{"database": "metadata", "table": "run_metadata", "rows": [[58897, "SRR11519038", "SRX8090383", "SRS6457235", "SRP255886", "PRJNA624126", "Early zebrafish development time course transcriptome", "GSE148391", "Transcriptome Analysis", "Early zebrafish development time course transcriptome Overall design: Three RNA seq datasets of zebrafish embryos expanding the first 8 hours of development. Wild type embryos were sequenced using two different RNA extractions protocols: poly A capture and ribosomal depletion. Also  we sequenced embryos  using poly A capture  that were treated with alpha amanitin 200ng/ul to inhibit zygotic transcription.", null, null, null, "TreatedAamanitin zfishPolyAalpha 6.5h", "GSM4467014", null, "tissue:zebrafish early embryo|developmental stage:early embryo|time post fertilization in hrs:6.5|treatment:alpha amanitin injected|rna extraction protocol:poly A capture", "TreatedAamanitin zfishPolyAalpha 6.5h", "Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a   using Ensembl 98 gene models. TPM values were generated using RSEM version v1.3.0 . Genome build: danRer11 Supplementary files format and content: comma delimited csv files include TPM values for each Sample", "zebrafish early embryo", "For treated embryos: \u03b1 amanitin was injected into single cell stage zebrafish embryos to inhibit zygotic transcription 200ng/ul.", "poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols", "Adults zebrafish females were crossed and fertilized embryos were collected and incubated at 28 degree Celsius. 25 embryos for each set with a biological replicate were collected from their respective plates at an interval of one hr. and up to 8hrs.", "developmental stage:early embryo|time post fertilization in hrs:6.5|treatment:alpha amanitin injected|rna extraction protocol:poly A capture", "GSM4467014", "GSM4467014: TreatedAamanitin zfishPolyAalpha 6.5h; Danio rerio; RNA Seq", "GSM4467014", null, "1", "poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM4467014", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP255886", null, null, "TreatedAamanitin_zfishPolyAalpha_6.5h.fastq.gz", "fastq", 2637121340.0, 34698965.0, "GSM4467014 r1", "0:76 1:0", "A:607991115;C:648768142;G:648963472;T:730955221;N:443390", 76, 0, null, null, 607991115, 648768142, 648963472, 730955221, 443390, "SRX8090383", "SRS6457235", "SRA1064259", "GEO", "Computational Biology, Stowers Institute for Medical Research", 1, 0.96223, null, 0.05876, null, 0.78693, null, 0.51118, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-04-09", "Adult", "Adult", "Embryo Imprecise", "All anatomical structures"]], "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": ["58897"], "units": {}, "query_ms": 8.823017007671297}