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| Status |
Public on Jan 29, 2024 |
| Title |
glp-1, L4440, day 3, rep2 |
| Sample type |
SRA |
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| Source name |
somatic cells
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| Organism |
Caenorhabditis elegans |
| Characteristics |
cell type: somatic cells
genotype: glp-1(e2141)
diet: L4440
time: day 3
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| Growth protocol |
All worms were grown on empty vector L4440 bacteria for ~48h at 25C until they reached the young adult/day 1 adult stage. Then, worms were split between L4440 and hda-1 RNAi bacteria for aging. Samples were collected at day 1, day 3, and day 12 of adulthood. All worms were germline-less, representing somatic-only samples.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Worms were frozen in Tri Reagent, and RNA was isolated with chloroform and isopropanol. RNA was treated with Dnase (TURBO Dnase kit, Invitrogen, AM1907), and cleaned with ethanol precipitation before library preparation.
315ng RNA from each sample was used for QuantSeq 3’ mRNA-Seq Library Prep Kit (Lexogen) following the manufacturer’s instructions and using 13 PCR cycles.
3' mRNA-seq
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
glp1_L4440_D3_rep2
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| Data processing |
Adaptor sequences were trimmed and low quality reads were filtered out from sequencing files using Trim Galore! (v0.6.5) with the settings –q 20 –fastqc.
Trimmed sequencing files were then aligned to the ce11/WBcel235 C. elegans reference genome using STAR (v2.7.9a) with the options –runThreadN 2 –quantMode GeneCounts —-outFilterMultiMapNmax 1 –outFilterMismatchNmax 2 –outSAMtype BAM SortedByCoordinate.
The resulting tab delimited text files containing read count per gene, with column 3 (the middle column of counts) representing the correct counts for 3’ RNA-seq data, were used to create a matrix of gene expression to compare multiple samples.
Assembly: WBcel235/ce11
Supplementary files format and content: tab-delimited text files include read count per gene
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| Submission date |
Jan 30, 2023 |
| Last update date |
Jan 29, 2024 |
| Contact name |
Siu Sylvia Lee |
| E-mail(s) |
[email protected]
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| Organization name |
Cornell University
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| Street address |
520 Campus road
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| City |
Ithaca |
| State/province |
NY |
| ZIP/Postal code |
14850 |
| Country |
USA |
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| Platform ID |
GPL19757 |
| Series (2) |
| GSE224075 |
The chromatin factors SET-26 and HCF-1 oppose the histone deacetylase HDA-1 in longevity and gene regulation in C. elegans [RNA-Seq] |
| GSE224078 |
The chromatin factors SET-26 and HCF-1 oppose the histone deacetylase HDA-1 in longevity and gene regulation in C. elegans |
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| Relations |
| BioSample |
SAMN32961670 |
| SRA |
SRX19217294 |
| 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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