Dm_y[1]cn[1] bw[1] sp[1]_larval_L3-gut-stage3_TotalRNA_p200_452-454-456_38bp
Ontology highlight
ABSTRACT:
ORGANISM(S): Drosophila melanogaster
SUBMITTER: DCC modENCODE
PROVIDER: E-GEOD-23221 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:modENCODE_submission_540 This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs. 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: Transcript tiling array analysis EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: Y cn bw sp; Developmental Stage: L3 stage larvae, dark blue gut PS(1-2) stage; Genotype: y[1] oc[R3.2]; Gr22b[1] Gr22d[1] cn[1] CG33964[R4.2] bw[1] sp[1]; LysC[1] lab[R4.2] MstProx[1] GstD5[1] Rh6[1]; NUMBER OF REPLICATES: 3; EXPERIMENTAL FACTORS: Strain Y cn bw sp; Developmental Stage L3 stage larvae, dark blue gut PS(1-2) stage
2010-08-05 | E-GEOD-23222 | biostudies-arrayexpress
Project description:modENCODE_submission_538 This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs. 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: Transcript tiling array analysis EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: Y cn bw sp; Developmental Stage: L3 stage larvae, 12 hr post-molt; Genotype: y[1] oc[R3.2]; Gr22b[1] Gr22d[1] cn[1] CG33964[R4.2] bw[1] sp[1]; LysC[1] lab[R4.2] MstProx[1] GstD5[1] Rh6[1]; NUMBER OF REPLICATES: 3; EXPERIMENTAL FACTORS: Strain Y cn bw sp; Developmental Stage L3 stage larvae, 12 hr post-molt
2010-08-05 | E-GEOD-23220 | biostudies-arrayexpress
Project description:Since their discovery, transposable elements have been proposed to play a central role in the evolution of their host genomes through their ability to regulate gene expression, in particular by providing transcription start sites (TSSs) for host genes. To investigate their contribution to developmental gene expression, we developed RAMPAGE, a high-throughput 5'-complete cDNA sequencing approach to accurately discover TSSs, characterize their transcripts, and quantify their expression. This strategy, which directly delineates the expression profiles of individual promoters and was designed to offer optimal sample multiplexing capabilities, represents an advantageous alternative to standard RNA-Seq for a wide range of transcriptome profiling applications. We used RAMPAGE in a genome-wide study of promoter activity throughout 36 stages of the life cycle of Drosophila melanogaster, and describe here a comprehensive dataset that represents the first developmental timecourse of promoter usage. We found that over 40% of developmentally expressed genes have at least 2 promoters, and that alternative promoters generally implement distinct regulatory programs. Transposons harbor TSSs driving the expression of hundreds of annotated genes, and they often impart their own expression specificity upon the genes they regulate. Detailed analysis of particular transposons identified sequence elements encoding these regulatory properties. Our results show that transposable elements contribute significantly to the generation of standing variation and to the evolution of gene regulatory networks, by distributing stereotyped regulatory modules throughout the genome. This dataset represents a whole-genome, single-base resolution profiling of transcription start site (TSS) expression throughout 36 stages of the life cycle of Drosophila melanogaster. These profiles were established using RAMPAGE, a high-throughput, high-accuracy 5'-complete cDNA sequencing method implemented on the Illumina platform. Embryos, larvae, pupae and adult flies were collected at specific stages of development, and RAMPAGE profiles were established for pools of whole organisms. The data was analyzed using custom scripts and algorithms that are all available upon request. Supplementary files: Dmel_Combined_+.bw: bigWig coverage by cDNA 5' ends (+ strand). Dmel_Combined_-.bw: bigWig coverage by cDNA 5' ends (- strand). Dmel_All_RAMPAGE_peaks.bed: BED file describing all RAMPAGE peaks. Dmel_GeneTSS_RAMPAGE_peaks.bed: BED file describing all peaks attributed to annotated genes. GeneTSS_expression_RAMPAGE_RPM.txt: Expression matrix for all genic peaks (RPM: reads per million). Transposon_expression_RAMPAGE_RPM.txt: Expression matrix for all RepeatMasker-annotated transposon classes (RPM: reads per million). Genome build: dm3
2012-08-30 | E-GEOD-36212 | biostudies-arrayexpress
Project description:modENCODE_submission_541 This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs. 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: Transcript tiling array analysis EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: Y cn bw sp; Developmental Stage: Pupae, WPP + 2 days; Genotype: y[1] oc[R3.2]; Gr22b[1] Gr22d[1] cn[1] CG33964[R4.2] bw[1] sp[1]; LysC[1] lab[R4.2] MstProx[1] GstD5[1] Rh6[1]; NUMBER OF REPLICATES: 3; EXPERIMENTAL FACTORS: Strain Y cn bw sp; Developmental Stage Pupae, WPP + 2 days
2010-08-04 | E-GEOD-23223 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE36200: RAMPAGE dataset for the human K562 cell line GSE36212: Promoter activity profiling throughout the Drosophila life cycle reveals role of transposons in regulatory innovation Refer to individual Series
2012-08-29 | E-GEOD-36213 | biostudies-arrayexpress
Project description:Low-oxygen tolerance is supported by an adaptive response that includes a coordinate shift in metabolism and the activation of a transcriptional program that is driven by the hypoxia-inducible factor (HIF) pathway. The precise contribution of HIF-1 in the adaptive response, however, has not been determined. Here we investigate how HIF-1 influences hypoxic adaptation throughout Drosophila development. We find that hypoxic-induced transcriptional changes are comprised of HIF-dependent and HIF-independent pathways that are distinct and separable. We show that normoxic set-points of carbohydrate metabolites are significantly altered in dHIF mutants and that these animals are unable to mobilize glycogen in hypoxia. Furthermore, we find that the estrogen-related receptor (dERR), which is a global regulator of aerobic glycolysis in larvae, is required for a competent hypoxic response. dERR binds to dHIF and participates in the HIF-dependent transcriptional program in hypoxia. In addition, dERR acts in the absence of dHIF in hypoxia and a significant portion of HIF-independent transcriptional responses can be attributed to dERR actions, including upregulation of glycolytic transcripts. These results indicate that competent hypoxic responses arise from complex interactions between HIF-dependent and -independent mechanisms, and that dERR plays a central role in both of these programs. Fly eggs were collected onto egg caps with yeast paste . The caps were replaced after overnight incubation periods and kept at 25M-BM-:C, until mid-L2. At mid-L2, larvae were transferred to a fresh egg cap with blue yeast paste (0.3% bromophenol blue), and allowed to develop until achieving the partial clear gut L3 stage (-10 to -4 hrs prior to metamorphic onset). Appropriately staged animals were moved to fresh agar plates and allowed to age an additional 6 hours at 25M-BM-:C (normoxic treatment). Alternatively, animals were placed in an airtight Modular Incubator Chamber for 6 hours at 25M-BM-:C after a gas mixture containing 4% oxygen balanced with nitrogen was flashed into the chamber (hypoxic treatment). Mutant larvae were sorted for the absence of GFP expression using dissecting stereoscope with fluorescence at mid-L2. Microarray analyses were performed on at least three biological replicates of w1118, dHIF mutants, or dERR mutants at the partial clear gut third instar larval stage and were treated for 6 hours in normoxia or 4% O2. For each biological replicate, at least 10 larvae were collected and washed with 1M-CM-^WPBS. Larvae were placed in TRIzol (Invitrogen, Carlsbad, CA) and homogenized using VWR disposable pellet mixer. Total RNA was isolated using a TRIzol/RQ1 DNase (Promega, Madison, WI) hybrid extraction protocol. Template labelings were performed using the GeneChip 3' IVT Express Kit according to the manufacturerM-bM-^@M-^Ys specifications (Affymetrix, Santa Clara, CA). Hybridizations to Affymetrix GeneChip Drosophila Genome 2.0 arrays were performed using the manufacturers recommendations. Every chip was scanned at a high resolution by the Affymetrix GeneChipM-BM-. Scanner 3000 according to the GeneChip Expression Analysis Technical Manual procedures (Affymetrix, Santa Clara, CA).
2013-02-05 | E-GEOD-33100 | biostudies-arrayexpress
Project description:modENCODE_submission_2342 This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs. 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: Transcript tiling array analysis EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: Oregon-R; Tissue: Female heads; Developmental Stage: Adult female, eclosion + 1 day; Genotype: wild type; Sex: Female; NUMBER OF REPLICATES: 2; EXPERIMENTAL FACTORS: Strain Oregon-R; Developmental Stage Adult female, eclosion + 1 day; Tissue Female heads
2010-08-05 | E-GEOD-23233 | biostudies-arrayexpress
Project description:modENCODE_submission_2340 This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs. 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: Transcript tiling array analysis EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: Oregon-R; Tissue: Adult ovaries; Developmental Stage: Adult female eclosion+4 day; Genotype: wild type; Sex: Female; NUMBER OF REPLICATES: 2; EXPERIMENTAL FACTORS: Strain Oregon-R; Developmental Stage Adult female eclosion+4 day; Tissue Adult ovaries
2010-08-05 | E-GEOD-23231 | biostudies-arrayexpress
Project description:modENCODE_submission_2341 This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs. 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: Transcript tiling array analysis EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: Oregon-R; Tissue: Female heads; Developmental Stage: Adult female, eclosion + 1 day; Genotype: wild type; Sex: Female; NUMBER OF REPLICATES: 2; EXPERIMENTAL FACTORS: Strain Oregon-R; Developmental Stage Adult female, eclosion + 1 day; Tissue Female heads
2010-08-05 | E-GEOD-23232 | biostudies-arrayexpress
Project description:modENCODE_submission_3248 This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs. 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: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: Y cn bw sp; Developmental Stage: Embryo 4-6h; Genotype: y[1] oc[R3.2]; Gr22b[1] Gr22d[1] cn[1] CG33964[R4.2] bw[1] sp[1]; LysC[1] lab[R4.2] MstProx[1] GstD5[1] Rh6[1]; NUMBER OF REPLICATES: 3; EXPERIMENTAL FACTORS: Strain Y cn bw sp; Developmental Stage Embryo 4-6h
2010-11-18 | E-GEOD-25347 | biostudies-arrayexpress