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Sample GSM3182557 Query DataSets for GSM3182557
Status Public on Feb 12, 2019
Title 164_1__2__1st Tri
Sample type SRA
 
Source name PTB_1st_Trimester_Patient_164
Organism Homo sapiens
Characteristics tissue: plasma
tissue compartment: exosome
full term (normal) vs preterm birth (ptb): PTB
trimester: 1st
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 SAMN09390412
SRA SRX4191530

Supplementary file Size Download File type/resource
GSM3182557_164_1_2_1st_Tri.csv.gz 8.5 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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