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36 rows where technology = "unknown", tissue_curation = "Pineal Gland" and tissue_curation_coarse = "Endocrine System"

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tissue_curation_coarse 1

  • Endocrine System · 36 ✖

tissue_curation 1

  • Pineal Gland · 36 ✖

technology 1

  • unknown · 36 ✖

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

experiment.library_layout 1

devstage_curation_coarse 1

devstage_curation 1

Link 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 …     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 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 …     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 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 …     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 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 …     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 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 …     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 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 …     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 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 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 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 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 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 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 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 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 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 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 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 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 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 ov…       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 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 ov…       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 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 ov…       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 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 ov…       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

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;