|
| Status |
Public on Feb 16, 2022 |
| Title |
OE GFP-1 in hiPSC-CMs (RNA-seq) |
| Sample type |
SRA |
| |
|
| Source name |
hiPSC-CMs overexpressed with GFP
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: hiPSC-derived cardioyocytes
differentiation: D24
genotype: overexpressed GFP
|
| Treatment protocol |
At D22, OE GFP or ERRg was performed using adenovirus expressing each gene. Two days after the infection, RNA samples were harvested.
|
| Growth protocol |
hiPSC were cultured in TeSR-E8 (StemCell Technologies) and differentiated toward cardiomyocytes with the method published by Dr. Joseph Wu (Nat Methods. 2014 Aug;11(8):855-60. PMID: 24930130).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Qiazol (QIAGEN). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
The quality of Total RNA was assessed by the Agilent Bioanalyzer Nano chip (Agilent Technologies). 1ug of Total RNA was used as starting material to construct RNA Seq library using Illumina's Truseq Stranded Total RNA Library preparation kit as per the instructions. First the total RNA is Ribo depleted to remove rRNA from total RNA. The remaining non-rRNA is fragmented into small pieces using divalent cations under elevated temperature. Following fragmentation, the first strand cDNA were synthesized using random primers and followed by second strand synthesis using DNA Polymerase I. The cDNA is then ligated with index adapters for each sample followed by purification and then enriched with PCR to create the final library. The quality and quantity of the libraries were detected by Agilent Bioanalyzer and Kapa Biosystems qPCR.
The quality and quantity of the libraries were detected by Agilent Bioanalyzer and Kapa Biosystems qPCR. Multiplexed libraries are pooled and single-end 50-bp sequencing was performed on one flow-cell of an Illumina Hiseq 2500.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Gene Expression Data
GFP-1
|
| Data processing |
Transcript-level gene expression was quantified using Salmon (Nat Methods. 2017 Apr;14(4):417-419. PMID: 28263959)
Transcript data was aggregated to produce gene-level quantifications, and tests for differential expression were performed using DESeq2 (Genome Biol. 2014;15(12):550. PMID: 25516281)
We considered genes with FDR < 0.05 and fold change at least 1.5 in any direction for further analyses.
Genome_build: GRCh38
Supplementary_files_format_and_content: Excel file contains significantly regulated gene name, log2 fold change (ERRg/GFP), and adjusted p-values.
|
| |
|
| Submission date |
Feb 02, 2021 |
| Last update date |
Feb 16, 2022 |
| Contact name |
Tomoya Sakamoto |
| Organization name |
University of Pennsylvania
|
| Department |
Cardiovascular Institute
|
| Lab |
Daniel Kelly lab
|
| Street address |
Smilow Center for Translational Research 11th FL (Room 11-172) 3400 Civic Center Blvd Bldg 421
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE165966 |
RNA-Seq transcriptome profiling of human iPS cell-derived cardiomyocytes (hiPSC-CMs) following overexpression (OE) of estrogen-related receptor gamma (ERRg) |
| GSE166064 |
The Nuclear Receptor ERR Cooperates with the Cardiogenic Factor GATA4 to Orchestrate Transcriptional Control of Cardiac Maturation |
|
| Relations |
| BioSample |
SAMN17736396 |
| SRA |
SRX10003032 |
