Pineal gland; day and night; and mixed tissue, day; Ribominus (Rat)

Specimens

Pools of 6 rat pineal glands were collected at mid-day (ZT7) and mid-night (ZT19) from animals housed in a 14:10 light:dark lighting cycle. In addition, a mixed tissue sample was prepared from material collected from three rats at ZT7. The tissues were: cortex, cerebellum, midbrain, hypothalamus, hindbrain, spinal cord, retina, pituitary, heart, liver, lung, kidney, skeletal muscle, small intestine, adrenal gland.

RNA Preparation

Samples of tissue from the three animals were mixed. Total RNA was extracted using an RNeasy Kit with on-column DNase treatment. To prepare the mixed tissue sample, equal amounts of RNA from each of the 15 tissues were combined.

RNA-Seq library preparation and sequencing

Total RNA (10 ug) from the pineal gland pools and mixed tissue samples was ribosomal RNA-depleted (=ribo), fragmented and sequenced on an Illumina GAII machine, yielding paired-end 51-mer reads.

Note: In some cases, the mixed tissue values for selected genes are exceptionally high because that gene is very highly expressed in only one tissue, e.g., Rho and GH are strongly expressed only in the retina and pituitary gland, respectively.

Bioinformatics methods

See bioinformatics methods for details.

Samples

The following table describes the sample metadata for this experiment. Accessions in GEO, BioProject, and SRA link to their resepective entries. Raw data were downloaded as FASTQ format using fastq-dump for each of the SRR run accessions.

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samplename	Label	BioSample	Experiment	SRRrun	SRA_Sample	Sample_Name	SRA_Study	BioProject	LoadDate	MBases	MBytes	Assay_Type	Center_Name	Consent	DATASTORE_filetype	DATASTORE_provider	Instrument	LibraryLayout	LibrarySelection	LibrarySource	Organism	Platform	ReleaseDate	AvgSpotLen	InsertSize	Library_Name

samplename	Label	BioSample	Experiment	SRRrun	SRA_Sample	Sample_Name	SRA_Study	BioProject	LoadDate	MBases	MBytes	Assay_Type	Center_Name	Consent	DATASTORE_filetype	DATASTORE_provider	Instrument	LibraryLayout	LibrarySelection	LibrarySource	Organism	Platform	ReleaseDate	AvgSpotLen	InsertSize	Library_Name
day_ribo	day_ribo	SAMN00627589	SRX076903	SRR279580	SRS212034	Rat pineal gland_ZT7_RiboMinus	SRP006893	PRJNA68065	2014-05-30	3205	1469	RNA-Seq	NICHD/PDEGEN	public	sra	ncbi	Illumina Genome Analyzer II	PAIRED	other	TRANSCRIPTOMIC	Rattus norvegicus	ILLUMINA	2012-08-28	102	375	DCK1r Pineal ZT7
mixed_ribo	mixed_ribo	SAMN00627591	SRX076921	SRR279588	SRS212036	Rat non-pineal mixed tissue_ZT7_RiboMinus	SRP006893	PRJNA68065	2014-05-30	2675	1168	RNA-Seq	NICHD/PDEGEN	public	sra	ncbi	Illumina Genome Analyzer II	PAIRED	other	TRANSCRIPTOMIC	Rattus norvegicus	ILLUMINA	2012-08-28	102	375	DCK3r mixed ZT7
night_ribo	night_ribo	SAMN00627590	SRX076913	SRR279581	SRS212035	Rat pineal gland_ZT19_RiboMinus	SRP006893	PRJNA68065	2014-05-30	1992	813	RNA-Seq	NICHD/PDEGEN	public	sra	ncbi	Illumina Genome Analyzer II	PAIRED	other	TRANSCRIPTOMIC	Rattus norvegicus	ILLUMINA	2012-08-28	102	375	DCK2r Pineal ZT19

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