{"database": "metadata", "table": "run_metadata", "rows": [[70805, "SRR20651072", "SRX16674145", "SRS14305694", "SRP388214", "PRJNA861969", "RNA seq in KLHL40 KO zebrafish muscle", "PRJNA861969", "Other", "Mutations in KLHL40 gene results in nemaline myopathy in affected patients. To identify the contribution of transcriptome on disease pathology  bulk RNA sequencing was performed in Control and KLHL40 knockout zebrafish at the onset of disease pathology at 3 month of age.", null, null, null, "klhl40a KO2", "klhl40a Mutant 2", null, "strain:TU|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:3 Months|dev stage:Adult|sex:not collected|tissue:Skeletal Muscle|disease:Nemaline Myopathy|disease stg:Disease onset|genotype:klhl40a|phenotype:Nemaline Myopathy|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "KO2", "klhl40a2", "klhl40a2", "A total amount of 1 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA. First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of 3 ends of DNA fragments  NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150200 bp in length  the library fragments were purified with AMPure XP system Beckman Coulter  Beverly  USA. Then 3 l USER Enzyme NEB  USA was used with size selected  adaptorligated cDNA at 37 C for 15 min followed by 5 min at 95 C before PCR. Then PCR was performed with Phusion High Fidelity DNA polymerase  Universal PCR primers and Index X Primer. At last  PCR products were purified AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system.  The clustering of the index coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot HS Illumina according to the manufacturers instructions. post cluster generation  the library preparations were sequenced on an Illumina platform and paired end reads were generated.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP388214", null, null, "KO2_1.fq.gz KO2_2.fq.gz", "fastq fastq", 6551044800.0, 21836816.0, "KO2 1.fq.gz", "0:150 1:150", "A:1793351007;C:1490899611;G:1511714794;T:1754976004;N:103384", 150, 150, null, null, 1793351007, 1490899611, 1511714794, 1754976004, 103384, "SRX16674145", "SRS14305694", null, null, "Brigham and Women's Hospital", 2, 0.95416, 0.953, 0.06534, 0.06511, 0.76678, 0.76668, 0.51901, 0.49628, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2022-07-26", "Adult", "Adult", "Muscle", "Muscular 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": ["70805"], "units": {}, "query_ms": 10.611918994982261}