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| Status |
Public on May 19, 2023 |
| Title |
Mechanistic impacts of bacterial diet on dopaminergic neurodegeneration in a Caenorhabditis elegans α-synuclein model of Parkinson's disease |
| Organism |
Caenorhabditis elegans |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Using distinct mutant strains deficient in key aspects of gene silencing machinery, we provide evidence that neuroprotection appears to stem from dsRNAs that originate from the bacteria themselves, and Systemic RNA Interference Defective (SID) mutants deficient in dsRNA-mediated gene silencing do not allow for neuroprotection from the bacteria.
Transcriptomic analysis between worms reared on OP50 and HB101 E. coli for multiple generations in an a-syn background revealed that the primary cellular processes involved in neuroprotection of this nature included but were not limited to endopeptidase activity, transcriptional regulation, calcium ion binding activity, and water channel activity.
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| Overall design |
Comparative gene expression profiling analysis of RNA-seq data for C. elegans in an a-synuclein background reared on OP50 or HB101 E. coli, 3 biological replicates.
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| Contributor(s) |
Gaeta AL, McKay LE, Keogh CM, Willicott K, Altman T, Caldwell GA, Caldwell KA |
| Citation(s) |
37260751 |
| Submission date |
Jul 28, 2022 |
| Last update date |
Aug 18, 2023 |
| Contact name |
Guy Caldwell |
| E-mail(s) |
gcaldwel@ua.edu
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| Organization name |
The University of Alabama
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| Department |
Biological Sciences
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| Street address |
300 Hackberry Lane
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| City |
Tuscaloosa |
| State/province |
AL |
| ZIP/Postal code |
35487 |
| Country |
USA |
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| Platforms (1) |
| GPL22765 |
Illumina HiSeq 4000 (Caenorhabditis elegans) |
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| Samples (12)
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| GSM6413337 |
UA44 strain, P0 generation, OP50 diet, rep1 |
| GSM6413338 |
UA44 strain, P0 generation, OP50 diet, rep2 |
| GSM6413339 |
UA44 strain, P0 generation, OP50 diet, rep3 |
| GSM6413340 |
UA44 strain, F3 generation, OP50 diet, rep1 |
| GSM6413341 |
UA44 strain, F3 generation, OP50 diet, rep2 |
| GSM6413342 |
UA44 strain, F3 generation, OP50 diet, rep3 |
| GSM6413343 |
UA44 strain, F3 generation, HB101 diet, rep1 |
| GSM6413344 |
UA44 strain, F3 generation, HB101 diet, rep2 |
| GSM6413345 |
UA44 strain, F3 generation, HB101 diet, rep3 |
| GSM6413346 |
UA44 strain, P0 generation, HB101 diet, rep1 |
| GSM6413347 |
UA44 strain, P0 generation, HB101 diet, rep2 |
| GSM6413348 |
UA44 strain, P0 generation, HB101 diet, rep3 |
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| Relations |
| BioProject |
PRJNA863300 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE210005_Diet_F3_Differential_analysis_results.txt.gz |
555.3 Kb |
(ftp)(http) |
TXT |
| GSE210005_Diet_F3_Readcount.txt.gz |
367.3 Kb |
(ftp)(http) |
TXT |
| GSE210005_Diet_F3_Significant_DEGs.txt.gz |
24.3 Kb |
(ftp)(http) |
TXT |
| GSE210005_Diet_P0_Differential_analysis_results.txt.gz |
537.1 Kb |
(ftp)(http) |
TXT |
| GSE210005_Diet_P0_Readcount.txt.gz |
369.8 Kb |
(ftp)(http) |
TXT |
| GSE210005_Diet_P0_Significant_DEGs.txt.gz |
3.7 Kb |
(ftp)(http) |
TXT |
| GSE210005_Diet_fpkm.txt.gz |
1.5 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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