rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.title,run.attributes,run.filename,run.semantic_name,run.total_bases,run.total_spots,run.alias,run.read_lengths,run.base_counts,run.r1_length,run.r2_length,run.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.mapping_rate.mate2,seqdetective.nofeature_rate.mate1,seqdetective.nofeature_rate.mate2,seqdetective.sparsity.mate1,seqdetective.sparsity.mate2,seqdetective.pos_strand_rate.mate1,seqdetective.pos_strand_rate.mate2,seqdetective.readlen.mate1,seqdetective.readlen.mate2,seqdetective.judgement.mate1,seqdetective.judgement.mate2,seqdetective.judgement.reason,platform_family,instrument_generation,read_bias,selection_class,prep_kit,sc_or_bulk,tech_class,technology,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse
36546,SRR4469353,SRX2278278,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,Control for deltaCLK experiment   pineal gland CT14b,Control for deltaCLK experiment   pineal gland CT14b,1,Overall  14 libraries [12 time points from Tgaanat2:EGFP ΔCLK fish and two control samples from Tgaanat2: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. postwards  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. post 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.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>102</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>52</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016132,,,cont-7_AGTTCC_L001_R1_001.fastq.gz cont-7_AGTTCC_L001_R2_001.fastq.gz cont-7_AGTTCC_L002_R1_001.fastq.gz cont-7_AGTTCC_L002_R2_001.fastq.gz,fastq fastq fastq fastq,1478016300.0,14780163.0,Control for deltaCLK experiment   pineal gland CT14b run,0:50 1:50,A:371860402;C:353565906;G:345517418;T:383732200;N:23340374,50,50,,,371860402,353565906,345517418,383732200,23340374,SRX2278278,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,2,0.90906,0.91515,0.20116,0.19445,0.72916,0.72835,0.49173,0.54608,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Israel,2014-07-23,Adult,Adult,Pineal Gland,Endocrine System
36547,SRR4469352,SRX2278277,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,Control for deltaCLK experiment   pineal gland CT2,Control for deltaCLK experiment   pineal gland CT2,1,Overall  14 libraries [12 time points from Tgaanat2:EGFP ΔCLK fish and two control samples from Tgaanat2: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. postwards  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. post 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.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>102</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>52</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016132,,,cont-4_AGTCAA_L001_R1_001.fastq.gz cont-4_AGTCAA_L001_R2_001.fastq.gz cont-4_AGTCAA_L002_R1_001.fastq.gz cont-4_AGTCAA_L002_R2_001.fastq.gz,fastq fastq fastq fastq,1470782400.0,14707824.0,Control for deltaCLK experiment   pineal gland CT2 run,0:50 1:50,A:391260359;C:331926713;G:321564174;T:402261946;N:23769208,50,50,,,391260359,331926713,321564174,402261946,23769208,SRX2278277,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,2,0.89527,0.90214,0.13737,0.13571,0.68087,0.68051,0.4788,0.49087,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Israel,2014-07-23,Adult,Adult,Pineal Gland,Endocrine System
36548,SRR4469348,SRX2278239,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,aanat2 deltaCLK pineal gland CT22b,aanat2 deltaCLK pineal gland CT22b,1,Overall  14 libraries [12 time points from Tgaanat2:EGFP ΔCLK fish and two control samples from Tgaanat2: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. postwards  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. post 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.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>102</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>52</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016132,,,dclk-9_GATCAG_L001_R1_001.fastq.gz dclk-9_GATCAG_L001_R2_001.fastq.gz dclk-9_GATCAG_L002_R1_001.fastq.gz dclk-9_GATCAG_L002_R2_001.fastq.gz,fastq fastq fastq fastq,1230723800.0,12307238.0,aanat2 deltaCLK pineal gland CT22b run,0:50 1:50,A:326116345;C:279149077;G:272739998;T:331989387;N:20728993,50,50,,,326116345,279149077,272739998,331989387,20728993,SRX2278239,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,2,0.90153,0.90798,0.12705,0.12581,0.69238,0.69124,0.45781,0.47401,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Israel,2014-07-23,Adult,Adult,Pineal Gland,Endocrine System
36549,SRR4469008,SRX2278238,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,aanat2 deltaCLK pineal gland CT18b,aanat2 deltaCLK pineal gland CT18b,1,Overall  14 libraries [12 time points from Tgaanat2:EGFP ΔCLK fish and two control samples from Tgaanat2: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. postwards  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. post 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.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>102</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>52</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016132,,,dclk-8_ACTTGA_L001_R1_001.fastq.gz dclk-8_ACTTGA_L001_R2_001.fastq.gz dclk-8_ACTTGA_L002_R1_001.fastq.gz dclk-8_ACTTGA_L002_R2_001.fastq.gz,fastq fastq fastq fastq,954886200.0,9548862.0,aanat2 deltaCLK pineal gland CT18b run,0:50 1:50,A:254282649;C:215854100;G:209622359;T:259594152;N:15532940,50,50,,,254282649,215854100,209622359,259594152,15532940,SRX2278238,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,2,0.90085,0.90415,0.14674,0.14451,0.68874,0.68856,0.47777,0.49043,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Israel,2014-07-23,Adult,Adult,Pineal Gland,Endocrine System
36550,SRR4468783,SRX2278237,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,aanat2 deltaCLK pineal gland CT14b,aanat2 deltaCLK pineal gland CT14b,1,Overall  14 libraries [12 time points from Tgaanat2:EGFP ΔCLK fish and two control samples from Tgaanat2: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. postwards  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. post 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.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>102</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>52</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016132,,,dclk-7_CAGATC_L001_R1_001.fastq.gz dclk-7_CAGATC_L001_R2_001.fastq.gz dclk-7_CAGATC_L002_R1_001.fastq.gz dclk-7_CAGATC_L002_R2_001.fastq.gz,fastq fastq fastq fastq,1513650800.0,15136508.0,aanat2 deltaCLK pineal gland CT14b run,0:50 1:50,A:397790485;C:347226977;G:333623071;T:410528680;N:24481587,50,50,,,397790485,347226977,333623071,410528680,24481587,SRX2278237,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,2,0.90378,0.90956,0.13414,0.13161,0.67927,0.67823,0.45986,0.47098,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Israel,2014-07-23,Adult,Adult,Pineal Gland,Endocrine System
36551,SRR4469351,SRX2278236,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,aanat2 deltaCLK pineal gland CT10b,aanat2 deltaCLK pineal gland CT10b,1,Overall  14 libraries [12 time points from Tgaanat2:EGFP ΔCLK fish and two control samples from Tgaanat2: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. postwards  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. post 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.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>102</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>52</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016132,,,dclk-12_CTTGTA_L001_R1_001.fastq.gz dclk-12_CTTGTA_L001_R2_001.fastq.gz dclk-12_CTTGTA_L002_R1_001.fastq.gz dclk-12_CTTGTA_L002_R2_001.fastq.gz,fastq fastq fastq fastq,1542083900.0,15420839.0,aanat2 deltaCLK pineal gland CT10b run,0:50 1:50,A:414372159;C:345091361;G:330865131;T:426545033;N:25210216,50,50,,,414372159,345091361,330865131,426545033,25210216,SRX2278236,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,2,0.89601,0.90164,0.1494,0.14679,0.68509,0.68249,0.46593,0.47633,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Israel,2014-07-23,Adult,Adult,Pineal Gland,Endocrine System
36552,SRR4469350,SRX2278235,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,aanat2 deltaCLK pineal gland CT6b,aanat2 deltaCLK pineal gland CT6b,1,Overall  14 libraries [12 time points from Tgaanat2:EGFP ΔCLK fish and two control samples from Tgaanat2: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. postwards  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. post 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.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>102</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>52</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016132,,,dclk-11_GGCTAC_L001_R1_001.fastq.gz dclk-11_GGCTAC_L001_R2_001.fastq.gz dclk-11_GGCTAC_L002_R1_001.fastq.gz dclk-11_GGCTAC_L002_R2_001.fastq.gz,fastq fastq fastq fastq,1470018300.0,14700183.0,aanat2 deltaCLK pineal gland CT6b run,0:50 1:50,A:390422751;C:333175699;G:322905954;T:399684708;N:23829188,50,50,,,390422751,333175699,322905954,399684708,23829188,SRX2278235,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,2,0.90133,0.90669,0.13486,0.13298,0.6802,0.67994,0.46476,0.47663,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Israel,2014-07-23,Adult,Adult,Pineal Gland,Endocrine System
36553,SRR4469349,SRX2278234,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,aanat2 deltaCLK pineal gland CT2b,aanat2 deltaCLK pineal gland CT2b,1,Overall  14 libraries [12 time points from Tgaanat2:EGFP ΔCLK fish and two control samples from Tgaanat2: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. postwards  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. post 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.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>102</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>52</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016132,,,dclk-10_TAGCTT_L001_R1_001.fastq.gz dclk-10_TAGCTT_L001_R2_001.fastq.gz dclk-10_TAGCTT_L002_R1_001.fastq.gz dclk-10_TAGCTT_L002_R2_001.fastq.gz,fastq fastq fastq fastq,1322705100.0,13227051.0,aanat2 deltaCLK pineal gland CT2b run,0:50 1:50,A:353320808;C:296680969;G:289897303;T:360502140;N:22303880,50,50,,,353320808,296680969,289897303,360502140,22303880,SRX2278234,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,2,0.89935,0.90337,0.138,0.13471,0.68761,0.68615,0.44537,0.48064,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Israel,2014-07-23,Adult,Adult,Pineal Gland,Endocrine System
36554,SRR4468779,SRX2278233,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,aanat2 deltaCLK pineal gland CT22,aanat2 deltaCLK pineal gland CT22,1,Overall  14 libraries [12 time points from Tgaanat2:EGFP ΔCLK fish and two control samples from Tgaanat2: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. postwards  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. post 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.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>102</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>52</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016132,,,dclk-3_TTAGGC_L001_R1_001.fastq.gz dclk-3_TTAGGC_L001_R2_001.fastq.gz dclk-3_TTAGGC_L002_R1_001.fastq.gz dclk-3_TTAGGC_L002_R2_001.fastq.gz,fastq fastq fastq fastq,1391437700.0,13914377.0,aanat2 deltaCLK pineal gland CT22 run,0:50 1:50,A:370600600;C:314791162;G:302422949;T:380945528;N:22677461,50,50,,,370600600,314791162,302422949,380945528,22677461,SRX2278233,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,2,0.90077,0.90663,0.13303,0.12983,0.68176,0.67927,0.46884,0.48222,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Israel,2014-07-23,Adult,Adult,Pineal Gland,Endocrine System
36555,SRR4468778,SRX2278232,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,aanat2 deltaCLK pineal gland CT18,aanat2 deltaCLK pineal gland CT18,1,Overall  14 libraries [12 time points from Tgaanat2:EGFP ΔCLK fish and two control samples from Tgaanat2: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. postwards  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. post 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.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>102</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>52</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016132,,,dclk-2_CGATGT_L001_R1_001.fastq.gz dclk-2_CGATGT_L001_R2_001.fastq.gz dclk-2_CGATGT_L002_R1_001.fastq.gz dclk-2_CGATGT_L002_R2_001.fastq.gz,fastq fastq fastq fastq,1566024800.0,15660248.0,aanat2 deltaCLK pineal gland CT18 run,0:50 1:50,A:419409692;C:351933648;G:338078927;T:431073653;N:25528880,50,50,,,419409692,351933648,338078927,431073653,25528880,SRX2278232,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,2,0.9,0.90492,0.13189,0.12932,0.68757,0.68743,0.45253,0.4674,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Israel,2014-07-23,Adult,Adult,Pineal Gland,Endocrine System
36556,SRR4468777,SRX2278214,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,aanat2 deltaCLK pineal gland CT14,aanat2 deltaCLK pineal gland CT14,1,Overall  14 libraries [12 time points from Tgaanat2:EGFP ΔCLK fish and two control samples from Tgaanat2: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. postwards  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. post 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.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>102</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>52</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016132,,,dclk-1_ATCACG_L001_R1_001.fastq.gz dclk-1_ATCACG_L001_R2_001.fastq.gz dclk-1_ATCACG_L002_R1_001.fastq.gz dclk-1_ATCACG_L002_R2_001.fastq.gz,fastq fastq fastq fastq,1072983800.0,10729838.0,aanat2 deltaCLK pineal gland CT14 run,0:50 1:50,A:285412675;C:241757167;G:239216359;T:289121128;N:17476471,50,50,,,285412675,241757167,239216359,289121128,17476471,SRX2278214,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,2,0.90548,0.91142,0.13613,0.13179,0.69808,0.69718,0.48357,0.48784,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Israel,2014-07-23,Adult,Adult,Pineal Gland,Endocrine System
36557,SRR4468782,SRX2278111,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,aanat2 deltaCLK pineal gland CT10,aanat2 deltaCLK pineal gland CT10,1,Overall  14 libraries [12 time points from Tgaanat2:EGFP ΔCLK fish and two control samples from Tgaanat2: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. postwards  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. post 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.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>102</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>52</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016132,,,dclk-6_GCCAAT_L001_R1_001.fastq.gz dclk-6_GCCAAT_L001_R2_001.fastq.gz dclk-6_GCCAAT_L002_R1_001.fastq.gz dclk-6_GCCAAT_L002_R2_001.fastq.gz,fastq fastq fastq fastq,1396334700.0,13963347.0,aanat2 deltaCLK pineal gland CT10 run,0:50 1:50,A:372017545;C:315699006;G:305209850;T:380695969;N:22712330,50,50,,,372017545,315699006,305209850,380695969,22712330,SRX2278111,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,2,0.90165,0.90375,0.13729,0.13572,0.68901,0.68887,0.47627,0.48756,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Israel,2014-07-23,Adult,Adult,Pineal Gland,Endocrine System
36558,SRR4468781,SRX2278008,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,aanat2 deltaCLK pineal gland CT6,aanat2 deltaCLK pineal gland CT6,1,Overall  14 libraries [12 time points from Tgaanat2:EGFP ΔCLK fish and two control samples from Tgaanat2: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. postwards  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. post 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.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>102</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>52</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016132,,,dclk-5_ACAGTG_L001_R1_001.fastq.gz dclk-5_ACAGTG_L001_R2_001.fastq.gz dclk-5_ACAGTG_L002_R1_001.fastq.gz dclk-5_ACAGTG_L002_R2_001.fastq.gz,fastq fastq fastq fastq,1400816900.0,14008169.0,aanat2 deltaCLK pineal gland CT6 run,0:50 1:50,A:372340894;C:317777109;G:301897255;T:386068427;N:22733215,50,50,,,372340894,317777109,301897255,386068427,22733215,SRX2278008,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,2,0.89908,0.9022,0.14682,0.14409,0.68012,0.67795,0.46353,0.47947,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Israel,2014-07-23,Adult,Adult,Pineal Gland,Endocrine System
36559,SRR4468780,SRX2277943,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,aanat2 deltaCLK pineal gland CT2,aanat2 deltaCLK pineal gland CT2,1,Overall  14 libraries [12 time points from Tgaanat2:EGFP ΔCLK fish and two control samples from Tgaanat2: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. postwards  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. post 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.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>102</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>52</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016132,,,dclk-4_TGACCA_L001_R1_001.fastq.gz dclk-4_TGACCA_L001_R2_001.fastq.gz dclk-4_TGACCA_L002_R1_001.fastq.gz dclk-4_TGACCA_L002_R2_001.fastq.gz,fastq fastq fastq fastq,1507598800.0,15075988.0,aanat2 deltaCLK pineal gland CT2 run,0:50 1:50,A:401061420;C:339329123;G:332045345;T:410675395;N:24487517,50,50,,,401061420,339329123,332045345,410675395,24487517,SRX2277943,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,2,0.90388,0.90981,0.12413,0.12289,0.68572,0.68532,0.47663,0.48902,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Israel,2014-07-23,Adult,Adult,Pineal Gland,Endocrine System
36563,SRR1048063,SRX363286,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,Zebrafish pineal gland dark replica 3,Pineal gland dark R3,1,Adult 0.5 1.5 years old Tgaanat2: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. postwards  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. post 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.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016132,,,d3_pineal_CAGATC_L002_R2_001.fastq d3_pineal_CAGATC_L002_R1_001.fastq,fastq fastq,1947522800.0,9737614.0,Pineal gland dark R3 run,0:101 1:99,A:510547277;C:456462539;G:450297233;T:513101663;N:17114088,101,99,,,510547277,456462539,450297233,513101663,17114088,SRX363286,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,2,0.92352,0.91715,0.10879,0.10898,0.6873,0.69023,0.48478,0.48106,101,99,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Israel,2013-12-12,Adult,Adult,Pineal Gland,Endocrine System
36564,SRR1048062,SRX363285,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,Zebrafish pineal gland dark replica 2,Pineal gland dark R2,1,Adult 0.5 1.5 years old Tgaanat2: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. postwards  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. post 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.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016132,,,d2_pineal_GCCAAT_L002_R2_001.fastq d2_pineal_GCCAAT_L002_R1_001.fastq,fastq fastq,1484149600.0,7420748.0,Pineal gland dark R2 run,0:101 1:99,A:385426867;C:351549544;G:346126979;T:388075322;N:12970888,101,99,,,385426867,351549544,346126979,388075322,12970888,SRX363285,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,2,0.92222,0.91476,0.10962,0.11121,0.68933,0.69359,0.48718,0.48244,101,99,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Israel,2013-12-12,Adult,Adult,Pineal Gland,Endocrine System
36565,SRR1048061,SRX363284,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,Zebrafish pineal gland dark replica 1,Pineal gland dark R1,1,Adult 0.5 1.5 years old Tgaanat2: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. postwards  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. post 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.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016132,,,d1_pineal_ACAGTG_L002_R1_001.fastq d1_pineal_ACAGTG_L002_R2_001.fastq,fastq fastq,1750757800.0,8753789.0,Pineal gland dark R1 run,0:101 1:99,A:458721893;C:411677417;G:404111686;T:460844026;N:15402778,101,99,,,458721893,411677417,404111686,460844026,15402778,SRX363284,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,2,0.91494,0.90596,0.11581,0.11538,0.69248,0.69481,0.4833,0.47732,101,99,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Israel,2013-12-12,Adult,Adult,Pineal Gland,Endocrine System
36566,SRR1048060,SRX363283,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,Zebrafish pineal gland light replica 3,Pineal gland light R3,1,Adult 0.5 1.5 years old Tgaanat2: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. postwards  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. post 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.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016132,,,l3_pineal_TGACCA_L002_R1_001.fastq l3_pineal_TGACCA_L002_R2_001.fastq,fastq fastq,1690222600.0,8451113.0,Pineal gland light R3 run,0:101 1:99,A:442363790;C:397493201;G:390948371;T:444488446;N:14928792,101,99,,,442363790,397493201,390948371,444488446,14928792,SRX363283,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,2,0.91881,0.91058,0.11743,0.11843,0.69629,0.69923,0.48757,0.48035,101,99,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Israel,2013-12-13,Adult,Adult,Pineal Gland,Endocrine System
36567,SRR1048059,SRX363282,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,Zebrafish pineal gland light replica 2,Pineal gland light R2,1,Adult 0.5 1.5 years old Tgaanat2: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. postwards  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. post 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.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016132,,,l2_pineal_TTAGGC_L002_R2_001.fastq l2_pineal_TTAGGC_L002_R1_001.fastq,fastq fastq,1014564400.0,5072822.0,Pineal gland light R2 run,0:101 1:99,A:276724352;C:226950331;G:223973268;T:276923072;N:9993377,101,99,,,276724352,226950331,223973268,276923072,9993377,SRX363282,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,2,0.90704,0.90364,0.13141,0.13204,0.68688,0.69061,0.48164,0.48436,101,99,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Israel,2013-12-12,Adult,Adult,Pineal Gland,Endocrine System
36568,SRR1048058,SRX363281,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,Zebrafish pineal gland light replica 1,Pineal gland light R1,1,Adult 0.5 1.5 years old Tgaanat2: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. postwards  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. post 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.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016132,,,l1_pineal_ATCACG_L002_R2_001.fastq l1_pineal_ATCACG_L002_R1_001.fastq,fastq fastq,157696200.0,788481.0,Pineal gland light R1 run,0:101 1:99,A:41851978;C:36357694;G:36173225;T:41883697;N:1429606,101,99,,,41851978,36357694,36173225,41883697,1429606,SRX363281,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,2,0.84634,0.81043,0.11575,0.11592,0.73397,0.73829,0.48622,0.48559,101,99,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Israel,2013-12-12,Adult,Adult,Pineal Gland,Endocrine System
36569,SRR592709,SRX195414,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,Zebrafish pineal gland CT10b,Pineal gland CT10b,1,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. postwards  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. post 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.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016132,,,12_zebrapg_CTTGTA_L001_R1.fastq,fastq,2267299914.0,11224257.0,Pineal gland CT10b run,0:101 1:101,A:607709328;C:525388699;G:526914662;T:602638305;N:4648920,101,101,,,607709328,525388699,526914662,602638305,4648920,SRX195414,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,2,0.91476,0.91223,0.13127,0.13216,0.69061,0.69357,0.4519,0.45883,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Israel,2012-10-23,Adult,Adult,Pineal Gland,Endocrine System
36570,SRR592708,SRX195413,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,Zebrafish pineal gland CT6b,Pineal gland CT6b,1,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. postwards  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. post 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.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016132,,,11_zebrapg_GGCTAC_L001_R1.fastq,fastq,1959732492.0,9701646.0,Pineal gland CT6b run,0:101 1:101,A:539256839;C:439457590;G:440064434;T:536966859;N:3986770,101,101,,,539256839,439457590,440064434,536966859,3986770,SRX195413,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,2,0.90016,0.89453,0.15085,0.15152,0.68669,0.68972,0.46594,0.46791,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Israel,2012-10-23,Adult,Adult,Pineal Gland,Endocrine System
36571,SRR592707,SRX195412,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,Zebrafish pineal gland CT2b,Pineal gland CT2b,1,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. postwards  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. post 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.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016132,,,,,2453741672.0,12147236.0,Pineal gland CT2b run,0:101 1:101,A:634387433;C:592849406;G:591345951;T:630233237;N:4925645,101,101,,,634387433,592849406,591345951,630233237,4925645,SRX195412,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,2,0.90708,0.90474,0.16568,0.16764,0.70755,0.70914,0.49572,0.50509,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Israel,2012-10-23,Adult,Adult,Pineal Gland,Endocrine System
36572,SRR592705,SRX195411,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,Zebrafish pineal gland CT18b,Pineal gland CT18b,1,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. postwards  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. post 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.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016132,,,,,2178785332.0,10786066.0,Pineal gland CT18b run,0:101 1:101,A:594834306;C:495808338;G:493409173;T:590321583;N:4411932,101,101,,,594834306,495808338,493409173,590321583,4411932,SRX195411,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,2,0.89881,0.89552,0.13767,0.13768,0.69215,0.69542,0.45042,0.45067,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Israel,2012-10-23,Adult,Adult,Pineal Gland,Endocrine System
36573,SRR592703,SRX195410,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,Zebrafish pineal gland CT10,Pineal gland CT10,1,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. postwards  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. post 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.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016132,,,6_zebrapg_GCCAAT_L001_R1.fastq,fastq,2264856522.0,11212161.0,Pineal gland CT10 run,0:101 1:101,A:618511903;C:514367008;G:514553380;T:612826453;N:4597778,101,101,,,618511903,514367008,514553380,612826453,4597778,SRX195410,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,2,0.9147,0.91201,0.14139,0.14232,0.66892,0.67225,0.46449,0.46385,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Israel,2012-12-14,Adult,Adult,Pineal Gland,Endocrine System
36574,SRR592702,SRX195409,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,Zebrafish pineal gland CT6,Pineal gland CT6,1,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. postwards  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. post 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.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016132,,,,,4862235950.0,24070475.0,Pineal gland CT6 run,0:101 1:101,A:1301039088;C:1130011170;G:1129039062;T:1292258043;N:9888587,101,101,,,1301039088,1130011170,1129039062,1292258043,9888587,SRX195409,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,2,0.91831,0.91455,0.12082,0.12144,0.6827,0.68625,0.46641,0.46572,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Israel,2012-10-23,Adult,Adult,Pineal Gland,Endocrine System
36575,SRR592701,SRX195408,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,Zebrafish pineal gland CT2,Pineal gland CT2,1,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. postwards  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. post 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.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016132,,,,,2765620178.0,13691189.0,Pineal gland CT2 run,0:101 1:101,A:732432924;C:649046085;G:650686268;T:727912942;N:5541959,101,101,,,732432924,649046085,650686268,727912942,5541959,SRX195408,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,2,0.91765,0.9136,0.10747,0.1072,0.67085,0.6733,0.46153,0.45978,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Israel,2012-10-23,Adult,Adult,Pineal Gland,Endocrine System
36576,SRR592700,SRX195407,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,Zebrafish pineal gland CT22,Pineal gland CT22,1,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. postwards  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. post 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.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016132,,,,,1547066490.0,7658745.0,Pineal gland CT22 run,0:101 1:101,A:420761054;C:353199899;G:352761515;T:417226020;N:3118002,101,101,,,420761054,353199899,352761515,417226020,3118002,SRX195407,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,2,0.89945,0.8894,0.13461,0.13453,0.67334,0.6772,0.47399,0.47311,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Israel,2012-10-23,Adult,Adult,Pineal Gland,Endocrine System
36577,SRR592706,SRX195406,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,Zebrafish pineal gland CT22b,Pineal gland CT22b,1,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. postwards  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. post 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.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>102</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>52</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016132,,,,,1732363308.0,16983954.0,Pineal gland CT22b run,0:51 1:51,A:460560266;C:406133382;G:400603421;T:464930271;N:135968,51,51,,,460560266,406133382,400603421,464930271,135968,SRX195406,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,2,0.89284,0.88902,0.1375,0.13615,0.68178,0.68138,0.46301,0.46538,51,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Israel,2012-10-23,Adult,Adult,Pineal Gland,Endocrine System
36578,SRR592704,SRX195405,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,Zebrafish pineal gland CT14b,Pineal gland CT14b,1,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. postwards  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. post 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.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>102</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>52</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016132,,,7_zebr_pg_CAGATC_L007_R1.fastq,fastq,1395806454.0,13684377.0,Pineal gland CT14b run,0:51 1:51,A:372939800;C:324349097;G:332976129;T:365435447;N:105981,51,51,,,372939800,324349097,332976129,365435447,105981,SRX195405,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,2,0.87193,0.87656,0.13322,0.13509,0.70084,0.70289,0.45121,0.45269,51,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Israel,2012-10-23,Adult,Adult,Pineal Gland,Endocrine System
36579,SRR592699,SRX195404,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,Zebrafish pineal gland CT18,Pineal gland CT18,1,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. postwards  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. post 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.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>102</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>52</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016132,,,,,1668838014.0,16361157.0,Pineal gland CT18 run,0:51 1:51,A:442604920;C:391602372;G:388058181;T:446247320;N:325221,51,51,,,442604920,391602372,388058181,446247320,325221,SRX195404,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,2,0.89426,0.89144,0.13522,0.13581,0.68499,0.6859,0.46605,0.46445,51,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Israel,2012-10-23,Adult,Adult,Pineal Gland,Endocrine System
36580,SRR592698,SRX195403,SRS369337,SRP016132,PRJNA177642,Danio rerio Transcriptome or Gene expression,PRJNA177642,Other,Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.,,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFPY8  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. Fish were raised under 12 hr light:12 hr dark LD cycles  in a temperature controlled room  and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma  sacrificed by decapitation  and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14  pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14  18  22  2  6  10  14b  18b  22b  2b  6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN  according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall  12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average  30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22  2  6  10  18b  2b  6b  10b and 2 x 50 base pairs for the remaining time points CTs 14  18  14b and 22b.,Zebrafish pineal gland,Pineal gland,,,,,,,,,,,Zebrafish pineal gland CT14,Pineal gland CT14,1,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. postwards  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. post 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.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>102</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>52</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP016132,,,1_zebr_pg_ATCACG_L006_R1.fastq,fastq,1426289358.0,13983229.0,Pineal gland CT14 run,0:51 1:51,A:378980680;C:335425123;G:329692368;T:381915783;N:275404,51,51,,,378980680,335425123,329692368,381915783,275404,SRX195403,SRS369337,SRA054264,Tel Aviv University,Tel Aviv University,2,0.85247,0.85003,0.12173,0.12294,0.69694,0.69781,0.46706,0.46744,51,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Israel,2012-12-14,Adult,Adult,Pineal Gland,Endocrine System
42457,SRR5599696,SRX2853245,SRS2224927,SRP107985,PRJNA387951,Next Generation Sequencing Study of Circadian Changes in Transcriptome of Zebrafish Pineal Gland and Eye,GSE99285,Transcriptome Analysis,Purpose: We performed an NGS study on the circadian changes in zebrafish eye and pineal gland transcriptome in order to elucidate novel and conserved elements in the circadian clock. Methods: Poly A selected RNA from zebrafish eyes and pineaal glands of animals eutanized at 2 timepoints Mid Day  Midnight  was deep sequenced  using Illumina HiSeq2000. Reads were aligned using STAR aligner and differential expression was asssessed using DESeq2. Results: We discover a variety of genes that show circadian activivty in both eye and pineal gland of Zebrafish. Conclusions: Our study represents part of a comparative analysis of retinaleye and pineal gland transcriptome of several species  generated by RNA seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFP  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. 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 Tricane 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 pool of 18 pineal glands 6 eyes and 4 8 of each peripheral tissue was collected at each time point. Total RNA for mRNA analysis was isolated using RNeasy Lipid Tissue Mini Kit Qiagen according to the manufacturer''s instructions. The mixed tissue samples consisted of equal amounts of total RNA 1mg from muscle  ovary  kidney  gill  liver  intestines  heart and brain.  Poly A selected RNA from zebrafish eyes  mixed tissue and pineaal glands of animals eutanized at 2 timepoints Mid Day  Midnight  was deep sequenced  using Illumina HiSeq2000. Reads were aligned using STAR aligner and differential expression was asssessed using DESeq2.,,,,Pineal Gland Night,GSM2640447,,source name:Pineal Gland|genotype/variation:Tgaanat2:EGFP|tissue:Pineal Gland|timepoint:night,Pineal Gland Night,Illumina Casava1.9 software used for basecalling. Reads were aligned with the RNA STAR aligner v. 2.3.0e   using a danRer10 genome build. STAR aligner parameters used:   runThreadN 8    outFilterMultimapNmax 1   outSAMunmapped Within   outStd SAM. Quality control metrics were calculated and visualized using FastQC software and in house written scripts  and no major artifacts or abnormalities were found Gene read counts were provided by R subreads package  featureCounts function with parameters specifying: paired end reads  and reverse complement for the second strand  p   S2.  Annotation for assigning the reads was derived from native annotation for danRer10 genome build.  Differential expression analysis was performed using DESeq2 software package. Genome build: danRer10 Supplementary files format and content: zebrafish FPKM.txt file includes FPKM values for all of the Samples,Pineal Gland,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFP  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. 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 Tricane 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 pool of 18 pineal glands 6 eyes and 4 8 of each peripheral tissue was collected at each time point. Total RNA for mRNA analysis was isolated using RNeasy Lipid Tissue Mini Kit Qiagen according to the manufacturer's instructions. The mixed tissue samples consisted of equal amounts of total RNA 1mg from muscle  ovary  kidney  gill  liver  intestines  heart and brain. Poly A RNA libraries were prepared for sequencing using standard Illumina protocols,,genotype/variation:Tgaanat2:EGFP|tissue:Pineal Gland|timepoint:night,GSM2640447,GSM2640447: Pineal Gland Night; Danio rerio; RNA Seq,GSM2640447,,1,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFP  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. 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 Tricane 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 pool of 18 pineal glands 6 eyes and 4 8 of each peripheral tissue was collected at each time point. Total RNA for mRNA analysis was isolated using RNeasy Lipid Tissue Mini Kit Qiagen according to the manufacturer's instructions. The mixed tissue samples consisted of equal amounts of total RNA 1mg from muscle  ovary  kidney  gill  liver  intestines  heart and brain. Poly A RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM2640447,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP107985,,,pineal_night_ACAGTG_L001_R2_001.fastq.gz pineal_night_ACAGTG_L001_R1_001.fastq.gz,fastq fastq,2524070600.0,12620353.0,GSM2640447 r1,0:100 1:100,A:741805672;C:522977974;G:524367955;T:733520495;N:1398504,100,100,,,741805672,522977974,524367955,733520495,1398504,SRX2853245,SRS2224927,SRA565720,GEO,"Christopher E. mason, Physiology and Biophysics, Weill Cornell Medicine",2,0.8882,0.89515,0.19772,0.1879,0.7021,0.70558,0.48908,0.487,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2017-05-24,Adult,Adult,Pineal Gland,Endocrine System
42458,SRR5599697,SRX2853245,SRS2224927,SRP107985,PRJNA387951,Next Generation Sequencing Study of Circadian Changes in Transcriptome of Zebrafish Pineal Gland and Eye,GSE99285,Transcriptome Analysis,Purpose: We performed an NGS study on the circadian changes in zebrafish eye and pineal gland transcriptome in order to elucidate novel and conserved elements in the circadian clock. Methods: Poly A selected RNA from zebrafish eyes and pineaal glands of animals eutanized at 2 timepoints Mid Day  Midnight  was deep sequenced  using Illumina HiSeq2000. Reads were aligned using STAR aligner and differential expression was asssessed using DESeq2. Results: We discover a variety of genes that show circadian activivty in both eye and pineal gland of Zebrafish. Conclusions: Our study represents part of a comparative analysis of retinaleye and pineal gland transcriptome of several species  generated by RNA seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFP  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. 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 Tricane 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 pool of 18 pineal glands 6 eyes and 4 8 of each peripheral tissue was collected at each time point. Total RNA for mRNA analysis was isolated using RNeasy Lipid Tissue Mini Kit Qiagen according to the manufacturer''s instructions. The mixed tissue samples consisted of equal amounts of total RNA 1mg from muscle  ovary  kidney  gill  liver  intestines  heart and brain.  Poly A selected RNA from zebrafish eyes  mixed tissue and pineaal glands of animals eutanized at 2 timepoints Mid Day  Midnight  was deep sequenced  using Illumina HiSeq2000. Reads were aligned using STAR aligner and differential expression was asssessed using DESeq2.,,,,Pineal Gland Night,GSM2640447,,source name:Pineal Gland|genotype/variation:Tgaanat2:EGFP|tissue:Pineal Gland|timepoint:night,Pineal Gland Night,Illumina Casava1.9 software used for basecalling. Reads were aligned with the RNA STAR aligner v. 2.3.0e   using a danRer10 genome build. STAR aligner parameters used:   runThreadN 8    outFilterMultimapNmax 1   outSAMunmapped Within   outStd SAM. Quality control metrics were calculated and visualized using FastQC software and in house written scripts  and no major artifacts or abnormalities were found Gene read counts were provided by R subreads package  featureCounts function with parameters specifying: paired end reads  and reverse complement for the second strand  p   S2.  Annotation for assigning the reads was derived from native annotation for danRer10 genome build.  Differential expression analysis was performed using DESeq2 software package. Genome build: danRer10 Supplementary files format and content: zebrafish FPKM.txt file includes FPKM values for all of the Samples,Pineal Gland,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFP  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. 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 Tricane 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 pool of 18 pineal glands 6 eyes and 4 8 of each peripheral tissue was collected at each time point. Total RNA for mRNA analysis was isolated using RNeasy Lipid Tissue Mini Kit Qiagen according to the manufacturer's instructions. The mixed tissue samples consisted of equal amounts of total RNA 1mg from muscle  ovary  kidney  gill  liver  intestines  heart and brain. Poly A RNA libraries were prepared for sequencing using standard Illumina protocols,,genotype/variation:Tgaanat2:EGFP|tissue:Pineal Gland|timepoint:night,GSM2640447,GSM2640447: Pineal Gland Night; Danio rerio; RNA Seq,GSM2640447,,1,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFP  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. 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 Tricane 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 pool of 18 pineal glands 6 eyes and 4 8 of each peripheral tissue was collected at each time point. Total RNA for mRNA analysis was isolated using RNeasy Lipid Tissue Mini Kit Qiagen according to the manufacturer's instructions. The mixed tissue samples consisted of equal amounts of total RNA 1mg from muscle  ovary  kidney  gill  liver  intestines  heart and brain. Poly A RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM2640447,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP107985,,,pineal_night_ACAGTG_L002_R1_001.fastq.gz pineal_night_ACAGTG_L002_R2_001.fastq.gz,fastq fastq,2481727800.0,12408639.0,GSM2640447 r2,0:100 1:100,A:729161022;C:514502873;G:515738117;T:720993212;N:1332576,100,100,,,729161022,514502873,515738117,720993212,1332576,SRX2853245,SRS2224927,SRA565720,GEO,"Christopher E. mason, Physiology and Biophysics, Weill Cornell Medicine",2,0.88828,0.89524,0.19981,0.18859,0.70418,0.70613,0.48446,0.49385,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2017-05-24,Adult,Adult,Pineal Gland,Endocrine System
42459,SRR5599694,SRX2853244,SRS2224926,SRP107985,PRJNA387951,Next Generation Sequencing Study of Circadian Changes in Transcriptome of Zebrafish Pineal Gland and Eye,GSE99285,Transcriptome Analysis,Purpose: We performed an NGS study on the circadian changes in zebrafish eye and pineal gland transcriptome in order to elucidate novel and conserved elements in the circadian clock. Methods: Poly A selected RNA from zebrafish eyes and pineaal glands of animals eutanized at 2 timepoints Mid Day  Midnight  was deep sequenced  using Illumina HiSeq2000. Reads were aligned using STAR aligner and differential expression was asssessed using DESeq2. Results: We discover a variety of genes that show circadian activivty in both eye and pineal gland of Zebrafish. Conclusions: Our study represents part of a comparative analysis of retinaleye and pineal gland transcriptome of several species  generated by RNA seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFP  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. 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 Tricane 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 pool of 18 pineal glands 6 eyes and 4 8 of each peripheral tissue was collected at each time point. Total RNA for mRNA analysis was isolated using RNeasy Lipid Tissue Mini Kit Qiagen according to the manufacturer''s instructions. The mixed tissue samples consisted of equal amounts of total RNA 1mg from muscle  ovary  kidney  gill  liver  intestines  heart and brain.  Poly A selected RNA from zebrafish eyes  mixed tissue and pineaal glands of animals eutanized at 2 timepoints Mid Day  Midnight  was deep sequenced  using Illumina HiSeq2000. Reads were aligned using STAR aligner and differential expression was asssessed using DESeq2.,,,,Pineal Gland Day,GSM2640446,,source name:Pineal Gland|genotype/variation:Tgaanat2:EGFP|tissue:Pineal Gland|timepoint:day,Pineal Gland Day,Illumina Casava1.9 software used for basecalling. Reads were aligned with the RNA STAR aligner v. 2.3.0e   using a danRer10 genome build. STAR aligner parameters used:   runThreadN 8    outFilterMultimapNmax 1   outSAMunmapped Within   outStd SAM. Quality control metrics were calculated and visualized using FastQC software and in house written scripts  and no major artifacts or abnormalities were found Gene read counts were provided by R subreads package  featureCounts function with parameters specifying: paired end reads  and reverse complement for the second strand  p   S2.  Annotation for assigning the reads was derived from native annotation for danRer10 genome build.  Differential expression analysis was performed using DESeq2 software package. Genome build: danRer10 Supplementary files format and content: zebrafish FPKM.txt file includes FPKM values for all of the Samples,Pineal Gland,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFP  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. 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 Tricane 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 pool of 18 pineal glands 6 eyes and 4 8 of each peripheral tissue was collected at each time point. Total RNA for mRNA analysis was isolated using RNeasy Lipid Tissue Mini Kit Qiagen according to the manufacturer's instructions. The mixed tissue samples consisted of equal amounts of total RNA 1mg from muscle  ovary  kidney  gill  liver  intestines  heart and brain. Poly A RNA libraries were prepared for sequencing using standard Illumina protocols,,genotype/variation:Tgaanat2:EGFP|tissue:Pineal Gland|timepoint:day,GSM2640446,GSM2640446: Pineal Gland Day; Danio rerio; RNA Seq,GSM2640446,,1,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFP  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. 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 Tricane 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 pool of 18 pineal glands 6 eyes and 4 8 of each peripheral tissue was collected at each time point. Total RNA for mRNA analysis was isolated using RNeasy Lipid Tissue Mini Kit Qiagen according to the manufacturer's instructions. The mixed tissue samples consisted of equal amounts of total RNA 1mg from muscle  ovary  kidney  gill  liver  intestines  heart and brain. Poly A RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM2640446,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP107985,,,pineal_day_TGACCA_L001_R1_001.fastq.gz pineal_day_TGACCA_L001_R2_001.fastq.gz,fastq fastq,2548229000.0,12741145.0,GSM2640446 r1,0:100 1:100,A:715059730;C:560972529;G:565884910;T:704927661;N:1384170,100,100,,,715059730,560972529,565884910,704927661,1384170,SRX2853244,SRS2224926,SRA565720,GEO,"Christopher E. mason, Physiology and Biophysics, Weill Cornell Medicine",2,0.90563,0.91317,0.14689,0.1416,0.69682,0.70329,0.47374,0.47931,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2017-05-24,Adult,Adult,Pineal Gland,Endocrine System
42460,SRR5599695,SRX2853244,SRS2224926,SRP107985,PRJNA387951,Next Generation Sequencing Study of Circadian Changes in Transcriptome of Zebrafish Pineal Gland and Eye,GSE99285,Transcriptome Analysis,Purpose: We performed an NGS study on the circadian changes in zebrafish eye and pineal gland transcriptome in order to elucidate novel and conserved elements in the circadian clock. Methods: Poly A selected RNA from zebrafish eyes and pineaal glands of animals eutanized at 2 timepoints Mid Day  Midnight  was deep sequenced  using Illumina HiSeq2000. Reads were aligned using STAR aligner and differential expression was asssessed using DESeq2. Results: We discover a variety of genes that show circadian activivty in both eye and pineal gland of Zebrafish. Conclusions: Our study represents part of a comparative analysis of retinaleye and pineal gland transcriptome of several species  generated by RNA seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFP  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. 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 Tricane 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 pool of 18 pineal glands 6 eyes and 4 8 of each peripheral tissue was collected at each time point. Total RNA for mRNA analysis was isolated using RNeasy Lipid Tissue Mini Kit Qiagen according to the manufacturer''s instructions. The mixed tissue samples consisted of equal amounts of total RNA 1mg from muscle  ovary  kidney  gill  liver  intestines  heart and brain.  Poly A selected RNA from zebrafish eyes  mixed tissue and pineaal glands of animals eutanized at 2 timepoints Mid Day  Midnight  was deep sequenced  using Illumina HiSeq2000. Reads were aligned using STAR aligner and differential expression was asssessed using DESeq2.,,,,Pineal Gland Day,GSM2640446,,source name:Pineal Gland|genotype/variation:Tgaanat2:EGFP|tissue:Pineal Gland|timepoint:day,Pineal Gland Day,Illumina Casava1.9 software used for basecalling. Reads were aligned with the RNA STAR aligner v. 2.3.0e   using a danRer10 genome build. STAR aligner parameters used:   runThreadN 8    outFilterMultimapNmax 1   outSAMunmapped Within   outStd SAM. Quality control metrics were calculated and visualized using FastQC software and in house written scripts  and no major artifacts or abnormalities were found Gene read counts were provided by R subreads package  featureCounts function with parameters specifying: paired end reads  and reverse complement for the second strand  p   S2.  Annotation for assigning the reads was derived from native annotation for danRer10 genome build.  Differential expression analysis was performed using DESeq2 software package. Genome build: danRer10 Supplementary files format and content: zebrafish FPKM.txt file includes FPKM values for all of the Samples,Pineal Gland,,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFP  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. 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 Tricane 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 pool of 18 pineal glands 6 eyes and 4 8 of each peripheral tissue was collected at each time point. Total RNA for mRNA analysis was isolated using RNeasy Lipid Tissue Mini Kit Qiagen according to the manufacturer's instructions. The mixed tissue samples consisted of equal amounts of total RNA 1mg from muscle  ovary  kidney  gill  liver  intestines  heart and brain. Poly A RNA libraries were prepared for sequencing using standard Illumina protocols,,genotype/variation:Tgaanat2:EGFP|tissue:Pineal Gland|timepoint:day,GSM2640446,GSM2640446: Pineal Gland Day; Danio rerio; RNA Seq,GSM2640446,,1,Adult 0.5 1.5 years old transgenic zebrafish  Tgaanat2:EGFP  which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions  were used. 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 Tricane 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 pool of 18 pineal glands 6 eyes and 4 8 of each peripheral tissue was collected at each time point. Total RNA for mRNA analysis was isolated using RNeasy Lipid Tissue Mini Kit Qiagen according to the manufacturer's instructions. The mixed tissue samples consisted of equal amounts of total RNA 1mg from muscle  ovary  kidney  gill  liver  intestines  heart and brain. Poly A RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM2640446,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP107985,,,pineal_day_TGACCA_L002_R1_001.fastq.gz pineal_day_TGACCA_L002_R2_001.fastq.gz,fastq fastq,2505604600.0,12528023.0,GSM2640446 r2,0:100 1:100,A:703028440;C:551757119;G:556590046;T:692921366;N:1307629,100,100,,,703028440,551757119,556590046,692921366,1307629,SRX2853244,SRS2224926,SRA565720,GEO,"Christopher E. mason, Physiology and Biophysics, Weill Cornell Medicine",2,0.90515,0.91255,0.14693,0.14214,0.69652,0.70313,0.47136,0.48018,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2017-05-24,Adult,Adult,Pineal Gland,Endocrine System