{"database": "metadata", "table": "run_metadata", "rows": [[41861, "SRR6384888", "SRX3478478", "SRS2764467", "SRP100425", "PRJNA376117", "Transcriptome Analysis of Zfpm1 Function in Early Zebrafish Embryogenesis and Postembryonic Heart Development", "GSE95118", "Transcriptome Analysis", "Through analyzing RNA seq datasets in zfpm1 mutant embryo 36hpf and maturing heart 21 dpf  we characterized the effects of loss of zfpm1 on the transcriptomic landscape. Overall design: Using RNA seq to identify the downstream genes of zfpm1 on embryogenesis and cardiac chamber maturation.", null, "pubmed:30611731", null, "Zfpm1 21dpf heart rep1", "GSM2892213", null, "source name:heart|strain:TU|tissue:heart|developmental stage:21dpf|genotype:zfpm1 mutant", "Zfpm1 21dpf heart rep1", "Illumina bcl2fastq2 v 2.16.0.10 software was used for base calling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.5. High quality reads were alligned to GRCz10 whole genome using tophat V2.2.1 and bowtie2 v2.2.3 with parameters  q  p 8   no novel juncs  G  o. Raw counts of sequencing reads were generated by using HTSeq v 0.6.1p1. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample", "heart", null, "36hpf zebrafish embryos and 21dpf heart were collected respectively  flash frozen on dry ice  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. Magnetic beads with oligodT were used to enrich the mRNAs  and then Frag/Prime Buffer was added to fragment the mRNAs. The short mRNA fragments were used as templates and random hexamers were used to synthesize first strand cDNA. Then double stranded cDNA was synthesized by adding buffer solution  dNTPs and DNA polymerase\u0399. The double stranded cDNAs were purified by DNA clean beads according to the manufacturer\u2019s instructions  then repaired at the tail ends  polyA added and enriched by PCR amplification. Finally  we tested the inserts sizes in the cDNA libraries on an Agilent 2100 Bioanalyzer.", null, "strain:TU|tissue:heart|developmental stage:21dpf|genotype:zfpm1 mutant", "GSM2892213", "GSM2892213: Zfpm1 21dpf heart rep1; Danio rerio; RNA Seq", "GSM2892213", null, "1", "36hpf zebrafish embryos and 21dpf heart were collected respectively  flash frozen on dry ice  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. Magnetic beads with oligodT were used to enrich the mRNAs  and then Frag/Prime Buffer was added to fragment the mRNAs. The short mRNA fragments were used as templates and random hexamers were used to synthesize first strand cDNA. Then double stranded cDNA was synthesized by adding buffer solution  dNTPs and DNA polymerase\u0399. The double stranded cDNAs were purified by DNA clean beads according to the manufacturer's instructions  then repaired at the tail ends  polyA added and enriched by PCR amplification. Finally  we tested the inserts sizes in the cDNA libraries on an Agilent 2100 Bioanalyzer.", "GEO Accession:GSM2892213", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP100425", null, null, "Zfpm1_heart_RNAseq_rep1_1.fq.gz Zfpm1_heart_RNAseq_rep1_2.fq.gz", "fastq fastq", 5936614800.0, 19788716.0, "GSM2892213 r1", "0:150 1:150", "A:1616123286;C:1354032331;G:1348383945;T:1617882201;N:193037", 150, 150, null, null, 1616123286, 1354032331, 1348383945, 1617882201, 193037, "SRX3478478", "SRS2764467", "SRA539171", "GEO", "Xin Lou Lab, Medical School, Nanjing University", 2, 0.93121, 0.93134, 0.08641, 0.08612, 0.69501, 0.69751, 0.51182, 0.50932, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "China", "2017-12-18", "Larval", "Larval", "Heart", "Cardiovascular 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": ["41861"], "units": {}, "query_ms": 11.951084999964223}