{"database": "metadata", "table": "run_metadata", "rows": [[64985, "SRR14867731", "SRX11185279", "SRS9242606", "SRP324746", "PRJNA739457", "Investigation of mettl4 mediated alterative splicing variation", "GSE178511", "Other", "We compare mettl4 KO and WT samples from different species to understand how mettl4 affects the alterative splicing Overall design: mRNA profiles of mettl4 KO and WT", null, null, null, "ZEBARFISH WT AB9  Sample 23", "GSM5393117", null, "tissue:ZEBARFISH|genotype:WT|cell line:AB9", "ZEBARFISH WT AB9\u00a0 Sample 23", "Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to mm8 whole genome using bowtie v0.12.2 with parameters  q  p 4  e 100  y  a  m 10   best   strata Reads Per Kilobase of exon per Megabase of library size RPKM were calculated. In short  exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: hg19 mm10  dm6  sacCer1  GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample", "ZEBARFISH", null, "RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "genotype:WT|cell line:AB9", "GSM5393117", "GSM5393117: ZEBARFISH WT AB9  Sample 23; Danio rerio; RNA Seq", "GSM5393117", null, "1", "RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5393117", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP324746", null, null, "ZEBRAFISH-WT-1_R1_001.fastq.gz ZEBRAFISH-WT-1_R2_001.fastq.gz", "fastq fastq", 8653301400.0, 28844338.0, "GSM5393117 r1", "0:150 1:150", "A:2002938965;C:2340373383;G:2308705634;T:2000755068;N:528350", 150, 150, null, null, 2002938965, 2340373383, 2308705634, 2000755068, 528350, "SRX11185279", "SRS9242606", "SRA1248203", "GEO", "Max Planck Institute for heart and lung research", 2, 0.03799, 0.045, 0.00894, 0.00762, 0.99744, 0.99754, 0.58095, 0.65007, 150, 150, "T", "T", "mates < 9% mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2021-06-20", "Undetermined", "Undetermined", "Cell Line", "Cell Line"]], "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": ["64985"], "units": {}, "query_ms": 11.184162000063225}