SRX066204 Rat pineal gland RNA-Seq PolyA project SRP006893 Rat pineal RNA-Seq For the mRNA-Seq sample preparation, the Illumina standard kit was used according to the manufacturer's protocol. Briefly, 10 micrograms of each total RNA sample was used for polyA mRNA selection using streptavidin-coated magnetic beads, followed by chemical mRNA fragmentation. The fragmented mRNA was subjected to cDNA synthesis using reverse transcriptase (SuperScript II) and random primers. The cDNA was further converted into double stranded cDNA and, after an end repair process (Klenow fragment, T4 polynucleotide kinase and T4 polymerase), was finally ligated to Illumina paired end (PE) adaptors. Size selection was performed using a 2% agarose gel. Finally, the libraries were enriched using 15 cycles of PCR and purified by the QIAquick PCR purification kit (Qiagen). The enriched libraries were diluted with Elution Buffer to a final concentration of 10 nM. Each library was run at a concentration of 7 pM on one Illumina Genome Analyzer II (GAii) lane using paired-end 51 base-pair sequencing. Image analysis and base calling was done by Illumina Genome Analyzer Pipeline software (GAPipeline) with default parameters. Three samples were analyzed in this manner. SRS210901 Rat pineal gland-ZT7-PolyA DCK1 Pineal ZT7 RNA-Seq TRANSCRIPTOMIC other 102 0 Application Read Forward 1 1 Application Read Reverse 52 Illumina Genome Analyzer II SRX069234 Rat pineal gland RNA-Seq PolyA ZT19 SRP006893 Rat pineal RNA-Seq For the mRNA-Seq sample preparation, the Illumina standard kit was used according to the manufacturer's protocol. Briefly, 10 microgram of each total RNA sample was used for polyA mRNA selection using streptavidin-coated magnetic beads, followed by chemical mRNA fragmentation. The fragmented mRNA was subjected to cDNA synthesis using reverse transcriptase (SuperScript II) and random primers. The cDNA was further converted into double stranded cDNA and, after an end repair process (Klenow fragment, T4 polynucleotide kinase and T4 polymerase), was finally ligated to Illumina paired end (PE) adaptors. Size selection was performed using a 2% agarose gel. Libraries were enriched using 15 cycles of PCR and purified by the QIAquick PCR purification kit (Qiagen). The enriched libraries were diluted with Elution Buffer to a final concentration of 10 nM. Each library was run at a concentration of 7 pM on one Illumina Genome Analyzer II (GAii) lane using paired-end 51 base-pair sequencing. Image analysis and base calling was done by Illumina Genome Analyzer Pipeline software (GAPipeline) with default parameters. SRS210902 Rat pineal gland_ZT19_PolyA DCK2 Pineal ZT19 RNA-Seq TRANSCRIPTOMIC other 102 0 Application Read Forward 1 1 Application Read Reverse 52 Illumina Genome Analyzer II SRX069235 Rat mixed tissue RNA-Seq PolyA ZT7 SRP006893 Rat pineal RNA-Seq For the mRNA-Seq sample preparation, the Illumina standard kit was used according to the manufacturer's protocol. Briefly, 10 *g of each total RNA sample was used for polyA mRNA selection using streptavidin-coated magnetic beads, followed by chemical mRNA fragmentation. The fragmented mRNA was subjected to cDNA synthesis using reverse transcriptase (SuperScript II) and random primers. The cDNA was further converted into double stranded cDNA and, after an end repair process (Klenow fragment, T4 polynucleotide kinase and T4 polymerase), was finally ligated to Illumina paired end (PE) adaptors. Size selection was performed using a 2% agarose gel.Finally, the libraries were enriched using 15 cycles of PCR and purified by the QIAquick PCR purification kit (Qiagen). The enriched libraries were diluted with Elution Buffer to a final concentration of 10 nM. Each library was run at a concentration of 7 pM on one Illumina Genome Analyzer II (GAii) lane using paired-end 51 base-pair sequencing. Image analysis and base calling was done by Illumina Genome Analyzer Pipeline software (GAPipeline) with default parameters. Three samples were analyzed in this manner. SRS210904 Rat non-pineal mixed tissue_ZT7_PolyA DCK3 mixed ZT7 RNA-Seq TRANSCRIPTOMIC other 102 0 Application Read Forward 1 1 Application Read Reverse 52 Illumina Genome Analyzer II SRX076903 Rat pineal gland RNA-Seq RiboMinus ZT7 SRP006893 Rat pineal RNA-Seq For the mRNA-Seq sample preparation, the Illumina standard kit was used according to the manufacturer's protocol. Briefly, 10 ug of each total RNA sample was depleted of ribosomal RNA using the RiboMinus kit (Invitrogen), followed by chemical mRNA fragmentation. The fragmented mRNA was used to synthesize cDNA using reverse transcriptase (SuperScript II) and random primers. The cDNA was further converted into double stranded cDNA and, after an end repair process (Klenow fragment, T4 polynucleotide kinase and T4 polymerase), was finally ligated to Illumina paired-end (PE) adaptors. Size selection was performed using a 2% agarose gel. Finally, the libraries were enriched using 15 cycles of PCR and purified by the QIAquick PCR purification kit (Qiagen). The enriched libraries were diluted with Elution Buffer to a final concentration of 10 nM. Each library was run at a concentration of 7 pM on one Illumina Genome Analyzer II (GAii) lane using paired-end 51 base-pair sequencing. Image analysis and base calling was done by Illumina Genome Analyzer Pipeline software (GAPipeline) with default parameters. Three samples were analyzed in this manner. SRS212034 Rat pineal gland_ZT7_RiboMinus DCK1r Pineal ZT7 RNA-Seq TRANSCRIPTOMIC other 102 0 Application Read Forward 1 1 Application Read Reverse 52 Illumina Genome Analyzer II SRX076913 Rat pineal gland RNA-Seq RiboMinus ZT19 SRP006893 Rat pineal RNA-Seq For the mRNA-Seq sample preparation, the Illumina standard kit was used according to the manufacturer's protocol. Briefly, 10 ug of each total RNA sample was depleted of ribosomal RNA using the RiboMinus kit (Invitrogen), followed by chemical mRNA fragmentation. The fragmented mRNA was used to synthesize cDNA using reverse transcriptase (SuperScript II) and random primers. The cDNA was further converted into double stranded cDNA and, after an end repair process (Klenow fragment, T4 polynucleotide kinase and T4 polymerase), was finally ligated to Illumina paired-end (PE) adaptors. Size selection was performed using a 2% agarose gel. Finally, the libraries were enriched using 15 cycles of PCR and purified by the QIAquick PCR purification kit (Qiagen). The enriched libraries were diluted with Elution Buffer to a final concentration of 10 nM. Each library was run at a concentration of 7 pM on one Illumina Genome Analyzer II (GAii) lane using paired-end 51 base-pair sequencing. Image analysis and base calling was done by Illumina Genome Analyzer Pipeline software (GAPipeline) with default parameters. Three samples were analyzed in this manner. SRS212035 Rat pineal gland_ZT19_RiboMinus DCK2r Pineal ZT19 RNA-Seq TRANSCRIPTOMIC other 102 0 Application Read Forward 1 1 Application Read Reverse 52 Illumina Genome Analyzer II SRX076921 Rat mixed tissue RNA-Seq RiboMinus ZT7 SRP006893 Rat pineal RNA-Seq For the mRNA-Seq sample preparation, the Illumina standard kit was used according to the manufacturer's protocol. Briefly, 10 ug of each total RNA sample was depleted of ribosomal RNA using the RiboMinus kit (Invitrogen), followed by chemical mRNA fragmentation. The fragmented mRNA was used to synthesize cDNA using reverse transcriptase (SuperScript II) and random primers. The cDNA was further converted into double stranded cDNA and, after an end repair process (Klenow fragment, T4 polynucleotide kinase and T4 polymerase), was finally ligated to Illumina paired-end (PE) adaptors. Size selection was performed using a 2% agarose gel. Finally, the libraries were enriched using 15 cycles of PCR and purified by the QIAquick PCR purification kit (Qiagen). The enriched libraries were diluted with Elution Buffer to a final concentration of 10 nM. Each library was run at a concentration of 7 pM on one Illumina Genome Analyzer II (GAii) lane using paired-end 51 base-pair sequencing. Image analysis and base calling was done by Illumina Genome Analyzer Pipeline software (GAPipeline) with default parameters. Three samples were analyzed in this manner. SRS212036 Rat non-pineal mixed tissue_ZT7_RiboMinus DCK3r mixed ZT7 RNA-Seq TRANSCRIPTOMIC other 102 0 Application Read Forward 1 1 Application Read Reverse 52 Illumina Genome Analyzer II