|
Status |
Public on Sep 01, 2024 |
Title |
SSC-PAH + PDE5i + Macitentan 3 |
Sample type |
SRA |
|
|
Source name |
PBMC
|
Organism |
Homo sapiens |
Characteristics |
disease state: scleroderma PAH cell type: PBMC treatment: PDE5i, Macitentan time: 3 months post treatment
|
Extracted molecule |
total RNA |
Extraction protocol |
Peripheral blood mononuclear cells (PBMCs) were isolated from peripheral venous blood drawn from patients seen at UPMC. Blood samples collected in EDTA purple top vacutainer were centrifuged at 2000 RPM for 15 minutes and plasma was removed for banking. Buffy coats were collected and used for Ficoll gradient to isolate PBMC which are used for the single cell RNA sequencing analysis. RNA libraries were prepared using Chromium Single Cell 3’ Reagent Kits V2 per manufacturer’s guidelines (10x Genomics manual CG00052, cat# PN-12237). Single cell RNA-sequencing was performed using the GemCodeTM Single Cell Instrument (Chromium, 10X Genomics) which included at least 800 cells (~50K reads per cell).
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic single cell |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 4000 |
|
|
Data processing |
The raw fastq reads were mapped against the human genome build hg38 and to generate raw counts using 10X Genomics Cell Ranger Raw counts were normalized for the library size and log2 transformed Then normalized counts were analyzed for potential batch effect corrections among different patient samples using SCTransform in Seurat v3 Assembly: hg38 Supplementary files format and content: Seurat object as R data serialization file
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|
|
Submission date |
Jul 28, 2023 |
Last update date |
Sep 01, 2024 |
Contact name |
Satoshi Okawa |
E-mail(s) |
okawas@pitt.edu
|
Organization name |
University of Pittsburgh
|
Street address |
200 Lothrop Street
|
City |
Pittsburgh |
State/province |
PA |
ZIP/Postal code |
15261 |
Country |
USA |
|
|
Platform ID |
GPL20301 |
Series (1) |
GSE239592 |
Serial mRNA profiling of peripheral blood monocytes from PAH patients treated with phosphodiesterase 5 inhibitors (PDE5i) and PDE5i+macitentan |
|
Relations |
BioSample |
SAMN36750667 |
SRA |
SRX21186851 |