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Series GSE25855 Query DataSets for GSE25855
Status Public on Feb 01, 2011
Title Empirical Annotation of the Daphnia pulex genome; Experiment A
Organism Daphnia pulex
Experiment type Expression profiling by genome tiling array
Summary 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.
Overall design 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).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.
Contributor(s) Colbourne JK, Lopez J, Choi J
Citation(s) 21292972
Submission date Dec 05, 2010
Last update date Jun 25, 2012
Contact name Jacqueline Lopez
Phone 574-631-1902
Organization name University of Notre Dame
Department Biology
Lab Pfrender Laboratory
Street address 019 Galvin Life Science Center
City Notre Dame
State/province Indiana
ZIP/Postal code 46556
Country USA
Platforms (2)
GPL11200 NimbleGen Daphnia pulex Whole-genome Tiling Array Set (1 of 2)
GPL11201 NimbleGen Daphnia pulex Whole-genome Tiling Array Set (2 of 2)
Samples (6)
GSM634925 Sample1_chip1_experimentA_replicate1
GSM634926 Sample2_chip1_experimentA_replicate2
GSM634927 Sample3_chip1_experimentA_replicate3
This SubSeries is part of SuperSeries:
GSE25823 The Ecoresponsive Genome of Daphnia pulex: Empirical annotation of the Daphnia pulex genome
BioProject PRJNA142497

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE25855_RAW.tar 660.3 Mb (http)(custom) TAR (of PAIR)
Processed data included within Sample table

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