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GSE51684

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Targeted degradation of sense and antisense C9orf72 RNA foci as therapy for amyotrophic lateral sclerosis and frontotemporal dementia (Multiplex Analysis of PolyA-linked Sequences)

Organism: Homo sapiens
Platform: GPL11154
Samples: 24
Experiment Types:
Expression profiling by high throughput sequencing
Submitted: Oct 24 2013
Last Updated: May 15 2019
Status: Public on Nov 12 2013
Contact: John,,Ravits (UCSD)

Relations

SubSeries of: GSE51741 BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA224740 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP032165

Summary

Purpose: The purpose of this experiment is to identify a C9-ALS/FTD specific genomic profile in fibroblast lines that is distinct from sporadic ALS without C9orf72 expansion and non-neurologic control cells. The study will then evaluate the effect on this identified profile of ASO treatment targeting the sense strand RNA transcript of the C9orf72 gene. Methods: Expression profiling was performed on RNAs from fibroblasts of four C9orf72 patients, four control individuals and four sporadic ALS patients using Multiplex Analysis of PolyA-linked Sequences method. Results: Hierarchical clustering of expression values for all genes showed that the four C9orf72 patient lines had an expression profile distinct from control and sporadic ALS lines. Statistical comparison of expression values between the four C9orf72 lines and the four control lines revealed that 122 genes were upregulated (defined by a False Discovery Rate FDR<0.05) and 34 genes were downregulated (defined by a False Discovery Rate FDR <0.05) in C9orf72 patient fibroblasts. Conclusions: A genome wide RNA signature can be defined in fibroblasts with C9orf72 expansion. ASO-mediated reduction of C9orf72 RNA levels in fibroblasts with the hexanucleotide expansion efficiently reduced accumulation of GGGGCC RNA foci. This did not, however, generate a reversal of the C9orf72 RNA profile.

Overall Design

Use of Multiplex Analysis of PolyA-linked Sequences to identify expression changes in fibroblasts from amyotrophic lateral sclerosis and frontotemporal dementia patients harboring an hexanucleotide expansion in the C9orf72 gene.

Analysis (4 steps)

View Data Processing
Processing steps for GSE51684
  1. Illumina Casava1.8.2 software used for basecalling.
  2. Demultiplexing based on index sequences
  3. Sequenced reads were mapped to Refseq RNA sequences using bowtie v0.12.7 with parameters -q -e 100 -m 10 --best --strata
  4. Count reads for each genes

Supplementary Files (1)

GSE51684_expression_table.txt.gz Download
GEO Samples (24)
GSM1250452 GSM1250453 GSM1250454 GSM1250455 GSM1250456 GSM1250457 GSM1250458 GSM1250459 GSM1250460 GSM1250461 GSM1250462 GSM1250463 GSM1250464 GSM1250465 GSM1250466 GSM1250467 GSM1250468 GSM1250469 GSM1250470 GSM1250471 GSM1250472 GSM1250473 GSM1250474 GSM1250475

Dataset Citations (1)

Targeted degradation of sense and antisense C9orf72 RNA foci as therapy for ALS and frontotemporal degeneration.
PMID 24170860 · 2013 · Proceedings of the National Academy of Sciences of the United States of America
Clotilde Lagier-Tourenne, Michael Baughn, Frank Rigo, Shuying Sun, Patrick Liu, Hai-Ri Li, Jie Jiang, Andrew T Watt, Seung Chun, Melanie Katz, Jinsong Qiu, Ying Sun, Shuo-Chien Ling, Qiang Zhu, Magdalini Polymenidou, Kevin Drenner, Jonathan W Artates, Melissa McAlonis-Downes, Sebastian Markmiller, Kasey R Hutt, Donald P Pizzo, Janet Cady, Matthew B Harms, Robert H Baloh, Scott R Vandenberg, Gene W Yeo, Xiang-Dong Fu, C Frank Bennett, Don W Cleveland, John Ravits

SRA Experiments (24) and Runs (24)

Total: 15358 MB
SRX368225 SRP032165 RNA-Seq SINGLE
GSM1250452: ALS14; Homo sapiens; RNA-Seq
Sample: SRS494267
BioProject: PRJNA224740
BioSample: SAMN02384545
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: Primary fibroblast cell cultures
tissue: Fibroblast
gender: male
age: 46 Years
genotype: Unknown Mutation
diagnosis: Sporadic ALS
disease onset: Bulbar
disease course: 6 years at time of biopsy
drug treatment: No ASO Treatment - Cells were exposed to cytofectin transfection reagent for four hours, but were not transfected with an ASO
Original files (1)
Primary fibroblast cell cultures
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR1017149 16362053 736292385 522.38 ALS14.fq.gz, SRR1017149, SRR1017149.sralite SRA
SRX368226 SRP032165 RNA-Seq SINGLE
GSM1250453: ALS20; Homo sapiens; RNA-Seq
Sample: SRS494266
BioProject: PRJNA224740
BioSample: SAMN02384544
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: Primary fibroblast cell cultures
tissue: Fibroblast
gender: male
age: 54 Years
genotype: Unknown Mutation
diagnosis: Sporadic ALS
disease onset: Arm
disease course: 10 months at time of biopsy
drug treatment: No ASO Treatment - Cells were exposed to cytofectin transfection reagent for four hours, but were not transfected with an ASO
Original files (1)
Primary fibroblast cell cultures
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR1017150 15460643 695728935 495.19 ALS20.fq.gz, SRR1017150, SRR1017150.sralite SRA
SRX368227 SRP032165 RNA-Seq SINGLE
GSM1250454: ALS25; Homo sapiens; RNA-Seq
Sample: SRS494269
BioProject: PRJNA224740
BioSample: SAMN02384546
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: Primary fibroblast cell cultures
tissue: Fibroblast
gender: male
age: 46 Years
genotype: Unknown Mutation
diagnosis: Sporadic ALS
disease onset: Bulbar
disease course: 2 years at time of biopsy
drug treatment: No ASO Treatment - Cells were exposed to cytofectin transfection reagent for four hours, but were not transfected with an ASO
Original files (1)
Primary fibroblast cell cultures
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR1017151 13903116 625640220 443.3 ALS25.fq.gz, SRR1017151, SRR1017151.sralite SRA
SRX368228 SRP032165 RNA-Seq SINGLE
GSM1250455: ALS2; Homo sapiens; RNA-Seq
Sample: SRS494268
BioProject: PRJNA224740
BioSample: SAMN02384549
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: Primary fibroblast cell cultures
tissue: Fibroblast
gender: male
age: 54 Years
genotype: Unknown Mutation
diagnosis: Sporadic ALS
disease onset: Bulbar
disease course: 2.5 years at time of biopsy
drug treatment: No ASO Treatment - Cells were exposed to cytofectin transfection reagent for four hours, but were not transfected with an ASO
Original files (1)
Primary fibroblast cell cultures
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR1017152 17001078 765048510 543.84 ALS2.fq.gz, SRR1017152, SRR1017152.sralite SRA
SRX368229 SRP032165 RNA-Seq SINGLE
GSM1250456: C9-1-Ctrl; Homo sapiens; RNA-Seq
Sample: SRS494270
BioProject: PRJNA224740
BioSample: SAMN02384547
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: Primary fibroblast cell cultures
tissue: Fibroblast
gender: male
age: 52 Years
genotype: C9orf72 Intron 1 Hexanucleotide Expansion
diagnosis: Familial ALS and Dementia
disease onset: Bulbar
disease course: 4 years at time of biopsy
drug treatment: No ASO Treatment - Cells were exposed to cytofectin transfection reagent for four hours, but were not transfected with an ASO
Original files (1)
Primary fibroblast cell cultures
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR1017153 18698729 841442805 594.96 C9-1-Ctrl.fq.gz, SRR1017153, SRR1017153.sralite SRA
SRX368230 SRP032165 RNA-Seq SINGLE
GSM1250457: C9-1-Mock; Homo sapiens; RNA-Seq
Sample: SRS494271
BioProject: PRJNA224740
BioSample: SAMN02384548
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: Primary fibroblast cell cultures
tissue: Fibroblast
gender: male
age: 52 Years
genotype: C9orf72 Intron 1 Hexanucleotide Expansion
diagnosis: Familial ALS and Dementia
disease onset: Bulbar
disease course: 4 years at time of biopsy
drug treatment: Transfection Control - Cells were treated with a control ASO which does not have any human genomic target.
Original files (1)
Primary fibroblast cell cultures
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR1017154 23092404 1039158180 734.76 C9-1-Mock.fq.gz, SRR1017154, SRR1017154.sralite SRA
SRX368231 SRP032165 RNA-Seq SINGLE
GSM1250458: C9-1-Tx; Homo sapiens; RNA-Seq
Sample: SRS494273
BioProject: PRJNA224740
BioSample: SAMN02384550
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: Primary fibroblast cell cultures
tissue: Fibroblast
gender: male
age: 52 Years
genotype: C9orf72 Intron 1 Hexanucleotide Expansion
diagnosis: Familial ALS and Dementia
disease onset: Bulbar
disease course: 4 years at time of biopsy
drug treatment: ASO Treatment - Cells were transfected with a nuclear RNase-H dependent antisense oligonucleotide targeting Exon 2 of Hs C9orf72. This ASO has been shown in previous work to efficiently knockdown all known isoforms of C9orf72.
Original files (1)
Primary fibroblast cell cultures
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR1017155 17900509 805522905 569.65 C9-1-Tx.fq.gz, SRR1017155, SRR1017155.sralite SRA
SRX368232 SRP032165 RNA-Seq SINGLE
GSM1250459: C9-2-Ctrl; Homo sapiens; RNA-Seq
Sample: SRS494272
BioProject: PRJNA224740
BioSample: SAMN02384552
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: Primary fibroblast cell cultures
tissue: Fibroblast
gender: male
age: 52 Years
genotype: C9orf72 Intron 1 Hexanucleotide Expansion
diagnosis: Sporadic ALS (C9orf72 expansion)
disease onset: Distal UE
disease course: 1 year at time of biopsy
drug treatment: No ASO Treatment - Cells were exposed to cytofectin transfection reagent for four hours, but were not transfected with an ASO
Original files (1)
Primary fibroblast cell cultures
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR1017156 17524371 788596695 558.85 C9-2-Ctrl.fq.gz, SRR1017156, SRR1017156.sralite SRA
SRX368233 SRP032165 RNA-Seq SINGLE
GSM1250460: C9-2-Mock; Homo sapiens; RNA-Seq
Sample: SRS494274
BioProject: PRJNA224740
BioSample: SAMN02384551
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: Primary fibroblast cell cultures
tissue: Fibroblast
gender: male
age: 52 Years
genotype: C9orf72 Intron 1 Hexanucleotide Expansion
diagnosis: Sporadic ALS (C9orf72 expansion)
disease onset: Distal UE
disease course: 1 year at time of biopsy
drug treatment: Transfection Control - Cells were treated with a control ASO which does not have any human genomic target.
Original files (1)
Primary fibroblast cell cultures
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR1017157 22101736 994578120 702.91 C9-2-Mock.fq.gz, SRR1017157, SRR1017157.sralite SRA
SRX368234 SRP032165 RNA-Seq SINGLE
GSM1250461: C9-2-Tx; Homo sapiens; RNA-Seq
Sample: SRS494275
BioProject: PRJNA224740
BioSample: SAMN02384553
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: Primary fibroblast cell cultures
tissue: Fibroblast
gender: male
age: 52 Years
genotype: C9orf72 Intron 1 Hexanucleotide Expansion
diagnosis: Sporadic ALS (C9orf72 expansion)
disease onset: Distal UE
disease course: 1 year at time of biopsy
drug treatment: ASO Treatment - Cells were transfected with a nuclear RNase-H dependent antisense oligonucleotide targeting Exon 2 of Hs C9orf72. This ASO has been shown in previous work to efficiently knockdown all known isoforms of C9orf72.
Original files (1)
Primary fibroblast cell cultures
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR1017158 24009506 1080427770 762.66 C9-2-Tx.fq.gz, SRR1017158, SRR1017158.sralite SRA
SRX368235 SRP032165 RNA-Seq SINGLE
GSM1250462: C9-3-Ctrl; Homo sapiens; RNA-Seq
Sample: SRS494276
BioProject: PRJNA224740
BioSample: SAMN02384555
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: Primary fibroblast cell cultures
tissue: Fibroblast
gender: male
age: 55 Years
genotype: C9orf72 Intron 1 Hexanucleotide Expansion
diagnosis: Familial ALS
disease onset: Unknown
disease course: 14 years at time of biopsy
drug treatment: No ASO Treatment - Cells were exposed to cytofectin transfection reagent for four hours, but were not transfected with an ASO
Original files (1)
Primary fibroblast cell cultures
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR1017159 27436986 1234664370 868.53 C9-3-Ctrl.fq.gz, SRR1017159, SRR1017159.sralite SRA
SRX368236 SRP032165 RNA-Seq SINGLE
GSM1250463: C9-3-Mock; Homo sapiens; RNA-Seq
Sample: SRS494277
BioProject: PRJNA224740
BioSample: SAMN02384557
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: Primary fibroblast cell cultures
tissue: Fibroblast
gender: male
age: 55 Years
genotype: C9orf72 Intron 1 Hexanucleotide Expansion
diagnosis: Familial ALS
disease onset: Unknown
disease course: 14 years at time of biopsy
drug treatment: Transfection Control - Cells were treated with a control ASO which does not have any human genomic target.
Original files (1)
Primary fibroblast cell cultures
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR1017160 15871571 714220695 509.1 C9-3-Mock.fq.gz, SRR1017160, SRR1017160.sralite SRA
SRX368237 SRP032165 RNA-Seq SINGLE
GSM1250464: C9-3-Tx; Homo sapiens; RNA-Seq
Sample: SRS494278
BioProject: PRJNA224740
BioSample: SAMN02384554
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: Primary fibroblast cell cultures
tissue: Fibroblast
gender: male
age: 55 Years
genotype: C9orf72 Intron 1 Hexanucleotide Expansion
diagnosis: Familial ALS
disease onset: Unknown
disease course: 14 years at time of biopsy
drug treatment: ASO Treatment - Cells were transfected with a nuclear RNase-H dependent antisense oligonucleotide targeting Exon 2 of Hs C9orf72. This ASO has been shown in previous work to efficiently knockdown all known isoforms of C9orf72.
Original files (1)
Primary fibroblast cell cultures
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR1017161 18236578 820646010 581.81 C9-3-Tx.fq.gz, SRR1017161, SRR1017161.sralite SRA
SRX368238 SRP032165 RNA-Seq SINGLE
GSM1250465: C9-4-Ctrl; Homo sapiens; RNA-Seq
Sample: SRS494279
BioProject: PRJNA224740
BioSample: SAMN02384556
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: Primary fibroblast cell cultures
tissue: Fibroblast
gender: male
age: 55 Years
genotype: C9orf72 Intron 1 Hexanucleotide Expansion
diagnosis: Familial ALS
disease onset: Leg
disease course: 2 years at time of biopsy
drug treatment: No ASO Treatment - Cells were exposed to cytofectin transfection reagent for four hours, but were not transfected with an ASO
Original files (1)
Primary fibroblast cell cultures
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR1017162 19745862 888563790 628.04 C9-4-Ctrl.fq.gz, SRR1017162, SRR1017162.sralite SRA
SRX368239 SRP032165 RNA-Seq SINGLE
GSM1250466: C9-4-Mock; Homo sapiens; RNA-Seq
Sample: SRS494280
BioProject: PRJNA224740
BioSample: SAMN02384561
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: Primary fibroblast cell cultures
tissue: Fibroblast
gender: male
age: 55 Years
genotype: C9orf72 Intron 1 Hexanucleotide Expansion
diagnosis: Familial ALS
disease onset: Leg
disease course: 2 years at time of biopsy
drug treatment: Transfection Control - Cells were treated with a control ASO which does not have any human genomic target.
Original files (1)
Primary fibroblast cell cultures
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR1017163 20022098 900994410 635.54 C9-4-Mock.fq.gz, SRR1017163, SRR1017163.sralite SRA
SRX368240 SRP032165 RNA-Seq SINGLE
GSM1250467: C9-4-Tx; Homo sapiens; RNA-Seq
Sample: SRS494281
BioProject: PRJNA224740
BioSample: SAMN02384559
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: Primary fibroblast cell cultures
tissue: Fibroblast
gender: male
age: 55 Years
genotype: C9orf72 Intron 1 Hexanucleotide Expansion
diagnosis: Familial ALS
disease onset: Leg
disease course: 2 years at time of biopsy
drug treatment: ASO Treatment - Cells were transfected with a nuclear RNase-H dependent antisense oligonucleotide targeting Exon 2 of Hs C9orf72. This ASO has been shown in previous work to efficiently knockdown all known isoforms of C9orf72.
Original files (1)
Primary fibroblast cell cultures
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR1017164 19031451 856415295 605.66 C9-4-Tx.fq.gz, SRR1017164, SRR1017164.sralite SRA
SRX368241 SRP032165 RNA-Seq SINGLE
GSM1250468: Kin1ALS17-Ctrl; Homo sapiens; RNA-Seq
Sample: SRS494282
BioProject: PRJNA224740
BioSample: SAMN02384558
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: Primary fibroblast cell cultures
tissue: Fibroblast
gender: female
age: 52 Years
genotype: No Known Relevant Mutations
diagnosis: Non-Neurologic Control
disease onset: N/A
disease course: N/A
drug treatment: No ASO Treatment - Cells were exposed to cytofectin transfection reagent for four hours, but were not transfected with an ASO
Original files (1)
Primary fibroblast cell cultures
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR1017165 22057144 992571480 705.68 Kin1ALS17-Ctrl.fq.gz, SRR1017165, SRR1017165.sralite SRA
SRX368242 SRP032165 RNA-Seq SINGLE
GSM1250469: Kin1ALS17-Tx; Homo sapiens; RNA-Seq
Sample: SRS494283
BioProject: PRJNA224740
BioSample: SAMN02384534
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: Primary fibroblast cell cultures
tissue: Fibroblast
gender: female
age: 52 Years
genotype: No Known Relevant Mutations
diagnosis: Non-Neurologic Control
disease onset: N/A
disease course: N/A
drug treatment: ASO Treatment - Cells were transfected with a nuclear RNase-H dependent antisense oligonucleotide targeting Exon 2 of Hs C9orf72. This ASO has been shown in previous work to efficiently knockdown all known isoforms of C9orf72.
Original files (1)
Primary fibroblast cell cultures
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR1017166 22005395 990242775 697.49 Kin1ALS17-Tx.fq.gz, SRR1017166, SRR1017166.sralite SRA
SRX368243 SRP032165 RNA-Seq SINGLE
GSM1250470: Kin1ALS6-Ctrl; Homo sapiens; RNA-Seq
Sample: SRS494284
BioProject: PRJNA224740
BioSample: SAMN02384531
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: Primary fibroblast cell cultures
tissue: Fibroblast
gender: female
age: 83 Years
genotype: No Known Relevant Mutations
diagnosis: Non-Neurologic Control
disease onset: N/A
disease course: N/A
drug treatment: No ASO Treatment - Cells were exposed to cytofectin transfection reagent for four hours, but were not transfected with an ASO
Original files (1)
Primary fibroblast cell cultures
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR1017167 24091533 1084118985 769.04 Kin1ALS6-Ctrl.fq.gz, SRR1017167, SRR1017167.sralite SRA
SRX368244 SRP032165 RNA-Seq SINGLE
GSM1250471: Kin1ALS6-Tx; Homo sapiens; RNA-Seq
Sample: SRS494285
BioProject: PRJNA224740
BioSample: SAMN02384533
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: Primary fibroblast cell cultures
tissue: Fibroblast
gender: female
age: 83 Years
genotype: No Known Relevant Mutations
diagnosis: Non-Neurologic Control
disease onset: N/A
disease course: N/A
drug treatment: ASO Treatment - Cells were transfected with a nuclear RNase-H dependent antisense oligonucleotide targeting Exon 2 of Hs C9orf72. This ASO has been shown in previous work to efficiently knockdown all known isoforms of C9orf72.
Original files (1)
Primary fibroblast cell cultures
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR1017168 23608468 1062381060 752.54 Kin1ALS6-Tx.fq.gz, SRR1017168, SRR1017168.sralite SRA
SRX368245 SRP032165 RNA-Seq SINGLE
GSM1250472: Kin2ALS6-Ctrl; Homo sapiens; RNA-Seq
Sample: SRS494286
BioProject: PRJNA224740
BioSample: SAMN02384532
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: Primary fibroblast cell cultures
tissue: Fibroblast
gender: male
age: 56 Years
genotype: No Known Relevant Mutations
diagnosis: Non-Neurologic Control
disease onset: N/A
disease course: N/A
drug treatment: No ASO Treatment - Cells were exposed to cytofectin transfection reagent for four hours, but were not transfected with an ASO
Original files (1)
Primary fibroblast cell cultures
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR1017169 19256902 866560590 615.44 Kin2ALS6-Ctrl.fastq, SRR1017169, SRR1017169.sralite SRA
SRX368246 SRP032165 RNA-Seq SINGLE
GSM1250473: Kin2ALS6-Tx; Homo sapiens; RNA-Seq
Sample: SRS494288
BioProject: PRJNA224740
BioSample: SAMN02384560
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: Primary fibroblast cell cultures
tissue: Fibroblast
gender: male
age: 56 Years
genotype: No Known Relevant Mutations
diagnosis: Non-Neurologic Control
disease onset: N/A
disease course: N/A
drug treatment: ASO Treatment - Cells were transfected with a nuclear RNase-H dependent antisense oligonucleotide targeting Exon 2 of Hs C9orf72. This ASO has been shown in previous work to efficiently knockdown all known isoforms of C9orf72.
Original files (1)
Primary fibroblast cell cultures
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR1017170 17727289 797728005 568.54 Kin2ALS6-Tx.fq.gz, SRR1017170, SRR1017170.sralite SRA
SRX368247 SRP032165 RNA-Seq SINGLE
GSM1250474: Kin4ALS6-Ctrl; Homo sapiens; RNA-Seq
Sample: SRS494287
BioProject: PRJNA224740
BioSample: SAMN02384562
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: Primary fibroblast cell cultures
tissue: Fibroblast
gender: male
age: 55 Years
genotype: No Known Relevant Mutations
diagnosis: Non-Neurologic Control
disease onset: N/A
disease course: N/A
drug treatment: No ASO Treatment - Cells were exposed to cytofectin transfection reagent for four hours, but were not transfected with an ASO
Original files (1)
Primary fibroblast cell cultures
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR1017171 18850727 848282715 599.49 Kin4ALS6-Ctrl.fq.gz, SRR1017171, SRR1017171.sralite SRA
SRX368248 SRP032165 RNA-Seq SINGLE
GSM1250475: Kin4ALS6-Tx; Homo sapiens; RNA-Seq
Sample: SRS494289
BioProject: PRJNA224740
BioSample: SAMN02384530
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: Primary fibroblast cell cultures
tissue: Fibroblast
gender: male
age: 55 Years
genotype: No Known Relevant Mutations
diagnosis: Non-Neurologic Control
disease onset: N/A
disease course: N/A
drug treatment: ASO Treatment - Cells were transfected with a nuclear RNase-H dependent antisense oligonucleotide targeting Exon 2 of Hs C9orf72. This ASO has been shown in previous work to efficiently knockdown all known isoforms of C9orf72.
Original files (1)
Primary fibroblast cell cultures
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR1017172 28162146 1267296570 892.56 Kin4ALS6-Tx.fq.gz, SRR1017172, SRR1017172.sralite SRA

Linked Publications (1)

Targeted degradation of sense and antisense C9orf72 RNA foci as therapy for ALS and frontotemporal degeneration.
Proceedings of the National Academy of Sciences of the United States of America · 2013

Data Files (30)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
— ALS14.fq.gz RNA-Seq 522.4 MB link
— ALS20.fq.gz RNA-Seq 495.2 MB link
— ALS25.fq.gz RNA-Seq 443.3 MB link
— ALS2.fq.gz RNA-Seq 543.8 MB link
— C9-1-Ctrl.fq.gz RNA-Seq 595.0 MB link
— C9-1-Mock.fq.gz RNA-Seq 734.8 MB link
— C9-1-Tx.fq.gz RNA-Seq 569.6 MB link
— C9-2-Ctrl.fq.gz RNA-Seq 558.8 MB link
— C9-2-Mock.fq.gz RNA-Seq 702.9 MB link
— C9-2-Tx.fq.gz RNA-Seq 762.7 MB link
— C9-3-Ctrl.fq.gz RNA-Seq 868.5 MB link
— C9-3-Mock.fq.gz RNA-Seq 509.1 MB link
— C9-3-Tx.fq.gz RNA-Seq 581.8 MB link
— C9-4-Ctrl.fq.gz RNA-Seq 628.0 MB link
— C9-4-Mock.fq.gz RNA-Seq 635.5 MB link
— C9-4-Tx.fq.gz RNA-Seq 605.7 MB link
— Kin1ALS17-Ctrl.fq.gz RNA-Seq 705.7 MB link
— Kin1ALS17-Tx.fq.gz RNA-Seq 697.5 MB link
— Kin1ALS6-Ctrl.fq.gz RNA-Seq 769.0 MB link
— Kin1ALS6-Tx.fq.gz RNA-Seq 752.5 MB link
— Kin2ALS6-Ctrl.fastq RNA-Seq 615.4 MB link
— Kin2ALS6-Tx.fq.gz RNA-Seq 568.5 MB link
— Kin4ALS6-Ctrl.fq.gz RNA-Seq 599.5 MB link
— Kin4ALS6-Tx.fq.gz RNA-Seq 892.6 MB link
— SRR1017149 RNA-Seq 522.4 MB link
— SRR1017151 RNA-Seq 443.3 MB link
— SRR1017157 RNA-Seq 702.9 MB link
— SRR1017158 RNA-Seq 762.7 MB link
— SRR1017159 RNA-Seq 868.5 MB link
— SRR1017160 RNA-Seq 509.1 MB link