|
Status |
Public on Feb 12, 2019 |
Title |
291_3__2__3rd tri |
Sample type |
SRA |
|
|
Source name |
PTB_3rd_Trimester_Patient_291
|
Organism |
Homo sapiens |
Characteristics |
tissue: plasma tissue compartment: exosome full term (normal) vs preterm birth (ptb): PTB trimester: 3rd patient id: 291
|
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.
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|
|
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
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|
|
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 |
SAMN09390420 |
SRA |
SRX4191547 |