|
| Status |
Public on Mar 21, 2016 |
| Title |
OMT924007 exosome |
| Sample type |
SRA |
| |
|
| Source name |
Cancer-associated adipocytes
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Cancer-associated adipocytes
sample type: exosome
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Exosomes were isolated from the conditioned medium by differential ultracentrifugation. Total RNAs were extracted from purified exosomes using the RNAqueous-Micro kit (Thermo Fisher Scientific), and the amount and quality of small RNA in the total RNA samples were determined using the Agilent small RNA kit on an Agilent 2100 Bioanalyzer. Five nanograms of small RNAs were subjected to library construction.
Library was constructed using the Ion Total RNA-Seq kit v2 (Life Technologies Corp.), according to the small RNA protocol.
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Ion Torrent PGM |
| |
|
| Description |
small RNA
|
| Data processing |
Ion Torrent reads were collected using Ion Torrent Suite software, which also sorted the data according to the barcodes.
The software scores the quality of the reads by assigning Q17 and Q20 scores according to the quality scoring computation.
Fastq files from the Ion Torrent server were imported to the CLC Genomics Workbench (version 5.1; Life Technologies Corp.).
Sequence reads were trimmed to remove reads with ambiguous nucleotides and to create a sequence length of 15 to 55 nucleotides. Trimmed sequence reads were aligned to a miRNA database (miRBase, release 18). Mapped reads were annotated and counted.
Genome_build: hg19
Supplementary_files_format_and_content: Ion Torrent reads were then normalized to the number of cells in each cell line used for exosome collection and presented as the total reads per 1000 cells in xlsx files.
|
| |
|
| Submission date |
Jan 27, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Chi Lam Au Yeung |
| Organization name |
UT MD Anderson Cancer Center
|
| Street address |
1515 Holcombe Blvd
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL17301 |
| Series (1) |
| GSE77318 |
Ion Torrent RNA-sequencing of exosomes isolated from ovarian cancer cells, fibroblasts and adipocytes |
|
| Relations |
| BioSample |
SAMN04446232 |
| SRA |
SRX1550585 |
