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Sample GSM6947105 Query DataSets for GSM6947105
Status Public on Oct 01, 2023
Title sRNAseq of Plasmids cd64_TP53 treated BMSC-derived EV
Sample type SRA
 
Source name Plasmids cd64_TP53 treated BMSC-derived EV
Organism Homo sapiens
Characteristics cell type: Bone Marrow Stem Cells (BMSCs)
tissue: extracellular vesicles (EVs)
treatment: Plasmids CD64 and TP53
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 SAMN32818003
SRA SRX19121024

Supplementary file Size Download File type/resource
GSM6947105_03_BMSC_64_53_S3_Processed.fa.gz 1.5 Mb (ftp)(http) FA
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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