{"database": "metadata", "table": "run_metadata", "rows": [[71045, "SRR21140655", "SRX17152942", "SRS14724787", "SRP393052", "PRJNA871254", "Mycn regulates intestinal development through ribosomal biogenesis in a zebrafish model of Feingold syndrome 1 RNA seq and Ribo seq", "GSE211652", "Other", "Purpose: To systematically investigate the molecular mechanisms resulting from Mycn loss of function. Methods:  Approximately 30 mycn mutant or WT zebrafish embryos at 72 hpf were harvested . Libraries were prepared using Chromium Controller and Chromium Single Cell three primeLibrary & Gel Bead Kit v3 10x Genomics  PN 1000074 according to the manufacturer's protocol for 10000 cells recovery. Results: More than 3 000 genes showed reduced tranlation efficiency in Mycn mutant. Conclusions: mTOR signaling was reduced in Mycn mutant. Overall design: wild type or mycn zebrafish embryos at 72 hpf were harvested for RNA seq and Ribo seq.", null, null, null, "Mycn mutant zebrafish embryos Ribo seq 72 hpf replicate 1", "GSM6482084", null, "source name:zebrafish cells|strain:Mycn mutant|tissue:embryonic cells|age:72 hpf", "Mycn mutant  zebrafish embryos Ribo seq 72 hpf replicate 1", "The sequencing reads were aligned to the zebrafish GRCz11 genome using STAR  and reads mapped to multiple genomic location were removed. Gene expression counts of each sample were calculated by featureCounts. Differential expression analysis was performed by limma package. Assembly: GRCz11", "zebrafish cells", "WT and Mycn mutant zebrafish embryos were collected for RNA sequencing or Ribo seq at 72 hpf", "For bulk RNA seq  RNA libraries were prepared for sequencing using standard Illumina protocols. For Ribo seq  WT and mycn mutant embryos were collected at 3 dpf  digested with cold 0.5% trypsin to a single cell suspension  and homogenized in lysis buffer for 20\u201350 times. The homogenate centrifuged at 12 000 g for 15 min at 4\u00b0C  and the supernatants were digested with RNase for 30 mins and aborted by 1M EGTA followed by layering on top of a 10%\u201350% sucrose gradient solution. Ultracentrifugation was performed at 36 000 rpm for 2 hrs hours at 4\u00b0C. post centrifugation  the fractions were collected according to the absorbance at optical density OD260 by a TRAIX detector. Then the RNA was purified and used to construct the library for sequencing.", "embryos were cultured in a Petri dish filled with 0.3X Danieau buffer", "strain:Mycn mutant|tissue:embryonic cells|age:72 hpf", "GSM6482084", "GSM6482084: Mycn mutant  zebrafish embryos Ribo seq 72 hpf replicate 1; Danio rerio; OTHER", "GSM6482084 r1", "GSM6482084", "1", "For bulk RNA seq  RNA libraries were prepared for sequencing using standard Illumina protocols. For Ribo seq  WT and mycn mutant embryos were collected at 3 dpf  digested with cold 0.5% trypsin to a single cell suspension  and homogenized in lysis buffer for 20\u201350 times. The homogenate centrifuged at 12 000 g for 15 min at 4\u00b0C  and the supernatants were digested with RNase for 30 mins and aborted by 1M EGTA followed by layering on top of a 10%\u201350% sucrose gradient solution. Ultracentrifugation was performed at 36 000 rpm for 2 hrs hours at 4\u00b0C. post centrifugation  the fractions were collected according to the absorbance at optical density OD260 by a TRAIX detector. Then the RNA was purified and used to construct the library for sequencing.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP393052", null, null, "mut1-riboseq_1.clean.fq.gz mut1-riboseq_2.clean.fq.gz", "fastq fastq", 491622744.0, 8480542.0, "GSM6482084 r1", "0:28.97 1:29.01", "A:119352696;C:126567605;G:126525090;T:119169287;N:8066", 28, 29, null, null, 119352696, 126567605, 126525090, 119169287, 8066, "SRX17152942", "SRS14724787", "SRA1479247", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", 2, 0.43508, 0.4326, 0.15983, 0.15894, 0.7388, 0.73939, 0.55997, 0.56089, 30, 30, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "other", "unknown", "sc", "bulk", "bulk", null, "China", "2022-08-19", "Larval", "Larval", "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": ["71045"], "units": {}, "query_ms": 6.854364997707307}