|
| Status |
Public on Apr 01, 2024 |
| Title |
EDTA-K3 plasma anticoagulant tubes [6-OSA16] |
| Sample type |
SRA |
| |
|
| Source name |
Plasma samples were collected in the early morning and after 10-14 h of overnight fasting and after sleep test.
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Plasma samples were collected in the early morning and after 10-14 h of overnight fasting and after sleep test.
Sex: female
age: 78
body mass_index: 36.11
apnea hypoapnea_index: 33.6
|
| Extracted molecule |
total RNA |
| Extraction protocol |
HTG EdgeSeq extraction-free chemistry can detect miRNA targets without the requirement for RNA extraction, adaptor ligation, cDNA synthesis or pre-amplification of the sample by PCR. Plasma samples were thawed and 15µl of each sample was plated in 24 wells and loaded onto the HTG EdgeSeq instrument.
HTG EdgeSeq miRNA following manufacture's protocols. Set of 2083 targets used, plus 5 negative controls, 1 positive control and 13 housekeeping genes - total of 2102 observations per sample
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
HTG EdgeSeq miRNA WTA Sequencer NB551420
GEO_data HTG OSA Processed TB.txt
|
| Data processing |
FASTQ files were processed by HTG EdgeSeq parser software. Parser produces text file of counts per target miRNA. Differential gene expression analysis based on the negative binomial distribution (DESeq package (R version 4.1.1)
biocLite("DESeq2"): 1. Quality assess and clean raw sequencing data; 2. Align reads to a reference; 3. Count the number of reads assigned to each contig/gene; 4. Extract counts and store in a matrix; 5. Create column metadata table; 6. Analyze count data using DESEQ2
Assembly: hg19
Supplementary files format and content: tab-delimited text files include RAW data (total counts) and analyzed count data for each sample
|
| |
|
| Submission date |
Apr 11, 2023 |
| Last update date |
Apr 05, 2024 |
| Contact name |
David de Gonzalo-Calvo |
| E-mail(s) |
dgonzalo@irblleida.cat
|
| Phone |
973702201
|
| Organization name |
IRBLleida
|
| Street address |
Rovira Roure 80
|
| City |
Lleida |
| State/province |
Lleida |
| ZIP/Postal code |
25196 |
| Country |
Spain |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE229362 |
microRNA signature to support clinical-decision making in patients with suspected Obstructive Sleep Apnea |
|
| Relations |
| SRA |
SRX19925386 |
| BioSample |
SAMN34137362 |
