GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM1412081 Query DataSets for GSM1412081
Status Public on Jun 14, 2014
Title MCF7_VN96
Sample type SRA
Source name breast
Organism Homo sapiens
Characteristics cell line: MCF7
exosome purification: VN96 method
Extracted molecule total RNA
Extraction protocol The conditioned cell culture media (from MCF-7 and MDA-MB-231 cells) were used to isolate EVs using the Vn96 peptide, ExoQuick and ultracentrifugation methods described above. RNA from the isolated EVs was harvested with TRIZOL reagent (Life Technologies)
Barcoded cDNA libraries were prepared using RNA-Seq Version 2 kit from Life Technologies following their recommended protocol. Library preparations were assayed for both quality control and quantity using Experion DNA 1K chip (Life Technologies) and diluted to 16 pM concentration. Samples were sequenced using a Proton Sequencer from Life Technologies on a PI chip following the manufacturer recommended protocol. Each chip was loaded with ten samples.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Ion Torrent Proton
Description exosomes are extracted from conditionned cell culture media
Data processing Torrent_Suite 3.4.2 used for basecalling
2 steps alignement for large RNA with tophat v2.0.6 and bowtie2 v2.0.2
alignement for small RNA with micro_razers v1.0
TMM normalization with edgeR for miRNA
RPKM normalisation
Genome_build: HG19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values or normalised values for each Sample ...
Submission date Jun 13, 2014
Last update date May 15, 2019
Contact name Nicolas Crapoulet
Organization name Atlantic cancer research institute
Street address 35 Providence street
City Moncton
State/province NB
ZIP/Postal code e1c 8x3
Country Canada
Platform ID GPL17303
Series (1)
GSE58464 Rapid isolation of extracellular vesicles from cell culture and biological fluids using a synthetic peptide with specific affinity for heat shock proteins
BioSample SAMN02854562
SRA SRX596351

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap