|
| Status |
Public on Oct 01, 2023 |
| Title |
sRNAseq of TP53 Plasmid treated BMSCs |
| Sample type |
SRA |
| |
|
| Source name |
TP53 Plasmid treated BMSCs
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Bone Marrow Stem Cells (BMSCs)
treatment: Plasmid53
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared from cells or cell-derived extracellular vesicles using miRNeasy Serum/Plasma advanced kit (Qiagen).
Small RNA (sRNA) libraries for sRNA-seq were prepared using NEXTFLEX Small RNA-seq kit v3 (PerkinElmer) following manufacturer's protocols (v19.01). The quality of libraries was assessed with the Agilent 2100 Bioanalyzer with the High Sensitivity DNA chip. The library concentrations were assessed by NEBNext Library Quant Kit (New Englans Biolabs). The libraries were pooled (2nM final concentration).
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
NextSeq 2000 |
| |
|
| Data processing |
small RNA analysis pipeline, sRNAnalyser (http://srnanalyzer.systemsbiology.net)
Small RNA sequence reads were trimmed for adaptor sequence/low-quality sequence using "Cutadapt" and "Prinseq"
Trimmed and duplicated sequence reads were merged into a single sequence while maintaining reads counts using "fastx_collapser" in FASTX_TOOLKIT.
Read count extraction was performed using sRNAnalyzer PisaR_v.1.6
Supplementary files format and content: processed data files represent the complete small RNA read counts
|
| |
|
| Submission date |
Jan 20, 2023 |
| Last update date |
Oct 02, 2023 |
| Contact name |
Inyoul Lee |
| Organization name |
Institute for Systems Biology
|
| Street address |
401 Terry Ave. North
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109 |
| Country |
USA |
| |
|
| Platform ID |
GPL30173 |
| Series (2) |
| GSE223397 |
Dual targeted extracellular vesicles regulating oncogenic genes in pancreatic cancer [sRNAseq] |
| GSE223409 |
Dual targeted extracellular vesicles regulating oncogenic genes in pancreatic cancer |
|
| Relations |
| BioSample |
SAMN32818002 |
| SRA |
SRX19121025 |
