|
| Status |
Public on Jun 14, 2014 |
| Title |
MDA-MB-231_Ultra |
| Sample type |
SRA |
| |
|
| Source name |
breast
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MDA-MB-231
exosome purification: ultracentrifugation 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 |
|
| Relations |
| BioSample |
SAMN02854565 |
| SRA |
SRX596354 |
