{"database": "metadata", "table": "run_metadata", "rows": [[74635, "SRR23908128", "SRX19719610", "SRS17086727", "SRP428084", "PRJNA946304", "Effect of sirt6 deficiency on gene expression in zebrafish at 3 dpf", "GSE227668", "Transcriptome Analysis", "To investigate the underlying  mechanisms of sirt6  in the regulation of HSCs and neutrophils lineage  expansion in zebrafish. Overall design: We generated a sirt6 mutant zebrafish line using CRISPR/Cas9 methods", null, null, null, "tail  WT 3", "GSM7104974", null, "source name:tail|tissue:tail|genotype:WT|developmental stage:larvae at 3 dpf|geo loc name:missing|collection date:missing", "tail  WT 3", "The generated fastq files were subjected to FastQC  to check sequencing quality. The clean reads were mapped onto the GRCz11 zebrafish reference genome using HISAT2 v2.0.5. The mapped reads were then counted using FeatureCounts. The counts matrix was applied to DESeq2 for normalization  differentially expressed genes identification. The resulting P values were adjusted using the Benjamini and Hochberg\u2019s approach for controlling the false discovery rate . Assembly: GRCz11 Supplementary files format and content: gene fpkm.txt", "tail", null, "Larvae were collected at 3 dpf  then grouped into sirt6 mutant and WT groups through genotyping  total RNA was extracted with TRIzol Invitrogen from the tails including hematopoietic tissue. The poly A selected RNA was applied to the NGS RNA Library Prep kits Novogene to construct Sequencing libraries.", null, "tissue:tail|genotype:WT|developmental stage:larvae at 3 dpf", "GSM7104974", "GSM7104974: tail  WT 3; Danio rerio; RNA Seq", "GSM7104974 r1", "GSM7104974", "1", "Larvae were collected at 3 dpf  then grouped into sirt6 mutant and WT groups through genotyping  total RNA was extracted with TRIzol Invitrogen from the tails including hematopoietic tissue. The poly A selected RNA was applied to the NGS RNA Library Prep kits Novogene to construct Sequencing libraries.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP428084", null, "loader:fastq load.py", "WT_3_1.fq.gz WT_3_2.fq.gz", "fastq fastq", 6599139300.0, 21997131.0, "GSM7104974 r1", "0:150 1:150", "A:1862099481;C:1460254817;G:1446030038;T:1828044493;N:2710471", 150, 150, null, null, 1862099481, 1460254817, 1446030038, 1828044493, 2710471, "SRX19719610", "SRS17086727", "SRA1606833", "South China University of Technology", "South China University of Technology", 2, 0.93499, 0.93641, 0.11822, 0.11847, 0.66561, 0.66636, 0.47204, 0.47094, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-03-19", "Larval", "Larval", "Tail", "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": ["74635"], "units": {}, "query_ms": 13.453135999952792}