|
| Status |
Public on May 20, 2019 |
| Title |
Primary keratinocytes (Exosomes) patient 377 |
| Sample type |
SRA |
| |
|
| Source name |
Conditioned media
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: primary keratinocytes
ev population: Exosomes
|
| Growth protocol |
Epidermal primary keratinocytes (PKCs) were freshly isolated from donor skin and propagated on i3T3 feeder cells using the method of Rheinwald and Green. HaCaT cells were purchased from CLS Cell Lines Service GmbH (Eppenheim, Germany). All keratinocyte cultures were maintained at 37 ºC in a 5% CO2 / 95% air atmosphere, with media changes every 2 days, and subcultured when the cultures became 80% confluent.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the Trizol™ method following the manufacturer’s protocol
Libraries were constructed using the TruSeq® SmallRNA Library Prep Kit, following the manufacturer’s instructions. A total of 1 µg RNA or 100 to 300 ng of exosomal RNA was used as input for library construction.
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
377_Ex
|
| Data processing |
Remove index and adaptor sequences using TagCleaner (version 0.16)
Trim reads to 28 nucleotides using FASTX-Toolkit (version 0.0.13)
miRNAs were identified using the miRDeep2 program (version 2.0.0.7), using the default parameters with the exception of allowing for 1 mismatch and discarding read less than 16 nucleotides in length.
Raw miRNA counts were normalized and statistically analyzed using the DESeq2 package (version 1.10.1) in R (version 3.2.2)
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited file containing raw miRNA counts
|
| |
|
| Submission date |
Nov 02, 2017 |
| Last update date |
May 20, 2019 |
| Contact name |
Dominic Guanzon |
| Organization name |
University of Queensland
|
| Department |
UQCCR
|
| Lab |
Exosome biology laboratory
|
| Street address |
Building 71/918 RBWH Herston
|
| City |
Brisbane |
| State/province |
Queensland |
| ZIP/Postal code |
4029 |
| Country |
Australia |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE106453 |
Differential expression of keratinocyte-derived extracellular vesicle miRNAs discriminate exosomes from apoptotic bodies and microvesicles |
|
| Relations |
| BioSample |
SAMN07967379 |
| SRA |
SRX3353439 |
