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GSE152033

GSE GEO
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RNA-targeting Cas9 corrects molecular and physiological features in pre-clinical model of myotonic dystrophy type 1

Organism: Mus musculus
Platform: GPL21103
Samples: 14
Experiment Types:
Expression profiling by high throughput sequencing
Submitted: Jun 08 2020
Last Updated: Jul 01 2020
Status: Public on Jul 01 2020
Contact: Gene,,Yeo (UCSD)

Relations

BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA638132 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP266474

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 in a mouse model of myotonic Dystrophy (DM1). Furthermore we show that gene expression is not altered with RCas9 treatment in WT mice with or without treatment with immunosuppression

Overall Design

We performed paired-end RNA-seq for either non-targeting (NT) and CTG-targeting (RCas9-CTG or PIN ) treated tibialis anterior muscles of myotonic dystrophy (DM1) mice called HSALR. Furthermore, we treated WT tibialis anterior muscle with either sgRNA only (G1), RCas9-CTG (G2) or RCas9-CTG along with immunosuppression with Tacrolimus and CTLA4-Ig. Following this we performed paired-end RNA-Seq

Analysis (8 steps)

View Data Processing
Processing steps for GSE152033
  1. RNA-seq data was aligned to the mouse mm10 genome build using Olego aligner, expression and alternative splicing were estimated using quantas as described below.
  2. Quantas software as described in Charizanis et al, 2012, Neuron, was used to estimate gene expression and alternative splicing.
  3. Olego aligned alignment files were used to count observed junction reads (for splicing) for each exon or RPKMs for each gene expression.
  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. Forcalculate gene expression between various groups edgeR was used which is a part of the Quantas suite.
  8. See documentation at http://zhanglab.c2b2.columbia.edu/index.php/Quantas_Documentation.

Supplementary Files (3)

GSE152033_Supplementary_Table_1.xlsx Download
GSE152033_Supplementary_Table_2.xlsx Download
GSE152033_Supplementary_Table_4.xlsx Download
GEO Samples (14)
GSM4600774 GSM4600775 GSM4600776 GSM4600777 GSM4600778 GSM4600779 GSM4600780 GSM4600781 GSM4600782 GSM4600783 GSM4600784 GSM4600785 GSM4600786 GSM4600787

SRA Experiments (14) and Runs (20)

Total: 69661 MB
SRX8499400 SRP266474 RNA-Seq PAIRED
GSM4600774: HSALR-NT1 Non-Targeting RCas9 -1; Mus musculus; RNA-Seq
Sample: SRS6798118
BioProject: PRJNA638132
BioSample: SAMN15169091
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Mouse Tibialis Anterior
tissue: Tibialis Anterior muscle
time point: 4 weeks post treatment
genotype: HSALR (DM1)
Original files (1)
Mouse Tibialis Anterior
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR11955144 18884105 3776821000 1848.69 NT-11_S3_L001_R1_001.fastq.gz, NT-11_S3_L001_R2_001.fastq.gz, SRR1195… SRA
SRR11955145 20290984 4058196800 2013.29 NT-11_S3_L002_R1_001.fastq.gz, NT-11_S3_L002_R2_001.fastq.gz, SRR1195… SRA
SRX8499401 SRP266474 RNA-Seq PAIRED
GSM4600775: HSALR-NT2 Non-Targeting RCas9 -2; Mus musculus; RNA-Seq
Sample: SRS6798119
BioProject: PRJNA638132
BioSample: SAMN15169090
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Mouse Tibialis Anterior
tissue: Tibialis Anterior muscle
time point: 4 weeks post treatment
genotype: HSALR (DM1)
Original files (1)
Mouse Tibialis Anterior
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR11955146 17202410 3440482000 1665.03 NT-F_S1_L001_R1_001.fastq.gz, NT-F_S1_L001_R2_001.fastq.gz, SRR119551… SRA
SRR11955147 18143648 3628729600 1780.75 NT-F_S1_L002_R1_001.fastq.gz, NT-F_S1_L002_R2_001.fastq.gz, SRR119551… SRA
SRX8499402 SRP266474 RNA-Seq PAIRED
GSM4600776: HSALR-PIN1 CTG-Targetting RCas9 -1; Mus musculus; RNA-Seq
Sample: SRS6798120
BioProject: PRJNA638132
BioSample: SAMN15169089
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Mouse Tibialis Anterior
tissue: Tibialis Anterior muscle
time point: 4 weeks post treatment
genotype: HSALR (DM1)
Original files (1)
Mouse Tibialis Anterior
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR11955148 18248957 3649791400 1784.73 Rcas9-PIN_S2_L001_R1_001.fastq.gz, Rcas9-PIN_S2_L001_R2_001.fastq.gz,… SRA
SRR11955149 19293477 3858695400 1914.53 Rcas9-PIN_S2_L002_R1_001.fastq.gz, Rcas9-PIN_S2_L002_R2_001.fastq.gz,… SRA
SRX8499403 SRP266474 RNA-Seq PAIRED
GSM4600777: HSALR-PIN2 CTG-Targetting RCas9 -2; Mus musculus; RNA-Seq
Sample: SRS6798121
BioProject: PRJNA638132
BioSample: SAMN15169088
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Mouse Tibialis Anterior
tissue: Tibialis Anterior muscle
time point: 4 weeks post treatment
genotype: HSALR (DM1)
Original files (1)
Mouse Tibialis Anterior
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR11955150 17883674 3576734800 1708.17 PIN2-10_S4_L001_R1_001.fastq.gz, PIN2-10_S4_L001_R2_001.fastq.gz, SRR… SRA
SRR11955151 19386875 3877375000 1877.87 PIN2-10_S4_L002_R1_001.fastq.gz, PIN2-10_S4_L002_R2_001.fastq.gz, SRR… SRA
SRX8499404 SRP266474 RNA-Seq PAIRED
GSM4600778: HSALR-PIN3 CTG-Targetting RCas9 -3; Mus musculus; RNA-Seq
Sample: SRS6798122
BioProject: PRJNA638132
BioSample: SAMN15169087
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Mouse Tibialis Anterior
tissue: Tibialis Anterior muscle
time point: 4 weeks post treatment
genotype: HSALR (DM1)
Original files (1)
Mouse Tibialis Anterior
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR11955152 20135327 4027065400 1937.16 PIN3-12_S6_L001_R1_001.fastq.gz, PIN3-12_S6_L001_R2_001.fastq.gz, SRR… SRA
SRR11955153 21645876 4329175200 2112.41 PIN3-12_S6_L002_R1_001.fastq.gz, PIN3-12_S6_L002_R2_001.fastq.gz, SRR… SRA
SRX8499405 SRP266474 RNA-Seq PAIRED
GSM4600779: HSALR-MBNL1; Mus musculus; RNA-Seq
Sample: SRS6798123
BioProject: PRJNA638132
BioSample: SAMN15169086
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Mouse Tibialis Anterior
tissue: Tibialis Anterior muscle
time point: 4 weeks post treatment
genotype: HSALR (DM1)
Original files (1)
Mouse Tibialis Anterior
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR11955154 16022999 3204599800 1559.06 MBNL-10_S7_L001_R1_001.fastq.gz, MBNL-10_S7_L001_R2_001.fastq.gz, SRR… SRA
SRR11955155 17236276 3447255200 1699.59 MBNL-10_S7_L002_R1_001.fastq.gz, MBNL-10_S7_L002_R2_001.fastq.gz, SRR… SRA
SRX8499406 SRP266474 RNA-Seq PAIRED
GSM4600780: Group_1_(guide_only)_1_week_post_injection; Mus musculus; RNA-Seq
Sample: SRS6798124
BioProject: PRJNA638132
BioSample: SAMN15169085
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Mouse Tibialis Anterior
tissue: Tibialis Anterior muscle
time point: 1 weeks post treatment
genotype: WT
strain: FVB/NJ
Original files (1)
Mouse Tibialis Anterior
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR11955156 56223824 16867147200 6998.24 G1-2-12w_R1_001.fastq.gz, G1-2-12w_R2_001.fastq.gz, SRR11955156, SRR1… SRA
SRX8499407 SRP266474 RNA-Seq PAIRED
GSM4600781: Group_2_(RCas9-CTG)_1_week_post_injection; Mus musculus; RNA-Seq
Sample: SRS6798125
BioProject: PRJNA638132
BioSample: SAMN15169084
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Mouse Tibialis Anterior
tissue: Tibialis Anterior muscle
time point: 1 weeks post treatment
genotype: WT
strain: FVB/NJ
Original files (1)
Mouse Tibialis Anterior
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR11955157 56823254 17046976200 7056.42 G1-6-12w_R1_001.fastq.gz, G1-6-12w_R2_001.fastq.gz, SRR11955157, SRR1… SRA
SRX8499408 SRP266474 RNA-Seq PAIRED
GSM4600782: Group_5_(RCas9-CTG_+_immunosuppression)_6_weeks_post_injection; Mus musculus; RNA-Seq
Sample: SRS6798126
BioProject: PRJNA638132
BioSample: SAMN15169083
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Mouse Tibialis Anterior
tissue: Tibialis Anterior muscle
time point: 6 weeks post treatment
genotype: WT
strain: FVB/NJ
Original files (1)
Mouse Tibialis Anterior
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR11955158 35911292 10773387600 4413.6 G1F1-6w_R1_001.fastq.gz, G1F1-6w_R2_001.fastq.gz, SRR11955158, SRR119… SRA
SRX8499409 SRP266474 RNA-Seq PAIRED
GSM4600783: Group_5_(RCas9-CTG_+_immunosuppression)_12_weeks_post_injection; Mus musculus; RNA-Seq
Sample: SRS6798127
BioProject: PRJNA638132
BioSample: SAMN15169082
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Mouse Tibialis Anterior
tissue: Tibialis Anterior muscle
time point: 12 weeks post treatment
genotype: WT
strain: FVB/NJ
Original files (1)
Mouse Tibialis Anterior
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR11955159 52242082 15672624600 6487.13 G1F2-1w_R1_001.fastq.gz, G1F2-1w_R2_001.fastq.gz, SRR11955159, SRR119… SRA
SRX8499410 SRP266474 RNA-Seq PAIRED
GSM4600784: Group_2_(RCas9-CTG)_6_week_post_injection; Mus musculus; RNA-Seq
Sample: SRS6798128
BioProject: PRJNA638132
BioSample: SAMN15169081
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Mouse Tibialis Anterior
tissue: Tibialis Anterior muscle
time point: 6 weeks post treatment
genotype: WT
strain: FVB/NJ
Original files (1)
Mouse Tibialis Anterior
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR11955160 43431930 13029579000 5432.39 G2F1-6w_R1_001.fastq.gz, G2F1-6w_R2_001.fastq.gz, SRR11955160, SRR119… SRA
SRX8499411 SRP266474 RNA-Seq PAIRED
GSM4600785: Group_1_(guide_only)_12_week_post_injection; Mus musculus; RNA-Seq
Sample: SRS6798129
BioProject: PRJNA638132
BioSample: SAMN15169080
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Mouse Tibialis Anterior
tissue: Tibialis Anterior muscle
time point: 12 weeks post treatment
genotype: WT
strain: FVB/NJ
Original files (1)
Mouse Tibialis Anterior
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR11955161 53508053 16052415900 6706.86 G2F2-1w_R1_001.fastq.gz, G2F2-1w_R2_001.fastq.gz, SRR11955161, SRR119… SRA
SRX8499412 SRP266474 RNA-Seq PAIRED
GSM4600786: Group_2_(RCas9)_12_week_post_injection; Mus musculus; RNA-Seq
Sample: SRS6798130
BioProject: PRJNA638132
BioSample: SAMN15169079
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Mouse Tibialis Anterior
tissue: Tibialis Anterior muscle
time point: 12 weeks post treatment
genotype: WT
strain: FVB/NJ
Original files (1)
Mouse Tibialis Anterior
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR11955162 43781088 13134326400 5444.93 G5-18-12w_R1_001.fastq.gz, G5-18-12w_R2_001.fastq.gz, SRR11955162, SR… SRA
SRX8499413 SRP266474 RNA-Seq PAIRED
GSM4600787: Group_1_(guide_only)_6_week_post_injection; Mus musculus; RNA-Seq
Sample: SRS6798131
BioProject: PRJNA638132
BioSample: SAMN15169078
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Mouse Tibialis Anterior
tissue: Tibialis Anterior muscle
time point: 6 weeks post treatment
genotype: WT
strain: FVB/NJ
Original files (1)
Mouse Tibialis Anterior
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR11955163 42232626 12669787800 5219.73 G5F2-6w_R1_001.fastq.gz, G5F2-6w_R2_001.fastq.gz, SRR11955163, SRR119… SRA

Linked Publications (1)

The sustained expression of Cas9 targeting toxic RNAs reverses disease phenotypes in mouse models of myotonic dystrophy type 1.
Nature biomedical engineering · 2021

Data Files (20)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
— G1-2-12w_R1_001.fastq.gz RNA-Seq 6.8 GB link
— G1-6-12w_R1_001.fastq.gz RNA-Seq 6.9 GB link
— G1F1-6w_R1_001.fastq.gz RNA-Seq 4.3 GB link
— G1F2-1w_R1_001.fastq.gz RNA-Seq 6.3 GB link
— G2F1-6w_R1_001.fastq.gz RNA-Seq 5.3 GB link
— G2F2-1w_R1_001.fastq.gz RNA-Seq 6.5 GB link
— G5-18-12w_R1_001.fastq.gz RNA-Seq 5.3 GB link
— G5F2-6w_R1_001.fastq.gz RNA-Seq 5.1 GB link
— MBNL-10_S7_L001_R1_001.fastq.gz RNA-Seq 1.5 GB link
— MBNL-10_S7_L002_R1_001.fastq.gz RNA-Seq 1.7 GB link
— NT-11_S3_L001_R1_001.fastq.gz RNA-Seq 1.8 GB link
— NT-11_S3_L002_R1_001.fastq.gz RNA-Seq 2.0 GB link
— NT-F_S1_L001_R1_001.fastq.gz RNA-Seq 1.6 GB link
— NT-F_S1_L002_R1_001.fastq.gz RNA-Seq 1.7 GB link
— PIN2-10_S4_L001_R1_001.fastq.gz RNA-Seq 1.7 GB link
— PIN2-10_S4_L002_R1_001.fastq.gz RNA-Seq 1.8 GB link
— PIN3-12_S6_L001_R1_001.fastq.gz RNA-Seq 1.9 GB link
— PIN3-12_S6_L002_R1_001.fastq.gz RNA-Seq 2.1 GB link
— Rcas9-PIN_S2_L001_R1_001.fastq.gz RNA-Seq 1.7 GB link
— Rcas9-PIN_S2_L002_R1_001.fastq.gz RNA-Seq 1.9 GB link