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Sample GSM7668443 Query DataSets for GSM7668443
Status Public on Sep 01, 2024
Title IPAH + PDE5i + Macitentan 3
Sample type SRA
 
Source name PBMC
Organism Homo sapiens
Characteristics disease state: IPAH
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
 
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 SAMN36750675
SRA SRX21186843

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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