|
| Status |
Public on Feb 12, 2019 |
| Title |
164_4_Delivery_PTB |
| Sample type |
SRA |
| |
|
| Source name |
PTB_Delivery_Patient_164
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: plasma
tissue compartment: exosome
full term (normal) vs preterm birth (ptb): PTB
trimester: Delivery
patient id: 164
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the miRNeasy Mini Kit and TRIzol LS Reagent following the manufacturer's instructions.
Libraries were constructed using the TruSeq® SmallRNA Library Prep Kit, following the manufacturer’s instructions. A total of 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 |
| |
|
| Data processing |
Remove index and adaptor sequences using TagCleaner (version 0.16)
Trim reads to 28 nucleotides using FASTX-Toolkit (version 0.0.14)
miRNAs were identified using the miRDeep2 program (version 2.0.0.7), using the deafult parameters with the exception of allowing for 1 mismatch and discarding read less than 16 nucleotides in length.
Raw miRNA counts were normalised and statistically anlaysed using the DESeq2 package (version 1.18.1) in R (version 3.2.2)
Genome_build: hg19
Supplementary_files_format_and_content: Comma-delimited file containing raw miRNA counts
|
| |
|
| Submission date |
Jun 11, 2018 |
| Last update date |
Feb 12, 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) |
| GSE115572 |
Circulating exosomal miRNA profile during term and preterm birth pregnancies – a longitudinal study |
|
| Relations |
| BioSample |
SAMN09390409 |
| SRA |
SRX4191533 |
