|
| Status |
Public on Feb 01, 2021 |
| Title |
016C [miRNA-Seq] |
| Sample type |
SRA |
| |
|
| Source name |
cancer kidney tissue
|
| Organism |
Homo sapiens |
| Characteristics |
cancer type: clear cell renal cell carcinoma (ccRCC)
fuhrman's grade: G2
Sex: Female
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For the preservation of RNA, tissue fragments were collected into tubes containing RNAlater (Sigma Aldrich) and stored at -80°C for further processing. Next, fragments of tissue were transferred into a sterile mortar and grinded in liquid nitrogen. RNA was extracted with Trizol.
TruSeq Small RNA Library Preparation Kit (Illumina, San Diego)
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiScanSQ |
| |
|
| Description |
library preparation kit: TruSeq Small RNA Library Preparation Kit (Illumina, San Diego)
|
| Data processing |
raw reads were trimmed with cutadapt (untrimmed reads and reads shorter than 10 nt were discarded)
Reads were aligned to Ensembl GRCh38 human genome with bowtie2
Raw read counts were generated with featureCounts v1.6.3
Genome_build: GRCh38
Supplementary_files_format_and_content: Table with microRNA expression raw reads in txt format.
|
| |
|
| Submission date |
May 29, 2020 |
| Last update date |
Feb 01, 2021 |
| Contact name |
Arkadiusz Kajdasz |
| E-mail(s) |
[email protected]
|
| Organization name |
Institute of Bioorganic Chemistry PAS
|
| Lab |
Laboratory of Bioinformatics
|
| Street address |
ul. Z. Noskowskiego 12/14
|
| City |
Poznań |
| State/province |
wielkopolskie |
| ZIP/Postal code |
61-704 |
| Country |
Poland |
| |
|
| Platform ID |
GPL15456 |
| Series (2) |
| GSE151423 |
Identification of RCC subtype-specific microRNAs – meta-analysis of high-throughput RCC tumor microRNA expression data [miRNA-Seq] |
| GSE151428 |
Identification of RCC subtype-specific microRNAs – meta-analysis of high-throughput RCC tumor microRNA expression data |
|
| Relations |
| BioSample |
SAMN15053655 |
| SRA |
SRX8423426 |
