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GSE176060

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

Organism: Homo sapiens
Platform: GPL16791
Samples: 8
Experiment Types:
Other
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/PRJNA734705 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP322566

Summary

Homozygous R636S mutation was created by genome editing in an iPS cell line generated from a healthy female patient. Mutant and wild-type cells were differentiated into cardiomyocytes by modulating the WNT signaling pathway, and then are subjected to the lactate purification method. eCLIP was performed to identify targets of RBM20 in mutant and wild-type iPSC-CMs.

Overall Design

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

Analysis (3 steps)

View Data Processing
Processing steps for GSE176060
  1. library strategy: eCLIP
  2. Reproducible RBM20 peaks (hg19) obtained from replicate WT and R636S HMZ iPSC-CMs compared to size-matched input controls, were used for all down-stream analyses.
  3. Downstream bioinformatics were performed according to the default ENCODE eCLIP bioinformatics pipeline as described at from https://www.encodeproject.org/eclip/.

Supplementary Files (2)

GSE176060_R636S_peaks.bed.gz Download
GSE176060_WT_peaks.bed.gz Download
GEO Samples (8)
GSM5354304 GSM5354305 GSM5354306 GSM5354307 GSM5354308 GSM5354309 GSM5354310 GSM5354311

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: 8194 MB
SRX11061409 SRP322566 OTHER SINGLE
GSM5354304: WTC11 eCLIP input-control wild-type replicate 1; Homo sapiens; OTHER
Sample: SRS9128594
BioProject: PRJNA734705
BioSample: SAMN19518954
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: Wild-Type iPSC-cardiomyocytes
cell line: WTC11
cell line source: a healthy male patient
cell type: iPS cell-derived cardiomyocytes
differentiation: WNT modulation method day 26
purification: Lactate method (PMID: 23168164)
Original files (1)
Wild-Type iPSC-cardiomyocytes
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR14724399 36294341 2722075575 1031.1 SB_RBM20_WT1_IN_R_S50_L003_R1_001.fastq.gz, SRR14724399, SRR14724399.… SRA
SRX11061410 SRP322566 OTHER SINGLE
GSM5354305: WTC11 RBM20 eCLIP wild-type replicate 1; Homo sapiens; OTHER
Sample: SRS9128596
BioProject: PRJNA734705
BioSample: SAMN19518953
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: Wild-Type iPSC-cardiomyocytes
cell line: WTC11
cell line source: a healthy male patient
cell type: iPS cell-derived cardiomyocytes
differentiation: WNT modulation method day 26
purification: Lactate method (PMID: 23168164)
Original files (1)
Wild-Type iPSC-cardiomyocytes
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR14724400 36733508 2755013100 1026.33 SB_RBM20_WT1_CLIP_R_S51_L003_R1_001.fastq.gz, SRR14724400, SRR1472440… SRA
SRX11061411 SRP322566 OTHER SINGLE
GSM5354306: WTC11 eCLIP input-control wild-type replicate 2; Homo sapiens; OTHER
Sample: SRS9128593
BioProject: PRJNA734705
BioSample: SAMN19518952
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: Wild-Type iPSC-cardiomyocytes
cell line: WTC11
cell line source: a healthy male patient
cell type: iPS cell-derived cardiomyocytes
differentiation: WNT modulation method day 26
purification: Lactate method (PMID: 23168164)
Original files (1)
Wild-Type iPSC-cardiomyocytes
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR14724401 42772874 3207965550 1135.73 SB_RBM20_WT2_IN_R_S64_L004_R1_001.fastq.gz, SRR14724401, SRR14724401.… SRA
SRX11061412 SRP322566 OTHER SINGLE
GSM5354307: WTC11 RBM20 eCLIP wild-type replicate 2; Homo sapiens; OTHER
Sample: SRS9128595
BioProject: PRJNA734705
BioSample: SAMN19518951
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: Wild-Type iPSC-cardiomyocytes
cell line: WTC11
cell line source: a healthy male patient
cell type: iPS cell-derived cardiomyocytes
differentiation: WNT modulation method day 26
purification: Lactate method (PMID: 23168164)
Original files (1)
Wild-Type iPSC-cardiomyocytes
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR14724402 40327456 3024559200 1057.76 SB_RBM20_WT2_CLIP_R_S65_L004_R1_001.fastq.gz, SRR14724402, SRR1472440… SRA
SRX11061413 SRP322566 OTHER SINGLE
GSM5354308: WTC11 eCLIP input-control R636S replicate 1; Homo sapiens; OTHER
Sample: SRS9128713
BioProject: PRJNA734705
BioSample: SAMN19518950
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: RBM20-R636S homozygous iPSC-cardiomyocytes
cell line: WTC11
cell line source: a healthy male patient
cell type: iPS cell-derived cardiomyocytes
differentiation: WNT modulation method day 26
purification: Lactate method (PMID: 23168164)
Original files (1)
RBM20-R636S homozygous iPSC-cardiomyocytes
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR14724403 35789903 2684242725 1008.39 SB_RBM20_Homo1_IN_R_S52_L003_R1_001.fastq.gz, SRR14724403, SRR1472440… SRA
SRX11061414 SRP322566 OTHER SINGLE
GSM5354309: WTC11 RBM20 eCLIP R636S replicate 1; Homo sapiens; OTHER
Sample: SRS9128597
BioProject: PRJNA734705
BioSample: SAMN19518949
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: RBM20-R636S homozygous iPSC-cardiomyocytes
cell line: WTC11
cell line source: a healthy male patient
cell type: iPS cell-derived cardiomyocytes
differentiation: WNT modulation method day 26
purification: Lactate method (PMID: 23168164)
Original files (1)
RBM20-R636S homozygous iPSC-cardiomyocytes
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR14724404 33244065 2493304875 955.42 SB_RBM20_Homo1_CLIP_R_S53_L003_R1_001.fastq.gz, SRR14724404, SRR14724… SRA
SRX11061415 SRP322566 OTHER SINGLE
GSM5354310: WTC11 eCLIP input-control R636S replicate 2; Homo sapiens; OTHER
Sample: SRS9128599
BioProject: PRJNA734705
BioSample: SAMN19518948
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: RBM20-R636S homozygous iPSC-cardiomyocytes
cell line: WTC11
cell line source: a healthy male patient
cell type: iPS cell-derived cardiomyocytes
differentiation: WNT modulation method day 26
purification: Lactate method (PMID: 23168164)
Original files (1)
RBM20-R636S homozygous iPSC-cardiomyocytes
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR14724405 38382402 2878680150 1009.89 SB_RBM20_Homo2_IN_R_S66_L004_R1_001.fastq.gz, SRR14724405, SRR1472440… SRA
SRX11061416 SRP322566 OTHER SINGLE
GSM5354311: WTC11 RBM20 eCLIP R636S replicate 2; Homo sapiens; OTHER
Sample: SRS9128598
BioProject: PRJNA734705
BioSample: SAMN19518947
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: RBM20-R636S homozygous iPSC-cardiomyocytes
cell line: WTC11
cell line source: a healthy male patient
cell type: iPS cell-derived cardiomyocytes
differentiation: WNT modulation method day 26
purification: Lactate method (PMID: 23168164)
Original files (1)
RBM20-R636S homozygous iPSC-cardiomyocytes
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR14724406 36852916 2763968700 969.07 SB_RBM20_Homo2_CLIP_R_S67_L004_R1_001.fastq.gz, SRR14724406, SRR14724… 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 (16)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
— SB_RBM20_Homo1_CLIP_R_S53_L003_R1_001.fastq.gz OTHER 955.4 MB link
— SB_RBM20_Homo1_CLIP_R_S53_L003_R1_001.fastq.gz OTHER 955.4 MB link
— SB_RBM20_Homo1_IN_R_S52_L003_R1_001.fastq.gz OTHER 1008.4 MB link
— SB_RBM20_Homo1_IN_R_S52_L003_R1_001.fastq.gz OTHER 1008.4 MB link
— SB_RBM20_Homo2_CLIP_R_S67_L004_R1_001.fastq.gz OTHER 969.1 MB link
— SB_RBM20_Homo2_CLIP_R_S67_L004_R1_001.fastq.gz OTHER 969.1 MB link
— SB_RBM20_Homo2_IN_R_S66_L004_R1_001.fastq.gz OTHER 1009.9 MB link
— SB_RBM20_Homo2_IN_R_S66_L004_R1_001.fastq.gz OTHER 1009.9 MB link
— SB_RBM20_WT1_CLIP_R_S51_L003_R1_001.fastq.gz OTHER 1.0 GB link
— SB_RBM20_WT1_CLIP_R_S51_L003_R1_001.fastq.gz OTHER 1.0 GB link
— SB_RBM20_WT1_IN_R_S50_L003_R1_001.fastq.gz OTHER 1.0 GB link
— SB_RBM20_WT1_IN_R_S50_L003_R1_001.fastq.gz OTHER 1.0 GB link
— SB_RBM20_WT2_CLIP_R_S65_L004_R1_001.fastq.gz OTHER 1.0 GB link
— SB_RBM20_WT2_CLIP_R_S65_L004_R1_001.fastq.gz OTHER 1.0 GB link
— SB_RBM20_WT2_IN_R_S64_L004_R1_001.fastq.gz OTHER 1.1 GB link
— SB_RBM20_WT2_IN_R_S64_L004_R1_001.fastq.gz OTHER 1.1 GB link