|
| Status |
Public on Aug 01, 2019 |
| Title |
3_Pten_Smad4_replicate3 |
| Sample type |
SRA |
| |
|
| Source name |
RNA-Seq of mus musculus prostate cancer
|
| Organism |
Mus musculus |
| Characteristics |
cell line: Pten Smad4
strain: FVB
tissue: Mouse prostate cancer primary site
age: 33 weeks
genotype: Pten[PC-/-]Smad4PC[-/-]
|
| Growth protocol |
Pten Smad4 cells are grown in DMEM 10% FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA are extracted by Maxwell® RSC simplyRNA Cells Kit.
Oligo (dT) magnetic beads are used to select mRNA with polyA tail, or hybridize the rRNA with DNA probe and digest the DNA/RNA hybrid strand, followed by DNase I reaction to remove DNA probe. Then obtain the target RNA after purification. 2) Fragment the target RNA and reverse transcription to doublestrand cDNA (dscDNA) by N6 random primer. 3) End repair the dscDNA with phosphate at 5' end and stickiness 'A' at 3' end, then ligate and adaptor with stickiness 'T' at 3' end to the dscDNA. 4) Two specific primers are used to amplify the ligation product. 5) Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase. 6) Perform sequencing on prepared library.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Description |
RNASeq_PTEN Smad4.txt
|
| Data processing |
Raw reads were quality-checked and subsequently mapped to the human genome (hg19) using Tophat2 (2.2.4) using default settings.
Differential gene expression was analyzed using the DESeq2 (1.8.1) package in R using default settings
Genome_build: hg19
Supplementary_files_format_and_content: txt
|
| |
|
| Submission date |
May 28, 2019 |
| Last update date |
Aug 01, 2019 |
| Contact name |
Filippo Giancotti |
| E-mail(s) |
[email protected]
|
| Organization name |
UT MD Anderson Cancer Center
|
| Department |
Cancer Biology
|
| Lab |
Dr. Giancotti Lab
|
| Street address |
1881 East Road
|
| City |
Houston |
| State/province |
Texas |
| ZIP/Postal code |
77054 |
| Country |
USA |
| |
|
| Platform ID |
GPL23479 |
| Series (2) |
| GSE131828 |
Transcriptomic data of established mouse prostate cancer cell lines like RM1 and Pten Smad4 |
| GSE131830 |
Transcriptomic data and Genome-wide maps of chromatin state in prostate cancer |
|
| Relations |
| BioSample |
SAMN11833243 |
| SRA |
SRX5884289 |
