run_metadata: 36560
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 |
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| 36560 | SRR1048073 | SRX363298 | 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 Brain miRNA | Brain miRNA | 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 and brains were removed under a fluorescent dissecting microscope; the use of transgenic fish expressing enhanced green fluorescent protein EGFP in the pineal gland enabled its selective removal. The tissues were collected from light and dark treated fish at 6 time points with 4 hr intervals throughout one daily cycle corresponding to CT2 6 10 14 18 and 22. For miR seq 18 pineal glands were pooled from the 6 sampling times for both light and dark treatments and one brain pool was composed of 4 brains that were collected from light and dark treated fish at CT2 and CT14. Brain samples were collected subsequent to the removal of pineal glands and therefore do not contain pineal tissues. Total RNA for miRNA analysis was isolated using miRNeasy Mini Kit Qiagen. miRNA capturing and library construction for the pineal light pineal dark and brain samples were conducted using Illumina's TruSeq Small RNA Sample Prep Kit according to the manufacturer’s protocol. Briefly three prime adapter was ligated to total RNA using truncated T4 RNA Ligase 2 without xxx then five prime adapter was added using T4 RNA Ligase with ATP. postwards reverse transcription followed by PCR was used to create cDNA constructs based on the small RNA ligated with three prime and five prime adapters. The introduction of index sequence bar codes was done at the PCR step. Finally gel electrophoresis was used to purify the amplified cDNA construct in preparation for subsequent cluster generation. 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 three mature miRNA libraries pineal light pineal dark and brain were sequenced with bar codes on one lane of an Illumina HiSeq2000 instrument following the manufacturer’s protocol. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline version 1.7. The reads were filtered using Illumina's HiSeq2000 softwares Illumina indexes separation was also performed. The total number of reads post filtering was 6 million 10.4 million and 14.8 million for the pineal light pineal dark and brain respectively. | miRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | SRP016132 | ZB_trimmed.fastq | fastq | 323899236.0 | 14781569.0 | Brain miRNA run | 0:21.91 1:0 | A:77705253;C:63882329;G:85902986;T:96383552;N:25116 | 21 | 0 | 77705253 | 63882329 | 85902986 | 96383552 | 25116 | SRX363298 | SRS369337 | SRA054264 | Tel Aviv University | Tel Aviv University | 1 | 0.88754 | 0.06569 | 0.96747 | 0.53358 | 23 | B | usable mapping rate | illumina | hiseq_era | unknown | size_fractionation | trueseq | bulk | unknown | unknown | Israel | 2015-07-22 | Adult | Adult | Multi-tissue | Multi-system |