|
| Status |
Public on Jun 16, 2024 |
| Title |
DMSOrep1tech1 |
| Sample type |
SRA |
| |
|
| Source name |
Cellular Dynamics iCell Cardiomyocytes
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Cellular Dynamics iCell Cardiomyocytes
treatment: DMSO
time: 24 h
|
| Treatment protocol |
Cellular Dynamics iCell Cardiomyocytes were treated with DMSO or 1 of 5 small molecules (C1, C2, C3, C4, C5) for 24 hours. Each condition had 3 replicates.
|
| Growth protocol |
manufacturer's instructions
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from hiPSC-CMs treated for 24 h using the mirVana microRNA Isolation Kit with phenol (Invitrogen) according to the manufacturer’s guidelines. Each sample was run with 3 biological replicates.
RNA sequencing libraries were generated and indexed using 200 ng of total RNA and the TruSeq Stranded mRNA LT Sample Prep Kit - Set B (Illumina) following the protocol provided by the manufacturer.
Resulting libraries were then assessed using the Agilent TapeStation 4200 (Agilent Technologies) and quantified by Qubit 2.0 (Thermo Fisher Scientific). The indexed libraries were pooled at equal molar concentrations and paired-end sequenced with 75 bp per read on the Illumina NextSeq 500 system using NextSeq 500 High Output 150 cycle cartridges (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Sequence read quality was assessed using the FastQC software (http://www.bioinformatics. babraham.ac.uk/projects/fastqc). All samples at all positions had Phred scores greater than 30. Paired-end reads were mapped to the human reference genome hg38 using the Bowtie2 aligner [66] and gene-level counts were quantified using the featureCounts program [67]. Genes with low counts were removed before normalizing by TMM.
Assembly: Paired-end reads were mapped to the human reference genome hg38 using the Bowtie2 aligner [66]
Supplementary files format and content: GEOreadcounts.csv contains the normalized gene counts from each sample.
|
| |
|
| Submission date |
May 30, 2024 |
| Last update date |
Jun 16, 2024 |
| Contact name |
Jeffrey John Saucerman |
| E-mail(s) |
jsaucerman@virginia.edu
|
| Organization name |
University of Virginia
|
| Department |
Biomedical Engineering
|
| Street address |
Box 800759
|
| City |
Charlottesville |
| State/province |
VA |
| ZIP/Postal code |
22908-0759 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE268693 |
Small molecules that induce proliferation of human iPSC-cardiomyocytes |
|
| Relations |
| BioSample |
SAMN41394233 |
| SRA |
SRX24566658 |
