{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation = \"Segmentation\" and experiment.library_strategy = \"RIP-Seq\"", "rows": [[70712, "SRR20077343", "SRX16115141", "SRS13777745", "SRP385866", "PRJNA857663", "RIP seq for Cpeb1b in zebrafish embryos", "GSE207904", "Transcriptome Analysis", "Cpeb1b mediated cytoplasmic polyadenylation modulates hematopoietic stem and progenitor cell development via translational control Overall design: RIP seq of 2 samples from Flag cpeb1b mRNA injected zebrafish embryos at xxx hpf including two biological replicates", "parent bioproject:PRJNA857656", null, null, "Flag Cpeb1b replicate 2", "GSM6322839", null, "source name:Flag Cpeb1b replicate 2|tissue:zebrafish embryos|genotype:wild type|age:16 hpf", "Flag Cpeb1b replicate 2", "The quality of raw sequencing reads was processed using FastQC and low quality bases were trimmed and filtered by cutadapt V 1.13 11 and Trimmomatic V 0.36 12. Processed reads were mapped to the zebrafish genome Zv9 using TopHat v2.1.1 18 with \u2018\u2018\u2013bowtie1\u2019\u2019. The target binding regions of Cpeb1b were identified using MACS2 software version 2.0.10. The target genes were annotated based on Ensembl release 79 gene annotation information by applying BEDTools\u2019 intersectBed version 2.16.2. Assembly: Zv9 Supplementary files format and content: rpkm for samples", "Flag Cpeb1b replicate 2", null, "Flag cpeb1b mRNA injected embryos were collected at xxx hpf and lysed in NETN lysis buffer 150 mM NaCl  0.5% NP 40  50 mM Tris HCl  pH 7.4  RNase inhibitor  Roche cocktail protease inhibitor. The lysate was incubated with anti FLAG M2 Magnetic Beads Merck for 4 h at 4 \u00b0C. Then  the beads were washed five times with the lysis buffer and five times with TBS buffer. For RIP seq assay  the bead bound RNA was extracted and then fragmented by RNA Fragmentation Reagent Ambion. 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Imprecise", "All anatomical structures"]], "truncated": false, "filtered_table_rows_count": 2, "expanded_columns": [], "expandable_columns": [], "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", 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