biostudies-arrayexpressMark SterkenCaenorhabditis eleganshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15535In this experiment we evaluate the transcriptional responses of C. elegans to 0 mM and 400 mM ethanol after 240 minutes by mapping expression quantitative trait loci. We used 70 mpRILs and their parental lines (JU1511, JU1926, JU1931, and JU1941). Animals were 3 day old when exposure and tissue collection took place. Growth, maintenance, and exposure was performed at 20 degrees Celsius, For this experiment we did not use biological replicates, except for the 4 parents that have 6 biological replicates. Worms underwent the treatment at VCU Richmond, Virginia, USA (Bettinger lab) and were sent to us (Wageningen, The Netherlands, Kammenga lab) on dry ice. RNA extraction was done in Wageningen. Sequencing was performed by BGI Hong Kong.biostudies-arrayexpressSample Collection - Because of the large size of this experiment, we needed to perform the ethanol exposure in batches. mpRILs were randomly assigned into six different batches. Each batch also contained each of the four founders as a control and reference (Supplemental Table 2). The experiment was started by age-synchronizing the parents and mpRIL populations. Age-synchronization was performed by allowing gravid adult hermaphrodites to lay eggs on an OP50 seeded NGM plate. After three hours, the adult hermaphrodites were removed and the remaining population was allowed to grow for three days at 20 °C until they were first day adults. In both the eQTL and the trans-band validation experiment, approximately 2000 age-synchronized well-fed young adult worms were washed off the NGM plates with M9 buffer into 15 mL conical tubes. The animals were allowed to settle for 2 minutes, and the supernatant was removed. Worms were washed with 5 mL M9, allowed to settle for 2 minutes, after which the supernatant was removed. Each population was divided equally over two 15 mL conical treatment tubes that were prepared by adding M9 + 100% ethanol to yield 0 mM or 400 mM ethanol solutions. Worms were placed on a rotator at room temperature for 240 minutes. After the exposure time, tubes were removed from the rotator and the worms were allowed to settle for 2 minutes. After settlement, the supernatant was removed and the animals were washed twice with 5 mL M9, allowed to settle for 2 minutes, and supernatant was removed. The remaining worms with M9 were then transferred to a microfuge tube and spun for one minute. The remaining supernatant was removed and the pellets were flash frozen in liquid nitrogen. Samples were stored at -80 ℃ until further use.Library Construction - Library preparation was done as follows: first, mRNA were enriched and purified by Oligo dT selection.Nucleic Acid Extraction - RNA was isolated as described previously (Jovic et al., 2017; Sterken et al., 2021). In short, a Maxwell 16 AS2000 (Promega) instrument with a Maxwell 16 Simply RNA kit (Promega) was used. The manufacturer’s instructions were followed with one modification: after the lysis step, 10 µL instead of 25 µL of a 20 mg/mL stock solution of proteinase K was added to each sample. Samples with the proteinase K were incubated for 10 minutes at 65 ℃ in a ThermoMixer (Eppendorf) at 1000 rpm, after which the samples were cooled on ice for 1 minutes before adding them in the cartridge and resuming with standard protocol. RNA samples were stored at -80 ℃ until further use. Out of 184 samples, 181 yielded sufficient RNA for library preparation.Sequencing - The mRNA fragments were reverse transcribed and a complementary strand was generated. Next, adaptors were ligated onto the fragments and a PCR was performed. PCR products were singled by heat separation and cyclized into a DNA nanoball which was sequenced. Per sample at least 20M clean paired end read of 100 bp were generated.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - The reads from the samples were mapped onto the annotated genome sequence of C. elegans (PRJNA13758_WS282) using HISAT2. Gene expression was quantified and TPM normalized.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsDNBSEQ-T7Maxwell® 16 AS2000RNA-seq of coding RNACaenorhabditis elegansStefan van de RuitenbeekJan KammengaLaura MathiesElizabeth QuammeMark SterkenBasten SnoekJill BettingerJoost RiksenMarijke van WijkAndrew DaviesfalseRNA-seq of 3 day old C. elegans RILs exposes for 240 minutes to 0 mM or 400 mM ethanolIn this experiment we evaluate the transcriptional responses of C. elegans to 0 mM and 400 mM ethanol after 240 minutes by mapping expression quantitative trait loci. We used 70 mpRILs and their parental lines (JU1511, JU1926, JU1931, and JU1941). Animals were 3 day old when exposure and tissue collection took place. Growth, maintenance, and exposure was performed at 20 degrees Celsius, For this experiment we did not use biological replicates, except for the 4 parents that have 6 biological replicates. Worms underwent the treatment at VCU Richmond, Virginia, USA (Bettinger lab) and were sent to us (Wageningen, The Netherlands, Kammenga lab) on dry ice. RNA extraction was done in Wageningen. Sequencing was performed by BGI Hong Kong.2026-06-30T00:00:00Z2026-06-30T01:00:56.065Z2025-09-02T21:12:23.691ZE-MTAB-15535ERP179533E-MTAB-9663EFO_0002944EFO_0004170EFO_0005518EFO_0003816EFO_0003738EFO_0004184