{"database": "metadata", "table": "run_metadata", "rows": [[71312, "SRR21487520", "SRX17491012", "SRS15043328", "SRP396256", "PRJNA878480", "Effect of nuclear pore complex NPC blockage by WGA treatment on zygotic genome activation ZGA during zebrafish early development", "GSE212929", "Transcriptome Analysis", "To investigate the function of nuclear pore complex NPC in the regulation of zygotic genome activation ZGA  we microinjected medium dosage of WGA in zebrafish embryos at xxx cell stage to block NPC function.  We then performed gene expression profiling analysis using data obtained from RNA seq of control or WGA treated embryo at comparable developmental time point 4.3 hpf  or develomental stage dome. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish control embryo at 4.3 hpf of dome stage and WGA treated embryos at 4.3 hpf developmental time matched or 5 hpf dome like stage.", null, "pubmed:36493774", null, "zebrafish early embryos  WGA treated  5 hpf  dome like stage", "GSM6562796", null, "source name:whole mount embryo|tissue:whole mount embryo|cell line:early embryo|cell type:embryonic cell|genotype:wildtype|treatment:0.65 ng WGA injected at 1 cell stage", "zebrafish early embryos  WGA treated  5 hpf  dome like stage", "BGISEQ 500 platform was used for base calling Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence on trimmomatic software v0.36 with paramwters ILLUMINACLIP:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50  then mapped to GRCz11 whole genome using Bowtie2 v2.2.5 with parameters  q   phred64   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 Fragments Per Kilobase of exon per Megabase of library size FPKM were calculated using software RSEM v1.2.8 from Langmead  B. et al.  Nat. Methods  2012  and Li  B. & Dewey  C. N.  BMC Bioinformatics  2011. Assembly: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample", "whole mount embryo", "1 nl WGA of 0.65 ng/nl dissolved in nuclease free water was microinjected into yolk of embryos at xxx cell stage.", "total RNAs were extracted from dechorionated whole embryos with RNeasy Mini Kit Qiagen RNA libraries were prepared for sequencing using standard protocols", null, "tissue:whole mount embryo|cell line:early embryo|cell type:embryonic cell|genotype:wildtype|treatment:0.65 ng WGA injected at 1 cell stage", "GSM6562796", "GSM6562796: zebrafish early embryos  WGA treated  5 hpf  dome like stage; Danio rerio; RNA Seq", "GSM6562796 r1", "GSM6562796", "1", "total RNAs were extracted from dechorionated whole embryos with RNeasy Mini Kit Qiagen RNA libraries were prepared for sequencing using standard protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP396256", null, null, "WGA_5h.fq.gz", "fastq", 1059386400.0, 21187728.0, "GSM6562796 r1", "0:50 1:0", "A:277040646;C:250203561;G:245816009;T:285209577;N:1116607", 50, 0, null, null, 277040646, 250203561, 245816009, 285209577, 1116607, "SRX17491012", "SRS15043328", "SRA1496611", "School of life science, Tsinghua University", "School of life science, Tsinghua University", 1, 0.94419, null, 0.03669, null, 0.74919, null, 0.48293, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-09-08", "Blastula", "Embryo", "Embryo Imprecise", "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": ["71312"], "units": {}, "query_ms": 8.184020000044256}