|
| Status |
Public on May 20, 2021 |
| Title |
C4-2B-ENZR cell as control 1 |
| Sample type |
SRA |
| |
|
| Source name |
C4-2B-ENZR
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: prostate cancer cell line C4-2B-ENZR
genotype/variation: negative control
|
| Treatment protocol |
C4-2B-ENZR cells transfected with siRNA are referred as C4-2B-ENZR_NC and C4-2B-ENZR_siKIF15.
|
| Growth protocol |
Cells were maintained in 1640 medium supplemented with 10% fetal bovine serum (FBS) and 100 U/mL penicillin and streptomycin. Cell cultures were held in a humid, 37℃ and 5% CO2 cell culture incubator.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
This sample is of C4-2B-ENZR transfected with siRNA of negtive control.
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
May 20, 2020 |
| Last update date |
May 20, 2021 |
| Contact name |
Lin Gao |
| E-mail(s) |
gaolin90@aliyun.com
|
| Organization name |
shandong university
|
| Street address |
No.44, Wenhua Xi Road
|
| City |
Jinan |
| ZIP/Postal code |
250012 |
| Country |
China |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE150895 |
KIF15 confers resistance to enzalutamide in castration resistant prostate cancer [RNA-Seq] |
| GSE150896 |
KIF15 promotes AR and AR-V7 protein stabilization in contribution to enzalutamide resistance of prostate cancers |
|
| Relations |
| BioSample |
SAMN14979359 |
| SRA |
SRX8367617 |
