|
| Status |
Public on Aug 05, 2023 |
| Title |
ARR2PBi-Cre;Ptenf/+;Ncoa6f/f _rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Prostate tumor
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Prostate
age: 9 months
genotype: Pten heterozygous KO; Ncoa6 homozygous KO
|
| Treatment protocol |
The prostate tissues and tumors were collected from untreated 9-month-old mice
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA samples were extracted from the mouse prostate tissues and tumors using the TRIzol reagent (15596018; Thermo Fisher) followed by purification with the RNeasy Mini Kit (74106; Qiagen) according to manufacturer's instructions. Quality of the samples were checked by using the NanoDrop spectrophotometer and Agilent Bioanalyzer 2100.
250 ng of total RNA samples (measured by picogreen) that had passed the quality check was used for creating a double-stranded DNA library. ERCC RNA Spike-In Controls were added to each sample according to the manufacturer’s protocol. The fragmented and 3’ poly (A)-selected portion of total RNA together with random primers were used to create the cDNA. In the process of second strand synthesis, dTTP was replaced with dUTP to quench the second strand during amplification amd thereby achieve strand specificity. The created cDNA fragments were blunt ended, attached with an adenosine to the 3' end, and finally ligated with unique adapters to the end. The ligated products were amplified with 15 PCR cycles. The resulting libraries were quantitated using the NanoDrop Spectrophotometer and the fragment sizes were assessed with the Agilent Bioanalyzer. To determine the concentration of adapter-ligated fragments, the libraries were further quantitated by qPCR by using the Applied Biosystems ViiA7 Real-Time PCR System and a KAPA Library Quant Kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
JX7832
|
| Data processing |
The paired-end reads were mapped to the mouse genome (UCSC mm10) using STAR with NCBI RefSeq genes as the reference. STAR generated read counts for each RNA was used as the measurement of gene expression.
DESeq2 was used to analyze the gene-based read counts to detect differentially expressed genes between the groups of interest.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include DESeq2 values.
|
| |
|
| Submission date |
Aug 05, 2020 |
| Last update date |
Aug 05, 2023 |
| Contact name |
Yonghong Liu |
| E-mail(s) |
yonghongliu2017@gmail.com
|
| Phone |
7137984684
|
| Organization name |
Baylor College of Medicne
|
| Department |
Molecular & Cellular Biology
|
| Lab |
N630
|
| Street address |
One Baylor Plaza
|
| City |
Houston |
| State/province |
Texas |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE155755 |
Identification of genes differentially expressed between the prostates of PtenPC+/- mice and the prostate tumors of PtenPC+/-;Ncoa6PC-/- mice at the age of 9 months |
| GSE155757 |
NCOA6 is a potent prostate cancer suppressor essential for NFY-mediated restriction of EGFR overexpression |
|
| Relations |
| BioSample |
SAMN15738135 |
| SRA |
SRX8894076 |
