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Sample GSM5059570 Query DataSets for GSM5059570
Status Public on Feb 16, 2022
Title OE ERRg-3 in hiPSC-CMs (RNA-seq)
Sample type SRA
 
Source name hiPSC-CMs overexpressed with ERRg
Organism Homo sapiens
Characteristics cell type: hiPSC-derived cardioyocytes
differentiation: D24
genotype: overexpressed ERRg
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
ERR-G-3
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 SAMN17736327
SRA SRX10003037

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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