Small RNA-seq during the ecdysone and heat-shock response in Drosophila Kc167 cells
Ontology highlight
ABSTRACT:
ORGANISM(S): Drosophila melanogaster
SUBMITTER: Kevin Van Bortle
PROVIDER: E-GEOD-69934 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Small RNA sequencing libraries at 0 h, 3 h, and 48 h time points after ecdysone treatment and 20min heat shock (37 degrees celcius) in Drosophila cell culture
2015-06-17 | GSE69934 | GEO
Project description:Kc167 cells were mock-treated/treated with combinations of steroid hormone ecdysone and gamma-irradiation, and harvested. The expression profiles were determined using Affymetrix Drosophila Genechip 1 arrays. Comparisons between the sample groups allow the identification of genes with ecdysone- and/or radiation-responsive expression patterns. Experiment Overall Design: 1 set of control, ecdysone, gamma-irradiated, ecdysone + irradiated samples was analyzed.
2008-06-12 | E-GEOD-3072 | biostudies-arrayexpress
Project description:Methoxyfenozide (RH-2485) represents the group of non-steroidal ecdysteroid agonists with a dibenzoylhydrazine structure, that are used as novel biorational insecticides in the control of insect pests. Here we report on the selection of Drosophila melanogaster S2 cells for resistance to inhibition of cell proliferation by methoxyfenozide by ~1000-fold over 4 months. Cells were exposed to gradually increasing concentrations of methoxyfenozide and selected out based on the ecdysteroid-sensitive response for cell proliferation. In the resistant cells, the ecdysteroid receptor (EcR/USP) complex was no longer active in the presence of methoxyfenozide. But when resistant cells were relaxed from pressure in methoxyfenozide-free medium, induction of the reporter construct was observed. In parallel, EcR/USP functionality was also restored when resistant cells were rescued by a Drosophila EcR plasmid. However, it was striking that in the resistant cells the ecdysteroid-sensitive response for cell proliferation was not restored upon methoxyfenozide withdrawal, indicating permanent changes in the physiology of the cells during selection. To investigate changes in gene expression caused by inactivation of the EcR/USP complex in resistant cells, Drosophila oligo 14kv1 microarrays were used and probed with cDNAs from resistant cells in the presence and absence of ecdysone agonist on one hand and from unselected sensitive cells on the other hand. A selection of 324 differentially expressed genes was assigned covering diverse functions as transport, enzyme activity, cytoskeleton organization, cell cycle machinery, transcription/translation and ecdysteroid signaling. Besides the identification of (primary and secondary) target genes of the EcR/USP signaling pathway, this analysis is also predicted to gain insights into the mechanism of resistance and the crosstalk between ecdysteroid signaling and cell proliferation-linked processes. In this microarray experiment three biological conditions were under study: (i) untreated S2 cells (S2), (ii) a subpopulation of these untreated cells, which were grown under continuous pressure of methoxyfenozide and which were shown to become resistant to this compound (S2res) and (iii) a subpopulation of the resistant cells, which were again cultured without methoxyfenozide added to the medium (S2res-woMF). For each condition, two subpopulations (which were treated as biological replicates, although they are not exactly independent), were isolated and used for the RNA extractions. The overall experimental design was an n+2 A-optimal design. When each hybridisation is respresented by an arrow (Cy5 ? Cy3), the design can be respresented as follows: First loop = S2.1 ? S2res.1 ? S2.2 ? S2res.2 ? S2.1; Second loop = S2.1 ? S2res-woMF.1 ? S2.2 ? S2res-woMF.2 ? S2.1 (numbers following the condition name correspond to the biological replicate numbers). The two loops are thus connected by S2.1 and S2.2. Two analyses were performed: S2res compared to S2 and S2res-woMF compared to S2.
2010-11-08 | E-GEOD-17748 | biostudies-arrayexpress
Project description:Previously we and other teams have found that 20E modulates the induction and expression of antimicrobial peptides (AMPs) in immune-challenged Drosophila cell culture or whole animals. To identify potential downstream targets of 20E involved in modulating the immune response we used Affymetrix gene chips (microarrays) to compare the transcriptomes of Drosophila S2* cells treated or not with 20E for 24 hours. Affymetrix Drosophila 2.0 Chips were probed in triplicate with RNA isolated from untreated S2* cells or cells treated with 1 microMolar 20E (Sigma) for 24 hours. cDNA products were hybridized at the Brown University Genomics Core Facility to Affymetrix GeneChip Drosophila_2.0 Genome Arrays (3 replicate chips per treatment).
2013-04-13 | E-GEOD-46020 | biostudies-arrayexpress
Project description:The changes in transcript titers are described for Drosophila Kc167 cells following 5-48 hr treatment with 20-hydroxyecdysone. Keywords: hormone response RNA from ecdysone-treated cells was compared to RNA from cells treated with carrier alone. A total of 3-13 slides were analyzed for each time point, each from a separate biological sample; dye-swaps were included.
2010-06-21 | E-GEOD-10926 | biostudies-arrayexpress
Project description:modENCODE_submission_2973 This submission comes from a modENCODE project of Eric Lai. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We plan to generate a comprehensive catalog of expressed and functional microRNAs, and generate biological evidence for their regulatory activity. We plan also to delineate the primary transcription units of microRNA genes. Finally, we plan to annotate other classes of non-miRNA expressed small RNAs, as least some of which may define novel classes of small RNA genes. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Keywords: RNA-seq EXPERIMENT TYPE: RNA-seq. BIOLOGICAL SOURCE: Cell Line: S2-Rubin; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Sex: Male; EXPERIMENTAL FACTORS: Cell Line S2-Rubin
2010-10-18 | E-GEOD-24542 | biostudies-arrayexpress
Project description:modENCODE_submission_2974 This submission comes from a modENCODE project of Eric Lai. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We plan to generate a comprehensive catalog of expressed and functional microRNAs, and generate biological evidence for their regulatory activity. We plan also to delineate the primary transcription units of microRNA genes. Finally, we plan to annotate other classes of non-miRNA expressed small RNAs, as least some of which may define novel classes of small RNA genes. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Keywords: RNA-seq EXPERIMENT TYPE: RNA-seq. BIOLOGICAL SOURCE: Cell Line: Kc-Rubin; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Genotype: se/e; Sex: Female; EXPERIMENTAL FACTORS: Cell Line Kc-Rubin
2010-10-18 | E-GEOD-24543 | biostudies-arrayexpress
Project description:Kc167 cells were mock-treated/treated with combinations of steroid hormone ecdysone and gamma-irradiation, and harvested. The expression profiles were determined using Affymetrix Drosophila Genechip 1 arrays. Comparisons between the sample groups allow the identification of genes with ecdysone- and/or radiation-responsive expression patterns. Keywords: response to hormone, stress response
2006-08-05 | GSE3072 | GEO
Project description:The changes in transcript titers are described for Drosophila ML-DmBG3-c2 cells following 5-48 hr treatment with 20-hydroxyecdysone. Keywords: hormone response RNA from ecdysone-treated cells was compared to RNA from cells treated with carrier alone. A total of 4 slides were analyzed for each time point, each from a separate biological sample; dye-swaps were included.
2009-03-19 | E-GEOD-11069 | biostudies-arrayexpress
Project description:The changes in transcript titers are described for Drosophila CME W1 Cl.8+ cells following 5-48 hr treatment with 20-hydroxyecdysone. Keywords: hormone response RNA from ecdysone-treated cells was compared to RNA from cells treated with carrier alone. A total of 4 slides were analyzed for each time point, each from a separate biological sample; dye-swaps were included.
2009-03-19 | E-GEOD-11068 | biostudies-arrayexpress