|
| Status |
Public on Mar 20, 2024 |
| Title |
SB-6 |
| Sample type |
SRA |
| |
|
| Source name |
Serum
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: pluripotent stem cells derived cardiomyocytes (PSC-CMs)
treated with: Serum
donor disease status: Mild COVID
|
| Treatment protocol |
All serum samples were obtained from different patients and media with serum was refreshed every 48 hours
|
| Growth protocol |
PSC-CMs were grown in serum free media (CMD-BSA or RPMI supplemented with B27) supplemented with 10% patient serum
|
| Extracted molecule |
total RNA |
| Extraction protocol |
GenElute Mammalian total RNA Miniprep Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Quality checks were performed using FastQC (v0.11.8), summarised with MultiQC (v1.9). Reads were then subsampled. Alignment to the human reference genome (build GRCh38.p13) was performed using STAR (v2.7.6a) with default parameters. The counts of the aligned reads corresponding to exons were obtained using featureCounts program against the exon annotations obtained from the ensembl database (annotation file Homo_sapiens.GRCh38.98.gtf). MA plots, JSIs and PCA were performed as further quality checks.
The resulting expression values were normalised using quantile normalisation [Bolstad2003] and noise was removed using noisyR count matrix approach [Moutsopoulos2021].
Differential expression analysis was performed using edgeR (v3.28.1) [Robinson2010] and DESeq2 1.26.0 [Love2014].
The visualisation, and community accessible overview were complied using bulkAnalyseR [Moutsopoulos2021].
Enrichment analysis on the set of differentially expressed genes against a background of all genes expressed in the dataset using the g:profiler (https://biit.cs.ut.ee/gprofiler/gost) R package (v0.1.9) [Raudvere2009].
Assembly: hg38 (GRCh38.p13)
Supplementary files format and content: count matrix containing raw gene expression
|
| |
|
| Submission date |
Jul 05, 2022 |
| Last update date |
Mar 20, 2024 |
| Contact name |
Irina Mohorianu |
| E-mail(s) |
data-submissions@stemcells.cam.ac.uk
|
| Organization name |
University of Cambridge
|
| Department |
Wellcome-MRC Cambridge Stem Cell Institute
|
| Street address |
Puddicombe Way
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 0AW |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE207473 |
Serological mechanisms driving cardiotoxicity in COVID-19 |
|
| Relations |
| BioSample |
SAMN29579989 |
| SRA |
SRX16060560 |
