run_metadata: 53147
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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| 53147 | SRR9685040 | SRX6444484 | SRS5098421 | SRP214637 | PRJNA554650 | Zebrafish whole brain single cell RNA seq of nr1d1:VNP fish | GSE134288 | Other | we report a transgenic zebrafish line using destabilized fluorescent protein Venus NLS PEST VNP driven by the promoter of a key circadian clock gene nr1d1. This system allows us to monitor the development of single cell circadian rhythm in live zebrafish larva in a cell type specific manner. To identify the cell types expressing nr1d1:VNP in the whole brain we conducted single cell RNA seq scRNA seq of 15 000 cells dissociated from the brain of Tgnr1d1:VNP larval fish at 6.5dpf. Among them 6514 cells were identified with number of genes > 500 and used for the following analysis. 26 cells clusters were classified from scRNAseq and manually annotated by comparing the marker genes with the adult zebrfiash whole brain single cell RNA seq data. The mRNA of nr1d1:VNP was enriched in photoreceptors in pineal gland granule cells and purkinje cells in cerebellum habenula cells as well as non neuron cell. Overall design: To identify the cell types expressing nr1d1:VNP in the whole brain we conducted single cell RNA seq scRNA seq of 15 000 cells dissociated from the brain of Tgnr1d1:VNP larval fish at 6.5dpf using 10X genomics. | pubmed:32168317 | whole brain single cell RNA seq of nr1d1:VNP fish | GSM3941431 | source name:Zebrafish brain|age:6.5dpf|genotype:nr1d1:VNP|tissue:brain|brain region:pineal | whole brain single cell RNA seq of nr1d1:VNP fish | Raw sequencing data was converted to matrices of expression counts using the cellranger software provided by 10X Chromium system. Reads were aligned to a zebrafish reference transcriptome ENSEMBL Zv11 release 95. The gene expression matrix were then loaded into Seurat package in R for clustering. Cells with less than 500 genes or percentage of mitochondiral genes>0.02 were excluded. Genome build: Zv11 Supplementary files format and content: processed data is a matrix each row represent one gene while each column represent one cell. | Zebrafish brain | The fish were untreated. | 6.5 dpf larval heads were dissected on dissection medium DMEF/F12 with 2% 100X penicillin streptomycin and pineal region were enriched by pipetting the pineal into the tube. Dissociation of the brain cells following the protocol from Miguel A. Lopez Ramirez et al. www.jove.com 2016. Briefly Add 300ul papain solution to the dissected tissue digest the tissue at 37 in water heater for 15 minute pipetting during digest. Then stop the digestion by adding 1.2ml of washing solution. Washing the cells twice using washing solution. In the end sterilize the cells using 40um pore size filter. Stain cells using trypan blue and count the living cells using a hemocytometer. The library were constructed following the instruction of 10X Chromium system. | Embryos were produced by natural spawning in the morning and raised in egg water containing methylene blue 0.3 ppm in a light controlled incubator under 12h/12h LD cycles at 28 oC. ZT0 is defined as the time when the lights are turned on 9 A.M.. | age:6.5dpf|genotype:nr1d1:VNP|tissue:brain|brain region:pineal | GSM3941431 | GSM3941431: whole brain single cell RNA seq of nr1d1:VNP fish; Danio rerio; RNA Seq | GSM3941431 | 1 | 6.5 dpf larval heads were dissected on dissection medium DMEF/F12 with 2% 100X penicillin streptomycin and pineal region were enriched by pipetting the pineal into the tube. Dissociation of the brain cells following the protocol from Miguel A. Lopez Ramirez et al. www.jove.com 2016. Briefly Add 300ul papain solution to the dissected tissue digest the tissue at 37 in water heater for 15 minute pipetting during digest. Then stop the digestion by adding 1.2ml of washing solution. Washing the cells twice using washing solution. In the end sterilize the cells using 40um pore size filter. Stain cells using trypan blue and count the living cells using a hemocytometer. The library were constructed following the instruction of 10X Chromium system. | GEO Accession:GSM3941431 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina Genome Analyzer IIx | SRP214637 | pineal_S1_L001_R1_001.fastq.gz pineal_S1_L001_R2_001.fastq.gz | fastq fastq | 40509923100.0 | 135033077.0 | GSM3941431 r1 | 0:150 1:150 | A:12010442156;C:5708633132;G:6678955522;T:16110568611;N:1323679 | 150 | 150 | 12010442156 | 5708633132 | 6678955522 | 16110568611 | 1323679 | SRX6444484 | SRS5098421 | SRA921010 | GEO | Institute of Neuroscience | 2 | 0.39852 | 0.8845 | 0.05199 | 0.15658 | 0.96644 | 0.78774 | 0.42222 | 0.51714 | 150 | 150 | B | B | mate1-mate2 similar by mapping diff | illumina | early_illumina | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | China | 2019-07-15 | Larval | Larval | Brain | Nervous System |