{"database": "metadata", "table": "run_metadata", "rows": [[33654, "SRR30355363", "SRX25813459", "SRS22443727", "SRP528295", "PRJNA1151638", "Expression profiling of whole kidney marrow cells derived from wild type and rad21 heterozygous mutant adult zebrafish [bulkRNA seq]", "GSE275536", "Transcriptome Analysis", "Bulk RNA sequencing analyses of whole kidney marrow tissue isolated from wild type and rad21 heterozygous mutant adult zebrafish. Overall design: RNA sequencing was carried out on whole kidney marrow tissue isolated from adult zebrafish that were wild type or carry germline heterozygous mutation in the rad21 gene. The zebrafish rad21 allele used in this study was rad21nz171  which contains a nonsense mutation in exon 8 of the zebrafish rad21a gene converting a glycine to a stop codon. The wild type zebrafish utilized were the wild type siblings obtained from in cross of rad21 heterozygous mutant zebrafish. RNA sequencing was carried out in triplicates and each replicate consisted of whole kidney marrow pooled from three adult zebrafish.", null, "pubmed:39548947", null, "Rad21het rep2", "GSM8479115", null, "source name:Whole kidney marrow|tissue:Whole kidney marrow|genotype:rad21+/ |geo loc name:missing|collection date:missing", "Rad21het rep2", "Sequencing reads were QC using FastQC. Sequencing adapter and low quality Q<20 were removed using fastq mcf. Cleaned reads were aligned using HISAT2 version 2.0.4. Read count were retrieved using FeatureCount summarising data at gene id level. Transcript per milion were generated using featureCount read count using R. Assembly: Danio Rerio genome GRCz11 Supplementary files format and content: tab delimited text file  contains the transcript parts million countsTPM for each sample", "Whole kidney marrow", null, "Whole kidney marrow tissue was isolated from adult zebrafish. Total RNA was extracted using the NucleoSpin RNA kit MACHEREY NAGEL. Libraries were prepared using the Illumina TruSeq\u00ae RNA Sample Preparation v2", null, "tissue:Whole kidney marrow|genotype:rad21+/ ", "GSM8479115", "GSM8479115: Rad21het rep2; Danio rerio; RNA Seq", "GSM8479115 r1", "GSM8479115", "1", "Whole kidney marrow tissue was isolated from adult zebrafish. Total RNA was extracted using the NucleoSpin RNA kit MACHEREY NAGEL. Libraries were prepared using the Illumina TruSeq\u00ae RNA Sample Preparation v2", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Five", null, "SRP528295", null, null, "Rad21het_rep2_L001_R1_001.fastq.gz Rad21het_rep2_L001_R2_001.fastq.gz", "fastq fastq", 15263700610.0, 50542055.0, "GSM8479115 r1", "0:151 1:151", "A:3934169632;C:3701506984;G:3857649812;T:3769115522;N:1258660", 151, 151, null, null, 3934169632, 3701506984, 3857649812, 3769115522, 1258660, "SRX25813459", "SRS22443727", "SRA1954177", "Horsfield, Pathology, University of Otago", "Horsfield, Pathology, University of Otago", 2, 0.9227, 0.92195, 0.02689, 0.02669, 0.72547, 0.73196, 0.47904, 0.48582, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "New Zealand", "2024-08-23", "Adult", "Adult", "Kidney", "Renal 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": ["33654"], "units": {}, "query_ms": 9.20792699616868}