run_metadata: 36548

This data as json

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
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