← All datasets

GSE125125

GSE GEO
View on GEO Export SRA CSV

Overriding FUS autoregulation triggers gain-of-toxic dysfunctions in autophagy-lysosome axis and RNA metabolism

Organism: Mus musculus
Platform: GPL21103
Samples: 14
Experiment Types:
Expression profiling by high throughput sequencing
Submitted: Jan 15 2019
Last Updated: Mar 19 2019
Status: Public on Jan 16 2019
Contact: Shuo-Chien,,Ling (National University of Singapore)

Relations

BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA515288 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP179634

Summary

Mutations in coding and non-coding regions of FUS cause amyotrophic lateral sclerosis (ALS). The latter mutations may exert toxicity by increasing FUS accumulation. We showhere that broad expression within the nervous system of wild type or either of two ALS-linkedmutants of human FUS produces progressive motor phenotypes accompanied bycharacteristic ALS-like pathology. FUS levels are autoregulated by a mechanism in whichwild type or ALS-linked mutants of human FUS downregulating endogenous FUS at bothmRNA and protein levels. Increasing wild type human FUS expression achieved bysaturating this autoregulatory mechanism produces a rapidly progressive neurologicalphenotype and dose-dependent lethality. Genome-wide expression analysis reveals mis-regulation of genes that are largely distinct from the alterations observed by the acute FUS reduction in the spinal cord. Among these are increased expression of lysosomal proteins,suggestive of disruption in protein homeostasis as a potential gain-of-toxic mechanism.Indeed, increased expression of wild type and ALS-linked mutations in FUS inhibitautophagy with accumulated p62/sequestosome observed in spinal cord motor neurons.Taken together, our data suggests that overriding FUS autoregulation triggers gain-of-toxicproperties in the autophagy-lysosome axis and deregulation of RNA metabolism, highlightinga disruption in protein and RNA homeostasis in FUS-mediated toxicity.

Overall Design

Differential gene expression analysis in spinal cord sections of <> mice

Analysis (3 steps)

View Data Processing
Processing steps for GSE125125
  1. Sequenced reads filtered for low quality reads with skewer 0.2.2 (-Q 5)
  2. RNA-seq read quantification was performed using Kallisto 0.44.0 (-b 50 –single -l 200 -s 20)
  3. DEG calling was performed using Sleuth 0.28.1 (Control contrast)

Supplementary Files (4)

GSE125125_base_nontg_FUS_wt_het_gene.tsv.gz Download
GSE125125_base_nontg_FUS_wt_homo_gene.tsv.gz Download
GSE125125_bs_control_fus_ko_wt_gene.tsv.gz Download
GSE125125_expression.tsv.gz Download
GEO Samples (14)

Dataset Citations (1)

Overriding FUS autoregulation in mice triggers gain-of-toxic dysfunctions in RNA metabolism and autophagy-lysosome axis.
PMID 30747709 · 2019 · eLife
Shuo-Chien Ling, Somasish Ghosh Dastidar, Seiya Tokunaga, Wan Yun Ho, Kenneth Lim, Hristelina Ilieva, Philippe A Parone, Sheue-Houy Tyan, Tsemay M Tse, Jer-Cherng Chang, Oleksandr Platoshyn, Ngoc B Bui, Anh Bui, Anne Vetto, Shuying Sun, Melissa McAlonis-Downes, Joo Seok Han, Debbie Swing, Katannya Kapeli, Gene W Yeo, Lino Tessarollo, Martin Marsala, Christopher E Shaw, Greg Tucker-Kellogg, Albert R La Spada, Clotilde Lagier-Tourenne, Sandrine Da Cruz, Don W Cleveland

SRA Experiments (14) and Runs (14)

Total: 10699 MB
SRX5252062 SRP179634 RNA-Seq SINGLE
GSM3563903: Nontransgenic, mouse ID 157; Mus musculus; RNA-Seq
Sample: SRS4253768
BioProject: PRJNA515288
BioSample: SAMN10752186
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Spinal cord
strain: C57BL/6
tissue: spinal cord
age: 30-day-old
genotype: non-transgenic control
Original files (1)
Spinal cord
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR8444929 28298537 1414926850 930.26 Sc_157.fastq.gz, SRR8444929, SRR8444929.sralite SRA
SRX5252063 SRP179634 RNA-Seq SINGLE
GSM3563904: Nontransgenic, mouse ID 163; Mus musculus; RNA-Seq
Sample: SRS4253769
BioProject: PRJNA515288
BioSample: SAMN10752185
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Spinal cord
strain: C57BL/6
tissue: spinal cord
age: 30-day-old
genotype: non-transgenic control
Original files (1)
Spinal cord
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR8444930 28127653 1406382650 927.02 Sc_163.fastq.gz, SRR8444930, SRR8444930.sralite SRA
SRX5252064 SRP179634 RNA-Seq SINGLE
GSM3563905: Nontransgenic, mouse ID 821; Mus musculus; RNA-Seq
Sample: SRS4253770
BioProject: PRJNA515288
BioSample: SAMN10752184
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Spinal cord
strain: C57BL/6
tissue: spinal cord
age: 30-day-old
genotype: non-transgenic control
Original files (1)
Spinal cord
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR8444931 24360938 1218046900 802.42 Sc_821.fastq.gz, SRR8444931, SRR8444931.sralite SRA
SRX5252065 SRP179634 RNA-Seq SINGLE
GSM3563906: hFUS overexpression Het (line 101), mouse ID 540; Mus musculus; RNA-Seq
Sample: SRS4253771
BioProject: PRJNA515288
BioSample: SAMN10752183
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Spinal cord
strain: C57BL/6
tissue: spinal cord
age: 30-day-old
genotype: wt-FUS transgene hemizygote
Original files (1)
Spinal cord
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR8444932 27007090 1350354500 884.32 SC_540.fastq.gz, SRR8444932, SRR8444932.sralite SRA
SRX5252066 SRP179634 RNA-Seq SINGLE
GSM3563907: hFUS overexpression Het (line 101), mouse ID 545; Mus musculus; RNA-Seq
Sample: SRS4253772
BioProject: PRJNA515288
BioSample: SAMN10752182
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Spinal cord
strain: C57BL/6
tissue: spinal cord
age: 30-day-old
genotype: wt-FUS transgene hemizygote
Original files (1)
Spinal cord
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR8444933 25780993 1289049650 851.46 Sc_545.fastq.gz, SRR8444933, SRR8444933.sralite SRA
SRX5252067 SRP179634 RNA-Seq SINGLE
GSM3563908: hFUS overexpression Het (line 101), mouse ID 825; Mus musculus; RNA-Seq
Sample: SRS4253773
BioProject: PRJNA515288
BioSample: SAMN10752181
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Spinal cord
strain: C57BL/6
tissue: spinal cord
age: 30-day-old
genotype: wt-FUS transgene hemizygote
Original files (1)
Spinal cord
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR8444934 35352805 1767640250 1159.23 Sc_825.fastq.gz, SRR8444934, SRR8444934.sralite SRA
SRX5252068 SRP179634 RNA-Seq SINGLE
GSM3563909: hFUS overexpression Homo (line 101), mouse ID 166; Mus musculus; RNA-Seq
Sample: SRS4253775
BioProject: PRJNA515288
BioSample: SAMN10752180
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Spinal cord
strain: C57BL/6
tissue: spinal cord
age: 30-day-old
genotype: wt-FUS transgene homozygote
Original files (1)
Spinal cord
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR8444935 26524434 1326221700 872.7 Sc_166.fastq.gz, SRR8444935, SRR8444935.sralite SRA
SRX5252069 SRP179634 RNA-Seq SINGLE
GSM3563910: hFUS overexpression Homo (line 101), mouse ID 858; Mus musculus; RNA-Seq
Sample: SRS4253774
BioProject: PRJNA515288
BioSample: SAMN10752179
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Spinal cord
strain: C57BL/6
tissue: spinal cord
age: 30-day-old
genotype: wt-FUS transgene homozygote
Original files (1)
Spinal cord
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR8444936 24418823 1220941150 803.89 Sc_858.fastq.gz, SRR8444936, SRR8444936.sralite SRA
SRX5252070 SRP179634 RNA-Seq SINGLE
GSM3563911: hFUS overexpression Homo (line 101), mouse ID 882; Mus musculus; RNA-Seq
Sample: SRS4253776
BioProject: PRJNA515288
BioSample: SAMN10752178
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Spinal cord
strain: C57BL/6
tissue: spinal cord
age: 30-day-old
genotype: wt-FUS transgene homozygote
Original files (1)
Spinal cord
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR8444937 27374910 1368745500 900.3 Sc_882.fastq.gz, SRR8444937, SRR8444937.sralite SRA
SRX5252071 SRP179634 RNA-Seq SINGLE
GSM3563912: control ASO treatment, biological recplicate 1; Mus musculus; RNA-Seq
Sample: SRS4253777
BioProject: PRJNA515288
BioSample: SAMN10752177
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Spinal cord
strain: C57BL/6
tissue: spinal cord
age: 60-day-old
genotype: C57BL/6 wild type mice
Original files (1)
Spinal cord
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR8444938 24916551 1245827550 384.95 KQ_23_ATCACG_L006_R1.fastq.gz, SRR8444938, SRR8444938.sralite SRA
SRX5252072 SRP179634 RNA-Seq SINGLE
GSM3563913: control ASO treatment, biological recplicate 2; Mus musculus; RNA-Seq
Sample: SRS4253778
BioProject: PRJNA515288
BioSample: SAMN10752176
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Spinal cord
strain: C57BL/6
tissue: spinal cord
age: 60-day-old
genotype: C57BL/6 wild type mice
Original files (1)
Spinal cord
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR8444939 30511896 1525594800 475.26 KQ_24_TTAGGC_L006_R1.fastq.gz, SRR8444939, SRR8444939.sralite SRA
SRX5252073 SRP179634 RNA-Seq SINGLE
GSM3563914: control ASO treatment, biological recplicate 3; Mus musculus; RNA-Seq
Sample: SRS4253779
BioProject: PRJNA515288
BioSample: SAMN10752175
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Spinal cord
strain: C57BL/6
tissue: spinal cord
age: 60-day-old
genotype: C57BL/6 wild type mice
Original files (1)
Spinal cord
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR8444940 42837543 2141877150 663.25 KQ_25_ACTTGA_L006_R1.fastq.gz, SRR8444940, SRR8444940.sralite SRA
SRX5252074 SRP179634 RNA-Seq SINGLE
GSM3563915: ASO Fus knockdown, biological recplicate 1; Mus musculus; RNA-Seq
Sample: SRS4253780
BioProject: PRJNA515288
BioSample: SAMN10752174
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Spinal cord
strain: C57BL/6
tissue: spinal cord
age: 60-day-old
genotype: C57BL/6 wild type mice
Original files (1)
Spinal cord
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR8444941 32303135 1615156750 496.18 KQ_27_TAGCTT_L006_R1.fastq.gz, SRR8444941, SRR8444941.sralite SRA
SRX5252075 SRP179634 RNA-Seq SINGLE
GSM3563916: ASO Fus knockdown, biological recplicate 2; Mus musculus; RNA-Seq
Sample: SRS4253781
BioProject: PRJNA515288
BioSample: SAMN10752173
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Spinal cord
strain: C57BL/6
tissue: spinal cord
age: 60-day-old
genotype: C57BL/6 wild type mice
Original files (1)
Spinal cord
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR8444942 35488691 1774434550 547.75 KQ_28_GGCTAC_L006_R1.fastq.gz, SRR8444942, SRR8444942.sralite SRA

Linked Publications (1)

Data Files (24)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
KQ_23_ATCACG_L006_R1.fastq.gz RNA-Seq 384.9 MB link
KQ_24_TTAGGC_L006_R1.fastq.gz RNA-Seq 475.3 MB link
KQ_25_ACTTGA_L006_R1.fastq.gz RNA-Seq 663.2 MB link
KQ_27_TAGCTT_L006_R1.fastq.gz RNA-Seq 496.2 MB link
KQ_28_GGCTAC_L006_R1.fastq.gz RNA-Seq 547.8 MB link
Sc_157.fastq.gz RNA-Seq 930.3 MB link
Sc_163.fastq.gz RNA-Seq 927.0 MB link
Sc_166.fastq.gz RNA-Seq 872.7 MB link
SC_540.fastq.gz RNA-Seq 884.3 MB link
Sc_545.fastq.gz RNA-Seq 851.5 MB link
Sc_821.fastq.gz RNA-Seq 802.4 MB link
Sc_825.fastq.gz RNA-Seq 1.1 GB link
Sc_858.fastq.gz RNA-Seq 803.9 MB link
Sc_882.fastq.gz RNA-Seq 900.3 MB link
SRR8444929 RNA-Seq 930.3 MB link
SRR8444930 RNA-Seq 927.0 MB link
SRR8444931 RNA-Seq 802.4 MB link
SRR8444932 RNA-Seq 884.3 MB link
SRR8444933 RNA-Seq 851.5 MB link
SRR8444935 RNA-Seq 872.7 MB link
SRR8444936 RNA-Seq 803.9 MB link
SRR8444938 RNA-Seq 384.9 MB link
SRR8444939.sralite RNA-Seq 475.3 MB link
SRR8444941 RNA-Seq 496.2 MB link