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Series GSE63309 Query DataSets for GSE63309
Status Public on Sep 02, 2015
Title RNA-Seq of the rat pineal transcriptome, with in-vivo and in-vitro samples, under various treatment and surgical conditions
Organism Rattus norvegicus
Experiment type Expression profiling by high throughput sequencing
Summary Pineal function follows a 24-hour schedule, dedicated to the conversion of night and day into a hormonal signal, melatonin. In mammals, 24-hour changes in pineal activity are controlled by a neural pathway that includes the central circadian oscillator in the suprachiasmatic nucleus and the superior cervical ganglia (SCG), which innervate the pineal gland. In this study, we have generated the first next-generation RNA sequencing evidence of neural control of the daily changes in the pineal transcriptome. We found over 3000 pineal transcripts that are differentially expressed (p <0.001) on a night/day basis (70% of these genes increase at night, 376 with fold change >4 or <1/4), the majority of which had not been previously identified as such. Nearly all night/day differences were eliminated by neonatal removal or decentralization of the SCG, confirming the importance of neural input for differential night/day changes in transcript abundance. In contrast, very few non-rhythmic genes showed evidence of changes in expression due to the surgical procedure itself, which is consistent with the hypothesis that post neonatal neural stimulation is not required for cell fate determination and maintenance of phenotype. Many of the transcripts that exhibit marked differential night/day expression exhibited similar changes in response to in vitro treatment with norepinephrine, the SCG neurotransmitter which mediates pineal regulation. Similar changes were also seen following treatment with an analog of the norepinephrine second messenger, cyclic AMP.
Overall design For the in vivo data, there were 8 biological conditions: day and night time points for each of four surgical groups: Control (Ctrl) Sham-surgery (Sham), Decentralized (DCN), and Ganglionectomized (SCGX). Samples were pooled into three biological replicates for each biological condition. For the in vitro data there were 3 biological conditions: Untreated control (CN), DBcAMP-treated (DB), and Norepinephrine-treated (NE). For the pineal enrichment comparison, three samples (i.e. no biological replicates) were used: pineal-day, pineal-night and mixed-tissue. For the mixed tissues sample, the following tissues from three rats sacrificed at ZT7 were used: cortex, cerebellum, midbrain, hypothalamus, hindbrain, spinal cord, retina, pituitary, heart, liver, lung, kidney, skeletal muscle, small intestine, adrenal gland. Total RNA was extracted from each tissue, and then equal amounts of each of the 15 tissues were combined for the final pooled sample.
Contributor(s) Hartley SW, Coon SL, Savastano LE, Mullikin J, Klein DC, Fu C
Citation(s) 26367423
Submission date Nov 14, 2014
Last update date May 15, 2019
Contact name Stephen William Hartley
Phone 301-451-0277
Organization name NHGRI, NIH
Department Cancer Genetics and Comparative Genomics Branch
Lab Comparative Genomics Analysis Unit
Street address 5625 Fishers Lane
City Rockville
State/province MD
ZIP/Postal code 20850
Country USA
Platforms (1)
GPL14844 Illumina HiSeq 2000 (Rattus norvegicus)
Samples (36)
GSM1545499 In Vitro, Untreated, Sample 1
GSM1545500 In Vitro, Untreated, Sample 2
GSM1545501 In Vitro, Untreated, Sample 3
BioProject PRJNA267246
SRA SRP049818

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Supplementary file Size Download File type/resource
GSE63309_DESeq2.results.all.v7.xlsx 75.7 Mb (ftp)(http) XLSX
GSE63309_RAW.tar 12.9 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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