In order to gain a broad sampling of the Drosophila transcriptome, RNA-Seq experiments were performed at all stages of the Drosophila life cycle, and 12 independent cDNA libraries were generated, including embryonic, larval, pupal, and adult. Some libraries were staged as specific windows: 2-4 hour embryo, 14-16 hour embryo, 3rd instar larva, 3-day pupa, and 17-day adult. Additional libraries were derived from broadly staged mixed samples: embryo, larvae, and pupa. Three-day old male and female adults were sequenced separately for discovery of sex-specific variation. Finally, one library of mixed-age pupal RNA was sequenced in replicate as a validation of the technology. A total of 272 million paired-end reads of 64-75 base pairs in length were obtained, representing greater than 690x sequence coverage of the 30Mb Drosophila melanogaster transcriptome.
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View SamplesThe regulation of transcriptome responses in zebrafish embryo exposure to triadimefon
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No sample metadata fields
View SamplesHigh-throughput approaches for profiling the 5'' ends of RNA degradation intermediates on a genome-wide scale are frequently applied in the validation of cleavage sites guided by microRNAs (miRNAs). However, the complexity of the RNA degradome beyond miRNA targets currently is largely unclear which limits the application of degradome. We provide multiple lines of evidence to show that ribosome footprints are widespread in the plant degradome. A 3-nt periodicity and a bias toward the translational frame were observed in the analysis of 5' truncated mRNA ends mapped to the coding sequence (CDS). In addition, predominant 5' termini of RNA degradation intermediates separated by a length equal to a ribosome-protected fragment were evident in the conserved peptide upstream open reading frames (uORFs). Through the analysis of degradome data, we uncovered novel ribosome stalling uORFs including a lineage specific uORF in the Brassicaceae family. Phased degradation signatures of stacked ribosomes were also identified in the CDS of multiple genes. Furthermore, we show that the binding of ARGONAUTE7 to a non-cleavable target site of miR390 might directly hinder ribosome movement. This work shows that the RNA degradome contains in vivo ribosome-protected mRNA fragments and demonstrates an alternative use of degradome data in the study of ribosome stalling.
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Specimen part
View SamplesThe mechanistic target of rapamycin complex 1 (mTORC1) regulates beta cell growth and mass; yet it remains unclear whether it also directs beta cell functional maturation. To understand the global molecular basis of the phenotype caused by the loss of Raptor in beta cells, we isolated pancreatic islets from 8-week-old RapKO and WT mice. We compared gene-expression profile by Affymetrix microarray of islets, which revealed that a number of mRNAs were dys-regulated in Raptor-deficient islets.
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Sex, Specimen part
View SamplesTotal RNA from lymphocytes derived from skin lesions of three pemphigus patients and three healthy control subjects was used for this study.
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Specimen part, Disease stage
View SamplesTranscriptional profiling of human acute myelogenous leukemia (AML) CD34+ cells treated with 5 M fenretinide. Two timepoints included are 6h, 12h, covering the apoptosis-induction time window of AML CD34+ cells responsing to the fenretinide treatment. We studied gene expression series in human AML CD34+ cells with or without 5 M fenretinide treatment by cDNA microarray analysis. Several signal transduction pathways are involve, including stress response, NF-kappaB inhibition and p53 inhibition (p<0.05). These findings indicate fenretinide may represent a promising candidate for targeting AML-initiating cells.
Preferential eradication of acute myelogenous leukemia stem cells by fenretinide.
Specimen part
View SamplesPML-RARa contributes to the development of APL through repression of genes important in myeloid development. Through a global approach, we have identified 2,979 high quality PML-RARa binding sites in ZnSO4 induced PR9 cells. By integration the gene expression data, we found that PML/RARa target genes are transcriptionally suppressed in primary APL cells and re-activated in ATRA treated NB4 cells.
PML/RARalpha targets promoter regions containing PU.1 consensus and RARE half sites in acute promyelocytic leukemia.
Cell line, Treatment, Time
View SamplesNB4 is an APL derived cell line, carrying the t(15;17) translocation and expressing the PML/RARa fusion protein. Still, an important question that remains to be addressed is whether PML/RARa target genes are transcriptionally suppressed in primary APL cells and re-activated in all-trans retinoic acid (ATRA) treated NB4 cells. Gene expression of NB4 cells treated with ATRA at different time points were analyzed.
PML/RARalpha targets promoter regions containing PU.1 consensus and RARE half sites in acute promyelocytic leukemia.
Cell line, Treatment, Time
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