{"database": "metadata", "table": "run_metadata", "rows": [[56881, "SRR11164689", "SRX7789373", "SRS6204771", "SRP250477", "PRJNA608279", "EPI 00649 2019 New insights into the early mechanisms of epileptogenesis in a zebrafish model of Dravet syndrome", "GSE145801", "Transcriptome Analysis", "We report early mechanisms of epileptogenesis in a zebrafish model of Dravet syndrome caused by missense mutation in scn1lab gene. Overall design: Single cell RNA Sequencing experiments were performed on a total of 4 samples. These correspond to zebrafish brain 5 dpf and 8 dpf comparing wild type to a scn1Lab homozygous mutation.", null, "pubmed:32096222", null, "Zebrafish Mutscn1Lab brain  5 dpf", "GSM4333120", null, "tissue:Mutscn1Lab brain  5 dpf dpf", "Zebrafish Mutscn1Lab brain  5 dpf", "R1 contains the cell barcode 1 12 bp and UMI 13 20 bp. R2 contains the cDNA sequence. Bcl2fastq ver 2.0 was used for the base calling Paired end sequencing reads were trimmed for adaptor sequence. Based on the original Dropseq implementation Macosko et al; 2015  the reads were demultiplexed for the cell barcode and UMI. The genes mapped to GRCz11 using STAR genome aligner   with default parameters Genome build: GRCz11 Supplementary files format and content: tab delimited text files include raw counts", "Mutscn1Lab brain  5 dpf", null, "Single cell RNA seq using Dropseq   three prime bead based enrichment technique  using SMART synthesis Macosko et al  2015 doi: 10.1016/j.cell.2015.05.002 Libraries were prepared according to Drop seq methods Macosko et al  2015 doi: 10.1016/j.cell.2015.05.002. post cDNA tagmenation  PCR amplification was performed using Illumina primers N701 N702  A501. The purified cDNA fragments of 600 bp were captured on an Illumina flow cell for cluster generation. Libraries were sequenced on Illumina NextSeq 500 following the manufacturer's protocols.", "as described in Tiraboschi et al.  EPI 00649 2019", "tissue:brain|genotype:scn1Lab|age:5 dpf", "GSM4333120", "GSM4333120: Zebrafish Mutscn1Lab brain  5 dpf Danio rerio; RNA Seq", "GSM4333120", null, "1", "Single cell RNA seq using Dropseq   three prime bead based enrichment technique  using SMART synthesis Macosko et al  2015 doi: 10.1016/j.cell.2015.05.002 Libraries were prepared according to Drop seq methods Macosko et al  2015 doi: 10.1016/j.cell.2015.05.002. post cDNA tagmenation  PCR amplification was performed using Illumina primers N701 N702  A501. The purified cDNA fragments of 600 bp were captured on an Illumina flow cell for cluster generation. Libraries were sequenced on Illumina NextSeq 500 following the manufacturer's protocols.", "GEO Accession:GSM4333120", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP250477", null, null, "5DPF2_S2_R1_001.fastq.gz 5DPF2_S2_R2_001.fastq.gz", "fastq fastq", 6663274080.0, 83290926.0, "GSM4333120 r1", "0:20 1:60", "A:1851799411;C:1470225216;G:1666931688;T:1673879241;N:438524", 20, 60, null, null, 1851799411, 1470225216, 1666931688, 1673879241, 438524, "SRX7789373", "SRS6204771", "SRA1047335", "GEO", "ICS, University of Luxembourg - LCSB", 2, 0.01151, 0.90584, 0.00724, 0.13592, 0.99022, 0.84784, 0.40101, 0.60276, 20, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "dropseq", null, "Luxembourg", "2020-02-24", "Larval", "Larval", "Brain", "Nervous System"]], "columns": ["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"], "primary_keys": ["rowid"], "primary_key_values": ["56881"], "units": {}, "query_ms": 7.4556740000844}