|
| Status |
Public on Jan 16, 2024 |
| Title |
COR-3013-D2 |
| Sample type |
SRA |
| |
|
| Source name |
plasma
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: plasma
timepoint: D2-24hPostCPET
disease state: control
|
| Treatment protocol |
Whole blood was collected in EDTA tubes before and 24h after subjects completed a cardiopulmonary exercise test (CPET). Plasma was separated from whole blood and stored frozen at -80C in 1 mL aliquots. Plasma was dilulted 3-fold in DMEM after thawing, and centrifuged at 100xg for 20 min at RT (no brake) to remove large debris. Supernatants were transfered to new tubes with wide-bore pipet and spun at 800xg for 20 min at RT (no brake) to pellet plasma particles containing platelets. Pellets were gently rinsed once with Tyrode's buffer, then resuspended in 1 mL of Tyrode's buffer. For RNA extraction, 250 uL of each sample was combined with 750 ul Trizol-LS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the Trizol protocol, with an extra chloroform extraction to remove residual phenol and addition of glyco-blue as a carrier to promote RNA precipitation. RNA concentration was determined with a HS RNA Qubit assay (ThermoFisher) and integrity assessed on a Fragment Analyzer (Agilent).
Directional RNA-seq libraries were prepared from 40ng total RNA using the NEBNext Directional Ultra II RNA Library Prep Kit for Illumina (New England Biolabs), with initial polyA+ isolation.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
raw_counts.txt:COR-3013-D2
|
| Data processing |
Illumina pipeline software was used for base calling.
Sequenced reads were trimmed for 3' adaptor sequence and low-quality sequence and filtered to remove reads < 50nt with TrimGalore/cutadapt.
Processed reads were mapped to the reference genome/transcriptome with STAR using --quantMode GeneCounts to generate raw counts per gene.
Assembly: hg38 (Ensembl genes)
Supplementary files format and content: Matrix table with raw gene counts for every annotated gene and every sample
|
| |
|
| Submission date |
Jul 03, 2023 |
| Last update date |
Jan 16, 2024 |
| Contact name |
Jennifer K Grenier |
| Organization name |
Cornell University
|
| Department |
Biomedical Sciences
|
| Lab |
Biotechnology Building rm 333
|
| Street address |
526 Campus Rd
|
| City |
Ithaca |
| State/province |
NY |
| ZIP/Postal code |
14853 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE214284 |
Transcriptomics of the immune system in ME/CFS at baseline and following symptom provocation |
| GSE236402 |
Transcriptome profiling of plasma-derived particles containing platelets in ME/CFS post exercise challenge |
|
| Relations |
| BioSample |
SAMN36275334 |
| SRA |
SRX20869901 |
