|
Status |
Public on Jan 16, 2024 |
Title |
COR-4361-D2 |
Sample type |
SRA |
|
|
Source name |
PBMCs
|
Organism |
Homo sapiens |
Characteristics |
cell type: PBMCs disease state: case
|
Treatment protocol |
Whole blood was collected in EDTA tubes 24h after subjects completed a cardiopulmonary exercise test (CPET). PBMCs were isolated using SepMate tubes and cryopreserved with 1-10 x10^6 cells per vial. Frozen PBMCs were recovered following the 10x Genomics Demonstrated Protocol: Fresh Frozen Human Peripheral Blood Mononuclear Cells for Single Cell RNA Sequencing (CG00039). Classical monocytes were isolated using the Miltenyi Biotec Classical Monocyte Isolation Kit (130-117-337) and CD14 MicroBeads (130-050-201).
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was isolated with Trizol, 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. Directional RNA-seq libraries were prepared from 25ng 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 |
COR.5655.D2 col in rawCounts.txt file
|
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. Raw counts were analyzed in R with DEseq2. Assembly: hg38 (Ensembl genes) Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
|
|
|
Submission date |
Sep 27, 2022 |
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) |
GSE214282 |
Transcriptome profiling of classical monocytes in ME/CFS post exercise challenge |
GSE214284 |
Transcriptomics of the immune system in ME/CFS at baseline and following symptom provocation |
|
Relations |
BioSample |
SAMN31037877 |
SRA |
SRX17723572 |