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GSE176045

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

Organism: Homo sapiens
Platform: GPL20301
Samples: 4
Experiment Types:
Expression profiling by high throughput sequencing
Submitted: Jun 02 2021
Last Updated: Dec 02 2021
Status: Public on Jun 03 2021
Contact: Nathan,,Salomonis (Cincinnati Children's Hospital)

Relations

SubSeries of: GSE175886 BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA734628 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP322397

Summary

RBM20 heterozygous (Het) mutation was created by genome editing in an iPS cell line generated from a healthy female 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 2 different genotypes as replicates

Analysis (4 steps)

View Data Processing
Processing steps for GSE176045
  1. RNA-Seq data was aligned to the human hg19 reference genome and transcriptome (Ensembl 72) using the software STAR.
  2. To accurately detect diverse alternative splicing events in iPSC-CM RNA-Seq, we adapted a recently developed Percent Spliced In (PSI) splicing method called MultiPath-PSI.
  3. MultiPath-PSI is available through AltAnalyze version 2.1.1, requiring aligned BAM files as input and was extensively benchmarked against other local splicing variation approaches (http://altanalyze.readthedocs.io/en/latest/Algorithms/#multipath-psi-splicing-algorithm).
  4. For gene expression Quantification Kallisto (https://pachterlab.github.io/kallisto/) was used.

Supplementary Files (1)

GSE176045_exp.WTB-PSI.txt.gz Download
GEO Samples (4)
GSM5353720 GSM5353721 GSM5353722 GSM5353723

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 (4) and Runs (4)

Total: 35227 MB
SRX11051163 SRP322397 RNA-Seq PAIRED
GSM5353720: WTB Wild-Type replicate 1; Homo sapiens; RNA-Seq
Sample: SRS9119082
BioProject: PRJNA734628
BioSample: SAMN19515205
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: iPS cell-derived cardiomyocytes
cell line: WTB from a healthy female patient
cell type: iPS cell-derived cardiomyocytes
differentiation: WNT modulation method day 26
purification: Lactate method (PMID: 23168164)
genotype: Wild-Type
Original files (1)
iPS cell-derived cardiomyocytes
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR14713281 91860275 18372055000 10121.73 WTB_WT-S1_r1_R1.fastq.gz, WTB_WT-S1_r1_R2.fastq.gz, SRR14713281, SRR1… SRA
SRX11051164 SRP322397 RNA-Seq PAIRED
GSM5353721: WTB Wild-Type replicate 2; Homo sapiens; RNA-Seq
Sample: SRS9119083
BioProject: PRJNA734628
BioSample: SAMN19515204
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: iPS cell-derived cardiomyocytes
cell line: WTB from a healthy female patient
cell type: iPS cell-derived cardiomyocytes
differentiation: WNT modulation method day 26
purification: Lactate method (PMID: 23168164)
genotype: Wild-Type
Original files (1)
iPS cell-derived cardiomyocytes
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR14713282 86218409 17243681800 9550.36 WTB_WT-S2_r1_R1.fastq.gz, WTB_WT-S2_r1_R2.fastq.gz, SRR14713282, SRR1… SRA
SRX11051165 SRP322397 RNA-Seq PAIRED
GSM5353722: WTB RBM20 R636S Het replicate 1; Homo sapiens; RNA-Seq
Sample: SRS9119084
BioProject: PRJNA734628
BioSample: SAMN19515203
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: iPS cell-derived cardiomyocytes
cell line: WTB from a healthy female patient
cell type: iPS cell-derived cardiomyocytes
differentiation: WNT modulation method day 26
purification: Lactate method (PMID: 23168164)
genotype: R636S Het
Original files (1)
iPS cell-derived cardiomyocytes
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR14713283 41289348 8257869600 4554.36 WTB_Het_R636-S1-r1_R1.fastq.gz, WTB_Het_R636-S1-r1_R2.fastq.gz, SRR14… SRA
SRX11051166 SRP322397 RNA-Seq PAIRED
GSM5353723: WTB RBM20 R636S Het replicate 2; Homo sapiens; RNA-Seq
Sample: SRS9119085
BioProject: PRJNA734628
BioSample: SAMN19515202
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: iPS cell-derived cardiomyocytes
cell line: WTB from a healthy female patient
cell type: iPS cell-derived cardiomyocytes
differentiation: WNT modulation method day 26
purification: Lactate method (PMID: 23168164)
genotype: R636S Het
Original files (1)
iPS cell-derived cardiomyocytes
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR14713284 98369742 19673948400 11000.5 WTB_Het_R636-S2_r1_R1.fastq.gz, WTB_Het_R636-S2_r1_R2.fastq.gz, SRR14… 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 (5)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
— SRR14713284.lite RNA-Seq 10.7 GB link
— WTB_Het_R636-S1-r1_R1.fastq.gz RNA-Seq 4.4 GB link
— WTB_Het_R636-S2_r1_R1.fastq.gz RNA-Seq 10.7 GB link
— WTB_WT-S1_r1_R1.fastq.gz RNA-Seq 9.9 GB link
— WTB_WT-S2_r1_R1.fastq.gz RNA-Seq 9.3 GB link