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| Status |
Public on Dec 31, 2023 |
| Title |
DNA methylome, R-loop and clinical exome profile of patients with sporadic Amyotrophic Lateral Sclerosis (RRBS) |
| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by high throughput sequencing
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| Summary |
Amyotrophic Lateral Sclerosis (ALS) is a fatal neurodegenerative disorder characterised by the death of motor neurons, the aetiology of which is essentially unknown. Here, we present an integrative epigenomic study in blood samples from seven clinically characterised sporadic ALS patients to elucidate molecular factors associated with the disease. We used clinical exome sequencing (CES) to study DNA variants, DNA-RNA hybrid immunoprecipitation sequencing (DRIP-seq) to assess R-loop distribution, and reduced representation bisulfite sequencing (RRBS) to examine DNA methylation changes. The above datasets were combined to create a comprehensive repository of genetic and epigenetic changes associated with the ALS cases studied. Our data descriptor is expected to guide further mechanistic studies on ALS to discover underlying genetic causes and develop new epigenetic therapies to combat this life-threatening disease.
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| Overall design |
To investigate the changes of DNA methylation in relation to ALS, we performed RRBS (reduced representation bisulfite sequencing) experiment on blood samples from 6 patients diagnosed with ALS (that had no other disease) and from 6 healthy individuals (control).
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| Contributor(s) |
Feró O, Varga D, Nagy É, Karányi Z, Sipos É, Engelhardt J, Török N, Balogh I, Vető B, Likó I, Fóthi Á, Szabó Z, Halmos G, Vécsei L, Arányi T, Székvölgyi L |
| Citation(s) |
38267456 |
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| Submission date |
Sep 06, 2023 |
| Last update date |
Feb 09, 2024 |
| Contact name |
Lorant Szekvolgyi |
| Organization name |
University of Debrecen
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| Department |
Department of Pharmacy
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| Lab |
Genome Architecture and Recombination Research Group
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| Street address |
Egyetem ter 1.
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| City |
Debrecen |
| ZIP/Postal code |
4032 |
| Country |
Hungary |
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| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (12)
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| GSM7764389 |
RRBS, ALS, ALS75 |
| GSM7764390 |
RRBS, ALS, ALS76 |
| GSM7764391 |
RRBS, ALS, ALS81 |
| GSM7764392 |
RRBS, Ctrl, K039 |
| GSM7764393 |
RRBS, Ctrl, K107 |
| GSM7764394 |
RRBS, Ctrl, K128 |
| GSM7764395 |
RRBS, Ctrl, K161 |
| GSM7764396 |
RRBS, Ctrl, K190 |
| GSM7764397 |
RRBS, Ctrl, K257 |
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| This SubSeries is part of SuperSeries: |
| GSE242475 |
DNA methylome, R-loop and clinical exome profiling of patients with sporadic Amyotrophic Lateral Sclerosis |
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| Relations |
| BioProject |
PRJNA1013553 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE242474_DMR_CpG_ALS_vs_Ctrl.tsv.gz |
8.2 Kb |
(ftp)(http) |
TSV |
| GSE242474_DMS_CpG_ALS_vs_Ctrl.tsv.gz |
396.9 Kb |
(ftp)(http) |
TSV |
| GSE242474_RAW.tar |
95.7 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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