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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