Eye, pineal gland and mixed tissue; day and night (Zebrafish)

Specimens

Experimental design: An NGS study on the daily changes in zebrafish eye, pineal gland and mixed tissue transcriptomes was performed to identify genes that are expressed selectively in the eye and pineal gland. Adult (0.5-1.5 years old) transgenic zebrafish, Tg(aanat2:EGFP), were used; these animals express enhanced green fluorescent protein (EGFP) in the pineal gland under the control of the aanat2 regulatory regions. Fish were raised under 12-hr light:12-hr dark (LD) cycles in a temperature-controlled room. For tissue collection fish were anesthetized in 1.5 mM Tricaine (Sigma) and sacrificed by decapitation. Dissections were conducted at mid-day (ZT6) and mid-night (ZT18). Fluorescent pineal glands, whole eyes and other tissues were removed under a dissecting microscope. A single pool of 18 pineal glands, 6 eyes and 4 to 8 of each peripheral tissue was collected at each time point. The mixed tissue samples consisted of equal amounts of total RNA (1 microgram) from muscle, ovary, kidney, gill, liver, intestines, heart and brain. Total RNA for mRNA analysis was isolated using RNeasy Lipid Tissue Mini Kit (Qiagen) according to the manufacturer's instructions.

Sequencing

Poly-A RNA libraries were prepared for sequencing using standard Illumina protocols. The 6 libraries were pooled and sequenced on two lanes of an Illumina HiSeq2000. This generated an average of 25.4 million reads per sample (paired-end, 100-bp). The data are referenced in GSE99285.

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.

Note: scroll to the right to see the full extent of the table.

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	layout	LibrarySelection	LibrarySource	Organism	Platform	ReleaseDate	AvgSpotLen	InsertSize
eye_day-1	eye_day	SAMN07163950	SRX2853242	SRR5599690	SRS2224925	Eye	SRP107985	PRJNA387951	NaN	2672	1092	RNA-Seq	GEO	public	sra	gs,ncbi,s3	Illumina HiSeq 2000	PAIRED	cDNA	TRANSCRIPTOMIC	Danio rerio	ILLUMINA	2018-02-01T00:00:00Z	200	NaN
eye_day-2	eye_day	SAMN07163950	SRX2853242	SRR5599691	SRS2224925	Eye	SRP107985	PRJNA387951	NaN	2621	1063	RNA-Seq	GEO	public	sra	gs,s3,ncbi	Illumina HiSeq 2000	PAIRED	cDNA	TRANSCRIPTOMIC	Danio rerio	ILLUMINA	2018-02-01T00:00:00Z	200	NaN
eye_night-1	eye_night	SAMN07163949	SRX2853243	SRR5599692	SRS2224924	Eye	SRP107985	PRJNA387951	NaN	2348	979	RNA-Seq	GEO	public	sra	gs,ncbi,s3	Illumina HiSeq 2000	PAIRED	cDNA	TRANSCRIPTOMIC	Danio rerio	ILLUMINA	2018-02-01T00:00:00Z	200	NaN
eye_night-2	eye_night	SAMN07163949	SRX2853243	SRR5599693	SRS2224924	Eye	SRP107985	PRJNA387951	NaN	2319	958	RNA-Seq	GEO	public	sra	ncbi,gs,s3	Illumina HiSeq 2000	PAIRED	cDNA	TRANSCRIPTOMIC	Danio rerio	ILLUMINA	2018-02-01T00:00:00Z	200	NaN
pineal_day-1	pineal_day	SAMN07163954	SRX2853244	SRR5599694	SRS2224926	Pineal Gland	SRP107985	PRJNA387951	NaN	2548	1054	RNA-Seq	GEO	public	sra	ncbi,gs,s3	Illumina HiSeq 2000	PAIRED	cDNA	TRANSCRIPTOMIC	Danio rerio	ILLUMINA	2018-02-01T00:00:00Z	200	NaN
pineal_day-2	pineal_day	SAMN07163954	SRX2853244	SRR5599695	SRS2224926	Pineal Gland	SRP107985	PRJNA387951	NaN	2505	1025	RNA-Seq	GEO	public	sra	ncbi,gs,s3	Illumina HiSeq 2000	PAIRED	cDNA	TRANSCRIPTOMIC	Danio rerio	ILLUMINA	2018-02-01T00:00:00Z	200	NaN
pineal_night-1	pineal_night	SAMN07163953	SRX2853245	SRR5599696	SRS2224927	Pineal Gland	SRP107985	PRJNA387951	NaN	2524	1026	RNA-Seq	GEO	public	sra	gs,ncbi,s3	Illumina HiSeq 2000	PAIRED	cDNA	TRANSCRIPTOMIC	Danio rerio	ILLUMINA	2018-02-01T00:00:00Z	200	NaN
pineal_night-2	pineal_night	SAMN07163953	SRX2853245	SRR5599697	SRS2224927	Pineal Gland	SRP107985	PRJNA387951	NaN	2481	996	RNA-Seq	GEO	public	sra	gs,ncbi,s3	Illumina HiSeq 2000	PAIRED	cDNA	TRANSCRIPTOMIC	Danio rerio	ILLUMINA	2018-02-01T00:00:00Z	200	NaN
mixed_day-1	mixed_day	SAMN07163952	SRX2853246	SRR5599698	SRS2224928	Mixed Tissue	SRP107985	PRJNA387951	NaN	2583	1047	RNA-Seq	GEO	public	sra	gs,ncbi,s3	Illumina HiSeq 2000	PAIRED	cDNA	TRANSCRIPTOMIC	Danio rerio	ILLUMINA	2018-02-01T00:00:00Z	200	NaN
mixed_day-2	mixed_day	SAMN07163952	SRX2853246	SRR5599699	SRS2224928	Mixed Tissue	SRP107985	PRJNA387951	NaN	2539	1021	RNA-Seq	GEO	public	sra	gs,s3,ncbi	Illumina HiSeq 2000	PAIRED	cDNA	TRANSCRIPTOMIC	Danio rerio	ILLUMINA	2018-02-01T00:00:00Z	200	NaN
mixed_night-1	mixed_night	SAMN07163951	SRX2853247	SRR5599700	SRS2224930	Mixed Tissue	SRP107985	PRJNA387951	NaN	2710	1096	RNA-Seq	GEO	public	sra	gs,s3,ncbi	Illumina HiSeq 2000	PAIRED	cDNA	TRANSCRIPTOMIC	Danio rerio	ILLUMINA	2018-02-01T00:00:00Z	200	NaN
mixed_night-2	mixed_night	SAMN07163951	SRX2853247	SRR5599701	SRS2224930	Mixed Tissue	SRP107985	PRJNA387951	NaN	2657	1068	RNA-Seq	GEO	public	sra	gs,ncbi,s3	Illumina HiSeq 2000	PAIRED	cDNA	TRANSCRIPTOMIC	Danio rerio	ILLUMINA	2018-02-01T00:00:00Z	200	NaN