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Series GSE46069 Query DataSets for GSE46069
Status Public on Feb 05, 2014
Title Whole transcriptome profiling of rat pineal glands and retinas collected throughout a 24-hour cycle
Organism Rattus norvegicus
Experiment type Expression profiling by high throughput sequencing
Summary The rat pineal transcriptome is highly dynamic, with many hundreds of transcripts changing more than two-fold on a 24-hr basis, as revealed earlier using Affymetrix GeneChip analysis. The retina is evolutionally related to the pineal gland so these two tissues share many gene expression patterns. This study more completely characterizes the temporally dynamic transcriptomes of these tissues using RNA-Seq to capture information regarding alternative splicing, novel exons, unannotated mRNAs, non-coding RNAs, and coding transcripts not represented on the Affymetrix chips. We also identified transcripts that were selectively expressed in the pineal gland relative to other tissues by comparing pineal samples to a sample of pooled non-pineal tissues.
Overall design The transcriptomes of the rat pineal gland and retina were sequenced using samples collected at 6 time points throughout a 24-hour cycle to identify rhythmically expressed transcripts. The transcriptomes of pools of mixed tissues collected at mid-day (ZT7) and mid-night (ZT19) were also sequenced for comparison to aid in determining pineal-enriched transcripts.
Contributor: NISC, Comparative Sequencing Program
Contributor(s) Coon SL, Fu C, Clokie SJ, Munson PJ, Cherukuri PF, Sugden D, Mullikin JC, Klein DC
Citation(s) 24351931
Submission date Apr 15, 2013
Last update date May 15, 2019
Contact name Steven Coon
Phone 3014516622
Organization name NIH
Lab Section on Neuroendocrinology
Street address 49 Convent Drive Room 6A83
City Bethesda
State/province MD
ZIP/Postal code 20892-4510
Country USA
Platforms (1)
GPL14844 Illumina HiSeq 2000 (Rattus norvegicus)
Samples (14)
GSM1122813 Rat pineal gland, Time series, ZT1 (1 hr after lights on)
GSM1122814 Rat pineal gland, Time series, ZT7 (mid-day)
GSM1122815 Rat pineal gland, Time series, ZT13 (1 hr before lights off)
BioProject PRJNA197149
SRA SRP021090

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Supplementary file Size Download File type/resource
GSE46069_FPKM_time_all.txt.gz 1.5 Mb (ftp)(http) TXT
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