Dataset Information

Expression profile of the first 24 hrs of Drosophila embryonic development using tiling arrays

ABSTRACT: Many animal and plant genomes are transcribed much more extensively than current annotations predict. However, the biological function of these unannotated transcribed regions is largely unknown. To begin to address this question, we have generated a series of transcription maps at an interrogation resolution of 35 base pairs (bp) across the Drosophila genome for the first 24 hrs of development in 2 hour increments, similar to maps we have created for regions of the human genome. Using a single tiling array, 3,075,693 probe pairs of twenty-five nucleotides (nts) in length were used to interrogate 105,897,358 non-repeat bp of the fly genome. Maps of the sites of transcription were made using total RNA greater than 200 nts. Approximately 7% and 23% of the detected transcribed nucleotides during D. melanogaster embryogenesis map to unannotated intergenic and intronic regions, respectively. Based on computational analysis of coordinated transcription, we conservatively estimate that 29% of all unannotated transcribed sequences function as missed or alternative exons of well-characterized protein coding genes. 15.6 % of intergenic transcribed regions function as missed or alternative transcription start sites utilized by 11.4% of the expressed protein-coding genes. Identification of P element mutations within or near newly identified 5' exons provides a strategy for mapping previously uncharacterized mutations to their respective genes. Collectively, these data indicate that at least 85% of the fly genome is transcribed and processed into mature transcripts representing at least 30% of the fly genome. Keywords: time course, Drosphila embryonic development, tiling array, expression profile

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE5514 | GEO | 2006/08/14

SECONDARY ACCESSION(S): PRJNA96067

REPOSITORIES: GEO

ACCESS DATA

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Project description:Experiments conducted on this tiling array are used to (1) validate the frozen gene sets of the current genome annotation, (2) improve the predicted gene structures by empirically determining UTRs and intron-exon boundaries, identifying missing upstream, internal, and downstream exons and alternative transcripts, (3) propose gene structure models in transcribed regions containing no predicted genes and (4) delineate transcriptionally active regions of the genome from intergenic, intronic and genic regions. Signal to background ratios were determined by first calling probes that fluoresced at intensities greater than 99% of the random probes’ signal intensities; therefore only 1% of fluorescing experimental probes should be false positives. We conducted two-color competitive hybridizations that measure differential expression from three replicates, each using RNA from independent biological extractions. Transcriptional active regions (TARs) were defined by stringing together overlapping probes showing fluorescence above a 1% false positive rate (FPR). Positive probes were joined into a TAR if they were adjacent (maxgap=0, no intermittent non-positive probe) and a TAR’s length had to be at least 45 bp (minrun=45, mid-point first positive probe to mid-point last positive probe, resulting in at least 3 adjacent positive probes for a TAR). Transcriptional active regions (TARs) were defined by stringing together overlapping probes showing fluorescence above a 1% false positive rate (FPR). The data analysis to measure differential expression of genes and of unannotated TARs was performed using the statistical software package R and Bioconductor with additions and modifications. The signal distributions across chips, samples and replicates were adjusted to be equal according to the mean fluorescence of the random probes on each array. All probes including random probes were quantile-normalized across replicates. Expression-level scores were assigned for each predicted gene based on the median log2 fluorescence over background intensity of probes falling within the exon boundaries.

Dataset Information

Expression profile of the first 24 hrs of Drosophila embryonic development using tiling arrays

Dataset's files

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets