|
| Status |
Public on Feb 01, 2024 |
| Title |
SAM_379_RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
primary bladder tumor
|
| Organism |
Homo sapiens |
| Characteristics |
age: 55
gender: female
histologic type: Non-muscle invasive bladder cancer (NMIBC)
progression: no
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from tissue using TRI reagent based method.
Total RNA (500 ng) was processed for preparing whole transcriptome sequencing library. Enrichment of whole transcriptome RNA by depleting ribosomal RNA ( rRNA ) was processed for preparing whole transcriptome sequencing library using MGIEasy RNA Directional Library Prep Kit (MGI) according to manufacturer’s instruction.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
MGISEQ-2000RS |
| |
|
| Data processing |
Reference genome sequence data from Homo sapiens were obtained from the NCBI Genome database (assembly ID: GRCh38). The reference genome indexing and read mapping of tissue samples were performed using STAR software (ver. 2.5.4b).
Then, the read counts per million fragments mapped (CPM) of each sample were estimated and were log2-transformed.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text format with log2 transformed CPM values of transcripts
|
| |
|
| Submission date |
Feb 01, 2023 |
| Last update date |
Feb 01, 2024 |
| Contact name |
sungghwan park |
| E-mail(s) |
sungghwan123@gmail.com
|
| Organization name |
Korea Research Institute of Bioscience and Biotechnology
|
| Street address |
Gwahak-ro, Yuseong-gu
|
| City |
Daejeon |
| ZIP/Postal code |
305-806 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL30209 |
| Series (1) |
| GSE224248 |
Development of a prognostic index for predicting disease progression in non-muscle invasive bladder cancer |
|
| Relations |
| BioSample |
SAMN33007292 |
| SRA |
SRX19246565 |
