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GSE100943

GSE GEO
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Microsatellite expansion RNA visualization, elimination, and reversal of molecular pathology by RNA-targeting Cas9

Organism: Homo sapiens
Platform: GPL20301
Samples: 9
Experiment Types:
Expression profiling by high throughput sequencing
Submitted: Jul 07 2017
Last Updated: May 15 2019
Status: Public on Aug 10 2017
Contact: Ranjan,,Batra (University of California San Diego)

Relations

BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA393468 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP111361

Summary

In this Study, we used RNA-targeting Cas9 (RCas9) to reverse characteristic Myotonic Dystrophy (DM1) cellular phenotypes such as elimination of RNA foci, MBNL relocalization, and reversal of transcriptome-wide splicing.

Overall Design

We performed RNA-seq for control and myotonic dystrophy (DM1) myoblasts and myotubes with various treatments including lentivirus mediated expression of either non-targeting (NT) or CTG-targeting (CTG) single guide RNA (sgRNA) and PIN-dCas9.Lentivirus mediated GFP expression was used as control.

Analysis (7 steps)

View Data Processing
Processing steps for GSE100943
  1. RNA-seq data was aligned to the human hg19 genome build using Olego alignes, and alternative splicing was estimated as described below.
  2. Quantas software as described in Charizanis et al, 2012, Neuron, was used to estimate alternative splicing.
  3. Olego aligned alignment files were used to count observed junction reads for each exon.
  4. Weighted number of exon or exon-junction fragments uniquely supporting the inclusion or skipping isoform of each cassette exon and a probability score was assigned to each isoform.
  5. A Fisher’s exact test was used to evaluate the statistical significance of splicing changes using both exon and exon-junction fragments, followed by Benjamini multiple testing correction to estimate the false discovery rate (FDR).
  6. In addition, inclusion or exclusion junction reads were used to calculate the proportional change of exon inclusion (dI).
  7. See documentation at http://zhanglab.c2b2.columbia.edu/index.php/Quantas_Documentation.

Supplementary Files (1)

GSE100943_RPKM_myo.txt.gz Download
GEO Samples (9)
GSM2696922 GSM2696923 GSM2696924 GSM2696925 GSM2696926 GSM2696927 GSM2696928 GSM2696929 GSM2696930

Dataset Citations (1)

Elimination of Toxic Microsatellite Repeat Expansion RNA by RNA-Targeting Cas9.
PMID 28803727 · 2017 · Cell
Ranjan Batra, David A Nelles, Elaine Pirie, Steven M Blue, Ryan J Marina, Harrison Wang, Isaac A Chaim, James D Thomas, Nigel Zhang, Vu Nguyen, Stefan Aigner, Sebastian Markmiller, Guangbin Xia, Kevin D Corbett, Maurice S Swanson, Gene W Yeo

SRA Experiments (9) and Runs (18)

Total: 36548 MB
SRX2990782 SRP111361 RNA-Seq PAIRED
GSM2696922: myoblast_Control-Non targeting; Homo sapiens; RNA-Seq
Sample: SRS2342765
BioProject: PRJNA393468
BioSample: SAMN07333951
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: Myoblasts
treatment: Lentivirus transduction with PIN-dCas9 and non targeting sgRNA
tag: Puromycin selection - 4 days
Original files (1)
Myoblasts
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR5812278 16236096 3225861912 1451.53 Myoblast1_S1_L001_R1_001.fastq.gz, Myoblast1_S1_L001_R2_001.fastq.gz,… SRA
SRR5812279 16605139 3299542067 1488.65 Myoblast1_S1_L002_R1_001.fastq.gz, Myoblast1_S1_L002_R2_001.fastq.gz,… SRA
SRX2990783 SRP111361 RNA-Seq PAIRED
GSM2696923: myoblast_Control-CTG targeting; Homo sapiens; RNA-Seq
Sample: SRS2342767
BioProject: PRJNA393468
BioSample: SAMN07333961
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: Myoblasts
treatment: Lentivirus transduction with PIN-dCas9 and CTG sgRNA
tag: Puromycin selection - 4 days
Original files (1)
Myoblasts
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR5812280 26724714 5311363747 2408.6 Myoblast2_S2_L001_R1_001.fastq.gz, Myoblast2_S2_L001_R2_001.fastq.gz,… SRA
SRR5812281 27239223 5414060318 2463.77 Myoblast2_S2_L002_R1_001.fastq.gz, Myoblast2_S2_L002_R2_001.fastq.gz,… SRA
SRX2990784 SRP111361 RNA-Seq PAIRED
GSM2696924: myoblast_Myotonic Dystriphy type I (DM1) GFP; Homo sapiens; RNA-Seq
Sample: SRS2342766
BioProject: PRJNA393468
BioSample: SAMN07333960
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: Myoblasts
treatment: Lentivirus transduction with GFP
tag: Puromycin selection - 4 days
Original files (1)
Myoblasts
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR5812282 26911183 5348735389 2411.12 Myoblast3_S3_L001_R1_001.fastq.gz, Myoblast3_S3_L001_R2_001.fastq.gz,… SRA
SRR5812283 27436366 5453526586 2466.18 Myoblast3_S3_L002_R1_001.fastq.gz, Myoblast3_S3_L002_R2_001.fastq.gz,… SRA
SRX2990785 SRP111361 RNA-Seq PAIRED
GSM2696925: myoblast_Myotonic Dystriphy type I (DM1) non targeting; Homo sapiens; RNA-Seq
Sample: SRS2342770
BioProject: PRJNA393468
BioSample: SAMN07333959
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: Myoblasts
treatment: Lentivirus transduction with PIN-dCas9 and non targeting sgRNA
tag: Puromycin selection - 4 days
Original files (1)
Myoblasts
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR5812284 16132608 3206248416 1434.79 Myoblast4_S4_L001_R1_001.fastq.gz, Myoblast4_S4_L001_R2_001.fastq.gz,… SRA
SRR5812285 16550333 3289509939 1474.98 Myoblast4_S4_L002_R1_001.fastq.gz, Myoblast4_S4_L002_R2_001.fastq.gz,… SRA
SRX2990786 SRP111361 RNA-Seq PAIRED
GSM2696926: myoblast_Myotonic Dystriphy type I (DM1) ctg targeting; Homo sapiens; RNA-Seq
Sample: SRS2342768
BioProject: PRJNA393468
BioSample: SAMN07333958
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: Myoblasts
treatment: Lentivirus transduction with PIN-dCas9 and CTG sgRNA
tag: Puromycin selection - 4 days
Original files (1)
Myoblasts
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR5812286 20325191 4040865009 1822.09 Myoblast5_S5_L001_R1_001.fastq.gz, Myoblast5_S5_L001_R2_001.fastq.gz,… SRA
SRR5812287 20863037 4148039539 1875.02 Myoblast5_S5_L002_R1_001.fastq.gz, Myoblast5_S5_L002_R2_001.fastq.gz,… SRA
SRX2990787 SRP111361 RNA-Seq PAIRED
GSM2696927: myotube_Control-Non targeting; Homo sapiens; RNA-Seq
Sample: SRS2342769
BioProject: PRJNA393468
BioSample: SAMN07333957
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: Myotubes
treatment: Lentivirus treatment with PIN-dCas9 and non targeting sgRNA
tag: Puromycin selection - 4 days
Original files (1)
Myotubes
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR5812288 25678992 5098229088 2329.04 Myotube1_S6_L001_R1_001.fastq.gz, Myotube1_S6_L001_R2_001.fastq.gz, S… SRA
SRR5812289 26242542 5211066775 2390.56 Myotube1_S6_L002_R1_001.fastq.gz, Myotube1_S6_L002_R2_001.fastq.gz, S… SRA
SRX2990788 SRP111361 RNA-Seq PAIRED
GSM2696928: myotube_Myotonic Dystriphy type I (DM1) non targeting; Homo sapiens; RNA-Seq
Sample: SRS2342772
BioProject: PRJNA393468
BioSample: SAMN07333956
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: Myotubes
treatment: Lentivirus transduction with PIN-dCas9 and CTG sgRNA
tag: Puromycin selection - 4 days
Original files (1)
Myotubes
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR5812290 28171474 2798164981 1264.1 Myotube2_S7_L001_R1_001.fastq.gz, Myotube2_S7_L001_R2_001.fastq.gz, S… SRA
SRR5812291 28718495 5704282525 2599.73 Myotube2_S7_L002_R1_001.fastq.gz, Myotube2_S7_L002_R2_001.fastq.gz, S… SRA
SRX2990789 SRP111361 RNA-Seq PAIRED
GSM2696929: myotube_Control-CTG targeting; Homo sapiens; RNA-Seq
Sample: SRS2342771
BioProject: PRJNA393468
BioSample: SAMN07333955
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: Myotubes
treatment: Lentivirus treatment with PIN-dCas9 and non targeting sgRNA
tag: Puromycin selection - 4 days
Original files (1)
Myotubes
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR5812292 22419494 4449210192 1992.34 Myotube3_S8_L001_R1_001.fastq.gz, Myotube3_S8_L001_R2_001.fastq.gz, S… SRA
SRR5812293 22895527 4544599638 2038.2 Myotube3_S8_L002_R1_001.fastq.gz, Myotube3_S8_L002_R2_001.fastq.gz, S… SRA
SRX2990790 SRP111361 RNA-Seq PAIRED
GSM2696930: myotube_Myotonic Dystriphy type I (DM1) ctg targeting; Homo sapiens; RNA-Seq
Sample: SRS2342773
BioProject: PRJNA393468
BioSample: SAMN07333954
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: Myotubes
treatment: Lentivirus transduction with PIN-dCas9 and CTG sgRNA
tag: Puromycin selection - 4 days
Original files (1)
Myotubes
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR5812294 25332398 5030790211 2288.7 Myotube4_S9_L001_R1_001.fastq.gz, Myotube4_S9_L001_R2_001.fastq.gz, S… SRA
SRR5812295 25892389 5142674717 2349.06 Myotube4_S9_L002_R1_001.fastq.gz, Myotube4_S9_L002_R2_001.fastq.gz, S… SRA

Linked Publications (1)

Elimination of Toxic Microsatellite Repeat Expansion RNA by RNA-Targeting Cas9.
Cell · 2017

Data Files (18)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
— Myoblast1_S1_L001_R1_001.fastq.gz RNA-Seq 1.4 GB link
— Myoblast1_S1_L002_R1_001.fastq.gz RNA-Seq 1.5 GB link
— Myoblast2_S2_L001_R1_001.fastq.gz RNA-Seq 2.4 GB link
— Myoblast2_S2_L002_R1_001.fastq.gz RNA-Seq 2.4 GB link
— Myoblast3_S3_L001_R1_001.fastq.gz RNA-Seq 2.4 GB link
— Myoblast3_S3_L002_R1_001.fastq.gz RNA-Seq 2.4 GB link
— Myoblast4_S4_L001_R1_001.fastq.gz RNA-Seq 1.4 GB link
— Myoblast4_S4_L002_R1_001.fastq.gz RNA-Seq 1.4 GB link
— Myoblast5_S5_L001_R1_001.fastq.gz RNA-Seq 1.8 GB link
— Myoblast5_S5_L002_R1_001.fastq.gz RNA-Seq 1.8 GB link
— Myotube1_S6_L001_R1_001.fastq.gz RNA-Seq 2.3 GB link
— Myotube1_S6_L002_R1_001.fastq.gz RNA-Seq 2.3 GB link
— Myotube2_S7_L001_R1_001.fastq.gz RNA-Seq 1.2 GB link
— Myotube2_S7_L002_R1_001.fastq.gz RNA-Seq 2.5 GB link
— Myotube3_S8_L001_R1_001.fastq.gz RNA-Seq 1.9 GB link
— Myotube3_S8_L002_R1_001.fastq.gz RNA-Seq 2.0 GB link
— Myotube4_S9_L001_R1_001.fastq.gz RNA-Seq 2.2 GB link
— Myotube4_S9_L002_R1_001.fastq.gz RNA-Seq 2.3 GB link