{"database": "metadata", "table": "run_metadata", "rows": [[53037, "SRR9674340", "SRX6434726", "SRS5089285", "SRP214428", "PRJNA554249", "the role of SMN complex in tissue regeneration", "GSE134187", "Transcriptome Analysis", "we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants.", null, null, null, "smn1 hom 2 [miRNA seq]", "GSM3938557", null, "source name:Homozygous smn1 mutants  repeat 2|strain background:TAB 5|genotype/variation:Homozygous smn1 mutants|Stage:7 dpf|tissue:whole fish embryos", "smn1 hom 2 [miRNA seq]", "Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or \"hisat2 2.2.1.0   no softclip   no spliced alignment    rna strandness R   new summary\" miRNA abundance is measured by RSEM \"rsem calculate expression   paired end   forward prob 0.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output\" for mRNA Seq  \"rsem calculate expression   forward prob 1.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output   fragment length mean 22   fragment length sd 10   seed length 15\" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq  miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output  gene abundance", "Homozygous smn1 mutants  repeat 2", null, "Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain background:TAB 5|genotype/variation:Homozygous smn1 mutants|Stage:7 dpf|tissue:whole fish embryos", "GSM3938557", "GSM3938557: smn1 hom 2 [miRNA seq]; Danio rerio; miRNA Seq", "GSM3938557", null, "1", "Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM3938557", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP214428", null, null, "mir_Smn1_2hom.fastq.gz", "fastq", 1625802786.0, 31878486.0, "GSM3938557 r1", "0:51", "A:376836190;C:399950981;G:453572869;T:395403783;N:38963", 51, null, null, null, 376836190, 399950981, 453572869, 395403783, 38963, "SRX6434726", "SRS5089285", "SRA920248", "GEO", "Burgess, NHGRI, NIH", 1, 0.00609, null, 0.00111, null, 0.99638, null, 0.63347, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-07-12", "Larval", "Larval", "Whole Organism", "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": ["53037"], "units": {}, "query_ms": 13.074628994218074}