|
| Status |
Public on Feb 16, 2022 |
| Title |
ERR_KO_hiPSC-CMs_KO6_rep1 (RNA-seq) |
| Sample type |
SRA |
| |
|
| Source name |
ERRa/g KO hiPSC-CMs line 6
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: hiPSC-derived cardiomyocytes
line: 6
differentiation: D22
genotype: ERRa/g KO
|
| Treatment protocol |
ERRg KO iPSCs were generated by pSpCas9n(BB)-2A-Puro plasmids (PX462, Addgene plasmid # 48141) containing distinct sgRNAs against ERRg. After generating ERRg KO hiPSCs, ERRa/g KO hiPSCs were generated by pCas9-EGFP and pGuide kindly provided by Dr. Kiran Musunuru (University of Pennsylvania, PA). Wild type control cells were processed with the same treatment using empty vectors without gRNA expression.
|
| 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 miRNeasy kit (QIAGEN) from hiPSC-CMs at day22.
RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina using manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Gene Expression Data
KO6-1
|
| 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 (WT/KO), 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 |
GPL24676 |
| Series (2) |
| GSE165963 |
RNA-Seq transcriptome profiling of estrogen-related receptor alpha and gamma (ERRa/g) knock out (KO) human iPS cell-derived cardiomyocytes (hiPSC-CMs) |
| GSE166064 |
The Nuclear Receptor ERR Cooperates with the Cardiogenic Factor GATA4 to Orchestrate Transcriptional Control of Cardiac Maturation |
|
| Relations |
| BioSample |
SAMN17736310 |
| SRA |
SRX10003046 |
