|
| Status |
Public on Aug 01, 2024 |
| Title |
T24si-SM-2 |
| Sample type |
SRA |
| |
|
| Source name |
bladder
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: bladder
cell line: T24
cell type: bladder cancer cell
genotype: SLC2A11-MIF knockdown
|
| Treatment protocol |
1 OD SiRNA was diluted at a stocking solution of 125 μL in sterile DEPC-treated water, and cells were treated for 48h with 5 μL of SiRNA.
|
| Growth protocol |
T24 was cultured in RPMI-1640 (Gibco) and UM-UC-3 was cultured in DMEM (Gibco) supplemented with 10% FBS (Biological Industries) 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 4000 |
| |
|
| Data processing |
Base-calling using bcl2fastq2 v2.19.1 with -r 4 -p 16 -w 4 --barcode-mismatches 0
Adaptor contamination was remove from reads (the number of bases contaminated by the adaptor in reads is greater than 5bp. For pair-end sequencing, if one end is contaminated by the adaptor, the Reads at both ends are removed)；Remove low-quality reads (Reads with more than 50% of the total bases are bases with a mass value of Q ≤ 19 . For pair-end sequencing, if one pair is low-quality reads, the both reads will be removed)；Remove the reads with N rate greater than 5% (For pair-end sequencing, if one pair contains more than 5% N, the both reads will be removed)
Fastq reads were mapped to genome using hisat2 v2.1.0 with default parameters
Reads count of echo gene was calculated using htseq-count v0.6.1 with -t exon -f bam -s no -a 10
Assembly: hg19(ftp://ftp.ensembl.org/pub/grch37/current/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.dna.toplevel.fa.gz)
Supplementary files format and content: excel files include normalize values for each Sample
|
| |
|
| Submission date |
Jun 30, 2024 |
| Last update date |
Aug 01, 2024 |
| Contact name |
Liang Cheng |
| E-mail(s) |
chengl33@mail2.sysu.edu.cn
|
| Phone |
18819254083
|
| Organization name |
Sun Yat-sen Memorial Hospital
|
| Department |
Department of Urology
|
| Street address |
107th Yanjiangxi Road
|
| City |
Guangzhou |
| State/province |
Guangdong |
| ZIP/Postal code |
510000 |
| Country |
China |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE271133 |
Oncogenic SLC2A11-MIF Fusion Protein Interacts with PTBP1 to Facilitate Bladder Cancer Proliferation and Metastasis by Regulating mRNA Stability |
|
| Relations |
| BioSample |
SAMN42180535 |
| SRA |
SRX25160118 |
