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GSE175885

GSE GEO
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RNA-Seq of isogenic human iPS cell-derived cardiomyocytes with RBM20 mutations created by genome editing (RiboMinus RNA-Seq)

Organism: Homo sapiens
Platform: GPL16791
Samples: 8
Experiment Types:
Expression profiling by high throughput sequencing
Submitted: Jun 01 2021
Last Updated: Dec 02 2021
Status: Public on Jun 01 2021
Contact: Nathan,,Salomonis (Cincinnati Children's Hospital)

Relations

SubSeries of: GSE175886 BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA734257 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP322106

Summary

RBM20 heterozygous (Het) and homozygous (Homo) R636S and homozygous 8-bp deletion (which causes nonsense-mediated decay) mutations were created by genome editing in an iPS cell line generated from a healthy male patient. Those cells were differentiated into cardiomyocytes by modulating the WNT signaling pathway, and then are subjected to the lactate purification method.

Overall Design

RNAseq of iPS cell-derived cardiomyocytes with 4 different genotypes as replicates

Analysis (5 steps)

View Data Processing
Processing steps for GSE175885
  1. To identify, quantify and annotate circular RNAs from back-splice junctions we first aligned the RNASeq results using TopHat2 on the RiboMinus depleted paired-end RNA-Seq FASTQ files, via the CIRCexplorer2 pipeline, on each individual sample (default options).
  2. This workflow identified far greater putative circRNAs than using the same pipeline with STAR 2.4.0.
  3. For differential circRNA analysis we ran RUVSEQ from the CSBB pipeline (https://github.com/csbbcompbio/CSBB-v3.0) on the back-splice junction counts for each sample for all relevant comparison groups.
  4. This workflow applies the software EdgeR to perform a differential expression analysis using a generalized linear model approach using the upper quartile normalization.
  5. All together, we identified circRNAs for 448 genes, with evidence of at least two reads per circRNA. circRNAs with a non-adjusted EdgeR p<0.1 were considered differentially expressed.

Supplementary Files (1)

GSE175885_RAW.tar Download
GEO Samples (8)
GSM5350776 GSM5350777 GSM5350778 GSM5350779 GSM5350780 GSM5350781 GSM5350782 GSM5350783

Dataset Citations (1)

Gain-of-function cardiomyopathic mutations in RBM20 rewire splicing regulation and re-distribute ribonucleoprotein granules within processing bodies.
PMID 34732726 · 2021 · Nature communications
Aidan M Fenix, Yuichiro Miyaoka, Alessandro Bertero, Steven M Blue, Matthew J Spindler, Kenneth K B Tan, Juan A Perez-Bermejo, Amanda H Chan, Steven J Mayerl, Trieu D Nguyen, Caitlin R Russell, Paweena P Lizarraga, Annie Truong, Po-Lin So, Aishwarya Kulkarni, Kashish Chetal, Shashank Sathe, Nathan J Sniadecki, Gene W Yeo, Charles E Murry, Bruce R Conklin, Nathan Salomonis

SRA Experiments (8) and Runs (8)

Total: 2567 MB
SRX11037735 SRP322106 RNA-Seq PAIRED
GSM5350776: WTC11 Wild-Type Ribo- replicate 1; Homo sapiens; RNA-Seq
Sample: SRS9107147
BioProject: PRJNA734257
BioSample: SAMN19487375
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: iPS cell-derived cardiomyocytes
cell line: WTC11 from a healthy male patient
differentiation: WNT modulation method day 26
genotype: Wild-Type
purification: Lactate method (PMID: 23168164)
Original files (1)
iPS cell-derived cardiomyocytes
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR14699656 10859015 1650570280 355.13 WT_GCaMP_1_S1.bam, SRR14699656, SRR14699656.lite SRA
SRX11037736 SRP322106 RNA-Seq PAIRED
GSM5350777: WTC11 Wild-Type Ribo- replicate 2; Homo sapiens; RNA-Seq
Sample: SRS9107148
BioProject: PRJNA734257
BioSample: SAMN19487374
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: iPS cell-derived cardiomyocytes
cell line: WTC11 from a healthy male patient
differentiation: WNT modulation method day 26
genotype: Wild-Type
purification: Lactate method (PMID: 23168164)
Original files (1)
iPS cell-derived cardiomyocytes
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR14699657 9392536 1427665472 304.87 WT_GCaMP_2_S3.bam, SRR14699657, SRR14699657.lite SRA
SRX11037737 SRP322106 RNA-Seq PAIRED
GSM5350778: WTC11 RBM20 R636S Het Ribo- replicate 1; Homo sapiens; RNA-Seq
Sample: SRS9107146
BioProject: PRJNA734257
BioSample: SAMN19487373
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: iPS cell-derived cardiomyocytes
cell line: WTC11 from a healthy male patient
differentiation: WNT modulation method day 26
genotype: RBM20 R636S Het
purification: Lactate method (PMID: 23168164)
Original files (1)
iPS cell-derived cardiomyocytes
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR14699658 9366672 1423734144 309.67 R636S_Het_1_S4.bam, SRR14699658, SRR14699658.lite SRA
SRX11037738 SRP322106 RNA-Seq PAIRED
GSM5350779: WTC11 RBM20 R636S Het Ribo- replicate 2; Homo sapiens; RNA-Seq
Sample: SRS9107149
BioProject: PRJNA734257
BioSample: SAMN19487372
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: iPS cell-derived cardiomyocytes
cell line: WTC11 from a healthy male patient
differentiation: WNT modulation method day 26
genotype: RBM20 R636S Het
purification: Lactate method (PMID: 23168164)
Original files (1)
iPS cell-derived cardiomyocytes
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR14699659 9668474 1469608048 312.05 R636S_Het_2_S5.bam, SRR14699659, SRR14699659.lite SRA
SRX11037739 SRP322106 RNA-Seq PAIRED
GSM5350780: WTC11 RBM20 R636S Het Ribo- replicate 3; Homo sapiens; RNA-Seq
Sample: SRS9107151
BioProject: PRJNA734257
BioSample: SAMN19487392
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: iPS cell-derived cardiomyocytes
cell line: WTC11 from a healthy male patient
differentiation: WNT modulation method day 26
genotype: RBM20 R636S Het
purification: Lactate method (PMID: 23168164)
Original files (1)
iPS cell-derived cardiomyocytes
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR14699660 7975515 1212278280 262.5 R636S_Het_3_S6.bam, SRR14699660, SRR14699660.lite SRA
SRX11037740 SRP322106 RNA-Seq PAIRED
GSM5350781: WTC11 RBM20 R636S Homo Ribo- replicate 1; Homo sapiens; RNA-Seq
Sample: SRS9107150
BioProject: PRJNA734257
BioSample: SAMN19487391
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: iPS cell-derived cardiomyocytes
cell line: WTC11 from a healthy male patient
differentiation: WNT modulation method day 26
genotype: RBM20 R636S Homo
purification: Lactate method (PMID: 23168164)
Original files (1)
iPS cell-derived cardiomyocytes
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR14699661 10638458 1617045616 341.04 R636S_Homo_S7.bam, SRR14699661, SRR14699661.lite SRA
SRX11037741 SRP322106 RNA-Seq PAIRED
GSM5350782: WTC11 RBM20 8-bp deletion Homo Ribo- replicate 1; Homo sapiens; RNA-Seq
Sample: SRS9107152
BioProject: PRJNA734257
BioSample: SAMN19487390
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: iPS cell-derived cardiomyocytes
cell line: WTC11 from a healthy male patient
differentiation: WNT modulation method day 26
genotype: RBM20 8-bp deletion Homo
purification: Lactate method (PMID: 23168164)
Original files (1)
iPS cell-derived cardiomyocytes
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR14699662 9627924 1463444448 309.54 8bp_del_Homo_1_S10.bam, SRR14699662, SRR14699662.lite SRA
SRX11037742 SRP322106 RNA-Seq PAIRED
GSM5350783: WTC11 RBM20 8-bp deletion Homo Ribo- replicate 2; Homo sapiens; RNA-Seq
Sample: SRS9107153
BioProject: PRJNA734257
BioSample: SAMN19487389
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: iPS cell-derived cardiomyocytes
cell line: WTC11 from a healthy male patient
differentiation: WNT modulation method day 26
genotype: RBM20 8-bp deletion Homo
purification: Lactate method (PMID: 23168164)
Original files (1)
iPS cell-derived cardiomyocytes
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR14699663 11745307 1785286664 372.03 8bp_del_Homo_2_S2.bam, SRR14699663, SRR14699663.lite SRA

Linked Publications (1)

Gain-of-function cardiomyopathic mutations in RBM20 rewire splicing regulation and re-distribute ribonucleoprotein granules within processing bodies.
Nature communications · 2021

Data Files (8)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
— 8bp_del_Homo_1_S10.bam RNA-Seq 309.5 MB link
— 8bp_del_Homo_2_S2.bam RNA-Seq 372.0 MB link
— R636S_Het_1_S4.bam RNA-Seq 309.7 MB link
— R636S_Het_2_S5.bam RNA-Seq 312.0 MB link
— R636S_Het_3_S6.bam RNA-Seq 262.5 MB link
— R636S_Homo_S7.bam RNA-Seq 341.0 MB link
— WT_GCaMP_1_S1.bam RNA-Seq 355.1 MB link
— WT_GCaMP_2_S3.bam RNA-Seq 304.9 MB link