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Sample GSM6947106 Query DataSets for GSM6947106
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 (
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
BioSample SAMN32818002
SRA SRX19121025

Supplementary file Size Download File type/resource
GSM6947106_44_cell_p53_S44_Processed.fa.gz 3.4 Mb (ftp)(http) FA
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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