|
| Status |
Public on Aug 27, 2024 |
| Title |
CMEC_Live_Plus_2 |
| Sample type |
SRA |
| |
|
| Source name |
iPSC
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: iPSC
cell type: iPSC-CM, iPSC-EC
genotype: control
treatment: Live COVID Virus
|
| Growth protocol |
SARS-CoV-2 pseudovirus was obtained commercially (Montana Molecular) where these pseudoviruses (as BSL-1 baculoviruses) were pseudotyped with Spike (S) proteins. As per manufacturer’s instructions, these pseudovirus does not replicate inside the cells, but exhibit high affinity for the host receptor ACE2 in ECs. iPSC-ECs or COs were infected with SARS-CoV-2 pseudovirus at the titer of 2x1010 VG/ml in EGM2 media (for iPSC-ECs) or a mixture of RPMI-B27 + EGM2 (for COs) for respective time periods.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from COs using RNeasy plus mini-Kit (Qiagen) as per manufacturer’s instructions
Dyna Oligo(dT) beads (Life technologies) were used to purify mRNA and then fragmentated to 200-300 bp fragments to prepare index-tagged paired-end cDNA libraries as previously descibed7. Illumina sequencing adapters were ligated to cDNA fragments through PCR and sequencing was performed on Novaseq 6000. Obtained fastq (paired end) sequencing reads were mapped to human reference genome (hg38) using STAR (2.5.4b), and quantified raw counts and RPKM values were annotated using Homer (analyzeRepeats.pl). Heatmaps were generated through normalized DESEQ2 counts. Gene ontology analysis was conducted using R package.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
RNAseq reads are trimmed using trimmomatic and HISAT2 tool is used for alignment
RPKM values are calculated using excel and read counts using featureCounts
differential analysis is perfomed using deseq2
Assembly: hg38
Supplementary files format and content: raw counts
|
| |
|
| Submission date |
Jan 03, 2024 |
| Last update date |
Aug 27, 2024 |
| Contact name |
Nazish Sayed |
| E-mail(s) |
sayedns@stanford.edu
|
| Organization name |
Stanford University
|
| Street address |
240 Pasteur Drive, 3500 BMI
|
| City |
Palo Alto |
| State/province |
California |
| ZIP/Postal code |
94303 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE252445 |
CCL2-mediated Endothelial Injury Drives Cardiac Dysfunction in Long COVID [LiveOrganoids] |
| GSE252448 |
CCL2-mediated Endothelial Injury Drives Cardiac Dysfunction in Long COVID |
|
| Relations |
| BioSample |
SAMN39243430 |
| SRA |
SRX23082918 |
