 |
| Sample type |
SRA |
| |
|
| Source name |
TRAMP-C2_control 8h
|
| Organism |
Mus musculus |
| Characteristics |
cell line: TRAMP-C2
cell type: mouse prostate cancer cells
passages: five to six
treated with: solvent (ethanol control) for 8hrs
|
| Treatment protocol |
For sutherlandia and Hh-CM treatment, cells are plated in 60mm petri dishes until confluent; TRAMPC2 cells are treated with ethnol control, 8ug/ml suterlandia extrat, 80ug/ml sutherlandia extract, Hh-CM, 8ug/ml suterlandia extrat+Hh-CM, 80ug/ml sutherlandia extract+Hh-CM for 8hr or 24 hr.
|
| Growth protocol |
TRAMPC2 cells were obtained from the American Type Culture Collection (ATCC). TRAMPC2 cells are cultured in RPMI1640 media with DHT and insulin(Invitrogen, Grand Island, NY) with 10% Fetal Bovine Serum (FBS) (GE Healthcare Life Sciences, Logan, Utah). 70% confluent TRAMPC2 cells were treated with indicated treatment.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted using Rneasy kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
TC2_2_ctrl_8h
TC2_2_ACTTGA_L001_R1_001.tar.gz
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequencing adaptor seuqence were trimmed off, then low qualtiy basecall was trimmed off, at last, low qualtiy sequence reads were filtered out.
Short sequencing reads were aligned to mus musculus genome mm9, gene expression value is quantified as raw read.
Differentially gene expression was analyzed using EdgeR
Genome_build: mm9
Supplementary_files_format_and_content: csv, raw gene expression read
|
| |
|
| Submission date |
Dec 07, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Yuan Lu |
| Organization name |
Xiphophorus Genetic Stock Center
|
| Street address |
university drive
|
| City |
San Marcos |
| State/province |
TX |
| ZIP/Postal code |
78666 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE75760 |
Sutherlanida extract inhibits Hedgehog signaling target genes |
|
| Relations |
| BioSample |
SAMN04323298 |
| SRA |
SRX1467123 |
