SRX195403 Pineal gland CT14 SRP016132 SUB135563 library construction was conducted using Illumina's TruSeq RNA Sample Prep Kit following the manufacture protocol. Briefly, starting from total RNA, the messenger RNA was purified using polyA selection, then chemically fragmented and converted into single-stranded cDNA using random hexamer priming. Afterwards, the second strand was generated to create double-stranded cDNA. Finally, adapters were added by ligation to the double-stranded cDNA, which prepared the samples for cluster generation. After library quality check by Bioanalyzer High Sensitivity chip, clusters were generated and libraries were run on HiSeq2000 by using standard Illumina sequencing workflow with the multiplexing option. The mRNA libraries from the zebrafish pineal glands were sequenced on two lanes of Illumina HiSeq2000 instrument following the manufacture protocol. In each sequencing lane six bar-codes were used, one for each tested sample. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline (version 1.7). The reads were filtered using Illumina's HiSeq2000 softwares, Illumina indexes separation was also performed. SRS369337 Pineal gland RNA-Seq TRANSCRIPTOMIC cDNA 102 0 Application Read Forward 1 1 Application Read Reverse 52 Illumina HiSeq 2000 SRX195404 Pineal gland CT18 SRP016132 SUB135563 library construction was conducted using Illumina's TruSeq RNA Sample Prep Kit following the manufacture protocol. Briefly, starting from total RNA, the messenger RNA was purified using polyA selection, then chemically fragmented and converted into single-stranded cDNA using random hexamer priming. Afterwards, the second strand was generated to create double-stranded cDNA. Finally, adapters were added by ligation to the double-stranded cDNA, which prepared the samples for cluster generation. After library quality check by Bioanalyzer High Sensitivity chip, clusters were generated and libraries were run on HiSeq2000 by using standard Illumina sequencing workflow with the multiplexing option. The mRNA libraries from the zebrafish pineal glands were sequenced on two lanes of Illumina HiSeq2000 instrument following the manufacture protocol. In each sequencing lane six bar-codes were used, one for each tested sample. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline (version 1.7). The reads were filtered using Illumina's HiSeq2000 softwares, Illumina indexes separation was also performed. SRS369337 Pineal gland RNA-Seq TRANSCRIPTOMIC cDNA 102 0 Application Read Forward 1 1 Application Read Reverse 52 Illumina HiSeq 2000 SRX195405 Pineal gland CT14b SRP016132 library construction was conducted using Illumina's TruSeq RNA Sample Prep Kit following the manufacture protocol. Briefly, starting from total RNA, the messenger RNA was purified using polyA selection, then chemically fragmented and converted into single-stranded cDNA using random hexamer priming. Afterwards, the second strand was generated to create double-stranded cDNA. Finally, adapters were added by ligation to the double-stranded cDNA, which prepared the samples for cluster generation. After library quality check by Bioanalyzer High Sensitivity chip, clusters were generated and libraries were run on HiSeq2000 by using standard Illumina sequencing workflow with the multiplexing option. The mRNA libraries from the zebrafish pineal glands were sequenced on two lanes of Illumina HiSeq2000 instrument following the manufacture protocol. In each sequencing lane six bar-codes were used, one for each tested sample. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline (version 1.7). The reads were filtered using Illumina's HiSeq2000 softwares, Illumina indexes separation was also performed. SRS369337 Pineal gland RNA-Seq TRANSCRIPTOMIC cDNA 102 0 Application Read Forward 1 1 Application Read Reverse 52 Illumina HiSeq 2000 SRX195406 Pineal gland CT22b SRP016132 library construction was conducted using Illumina's TruSeq RNA Sample Prep Kit following the manufacture protocol. Briefly, starting from total RNA, the messenger RNA was purified using polyA selection, then chemically fragmented and converted into single-stranded cDNA using random hexamer priming. Afterwards, the second strand was generated to create double-stranded cDNA. Finally, adapters were added by ligation to the double-stranded cDNA, which prepared the samples for cluster generation. After library quality check by Bioanalyzer High Sensitivity chip, clusters were generated and libraries were run on HiSeq2000 by using standard Illumina sequencing workflow with the multiplexing option. The mRNA libraries from the zebrafish pineal glands were sequenced on two lanes of Illumina HiSeq2000 instrument following the manufacture protocol. In each sequencing lane six bar-codes were used, one for each tested sample. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline (version 1.7). The reads were filtered using Illumina's HiSeq2000 softwares, Illumina indexes separation was also performed. SRS369337 Pineal gland RNA-Seq TRANSCRIPTOMIC cDNA 102 0 Application Read Forward 1 1 Application Read Reverse 52 Illumina HiSeq 2000 SRX195407 Pineal gland CT22 SRP016132 library construction was conducted using Illumina's TruSeq RNA Sample Prep Kit following the manufacture protocol. Briefly, starting from total RNA, the messenger RNA was purified using polyA selection, then chemically fragmented and converted into single-stranded cDNA using random hexamer priming. Afterwards, the second strand was generated to create double-stranded cDNA. Finally, adapters were added by ligation to the double-stranded cDNA, which prepared the samples for cluster generation. After library quality check by Bioanalyzer High Sensitivity chip, clusters were generated and libraries were run on HiSeq2000 by using standard Illumina sequencing workflow with the multiplexing option. The mRNA libraries from the zebrafish pineal glands were sequenced on two lanes of Illumina HiSeq2000 instrument following the manufacture protocol. In each sequencing lane six bar-codes were used, one for each tested sample. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline (version 1.7). The reads were filtered using Illumina's HiSeq2000 softwares, Illumina indexes separation was also performed. SRS369337 Pineal gland RNA-Seq TRANSCRIPTOMIC cDNA 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX195408 Pineal gland CT2 SRP016132 library construction was conducted using Illumina's TruSeq RNA Sample Prep Kit following the manufacture protocol. Briefly, starting from total RNA, the messenger RNA was purified using polyA selection, then chemically fragmented and converted into single-stranded cDNA using random hexamer priming. Afterwards, the second strand was generated to create double-stranded cDNA. Finally, adapters were added by ligation to the double-stranded cDNA, which prepared the samples for cluster generation. After library quality check by Bioanalyzer High Sensitivity chip, clusters were generated and libraries were run on HiSeq2000 by using standard Illumina sequencing workflow with the multiplexing option. The mRNA libraries from the zebrafish pineal glands were sequenced on two lanes of Illumina HiSeq2000 instrument following the manufacture protocol. In each sequencing lane six bar-codes were used, one for each tested sample. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline (version 1.7). The reads were filtered using Illumina's HiSeq2000 softwares, Illumina indexes separation was also performed. SRS369337 Pineal gland RNA-Seq TRANSCRIPTOMIC cDNA 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX195409 Pineal gland CT6 SRP016132 library construction was conducted using Illumina's TruSeq RNA Sample Prep Kit following the manufacture protocol. Briefly, starting from total RNA, the messenger RNA was purified using polyA selection, then chemically fragmented and converted into single-stranded cDNA using random hexamer priming. Afterwards, the second strand was generated to create double-stranded cDNA. Finally, adapters were added by ligation to the double-stranded cDNA, which prepared the samples for cluster generation. After library quality check by Bioanalyzer High Sensitivity chip, clusters were generated and libraries were run on HiSeq2000 by using standard Illumina sequencing workflow with the multiplexing option. The mRNA libraries from the zebrafish pineal glands were sequenced on two lanes of Illumina HiSeq2000 instrument following the manufacture protocol. In each sequencing lane six bar-codes were used, one for each tested sample. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline (version 1.7). The reads were filtered using Illumina's HiSeq2000 softwares, Illumina indexes separation was also performed. SRS369337 Pineal gland RNA-Seq TRANSCRIPTOMIC cDNA 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX195410 Pineal gland CT10 SRP016132 library construction was conducted using Illumina's TruSeq RNA Sample Prep Kit following the manufacture protocol. Briefly, starting from total RNA, the messenger RNA was purified using polyA selection, then chemically fragmented and converted into single-stranded cDNA using random hexamer priming. Afterwards, the second strand was generated to create double-stranded cDNA. Finally, adapters were added by ligation to the double-stranded cDNA, which prepared the samples for cluster generation. After library quality check by Bioanalyzer High Sensitivity chip, clusters were generated and libraries were run on HiSeq2000 by using standard Illumina sequencing workflow with the multiplexing option. The mRNA libraries from the zebrafish pineal glands were sequenced on two lanes of Illumina HiSeq2000 instrument following the manufacture protocol. In each sequencing lane six bar-codes were used, one for each tested sample. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline (version 1.7). The reads were filtered using Illumina's HiSeq2000 softwares, Illumina indexes separation was also performed. SRS369337 Pineal gland RNA-Seq TRANSCRIPTOMIC cDNA 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX195411 Pineal gland CT18b SRP016132 library construction was conducted using Illumina's TruSeq RNA Sample Prep Kit following the manufacture protocol. Briefly, starting from total RNA, the messenger RNA was purified using polyA selection, then chemically fragmented and converted into single-stranded cDNA using random hexamer priming. Afterwards, the second strand was generated to create double-stranded cDNA. Finally, adapters were added by ligation to the double-stranded cDNA, which prepared the samples for cluster generation. After library quality check by Bioanalyzer High Sensitivity chip, clusters were generated and libraries were run on HiSeq2000 by using standard Illumina sequencing workflow with the multiplexing option. The mRNA libraries from the zebrafish pineal glands were sequenced on two lanes of Illumina HiSeq2000 instrument following the manufacture protocol. In each sequencing lane six bar-codes were used, one for each tested sample. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline (version 1.7). The reads were filtered using Illumina's HiSeq2000 softwares, Illumina indexes separation was also performed. SRS369337 Pineal gland RNA-Seq TRANSCRIPTOMIC cDNA 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX195412 Pineal gland CT2b SRP016132 library construction was conducted using Illumina's TruSeq RNA Sample Prep Kit following the manufacture protocol. Briefly, starting from total RNA, the messenger RNA was purified using polyA selection, then chemically fragmented and converted into single-stranded cDNA using random hexamer priming. Afterwards, the second strand was generated to create double-stranded cDNA. Finally, adapters were added by ligation to the double-stranded cDNA, which prepared the samples for cluster generation. After library quality check by Bioanalyzer High Sensitivity chip, clusters were generated and libraries were run on HiSeq2000 by using standard Illumina sequencing workflow with the multiplexing option. The mRNA libraries from the zebrafish pineal glands were sequenced on two lanes of Illumina HiSeq2000 instrument following the manufacture protocol. In each sequencing lane six bar-codes were used, one for each tested sample. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline (version 1.7). The reads were filtered using Illumina's HiSeq2000 softwares, Illumina indexes separation was also performed. SRS369337 Pineal gland RNA-Seq TRANSCRIPTOMIC cDNA 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX195413 Pineal gland CT6b SRP016132 library construction was conducted using Illumina's TruSeq RNA Sample Prep Kit following the manufacture protocol. Briefly, starting from total RNA, the messenger RNA was purified using polyA selection, then chemically fragmented and converted into single-stranded cDNA using random hexamer priming. Afterwards, the second strand was generated to create double-stranded cDNA. Finally, adapters were added by ligation to the double-stranded cDNA, which prepared the samples for cluster generation. After library quality check by Bioanalyzer High Sensitivity chip, clusters were generated and libraries were run on HiSeq2000 by using standard Illumina sequencing workflow with the multiplexing option. The mRNA libraries from the zebrafish pineal glands were sequenced on two lanes of Illumina HiSeq2000 instrument following the manufacture protocol. In each sequencing lane six bar-codes were used, one for each tested sample. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline (version 1.7). The reads were filtered using Illumina's HiSeq2000 softwares, Illumina indexes separation was also performed. SRS369337 Pineal gland RNA-Seq TRANSCRIPTOMIC cDNA 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX195414 Pineal gland CT10b SRP016132 library construction was conducted using Illumina's TruSeq RNA Sample Prep Kit following the manufacture protocol. Briefly, starting from total RNA, the messenger RNA was purified using polyA selection, then chemically fragmented and converted into single-stranded cDNA using random hexamer priming. Afterwards, the second strand was generated to create double-stranded cDNA. Finally, adapters were added by ligation to the double-stranded cDNA, which prepared the samples for cluster generation. After library quality check by Bioanalyzer High Sensitivity chip, clusters were generated and libraries were run on HiSeq2000 by using standard Illumina sequencing workflow with the multiplexing option. The mRNA libraries from the zebrafish pineal glands were sequenced on two lanes of Illumina HiSeq2000 instrument following the manufacture protocol. In each sequencing lane six bar-codes were used, one for each tested sample. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline (version 1.7). The reads were filtered using Illumina's HiSeq2000 softwares, Illumina indexes separation was also performed. SRS369337 Pineal gland RNA-Seq TRANSCRIPTOMIC cDNA 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX363281 Pineal gland light R1 SRP016132 PRJNA177642 Adult (0.5-1.5 years old) Tg(aanat2:EGFP) zebrafish (Gothilf et al., 2002) were raised in a temperature controlled recirculation water system under 12-hr light: 12-hr dark (LD) cycles, and transferred to constant darkness (DD) at the end of the day prior to the experiment. Fish were exposed to a 1-hr light pulse (light intensity of 12 W/m2) prior to sampling (light treatment) or kept under constant darkness for control (dark treatment). The fish were anesthetized in 1.5mM Tricane (Sigma) and sacrificed by decapitation. Pineal glands were removed under a fluorescent dissecting microscope; the use of transgenic fish expressing enhanced green fluorescent protein (EGFP) in the pineal gland enabled its selective removal. The tissues were collected from light- and dark-treated fish at 6 time points with 4-hr intervals throughout one daily cycle, corresponding to CT2, 6, 10, 14, 18 and 22. For mRNA-seq, pineal glands were collected at the 6 sampling times and pooled together to establish triplicates of 15 pineal glands for every treatment. Total RNA for mRNA analysis was isolated using RNeasy Lipid Tissue Mini Kit (Qiagen). library construction was conducted using Illumina's TruSeq RNA Sample Prep Kit following the manufacture protocol. Briefly, starting from total RNA, the messenger RNA was purified using polyA selection, then chemically fragmented and converted into single-stranded cDNA using random hexamer priming. Afterwards, the second strand was generated to create double-stranded cDNA. Finally, adapters were added by ligation to the double-stranded cDNA, which prepared the samples for cluster generation. After library quality check by Bioanalyzer High Sensitivity chip, clusters were generated and libraries were run on HiSeq2000 by using standard Illumina sequencing workflow. Overall, 6 libraries (3 light groups and 3 dark groups) were run on one lane of an Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol (Institute of Applied Genomics, Italy). Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline (version 1.7). The reads were filtered using Illumina's HiSeq2000 softwares, Illumina indexes separation was also performed. On average, ~6.7 million paired-end reads were obtained for each library. The reads were of 2x100 base pairs. SRS369337 Pineal gland RNA-Seq TRANSCRIPTOMIC cDNA 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX363282 Pineal gland light R2 SRP016132 PRJNA177642 Adult (0.5-1.5 years old) Tg(aanat2:EGFP) zebrafish (Gothilf et al., 2002) were raised in a temperature controlled recirculation water system under 12-hr light: 12-hr dark (LD) cycles, and transferred to constant darkness (DD) at the end of the day prior to the experiment. Fish were exposed to a 1-hr light pulse (light intensity of 12 W/m2) prior to sampling (light treatment) or kept under constant darkness for control (dark treatment). The fish were anesthetized in 1.5mM Tricane (Sigma) and sacrificed by decapitation. Pineal glands were removed under a fluorescent dissecting microscope; the use of transgenic fish expressing enhanced green fluorescent protein (EGFP) in the pineal gland enabled its selective removal. The tissues were collected from light- and dark-treated fish at 6 time points with 4-hr intervals throughout one daily cycle, corresponding to CT2, 6, 10, 14, 18 and 22. For mRNA-seq, pineal glands were collected at the 6 sampling times and pooled together to establish triplicates of 15 pineal glands for every treatment. Total RNA for mRNA analysis was isolated using RNeasy Lipid Tissue Mini Kit (Qiagen). library construction was conducted using Illumina's TruSeq RNA Sample Prep Kit following the manufacture protocol. Briefly, starting from total RNA, the messenger RNA was purified using polyA selection, then chemically fragmented and converted into single-stranded cDNA using random hexamer priming. Afterwards, the second strand was generated to create double-stranded cDNA. Finally, adapters were added by ligation to the double-stranded cDNA, which prepared the samples for cluster generation. After library quality check by Bioanalyzer High Sensitivity chip, clusters were generated and libraries were run on HiSeq2000 by using standard Illumina sequencing workflow. Overall, 6 libraries (3 light groups and 3 dark groups) were run on one lane of an Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol (Institute of Applied Genomics, Italy). Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline (version 1.7). The reads were filtered using Illumina's HiSeq2000 softwares, Illumina indexes separation was also performed. On average, ~6.7 million paired-end reads were obtained for each library. The reads were of 2x100 base pairs. SRS369337 Pineal gland RNA-Seq TRANSCRIPTOMIC cDNA 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX363283 Pineal gland light R3 SRP016132 PRJNA177642 Adult (0.5-1.5 years old) Tg(aanat2:EGFP) zebrafish (Gothilf et al., 2002) were raised in a temperature controlled recirculation water system under 12-hr light: 12-hr dark (LD) cycles, and transferred to constant darkness (DD) at the end of the day prior to the experiment. Fish were exposed to a 1-hr light pulse (light intensity of 12 W/m2) prior to sampling (light treatment) or kept under constant darkness for control (dark treatment). The fish were anesthetized in 1.5mM Tricane (Sigma) and sacrificed by decapitation. Pineal glands were removed under a fluorescent dissecting microscope; the use of transgenic fish expressing enhanced green fluorescent protein (EGFP) in the pineal gland enabled its selective removal. The tissues were collected from light- and dark-treated fish at 6 time points with 4-hr intervals throughout one daily cycle, corresponding to CT2, 6, 10, 14, 18 and 22. For mRNA-seq, pineal glands were collected at the 6 sampling times and pooled together to establish triplicates of 15 pineal glands for every treatment. Total RNA for mRNA analysis was isolated using RNeasy Lipid Tissue Mini Kit (Qiagen). library construction was conducted using Illumina's TruSeq RNA Sample Prep Kit following the manufacture protocol. Briefly, starting from total RNA, the messenger RNA was purified using polyA selection, then chemically fragmented and converted into single-stranded cDNA using random hexamer priming. Afterwards, the second strand was generated to create double-stranded cDNA. Finally, adapters were added by ligation to the double-stranded cDNA, which prepared the samples for cluster generation. After library quality check by Bioanalyzer High Sensitivity chip, clusters were generated and libraries were run on HiSeq2000 by using standard Illumina sequencing workflow. Overall, 6 libraries (3 light groups and 3 dark groups) were run on one lane of an Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol (Institute of Applied Genomics, Italy). Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline (version 1.7). The reads were filtered using Illumina's HiSeq2000 softwares, Illumina indexes separation was also performed. On average, ~6.7 million paired-end reads were obtained for each library. The reads were of 2x100 base pairs. SRS369337 Pineal gland RNA-Seq TRANSCRIPTOMIC cDNA 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX363284 Pineal gland dark R1 SRP016132 PRJNA177642 Adult (0.5-1.5 years old) Tg(aanat2:EGFP) zebrafish (Gothilf et al., 2002) were raised in a temperature controlled recirculation water system under 12-hr light: 12-hr dark (LD) cycles, and transferred to constant darkness (DD) at the end of the day prior to the experiment. Fish were exposed to a 1-hr light pulse (light intensity of 12 W/m2) prior to sampling (light treatment) or kept under constant darkness for control (dark treatment). The fish were anesthetized in 1.5mM Tricane (Sigma) and sacrificed by decapitation. Pineal glands were removed under a fluorescent dissecting microscope; the use of transgenic fish expressing enhanced green fluorescent protein (EGFP) in the pineal gland enabled its selective removal. The tissues were collected from light- and dark-treated fish at 6 time points with 4-hr intervals throughout one daily cycle, corresponding to CT2, 6, 10, 14, 18 and 22. For mRNA-seq, pineal glands were collected at the 6 sampling times and pooled together to establish triplicates of 15 pineal glands for every treatment. Total RNA for mRNA analysis was isolated using RNeasy Lipid Tissue Mini Kit (Qiagen). library construction was conducted using Illumina's TruSeq RNA Sample Prep Kit following the manufacture protocol. Briefly, starting from total RNA, the messenger RNA was purified using polyA selection, then chemically fragmented and converted into single-stranded cDNA using random hexamer priming. Afterwards, the second strand was generated to create double-stranded cDNA. Finally, adapters were added by ligation to the double-stranded cDNA, which prepared the samples for cluster generation. After library quality check by Bioanalyzer High Sensitivity chip, clusters were generated and libraries were run on HiSeq2000 by using standard Illumina sequencing workflow. Overall, 6 libraries (3 light groups and 3 dark groups) were run on one lane of an Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol (Institute of Applied Genomics, Italy). Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline (version 1.7). The reads were filtered using Illumina's HiSeq2000 softwares, Illumina indexes separation was also performed. On average, ~6.7 million paired-end reads were obtained for each library. The reads were of 2x100 base pairs. SRS369337 Pineal gland RNA-Seq TRANSCRIPTOMIC cDNA 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX363285 Pineal gland dark R2 SRP016132 PRJNA177642 Adult (0.5-1.5 years old) Tg(aanat2:EGFP) zebrafish (Gothilf et al., 2002) were raised in a temperature controlled recirculation water system under 12-hr light: 12-hr dark (LD) cycles, and transferred to constant darkness (DD) at the end of the day prior to the experiment. Fish were exposed to a 1-hr light pulse (light intensity of 12 W/m2) prior to sampling (light treatment) or kept under constant darkness for control (dark treatment). The fish were anesthetized in 1.5mM Tricane (Sigma) and sacrificed by decapitation. Pineal glands were removed under a fluorescent dissecting microscope; the use of transgenic fish expressing enhanced green fluorescent protein (EGFP) in the pineal gland enabled its selective removal. The tissues were collected from light- and dark-treated fish at 6 time points with 4-hr intervals throughout one daily cycle, corresponding to CT2, 6, 10, 14, 18 and 22. For mRNA-seq, pineal glands were collected at the 6 sampling times and pooled together to establish triplicates of 15 pineal glands for every treatment. Total RNA for mRNA analysis was isolated using RNeasy Lipid Tissue Mini Kit (Qiagen). library construction was conducted using Illumina's TruSeq RNA Sample Prep Kit following the manufacture protocol. Briefly, starting from total RNA, the messenger RNA was purified using polyA selection, then chemically fragmented and converted into single-stranded cDNA using random hexamer priming. Afterwards, the second strand was generated to create double-stranded cDNA. Finally, adapters were added by ligation to the double-stranded cDNA, which prepared the samples for cluster generation. After library quality check by Bioanalyzer High Sensitivity chip, clusters were generated and libraries were run on HiSeq2000 by using standard Illumina sequencing workflow. Overall, 6 libraries (3 light groups and 3 dark groups) were run on one lane of an Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol (Institute of Applied Genomics, Italy). Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline (version 1.7). The reads were filtered using Illumina's HiSeq2000 softwares, Illumina indexes separation was also performed. On average, ~6.7 million paired-end reads were obtained for each library. The reads were of 2x100 base pairs. SRS369337 Pineal gland RNA-Seq TRANSCRIPTOMIC cDNA 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX363286 Pineal gland dark R3 SRP016132 PRJNA177642 Adult (0.5-1.5 years old) Tg(aanat2:EGFP) zebrafish (Gothilf et al., 2002) were raised in a temperature controlled recirculation water system under 12-hr light: 12-hr dark (LD) cycles, and transferred to constant darkness (DD) at the end of the day prior to the experiment. Fish were exposed to a 1-hr light pulse (light intensity of 12 W/m2) prior to sampling (light treatment) or kept under constant darkness for control (dark treatment). The fish were anesthetized in 1.5mM Tricane (Sigma) and sacrificed by decapitation. Pineal glands were removed under a fluorescent dissecting microscope; the use of transgenic fish expressing enhanced green fluorescent protein (EGFP) in the pineal gland enabled its selective removal. The tissues were collected from light- and dark-treated fish at 6 time points with 4-hr intervals throughout one daily cycle, corresponding to CT2, 6, 10, 14, 18 and 22. For mRNA-seq, pineal glands were collected at the 6 sampling times and pooled together to establish triplicates of 15 pineal glands for every treatment. Total RNA for mRNA analysis was isolated using RNeasy Lipid Tissue Mini Kit (Qiagen). library construction was conducted using Illumina's TruSeq RNA Sample Prep Kit following the manufacture protocol. Briefly, starting from total RNA, the messenger RNA was purified using polyA selection, then chemically fragmented and converted into single-stranded cDNA using random hexamer priming. Afterwards, the second strand was generated to create double-stranded cDNA. Finally, adapters were added by ligation to the double-stranded cDNA, which prepared the samples for cluster generation. After library quality check by Bioanalyzer High Sensitivity chip, clusters were generated and libraries were run on HiSeq2000 by using standard Illumina sequencing workflow. Overall, 6 libraries (3 light groups and 3 dark groups) were run on one lane of an Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol (Institute of Applied Genomics, Italy). Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline (version 1.7). The reads were filtered using Illumina's HiSeq2000 softwares, Illumina indexes separation was also performed. On average, ~6.7 million paired-end reads were obtained for each library. The reads were of 2x100 base pairs. SRS369337 Pineal gland RNA-Seq TRANSCRIPTOMIC cDNA 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 SRX363296 Pineal gland light miRNA SRP016132 PRJNA177642 Adult (0.5-1.5 years old) Tg(aanat2:EGFP) zebrafish (Gothilf et al., 2002) were raised in a temperature controlled recirculation water system under 12-hr light: 12-hr dark (LD) cycles, and transferred to constant darkness (DD) at the end of the day prior to the experiment. Fish were exposed to a 1-hr light pulse (light intensity of 12 W/m2) prior to sampling (light treatment) or kept under constant darkness for control (dark treatment). The fish were anesthetized in 1.5mM Tricane (Sigma) and sacrificed by decapitation. Pineal glands and brains were removed under a fluorescent dissecting microscope; the use of transgenic fish expressing enhanced green fluorescent protein (EGFP) in the pineal gland enabled its selective removal. The tissues were collected from light- and dark-treated fish at 6 time points with 4-hr intervals throughout one daily cycle, corresponding to CT2, 6, 10, 14, 18 and 22. For miR-seq, 18 pineal glands were pooled from the 6 sampling times for both light and dark treatments, and one brain pool was composed of 4 brains that were collected from light- and dark-treated fish at CT2 and CT14. Brain samples were collected subsequent to the removal of pineal glands and therefore do not contain pineal tissues. Total RNA for miRNA analysis was isolated using miRNeasy Mini Kit (Qiagen). miRNA capturing and library construction, for the pineal light, pineal dark and brain samples, were conducted using Illumina's TruSeq Small RNA Sample Prep Kit according to the manufacturer’s protocol. Briefly, 3' adapter was ligated to total RNA using truncated T4 RNA Ligase 2 without ATP, then 5' adapter was added using T4 RNA Ligase with ATP. Afterwards, reverse transcription followed by PCR was used to create cDNA constructs based on the small RNA ligated with 3' and 5' adapters. The introduction of index sequence (bar-codes) was done at the PCR step. Finally, gel electrophoresis was used to purify the amplified cDNA construct in preparation for subsequent cluster generation. After library quality check by Bioanalyzer High Sensitivity chip, clusters were generated and libraries were run on HiSeq2000 by using standard Illumina sequencing workflow with the multiplexing option. The three mature miRNA libraries (pineal light, pineal dark, and brain) were sequenced with bar-codes on one lane of an Illumina HiSeq2000 instrument following the manufacturer’s protocol. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline (version 1.7). The reads were filtered using Illumina's HiSeq2000 softwares, Illumina indexes separation was also performed. The total number of reads after filtering was ~6 million, ~10.4 million and ~14.8 million for the pineal light, pineal dark and brain, respectively. SRS369337 Pineal gland miRNA-Seq TRANSCRIPTOMIC size fractionation 50 0 Application Read Forward 1 Illumina HiSeq 2000 SRX363297 Pineal gland dark miRNA SRP016132 PRJNA177642 Adult (0.5-1.5 years old) Tg(aanat2:EGFP) zebrafish (Gothilf et al., 2002) were raised in a temperature controlled recirculation water system under 12-hr light: 12-hr dark (LD) cycles, and transferred to constant darkness (DD) at the end of the day prior to the experiment. Fish were exposed to a 1-hr light pulse (light intensity of 12 W/m2) prior to sampling (light treatment) or kept under constant darkness for control (dark treatment). The fish were anesthetized in 1.5mM Tricane (Sigma) and sacrificed by decapitation. Pineal glands and brains were removed under a fluorescent dissecting microscope; the use of transgenic fish expressing enhanced green fluorescent protein (EGFP) in the pineal gland enabled its selective removal. The tissues were collected from light- and dark-treated fish at 6 time points with 4-hr intervals throughout one daily cycle, corresponding to CT2, 6, 10, 14, 18 and 22. For miR-seq, 18 pineal glands were pooled from the 6 sampling times for both light and dark treatments, and one brain pool was composed of 4 brains that were collected from light- and dark-treated fish at CT2 and CT14. Brain samples were collected subsequent to the removal of pineal glands and therefore do not contain pineal tissues. Total RNA for miRNA analysis was isolated using miRNeasy Mini Kit (Qiagen). miRNA capturing and library construction, for the pineal light, pineal dark and brain samples, were conducted using Illumina's TruSeq Small RNA Sample Prep Kit according to the manufacturer’s protocol. Briefly, 3' adapter was ligated to total RNA using truncated T4 RNA Ligase 2 without ATP, then 5' adapter was added using T4 RNA Ligase with ATP. Afterwards, reverse transcription followed by PCR was used to create cDNA constructs based on the small RNA ligated with 3' and 5' adapters. The introduction of index sequence (bar-codes) was done at the PCR step. Finally, gel electrophoresis was used to purify the amplified cDNA construct in preparation for subsequent cluster generation. After library quality check by Bioanalyzer High Sensitivity chip, clusters were generated and libraries were run on HiSeq2000 by using standard Illumina sequencing workflow with the multiplexing option. The three mature miRNA libraries (pineal light, pineal dark, and brain) were sequenced with bar-codes on one lane of an Illumina HiSeq2000 instrument following the manufacturer’s protocol. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline (version 1.7). The reads were filtered using Illumina's HiSeq2000 softwares, Illumina indexes separation was also performed. The total number of reads after filtering was ~6 million, ~10.4 million and ~14.8 million for the pineal light, pineal dark and brain, respectively. SRS369337 Pineal gland miRNA-Seq TRANSCRIPTOMIC size fractionation 50 0 Application Read Forward 1 Illumina HiSeq 2000 SRX363298 Brain miRNA SRP016132 PRJNA177642 Adult (0.5-1.5 years old) Tg(aanat2:EGFP) zebrafish (Gothilf et al., 2002) were raised in a temperature controlled recirculation water system under 12-hr light: 12-hr dark (LD) cycles, and transferred to constant darkness (DD) at the end of the day prior to the experiment. Fish were exposed to a 1-hr light pulse (light intensity of 12 W/m2) prior to sampling (light treatment) or kept under constant darkness for control (dark treatment). The fish were anesthetized in 1.5mM Tricane (Sigma) and sacrificed by decapitation. Pineal glands and brains were removed under a fluorescent dissecting microscope; the use of transgenic fish expressing enhanced green fluorescent protein (EGFP) in the pineal gland enabled its selective removal. The tissues were collected from light- and dark-treated fish at 6 time points with 4-hr intervals throughout one daily cycle, corresponding to CT2, 6, 10, 14, 18 and 22. For miR-seq, 18 pineal glands were pooled from the 6 sampling times for both light and dark treatments, and one brain pool was composed of 4 brains that were collected from light- and dark-treated fish at CT2 and CT14. Brain samples were collected subsequent to the removal of pineal glands and therefore do not contain pineal tissues. Total RNA for miRNA analysis was isolated using miRNeasy Mini Kit (Qiagen). miRNA capturing and library construction, for the pineal light, pineal dark and brain samples, were conducted using Illumina's TruSeq Small RNA Sample Prep Kit according to the manufacturer’s protocol. Briefly, 3' adapter was ligated to total RNA using truncated T4 RNA Ligase 2 without ATP, then 5' adapter was added using T4 RNA Ligase with ATP. Afterwards, reverse transcription followed by PCR was used to create cDNA constructs based on the small RNA ligated with 3' and 5' adapters. The introduction of index sequence (bar-codes) was done at the PCR step. Finally, gel electrophoresis was used to purify the amplified cDNA construct in preparation for subsequent cluster generation. After library quality check by Bioanalyzer High Sensitivity chip, clusters were generated and libraries were run on HiSeq2000 by using standard Illumina sequencing workflow with the multiplexing option. The three mature miRNA libraries (pineal light, pineal dark, and brain) were sequenced with bar-codes on one lane of an Illumina HiSeq2000 instrument following the manufacturer’s protocol. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline (version 1.7). The reads were filtered using Illumina's HiSeq2000 softwares, Illumina indexes separation was also performed. The total number of reads after filtering was ~6 million, ~10.4 million and ~14.8 million for the pineal light, pineal dark and brain, respectively. SRS369337 Pineal gland miRNA-Seq TRANSCRIPTOMIC size fractionation 50 0 Application Read Forward 1 Illumina HiSeq 2000 SRX2277943 aanat2-deltaCLK pineal gland CT2 SRP016132 Overall, 14 libraries [12 time points from Tg(aanat2:EGFP-ΔCLK) fish and two control samples from Tg(aanat2:EGFP) fish] were run on a single flow cell of an Illumina HiSeq2500 machine (rapid run mode) using the multiplexing strategy of the TruSeq protocol (Institute of Applied Genomics, Italy). Library construction was conducted using Illumina's TruSeq RNA Sample Prep Kit following the manufacture protocol. Briefly, starting from total RNA, the messenger RNA was purified using polyA selection, then chemically fragmented and converted into single-stranded cDNA using random hexamer priming. Afterwards, the second strand was generated to create double-stranded cDNA. Finally, adapters were added by ligation to the double-stranded cDNA, which prepared the samples for cluster generation. After library quality check by Bioanalyzer High Sensitivity chip, clusters were generated and libraries were run on HiSeq2500 by using standard Illumina sequencing workflow with the multiplexing option. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline . The reads were filtered using Illumina's HiSeq2500 softwares, Illumina indexes separation was also performed. SRS369337 RNA-Seq TRANSCRIPTOMIC cDNA 102 0 Application Read Forward 1 1 Application Read Reverse 52 Illumina HiSeq 2500 SRX2278008 aanat2-deltaCLK pineal gland CT6 SRP016132 Overall, 14 libraries [12 time points from Tg(aanat2:EGFP-ΔCLK) fish and two control samples from Tg(aanat2:EGFP) fish] were run on a single flow cell of an Illumina HiSeq2500 machine (rapid run mode) using the multiplexing strategy of the TruSeq protocol (Institute of Applied Genomics, Italy). Library construction was conducted using Illumina's TruSeq RNA Sample Prep Kit following the manufacture protocol. Briefly, starting from total RNA, the messenger RNA was purified using polyA selection, then chemically fragmented and converted into single-stranded cDNA using random hexamer priming. Afterwards, the second strand was generated to create double-stranded cDNA. Finally, adapters were added by ligation to the double-stranded cDNA, which prepared the samples for cluster generation. After library quality check by Bioanalyzer High Sensitivity chip, clusters were generated and libraries were run on HiSeq2500 by using standard Illumina sequencing workflow with the multiplexing option. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline . The reads were filtered using Illumina's HiSeq2500 softwares, Illumina indexes separation was also performed. SRS369337 RNA-Seq TRANSCRIPTOMIC cDNA 102 0 Application Read Forward 1 1 Application Read Reverse 52 Illumina HiSeq 2500 SRX2278111 aanat2-deltaCLK pineal gland CT10 SRP016132 Overall, 14 libraries [12 time points from Tg(aanat2:EGFP-ΔCLK) fish and two control samples from Tg(aanat2:EGFP) fish] were run on a single flow cell of an Illumina HiSeq2500 machine (rapid run mode) using the multiplexing strategy of the TruSeq protocol (Institute of Applied Genomics, Italy). Library construction was conducted using Illumina's TruSeq RNA Sample Prep Kit following the manufacture protocol. Briefly, starting from total RNA, the messenger RNA was purified using polyA selection, then chemically fragmented and converted into single-stranded cDNA using random hexamer priming. Afterwards, the second strand was generated to create double-stranded cDNA. Finally, adapters were added by ligation to the double-stranded cDNA, which prepared the samples for cluster generation. After library quality check by Bioanalyzer High Sensitivity chip, clusters were generated and libraries were run on HiSeq2500 by using standard Illumina sequencing workflow with the multiplexing option. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline . The reads were filtered using Illumina's HiSeq2500 softwares, Illumina indexes separation was also performed. SRS369337 RNA-Seq TRANSCRIPTOMIC cDNA 102 0 Application Read Forward 1 1 Application Read Reverse 52 Illumina HiSeq 2500 SRX2278214 aanat2-deltaCLK pineal gland CT14 SRP016132 Overall, 14 libraries [12 time points from Tg(aanat2:EGFP-ΔCLK) fish and two control samples from Tg(aanat2:EGFP) fish] were run on a single flow cell of an Illumina HiSeq2500 machine (rapid run mode) using the multiplexing strategy of the TruSeq protocol (Institute of Applied Genomics, Italy). Library construction was conducted using Illumina's TruSeq RNA Sample Prep Kit following the manufacture protocol. Briefly, starting from total RNA, the messenger RNA was purified using polyA selection, then chemically fragmented and converted into single-stranded cDNA using random hexamer priming. Afterwards, the second strand was generated to create double-stranded cDNA. Finally, adapters were added by ligation to the double-stranded cDNA, which prepared the samples for cluster generation. After library quality check by Bioanalyzer High Sensitivity chip, clusters were generated and libraries were run on HiSeq2500 by using standard Illumina sequencing workflow with the multiplexing option. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline . The reads were filtered using Illumina's HiSeq2500 softwares, Illumina indexes separation was also performed. SRS369337 RNA-Seq TRANSCRIPTOMIC cDNA 102 0 Application Read Forward 1 1 Application Read Reverse 52 Illumina HiSeq 2500 SRX2278232 aanat2-deltaCLK pineal gland CT18 SRP016132 Overall, 14 libraries [12 time points from Tg(aanat2:EGFP-ΔCLK) fish and two control samples from Tg(aanat2:EGFP) fish] were run on a single flow cell of an Illumina HiSeq2500 machine (rapid run mode) using the multiplexing strategy of the TruSeq protocol (Institute of Applied Genomics, Italy). Library construction was conducted using Illumina's TruSeq RNA Sample Prep Kit following the manufacture protocol. Briefly, starting from total RNA, the messenger RNA was purified using polyA selection, then chemically fragmented and converted into single-stranded cDNA using random hexamer priming. Afterwards, the second strand was generated to create double-stranded cDNA. Finally, adapters were added by ligation to the double-stranded cDNA, which prepared the samples for cluster generation. After library quality check by Bioanalyzer High Sensitivity chip, clusters were generated and libraries were run on HiSeq2500 by using standard Illumina sequencing workflow with the multiplexing option. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline . The reads were filtered using Illumina's HiSeq2500 softwares, Illumina indexes separation was also performed. SRS369337 RNA-Seq TRANSCRIPTOMIC cDNA 102 0 Application Read Forward 1 1 Application Read Reverse 52 Illumina HiSeq 2500 SRX2278233 aanat2-deltaCLK pineal gland CT22 SRP016132 Overall, 14 libraries [12 time points from Tg(aanat2:EGFP-ΔCLK) fish and two control samples from Tg(aanat2:EGFP) fish] were run on a single flow cell of an Illumina HiSeq2500 machine (rapid run mode) using the multiplexing strategy of the TruSeq protocol (Institute of Applied Genomics, Italy). Library construction was conducted using Illumina's TruSeq RNA Sample Prep Kit following the manufacture protocol. Briefly, starting from total RNA, the messenger RNA was purified using polyA selection, then chemically fragmented and converted into single-stranded cDNA using random hexamer priming. Afterwards, the second strand was generated to create double-stranded cDNA. Finally, adapters were added by ligation to the double-stranded cDNA, which prepared the samples for cluster generation. After library quality check by Bioanalyzer High Sensitivity chip, clusters were generated and libraries were run on HiSeq2500 by using standard Illumina sequencing workflow with the multiplexing option. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline . The reads were filtered using Illumina's HiSeq2500 softwares, Illumina indexes separation was also performed. SRS369337 RNA-Seq TRANSCRIPTOMIC cDNA 102 0 Application Read Forward 1 1 Application Read Reverse 52 Illumina HiSeq 2500 SRX2278234 aanat2-deltaCLK pineal gland CT2b SRP016132 Overall, 14 libraries [12 time points from Tg(aanat2:EGFP-ΔCLK) fish and two control samples from Tg(aanat2:EGFP) fish] were run on a single flow cell of an Illumina HiSeq2500 machine (rapid run mode) using the multiplexing strategy of the TruSeq protocol (Institute of Applied Genomics, Italy). Library construction was conducted using Illumina's TruSeq RNA Sample Prep Kit following the manufacture protocol. Briefly, starting from total RNA, the messenger RNA was purified using polyA selection, then chemically fragmented and converted into single-stranded cDNA using random hexamer priming. Afterwards, the second strand was generated to create double-stranded cDNA. Finally, adapters were added by ligation to the double-stranded cDNA, which prepared the samples for cluster generation. After library quality check by Bioanalyzer High Sensitivity chip, clusters were generated and libraries were run on HiSeq2500 by using standard Illumina sequencing workflow with the multiplexing option. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline . The reads were filtered using Illumina's HiSeq2500 softwares, Illumina indexes separation was also performed. SRS369337 RNA-Seq TRANSCRIPTOMIC cDNA 102 0 Application Read Forward 1 1 Application Read Reverse 52 Illumina HiSeq 2500 SRX2278235 aanat2-deltaCLK pineal gland CT6b SRP016132 Overall, 14 libraries [12 time points from Tg(aanat2:EGFP-ΔCLK) fish and two control samples from Tg(aanat2:EGFP) fish] were run on a single flow cell of an Illumina HiSeq2500 machine (rapid run mode) using the multiplexing strategy of the TruSeq protocol (Institute of Applied Genomics, Italy). Library construction was conducted using Illumina's TruSeq RNA Sample Prep Kit following the manufacture protocol. Briefly, starting from total RNA, the messenger RNA was purified using polyA selection, then chemically fragmented and converted into single-stranded cDNA using random hexamer priming. Afterwards, the second strand was generated to create double-stranded cDNA. Finally, adapters were added by ligation to the double-stranded cDNA, which prepared the samples for cluster generation. After library quality check by Bioanalyzer High Sensitivity chip, clusters were generated and libraries were run on HiSeq2500 by using standard Illumina sequencing workflow with the multiplexing option. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline . The reads were filtered using Illumina's HiSeq2500 softwares, Illumina indexes separation was also performed. SRS369337 RNA-Seq TRANSCRIPTOMIC cDNA 102 0 Application Read Forward 1 1 Application Read Reverse 52 Illumina HiSeq 2500 SRX2278236 aanat2-deltaCLK pineal gland CT10b SRP016132 Overall, 14 libraries [12 time points from Tg(aanat2:EGFP-ΔCLK) fish and two control samples from Tg(aanat2:EGFP) fish] were run on a single flow cell of an Illumina HiSeq2500 machine (rapid run mode) using the multiplexing strategy of the TruSeq protocol (Institute of Applied Genomics, Italy). Library construction was conducted using Illumina's TruSeq RNA Sample Prep Kit following the manufacture protocol. Briefly, starting from total RNA, the messenger RNA was purified using polyA selection, then chemically fragmented and converted into single-stranded cDNA using random hexamer priming. Afterwards, the second strand was generated to create double-stranded cDNA. Finally, adapters were added by ligation to the double-stranded cDNA, which prepared the samples for cluster generation. After library quality check by Bioanalyzer High Sensitivity chip, clusters were generated and libraries were run on HiSeq2500 by using standard Illumina sequencing workflow with the multiplexing option. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline . The reads were filtered using Illumina's HiSeq2500 softwares, Illumina indexes separation was also performed. SRS369337 RNA-Seq TRANSCRIPTOMIC cDNA 102 0 Application Read Forward 1 1 Application Read Reverse 52 Illumina HiSeq 2500 SRX2278237 aanat2-deltaCLK pineal gland CT14b SRP016132 Overall, 14 libraries [12 time points from Tg(aanat2:EGFP-ΔCLK) fish and two control samples from Tg(aanat2:EGFP) fish] were run on a single flow cell of an Illumina HiSeq2500 machine (rapid run mode) using the multiplexing strategy of the TruSeq protocol (Institute of Applied Genomics, Italy). Library construction was conducted using Illumina's TruSeq RNA Sample Prep Kit following the manufacture protocol. Briefly, starting from total RNA, the messenger RNA was purified using polyA selection, then chemically fragmented and converted into single-stranded cDNA using random hexamer priming. Afterwards, the second strand was generated to create double-stranded cDNA. Finally, adapters were added by ligation to the double-stranded cDNA, which prepared the samples for cluster generation. After library quality check by Bioanalyzer High Sensitivity chip, clusters were generated and libraries were run on HiSeq2500 by using standard Illumina sequencing workflow with the multiplexing option. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline . The reads were filtered using Illumina's HiSeq2500 softwares, Illumina indexes separation was also performed. SRS369337 RNA-Seq TRANSCRIPTOMIC cDNA 102 0 Application Read Forward 1 1 Application Read Reverse 52 Illumina HiSeq 2500 SRX2278238 aanat2-deltaCLK pineal gland CT18b SRP016132 Overall, 14 libraries [12 time points from Tg(aanat2:EGFP-ΔCLK) fish and two control samples from Tg(aanat2:EGFP) fish] were run on a single flow cell of an Illumina HiSeq2500 machine (rapid run mode) using the multiplexing strategy of the TruSeq protocol (Institute of Applied Genomics, Italy). Library construction was conducted using Illumina's TruSeq RNA Sample Prep Kit following the manufacture protocol. Briefly, starting from total RNA, the messenger RNA was purified using polyA selection, then chemically fragmented and converted into single-stranded cDNA using random hexamer priming. Afterwards, the second strand was generated to create double-stranded cDNA. Finally, adapters were added by ligation to the double-stranded cDNA, which prepared the samples for cluster generation. After library quality check by Bioanalyzer High Sensitivity chip, clusters were generated and libraries were run on HiSeq2500 by using standard Illumina sequencing workflow with the multiplexing option. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline . The reads were filtered using Illumina's HiSeq2500 softwares, Illumina indexes separation was also performed. SRS369337 RNA-Seq TRANSCRIPTOMIC cDNA 102 0 Application Read Forward 1 1 Application Read Reverse 52 Illumina HiSeq 2500 SRX2278239 aanat2-deltaCLK pineal gland CT22b SRP016132 Overall, 14 libraries [12 time points from Tg(aanat2:EGFP-ΔCLK) fish and two control samples from Tg(aanat2:EGFP) fish] were run on a single flow cell of an Illumina HiSeq2500 machine (rapid run mode) using the multiplexing strategy of the TruSeq protocol (Institute of Applied Genomics, Italy). Library construction was conducted using Illumina's TruSeq RNA Sample Prep Kit following the manufacture protocol. Briefly, starting from total RNA, the messenger RNA was purified using polyA selection, then chemically fragmented and converted into single-stranded cDNA using random hexamer priming. Afterwards, the second strand was generated to create double-stranded cDNA. Finally, adapters were added by ligation to the double-stranded cDNA, which prepared the samples for cluster generation. After library quality check by Bioanalyzer High Sensitivity chip, clusters were generated and libraries were run on HiSeq2500 by using standard Illumina sequencing workflow with the multiplexing option. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline . The reads were filtered using Illumina's HiSeq2500 softwares, Illumina indexes separation was also performed. SRS369337 RNA-Seq TRANSCRIPTOMIC cDNA 102 0 Application Read Forward 1 1 Application Read Reverse 52 Illumina HiSeq 2500 SRX2278277 Control for deltaCLK experiment - pineal gland CT2 SRP016132 Overall, 14 libraries [12 time points from Tg(aanat2:EGFP-ΔCLK) fish and two control samples from Tg(aanat2:EGFP) fish] were run on a single flow cell of an Illumina HiSeq2500 machine (rapid run mode) using the multiplexing strategy of the TruSeq protocol (Institute of Applied Genomics, Italy). Library construction was conducted using Illumina's TruSeq RNA Sample Prep Kit following the manufacture protocol. Briefly, starting from total RNA, the messenger RNA was purified using polyA selection, then chemically fragmented and converted into single-stranded cDNA using random hexamer priming. Afterwards, the second strand was generated to create double-stranded cDNA. Finally, adapters were added by ligation to the double-stranded cDNA, which prepared the samples for cluster generation. After library quality check by Bioanalyzer High Sensitivity chip, clusters were generated and libraries were run on HiSeq2500 by using standard Illumina sequencing workflow with the multiplexing option. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline . The reads were filtered using Illumina's HiSeq2500 softwares, Illumina indexes separation was also performed. SRS369337 RNA-Seq TRANSCRIPTOMIC cDNA 102 0 Application Read Forward 1 1 Application Read Reverse 52 Illumina HiSeq 2500 SRX2278278 Control for deltaCLK experiment - pineal gland CT14b SRP016132 Overall, 14 libraries [12 time points from Tg(aanat2:EGFP-ΔCLK) fish and two control samples from Tg(aanat2:EGFP) fish] were run on a single flow cell of an Illumina HiSeq2500 machine (rapid run mode) using the multiplexing strategy of the TruSeq protocol (Institute of Applied Genomics, Italy). Library construction was conducted using Illumina's TruSeq RNA Sample Prep Kit following the manufacture protocol. Briefly, starting from total RNA, the messenger RNA was purified using polyA selection, then chemically fragmented and converted into single-stranded cDNA using random hexamer priming. Afterwards, the second strand was generated to create double-stranded cDNA. Finally, adapters were added by ligation to the double-stranded cDNA, which prepared the samples for cluster generation. After library quality check by Bioanalyzer High Sensitivity chip, clusters were generated and libraries were run on HiSeq2500 by using standard Illumina sequencing workflow with the multiplexing option. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline . The reads were filtered using Illumina's HiSeq2500 softwares, Illumina indexes separation was also performed. SRS369337 RNA-Seq TRANSCRIPTOMIC cDNA 102 0 Application Read Forward 1 1 Application Read Reverse 52 Illumina HiSeq 2500