{"database": "metadata", "table": "run_metadata", "rows": [[67550, "SRR17201124", "SRX13381108", "SRS11285137", "SRP350317", "PRJNA788011", "pharyngeal arch region in zebrafish embryos at 48 hpf", "PRJNA788011", "Other", "pharyngeal arch regions in wild type sibling and mutant zebrafish embryos at 48 hpf", null, null, null, null, "homo 48h2", null, "strain:Tubingen|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:48 hpf stage:not applicable|sex:not determined|tissue:pharyngeal arch|genotype:homozygotic mutant 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio: 48hpf homozygotic mutant pharyngeal arch 2", "homo 48h2", "homo 48h2", "Poly A RNA is purified from 1g total RNA using Dynabeads Oligo dT25 61005 Thermo Fisher  CA  USA using two rounds of purification. Then the polyA RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module NEB  cat.e6150  USA under 94 5 7min. Then the cleaved RNA fragments were reverse transcribed to create the cDNA by SuperScript II Reverse Transcriptase Invitrogen  cat. 1896649  USA  which were next used to synthesise U labeled second stranded DNAs with E. coli DNA polymerase I NEB  cat.m0209  USA  RNase H NEB  cat.m0297  USA and dUTP Solution Thermo Fisher  cat.R0133  USA. An A base is then added to the blunt ends of each strand  preparing them for ligation to the indexed adapters. Each adapter contains a T base overhang for ligating the adapter to the A tailed fragmented DNA. Single  or dual index adapters are ligated to the fragments  and size selection was performed with AMPureXP beads. post the heat labile UDG enzyme NEB  cat.m0280  USA treatment of the U labeled second stranded DNAs  the ligated products are amplified with PCR by the following conditions: initial denaturation at 95 for 3 min; 8 cycles of denaturation at 98 for 15 sec  annealing at 60 for 15 sec  and extension at 72 for 30 sec; and then final extension at 72 for 5 min. The average insert size for the final cDNA library was 30050 bp.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP350317", null, null, "homo_48h2_Clean_Data1.fq.gz homo_48h2_Clean_Data2.fq.gz", "fastq fastq", 5736708800.0, 20741445.0, "homo 48h2 Clean Data1.fq.gz", "0:138.30 1:138.28", "A:1509851615;C:1356120916;G:1368270971;T:1502443004;N:22294", 138, 138, null, null, 1509851615, 1356120916, 1368270971, 1502443004, 22294, "SRX13381108", "SRS11285137", "SRA1341839", "Ocean University of China|School of Medicine and Pharmacy", "Ocean University of China", 2, 0.95037, 0.95325, 0.06985, 0.06953, 0.68763, 0.68678, 0.47361, 0.46423, 141, 141, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2021-12-11", "Hatching", "Embryo", "Pharyngeal Arch", "Multi-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": ["67550"], "units": {}, "query_ms": 12.297115987166762}