SR proteins control a complex network of RNA-processing events
Ontology highlight
ABSTRACT:
ORGANISM(S): Drosophila melanogaster
SUBMITTER: Marco Blanchette
PROVIDER: E-GEOD-63261 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:We identified the precise genome-wide binding sites for all SR proteins, using iCLIP-seq SR proteins were encoded on stable transgenes, transfected in S2 cells, FLAG-tag immunopurified, and the bound RNA purified and subjected to RNA-seq. The resulting reads (CLIP tags) were aligned to the Drosophila genome and generated 38,695-5,900,000 unique CLIP tags for each SR-protein replicate.
2014-11-23 | E-GEOD-63262 | biostudies-arrayexpress
Project description:Using RNA-seq, we characterize the global AS regulation of the eight Drosophila SR protein family members RNA-seq experiments on two replicate samples from 8 individual SR protein knockdown (exptGroup=S), two replicates of simultaneous SR protein knockdown (XL6:B52 & SC35:B52) (exptGroup=D). Each exptGroup includes duplicate of its own non-specific (NS) controls.
2014-11-23 | E-GEOD-63263 | biostudies-arrayexpress
Project description:Six different endogenous Drosophila proteins (all potential export factors) have been inactivated using RNAi and leptomycin B (LMB) treatments. Five different endogenous Drosophila proteins (all potential export factors) have been targeted by RNAi. The effect on mRNA export is analyzed by monitoring the levels of mRNAs in cytoplasmic and total samples. Samples from knock-downs are compared to samples obtained from (GFP transfected) control cells processed in parallel. [The two samples compared have the same name, but the suffix _KD for knock down and _ctrl for the control]. The potential export factors targeted by RNAi are: NXF1, NXF2, NXF3, p15 and UAP56. In an additional control experiment the translation initiation factor eIF4G was targeted by RNAi (to control for the specificity of the observed effects). The samples were taken 2 (nxf1_d2), 4 (nxf1_d4, p15_d4, uap56_d4), 5 (nxf2_d5, nxf3_d5) or 6 (IF_d6) days after transfecting with dsRNA. Crm1, a transport factor responsible for protein export and the export of UsnRNAs and ribosomal subunits, has been specifically inactivated using LMB (instead of RNAi).
2003-05-15 | E-MEXP-4 | biostudies-arrayexpress
Project description:2 million cells were seeded in a 2 ml medium containing 58 µg of total dsRNA. For coRNAi treatments 28 µg of each single dsRNA were used. After treatment cells were left to incubate 4 d at 25 °C, and plates were sealed with Parafilm to avoid medium evaporation. 8 samples were prepared with the following dsRNA treatment combinations: RLUC/RLUC x 2, CSN5/RLUC, CSN8/RLUC, CDK2/CSN5, CDK2/CSN8, CDK2/RLUC 2x . dsRNAs were taken from the HD3-dsRNA-library. Two dsRNAs per gene were pooled. The single-cell transcriptomic sequencing experiment was performed with 10x Genomics technology according to the manufacturer’s protocol.
2022-01-03 | E-MTAB-11196 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE30989: MOF-containing NSL complex specifically binds promoters of most, but stimulates only a specific subset of, housekeeping genes (ChIP-chip dataset) GSE30990: MOF-containing NSL complex specifically binds promoters of most, but stimulates only a specific subset of, housekeeping genes (expression dataset) Refer to individual Series
2011-10-28 | E-GEOD-30991 | biostudies-arrayexpress
Project description:In honey bees, Vitellogenin (Vg) is hypothesized to be a major factor affecting hormone signaling, food-related behavior, immunity, stress resistance and lifespan. Likewise microRNAs play important roles in posttranscriptional gene regulation and affect many biological processes thereby showing many parallels to Vg functions. The molecular basis of Vg and microRNA interactions is largely unknown. Here, we exploited the well-established RNA interference (RNAi) protocol for Vg knockdown to investigate its effects on microRNA population in honey bee foragerM-bM-^@M-^Ys brain and fat body tissue. To identify microRNAs that are differentially expressed between tissues in control and knockdown foragers, we used M-BM-5ParafloM-BM-. microfluidic oligonucleotide microRNA microarrays. Our results show 76 and 74 miRNAs were expressed in the brain of control and knockdown foragers whereas 66 and 69 miRNAs were expressed in the fat body of control and knockdown foragers respectively. Target prediction identified potential seed matches for differentially expressed subset of microRNAs affected by Vg knockdown. These candidate genes are involved in a broad range of biological processes including insulin signaling, juvenile hormone (JH) and ecdysteroid signaling previously shown to affect foraging behavior. Thus, here we demonstrate a causal link between Vg expression-variation and variation in the abundance of microRNAs in different tissues with possible consequences for regulation of foraging behavior. We knocked down Vitellogenin (Vg) gene expression (using RNAi) in adult workers to identify potential downstream consequences on the expression of microRNA population in the fat body compared to control group (dsRNA-GFP injected bees). Six biological samples of fat body-derived small RNA fraction were prepared for each treatment group (dsRNA-Vg and dsRNA-GFP). Each biological sample contained pooled RNA from 5 unique individuals. Each fat body pool contained a total of 2 M-BM-5g of small RNA fraction, to which each of the 5 individuals contributed equally (400 ng). Pools were named as M-bM-^@M-^\control forager fat bodyM-bM-^@M-^] (GFFb) and M-bM-^@M-^\knockdown forager fat bodyM-bM-^@M-^] (VFFb), followed by a number from 1 to 6.
2013-03-07 | E-GEOD-44916 | biostudies-arrayexpress
Project description:In honey bees, Vitellogenin (Vg) is hypothesized to be a major factor affecting hormone signaling, food-related behavior, immunity, stress resistance and lifespan. Likewise microRNAs play important roles in posttranscriptional gene regulation and affect many biological processes thereby showing many parallels to Vg functions. The molecular basis of Vg and microRNA interactions is largely unknown. Here, we exploited the well-established RNA interference (RNAi) protocol for Vg knockdown to investigate its effects on microRNA population in honey bee foragerM-bM-^@M-^Ys brain and fat body tissue. To identify microRNAs that are differentially expressed between tissues in control and knockdown foragers, we used M-BM-5ParafloM-BM-. microfluidic oligonucleotide microRNA microarrays. Our results show 76 and 74 miRNAs were expressed in the brain of control and knockdown foragers whereas 66 and 69 miRNAs were expressed in the fat body of control and knockdown foragers respectively. Target prediction identified potential seed matches for differentially expressed subset of microRNAs affected by Vg knockdown. These candidate genes are involved in a broad range of biological processes including insulin signaling, juvenile hormone (JH) and ecdysteroid signaling previously shown to affect foraging behavior. Thus, here we demonstrate a causal link between Vg expression-variation and variation in the abundance of microRNAs in different tissues with possible consequences for regulation of foraging behavior. We knocked down Vitellogenin (Vg) gene expression (using RNAi) in adult workers to identify potential downstream consequences on the expression of microRNA population in the brain compared to control group (dsRNA-GFP injected bees). Six biological samples of brain-derived small RNA fraction were prepared for each treatment group (dsRNA-Vg and dsRNA-GFP). Each biological sample contained pooled RNA from 5 unique individuals. Each brain pool contained a total of 1 M-BM-5g of small RNA fraction, to which each of the 5 individuals contributed equally (200 ng). Pools were named as M-bM-^@M-^\control forager brainM-bM-^@M-^] (GFBr) and M-bM-^@M-^\knockdown forager brainM-bM-^@M-^] (VFBr), followed by a number from 1 to 6.
2013-03-07 | E-GEOD-44915 | biostudies-arrayexpress
Project description:The MOF-containing NSL complex binds to many but not all promoters of active genes and potentially contributes to their proper gene expression. It is currently unknown what determines whether an active gene is bound or not. Here, we provide evidence that the NSL complex primarily targets active promoters of most housekeeping genes. There, it co-localizes with the chromatin remodeler NURF and the histone methyltransferase Trithorax. Moreover, despite binding to most housekeeping genes, the NSL complex regulates only a subset of them, which are depleted for certain insulator binding-proteins and enriched for the core promoter motif “Ohler 5”. We suggest that the combination of general chromatin factors and core promoter motifs is predictive for whether a housekeeping gene is transcriptionally regulated by the NSL complex. Transcriptome expression profiling comparing NSL1 RNAi-depleted cells with control RNAi cells using Affymetrix microarrays.
2011-10-28 | E-GEOD-30990 | biostudies-arrayexpress
Project description:modENCODE_submission_5596 This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: The goal of these experiments are to a) validate/confirm the locations of 125 chromosomal proteins across the Drosophila melanogaster genome and b) evaluate their biological significance by assaying the impact of depletion on other proteins/marks. We are using RNAi to deplete individual non-histone chromosomal proteins in Drosophila BG3 and S2 tissue culture cells, followed by Chromatin ImmunoPrecipitation (ChIP) assayed on genomic tiling arrays. Comparison of a protein factor's binding profiles before and after depletion will increase the confidence of our predictions. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Cell Line: S2-DRSC; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Sex: Male; EXPERIMENTAL FACTORS: Cell Line S2-DRSC; Antibody H2AV 9751 (target is H2AV); dsRNA (RNAi_reagent) Fly_GFP_RNAi_2&oldid=76949
2013-11-01 | E-GEOD-51991 | biostudies-arrayexpress
Project description:modENCODE_submission_5595 This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: The goal of these experiments are to a) validate/confirm the locations of 125 chromosomal proteins across the Drosophila melanogaster genome and b) evaluate their biological significance by assaying the impact of depletion on other proteins/marks. We are using RNAi to deplete individual non-histone chromosomal proteins in Drosophila BG3 and S2 tissue culture cells, followed by Chromatin ImmunoPrecipitation (ChIP) assayed on genomic tiling arrays. Comparison of a protein factor's binding profiles before and after depletion will increase the confidence of our predictions. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Cell Line: S2-DRSC; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Sex: Male; EXPERIMENTAL FACTORS: Cell Line S2-DRSC; Antibody H2AV 9751 (target is H2AV); dsRNA (RNAi_reagent) CG5499_RNAi_2&oldid=76948
2013-11-01 | E-GEOD-51990 | biostudies-arrayexpress