RNA-seq of Caenorhabditis elegans at Late L4 stage of WT, daf-2(e1370), daf-16(mgDf50);daf-2(e1370) on control RNAi and cdk-12 RNAi
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina HiSeq 2500, Illumina NovaSeq 6000
ORGANISM(S): Caenorhabditis elegans
SUBMITTER: Arnab Mukhopadhyay
PROVIDER: E-MTAB-11189 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Comparison of sterile worms grown on Control Vector, daf-2 RNAi, and daf-2 + daf-16 RNAi. Synchronized fer-15(b26); fem-1(hc17) animals were grown on RNAi bacteria at 25ºC, induced with IPTG on Day 1 of adulthood, and collected from 0-48 hours (10 time points) and 0-196 hours (10 time points); RNAi bacteria was supplemented as necessary for later time points. Worms were floated off lawns with M9 buffer, centrifuged, and washed again in M9. The pelleted worms were dissolved in Trizol (Gibco) and frozen in liquid nitrogen.Time courses were compared with mixed references (collected from 1/2 of each of the time course samples)
2003-07-17 | E-MEXP-8 | biostudies-arrayexpress
Project description:Comparison of sterile worms grown on Control Vector, daf-2 RNAi, and daf-2 + daf-16 RNAi. Synchronized fer-15(b26); fem-1(hc17) animals were grown on RNAi bacteria at 25ºC, induced with IPTG on Day 1 of adulthood, and collected from 0-48 hours (10 time points) and 0-196 hours (10 time points); RNAi bacteria was supplemented as necessary for later time points. Worms were floated off lawns with M9 buffer, centrifuged, and washed again in M9. The pelleted worms were dissolved in Trizol (Gibco) and frozen in liquid nitrogen.Time courses were compared with mixed references (collected from 1/2 of each of the time course samples)
2003-07-17 | E-MEXP-9 | biostudies-arrayexpress
Project description:We identified the DNA binding sites of DAF-16 in transgenic line TJ356 (daf-16::gfp) that carries high-copy number daf-16. The expression pattern was examined through fluorescent microscopy. The binding sites were determined using chromatin immunoprecipitation with anti-GFP antibody and anti-POL II antibody followed by illumina high-throughput sequencing (ChIP-seq). For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Identification of DAF-16 binding sites at L4/Young adult stage when DAF-16 was highly overexpressed
2009-04-11 | E-GEOD-15567 | biostudies-arrayexpress
Project description:Most aging hypotheses revolve around the accumulation of some sort of damage resulting in gradual physiological decline and ultimately death. Avoiding protein damage accumulation by enhanced turnover should slow down the aging process and extend lifespan. However, lowering translational efficiency extends rather than shortens lifespan in C. elegans. We studied turnover of individual proteins in the conserved Insulin/Insulin-like Growth Factor (IGF-1) receptor mutant daf-2 by combining Stable Isotope Labeling by Nitrogen-15 in Caenorhabditis elegans and LC-MS/MS. Intriguingly, the majority of proteins displayed prolonged half-lives in daf-2, while others remained unchanged, signifying that longevity is not supported by high protein turnover. This slow-down of protein turnover was most prominent for components of the translation machinery and mitochondria. In contrast, the high turnover of lysosomal hydrolases and very low turnover of cytoskeletal proteins remained largely unchanged in daf-2. The slow-down of protein dynamics and decreased abundance of the translational machinery may point at the importance of anabolic attenuation in lifespan extension as suggested by the hyperfunction theory.
2016-09-27 | PXD002317 | Pride
Project description:The plant immune hormone salicylic acid (SA) modulates transcriptional reprogramming via controlling the master transcriptional coactivator, NPR1. Here we examined the role of HECT-type ubiquitin ligases, UPL1 and UPL5, in SA/NPR1-dependent transcriptional control. We showed that UPL1 and UPL5 are essential regulators of SA-responsive genes, and regulate SA-induced transcriptional reprogramming in a NPR1-dependent manner. Four-week old Arabidopsis thaliana plants of wild-type Col-0, mutant upl1, mutant upl5, and mutant npr1-1 genotypes were germinated on soil in 100% relative humidity. Plants were continuously grown in an environmental chamber with 16/8 hour day/night light regime (120 mol m-2 s-1 light intensity), 21/18 degrees celcius day/night cycle and 65% relative humidity. 4-week-old plants were sprayed with water or 0.5 mM SA until all leaves were thoroughly covered with fine droplets, samples were collected after 24 hours treatment. In total two independent biological repeats were collected.
2021-10-05 | E-MTAB-10963 | biostudies-arrayexpress
Project description:The plant hormone ethylene is involved in plant developmental, stress and environmental signalling. The ethylene signalling pathway is modulated by the master transcription factor EIN3. Here we examined the involvement of proteasome-associated UPL3 and UPL4 ubiquitin ligases in ethylene-responsive gene expression. We reveal that in absence of functional UPL3 and UPL4, plants show constitutive and enhanced activation or repression of ethylene-responsive genes in an EIN3-dependent manner. Ten-day old Arabidopsis thaliana seedlings of wild-type Col-0, mutant upl3 upl4, mutant ein3-1, and mutant upl3 upl4 ein3-1 were grown on MS media in an environmental chamber with 16/8 hour day/night light regime (120 mol m-2 s-1 light intensity) and 22 degrees Celsius. Seedlings were then transferred to 6-well plates and floated on the surface of water or 50 uM 1-aminocyclopropane-1-carboxylic acid (ACC). After 3 hours seedlings were harvested and for each treatment ~50 seedlings were pooled together into a single biological repeat. In total three independent biological repeats were collected. After harvesting seedlings were briefly dried on tissue and immediately frozen in liquid nitrogen until further analysis.
2021-10-05 | E-MTAB-10964 | biostudies-arrayexpress
Project description:Activation of plant immunity is associated with dramatic transcriptome reprogramming to prioritise immune responses over normal cellular functions. Changes in gene expression are coordinated by the immune hormone salicylic acid (SA). Here we investigated the involvement of the E4 ubiquitin ligase UBE4/MUSE3 in SA-induced transcriptional reprogramming. We show that loss of UBE4 function results in amplified expression of SA-induced, NPR1-dependent gene expression. Twelve-day old Arabidopsis thaliana seedlings of wild-type Col-0, mutant ube4 (SAIL_713_A12) and mutant npr1-1 genotypes were grown on MS media supplemented with 1X Gamborg vitamins in an environmental chamber with 16/8 hour day/night light regime (120 mol m-2 s-1 light intensity) and 22 degrees Celcius. Seedlings were then transferred to 6-well plates and immersed in 10 ml of 0.5 mM SA or water. After 12 hours seedlings were harvested and for each treatment ~50 seedlings were pooled together into a single biological repeat. In total two independent biological repeats were collected. After harvesting seedlings were briefly dried on tissue and immediately frozen in liquid nitrogen until further analysis.
2019-03-20 | E-MTAB-7369 | biostudies-arrayexpress
Project description:RNA-seq of zebrafish embryos with mutations in srpk3 (sa1890 allele) and/or ttn.1 (sa5562 allele). Each of the 24 samples (six samples for each of four genotypes) represents RNA from a pool of three 5 dpf zebrafish embryos.
2024-02-09 | E-MTAB-12934 | biostudies-arrayexpress
Project description:Activation of plant immunity is associated with dramatic transcriptome reprogramming to prioritise immune responses over normal cellular functions. Changes in gene expression are coordinated by the immune hormone salicylic acid (SA). Here we investigated the involvement of the HECT-type ligase Ubiquitin Protein Ligase 3 (UPL3) in SA-induced transcriptional reprogramming. We show that UPL3 acts as an amplifier of SA-induced changes in gene expression. Four-week old Arabidopsis thaliana plants of wild-type Col-0 and mutant upl3-4 genotypes were germinated on soil in 100% relative humidity. After 12 days plants were transplanted to larger pots (six plants per pot) and grown for an additional 3 weeks before experimental treatment. Plants were continuously grown in an environmental chamber with 16/8 hour day/night light regime (120 mol m-2 s-1 light intensity), 21/18 degrees celcius day/night cycle and 65% relative humidity. Plants were then sprayed with water or 0.5 mM SA until all leaves were thoroughly covered with fine droplets. After 24 hours leaf tissue was harvested from 6 plants per treatment and pooled together into a single biological repeat. In total two or three independent biological repeats were collected. After harvesting leaf tissue was immediately frozen in liquid nitrogen until further analysis.
2018-11-09 | E-MTAB-7374 | biostudies-arrayexpress
Project description:Chemo-resistance is the major cause of death in advanced prostate cancer (PCa), especially in metastatic PCa (mPCa). However, the molecular mechanisms behind chemo-resistance of PCa have not been clarified so far. Here we found GADD45B was significantly low expressed in metastasis PCa and it could promote chemotherapy sensitivity. So we further constructed GADD45B overexpressed cell line to investigate the possible mechanism.
2021-07-01 | E-MTAB-10704 | biostudies-arrayexpress