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| Status |
Public on Oct 26, 2023 |
| Title |
NV50_untreated_rep4 [248-19] |
| Sample type |
SRA |
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| Source name |
whole nematode pellet, RNA extracted
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| Organism |
Caenorhabditis elegans |
| Characteristics |
cell line: NV50: abl-1 KO, isolated from crossing XR1 with GRU102,
treatment: untreated
time point: 3 days old worms on Empty vector (pL4440)
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| Treatment protocol |
Quercetin (Q4951 Sigma-Aldrich), Lutein (PHR1699 Sigma-Aldrich), where dissolved in a solution of Dimethylsulfoxid (DMSO, 276855 Sigma-Aldrich) containing 1% of Tween 80 (P1754 Sigma-Aldrich) and mixed with bacteria to the following concentrations: Quercetin 100µM, lutein µM100. Control worms were fed bacteria containing the same amount of solvent (0.5% DMSO plus 0.005% Tween 80) used to prepare the above compound. Treatement started from eggs on plates seeded with HT115 (pl4440)
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| Growth protocol |
All strains were maintained and kept synchronized by egg lay at 20 °C on Nematode Growth Media (NGM) agar supplemented with Escherichia coli OP50 unless otherwise indicated. Worms
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNeasy Mini Plus Kit, Qiagen according to manufacturer with optional DNAse treatment
Libraries were prepared according to Illumina instructions accompanying the Illumina® ‘TruSeq Stranded mRNA Library Prep’ Kit. Briefly, 350 ng total RNA were used for mRNA capturing, fragmentation, the synthesis of cDNA, adapter ligation and library amplification. Bead purified libraries were normalized and finally sequenced on the HiSeq 3000/4000 system (Illumina Inc. San Diego, CA, USA), following the manufacturer's protocols, with a read setup of 1 × 150 bp.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
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| Data processing |
Illumina bcl2fastq v2.20.0.422 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence (Illumina TrueSeq) and quality trimmed (using the default parameters: bases below Q13 were trimmed from the end of the reads, ambiguous nucleotides maximal 2), then mapped to C. elegans (WBcel235.99) (March 26, 2020) genome sequence using CLC Genomics Workbench v20.0.4 and v21.0.4 with standard parameters.
Reads Per Kilobase and per Megabase (RPKM) were calculated using CLC Genomics Workbench v21.0.4 with standard parameters. After grouping of samples according to their respective experimental condition, the statistical differential expression was determined using the CLC Differential Expression for RNA-Seq tool (version 2.5). The resulting p values were corrected for multiple testing by FDR and Bonferroni-correction. A p value of ≤ 0.05 was considered significant.
Assembly: WBcel235.99
Supplementary files format and content: The Excel file includes RPKM values for every gene and each sample.
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| Submission date |
Jun 20, 2023 |
| Last update date |
Oct 26, 2023 |
| Contact name |
Natascia Ventura |
| Organization name |
Heinrich Heine University and the IUF- Leibniz Research Institute for Environmental Medicine
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| Street address |
Auf'm Hennekamp 50
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| City |
Düsseldorf |
| ZIP/Postal code |
40225 |
| Country |
Germany |
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| Platform ID |
GPL24892 |
| Series (1) |
| GSE235199 |
Abl depletion via autophagy mediates the beneficial effects of quercetin against Alzheimer pathology across species |
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| Relations |
| BioSample |
SAMN35798004 |
| SRA |
SRX20725007 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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