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GSE175886

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

Organism: Homo sapiens
Platform: GPL16791
Samples: 41
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

SuperSeries of: GSE113947 SuperSeries of: GSE175885 SuperSeries of: GSE176045 SuperSeries of: GSE176060 BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA734252

Summary

This SuperSeries is composed of the SubSeries listed below.

Overall Design

Refer to individual Series

Analysis (4 steps)

View Data Processing
Processing steps for GSE175886
  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)

GSE175886_RAW.tar Download
GEO Samples (41)
GSM3124390 GSM3124391 GSM3124392 GSM3124393 GSM3124394 GSM3124395 GSM3124396 GSM3124397 GSM3124398 GSM3124399 GSM3124400 GSM3124401 GSM3124402 GSM3124403 GSM3124404 GSM3124405 GSM3124406 GSM3124407 GSM3124408 GSM3124409 GSM3124410 GSM5350776 GSM5350777 GSM5350778 GSM5350779 GSM5350780 GSM5350781 GSM5350782 GSM5350783 GSM5353720 GSM5353721 GSM5353722 GSM5353723 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

Linked Publications (1)

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