RNA-Seq of the rat pineal transcriptome, with in-vivo and in-vitro samples, under various treatment and surgical conditions

Experiment ID:SRP049818
Technology:RNA-Seq
Description: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.
Source:SRP049818  SRA
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Bulk RNA-Seq processed expression values in Rattus norvegicus

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Library ID
Identifier of the RNA-Seq library
Anat. entity ID
ID of the anatomical localization of the sample
Anat. entity name
Name of the anatomical localization of the sample
Anat. entity author annotation
Free text annotation of anatomical localization of the sample as provided by authors
Stage ID
ID of the developmental and life stage of the sample
Stage name
Name of the developmental and life stage of the sample
Stage author annotation
Free text annotation of the developmental and life stage of the sample as provided by authors
Sex
Annotation of the sex of the sample
Strain
Annotation of the strain of the sample
Time
Free text annotation of the time of sampling as provided by authors
Time unit
Unit for the time of sampling as provided by authors
Species
Physiological status
Physiological status of the organism at time of sampling
Technology
Sequencing platform
Sequenced transcript part
Possible values are: full length, all parts of the transcript are sequenced; 3': only the 3' end of the transcript is sequenced; 5': only the 5' end of the transcript is sequenced.
Fragmentation
Size of the RNA fragmentation
Run sequencing type
Paired-end or single-read run
Total read count
Total number of reads for the library.
Mapped read count
Number of reads that could be mapped to the transcriptome.
Total UMI count
Total number of individual RNA molecules (UMI) for the annotated sample. Only applicable for libraries producing UMIs.
Mapped UMI count
Number of UMIs that could be mapped to the transcriptome. Only applicable for libraries producing UMIs.
Distinct rank count
When performing a fractional ranking of the genes in the annotated sample, based on their expression level, number of distinct ranks observed, to have a value of the power for distinguishing expression levels. Used as a weight to compute a weighted mean rank accross samples for each gene and compute expression scores in Bgee.
Max rank
When performing a fractional ranking of the genes in the annotated sample, based on their expression level, maximum rank attained in the sample. Used to normalize ranks accross samples and compute expression scores in Bgee.
Link to processed expression values
See the processed expression value results for this assay
SRX759817UBERON:0001905 pineal bodypineal glandUBERON:0034919 juvenile stage45 days oldNASprague-DawleyNANARattus norvegicusNAIlluminaIllumina HiSeq 2000FULL_LENGTH101paired4645277222943223002015223810Browse results
SRX759818UBERON:0001905 pineal bodypineal glandUBERON:0034919 juvenile stage45 days oldNASprague-DawleyNANARattus norvegicusNAIlluminaIllumina HiSeq 2000FULL_LENGTH101paired4715269422773710001996223653.5Browse results
SRX759819UBERON:0001905 pineal bodypineal glandUBERON:0034919 juvenile stage45 days oldNASprague-DawleyNANARattus norvegicusNAIlluminaIllumina HiSeq 2000FULL_LENGTH101paired4993646723716140002013323789Browse results
SRX759820UBERON:0001905 pineal bodypineal glandUBERON:0034919 juvenile stage45 days oldNASprague-DawleyNANARattus norvegicusNAIlluminaIllumina HiSeq 2000FULL_LENGTH101paired4849250223763211001990623662Browse results
SRX759821UBERON:0001905 pineal bodypineal glandUBERON:0034919 juvenile stage45 days oldNASprague-DawleyNANARattus norvegicusNAIlluminaIllumina HiSeq 2000FULL_LENGTH101paired5108205323503661001977023493.5Browse results
SRX759822UBERON:0001905 pineal bodypineal glandUBERON:0034919 juvenile stage45 days oldNASprague-DawleyNANARattus norvegicusNAIlluminaIllumina HiSeq 2000FULL_LENGTH101paired4829750322957065001965423501.5Browse results
SRX759841UBERON:0001905 pineal bodypineal glandUBERON:0034919 juvenile stage45 days oldNASprague-DawleyNANARattus norvegicusNAIlluminaIllumina HiSeq 2000FULL_LENGTH101paired5560725935153628002055023953Browse results
SRX759842UBERON:0001905 pineal bodypineal glandUBERON:0034919 juvenile stage45 days oldNASprague-DawleyNANARattus norvegicusNAIlluminaIllumina HiSeq 2000FULL_LENGTH101paired6906221944938091002032823772.5Browse results
SRX759843UBERON:0000468 multicellular organismmixed-tissueUBERON:0034919 juvenile stage45 days oldNASprague-DawleyNANARattus norvegicusNAIlluminaIllumina HiSeq 2000FULL_LENGTH101paired6376392845463351002173324869Browse results

Showing 1 to 9 of 9 entries