run_metadata: 42459
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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| 42459 | SRR5599694 | SRX2853244 | SRS2224926 | SRP107985 | PRJNA387951 | Next Generation Sequencing Study of Circadian Changes in Transcriptome of Zebrafish Pineal Gland and Eye | GSE99285 | Transcriptome Analysis | Purpose: We performed an NGS study on the circadian changes in zebrafish eye and pineal gland transcriptome in order to elucidate novel and conserved elements in the circadian clock. Methods: Poly A selected RNA from zebrafish eyes and pineaal glands of animals eutanized at 2 timepoints Mid Day Midnight was deep sequenced using Illumina HiSeq2000. Reads were aligned using STAR aligner and differential expression was asssessed using DESeq2. Results: We discover a variety of genes that show circadian activivty in both eye and pineal gland of Zebrafish. Conclusions: Our study represents part of a comparative analysis of retinaleye and pineal gland transcriptome of several species generated by RNA seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: Adult 0.5 1.5 years old transgenic zebrafish Tgaanat2:EGFP which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions were used. Fish were raised under 12 hr light:12 hr dark LD cycles in a temperature controlled room. For tissue collection fish were anesthetized in 1.5 mM Tricane Sigma and sacrificed by decapitation. Dissections were conducted at mid day ZT6 and mid night ZT18. Fluorescent pineal glands whole eyes and other tissues were removed under a dissecting microscope. A pool of 18 pineal glands 6 eyes and 4 8 of each peripheral tissue was collected at each time point. Total RNA for mRNA analysis was isolated using RNeasy Lipid Tissue Mini Kit Qiagen according to the manufacturer''s instructions. The mixed tissue samples consisted of equal amounts of total RNA 1mg from muscle ovary kidney gill liver intestines heart and brain. Poly A selected RNA from zebrafish eyes mixed tissue and pineaal glands of animals eutanized at 2 timepoints Mid Day Midnight was deep sequenced using Illumina HiSeq2000. Reads were aligned using STAR aligner and differential expression was asssessed using DESeq2. | Pineal Gland Day | GSM2640446 | source name:Pineal Gland|genotype/variation:Tgaanat2:EGFP|tissue:Pineal Gland|timepoint:day | Pineal Gland Day | Illumina Casava1.9 software used for basecalling. Reads were aligned with the RNA STAR aligner v. 2.3.0e using a danRer10 genome build. STAR aligner parameters used: runThreadN 8 outFilterMultimapNmax 1 outSAMunmapped Within outStd SAM. Quality control metrics were calculated and visualized using FastQC software and in house written scripts and no major artifacts or abnormalities were found Gene read counts were provided by R subreads package featureCounts function with parameters specifying: paired end reads and reverse complement for the second strand p S2. Annotation for assigning the reads was derived from native annotation for danRer10 genome build. Differential expression analysis was performed using DESeq2 software package. Genome build: danRer10 Supplementary files format and content: zebrafish FPKM.txt file includes FPKM values for all of the Samples | Pineal Gland | Adult 0.5 1.5 years old transgenic zebrafish Tgaanat2:EGFP which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions were used. Fish were raised under 12 hr light:12 hr dark LD cycles in a temperature controlled room. For tissue collection fish were anesthetized in 1.5 mM Tricane Sigma and sacrificed by decapitation. Dissections were conducted at mid day ZT6 and mid night ZT18. Fluorescent pineal glands whole eyes and other tissues were removed under a dissecting microscope. A pool of 18 pineal glands 6 eyes and 4 8 of each peripheral tissue was collected at each time point. Total RNA for mRNA analysis was isolated using RNeasy Lipid Tissue Mini Kit Qiagen according to the manufacturer's instructions. The mixed tissue samples consisted of equal amounts of total RNA 1mg from muscle ovary kidney gill liver intestines heart and brain. Poly A RNA libraries were prepared for sequencing using standard Illumina protocols | genotype/variation:Tgaanat2:EGFP|tissue:Pineal Gland|timepoint:day | GSM2640446 | GSM2640446: Pineal Gland Day; Danio rerio; RNA Seq | GSM2640446 | 1 | Adult 0.5 1.5 years old transgenic zebrafish Tgaanat2:EGFP which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions were used. Fish were raised under 12 hr light:12 hr dark LD cycles in a temperature controlled room. For tissue collection fish were anesthetized in 1.5 mM Tricane Sigma and sacrificed by decapitation. Dissections were conducted at mid day ZT6 and mid night ZT18. Fluorescent pineal glands whole eyes and other tissues were removed under a dissecting microscope. A pool of 18 pineal glands 6 eyes and 4 8 of each peripheral tissue was collected at each time point. Total RNA for mRNA analysis was isolated using RNeasy Lipid Tissue Mini Kit Qiagen according to the manufacturer's instructions. The mixed tissue samples consisted of equal amounts of total RNA 1mg from muscle ovary kidney gill liver intestines heart and brain. Poly A RNA libraries were prepared for sequencing using standard Illumina protocols | GEO Accession:GSM2640446 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP107985 | pineal_day_TGACCA_L001_R1_001.fastq.gz pineal_day_TGACCA_L001_R2_001.fastq.gz | fastq fastq | 2548229000.0 | 12741145.0 | GSM2640446 r1 | 0:100 1:100 | A:715059730;C:560972529;G:565884910;T:704927661;N:1384170 | 100 | 100 | 715059730 | 560972529 | 565884910 | 704927661 | 1384170 | SRX2853244 | SRS2224926 | SRA565720 | GEO | Christopher E. mason, Physiology and Biophysics, Weill Cornell Medicine | 2 | 0.90563 | 0.91317 | 0.14689 | 0.1416 | 0.69682 | 0.70329 | 0.47374 | 0.47931 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | United States | 2017-05-24 | Adult | Adult | Pineal Gland | Endocrine System |