|
| Status |
Public on Aug 13, 2017 |
| Title |
UM-UC-3_si-hnRNPK |
| Sample type |
SRA |
| |
|
| Source name |
bladder cancer cell line UM-UC-3
|
| Organism |
Homo sapiens |
| Characteristics |
sirna: Two different siRNAs targeting hnRNPK were transfected in the cell
sirna sequence: GGGUUGUAGAGUGCAUAAATT ; GCCUCCAUCUAGAAGAGAUTT
inhibition rate (relative to control sirna) detected by qpcr: 0.08
|
| Treatment protocol |
siRNA transfections were done with 75 nM siRNA and Lipofectamine RNAimax (Life technologies) following manufacturer's instructions.
|
| Growth protocol |
UM-UC-3 was cultured in DMEM (Gibco) supplemented with 10% FBS (Shanghai ExCell Biology, China) and 1% penicillin/streptomycin (Gibco). Cells were grown in a humidified atmosphere of 5% CO2 at 37°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol reagent and was further purified using Qiagen RNeasy Mini Kit according to the manufactures’ instructions. The RNA quality was assessed by formaldehyde agarose gel electrophoresis and was quantitated spectrophotometrically.
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 |
| |
|
| Data processing |
Base-calling: CASAVA1.8
Data filtering : in house
Read alignment: tophat2.0.12
transcript assemble: cufflink2.2.1
Genome_build: genome build: hg19
Supplementary_files_format_and_content: txt files include normalize values for each Sample
|
| |
|
| Submission date |
Apr 01, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Xu Chen |
| E-mail(s) |
joshua_18chen@163.com
|
| Organization name |
Sun Yat-sen Memorial Hospital
|
| Department |
Department of Urology
|
| Street address |
107. W. Yanjiang Road
|
| City |
Guangzhou |
| State/province |
Guangdong |
| ZIP/Postal code |
510120 |
| Country |
China |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE79832 |
Altered expression of genes in lncRNA-LBCS, hnRNPK and PTBP1 knockdown |
|
| Relations |
| BioSample |
SAMN04545463 |
| SRA |
SRX1629964 |
