{"database": "metadata", "table": "run_metadata", "rows": [[75396, "SRR24497420", "SRX20282374", "SRS17609397", "SRP436940", "PRJNA971233", "MCPIP1 functions as a safeguard of early embryonic development", "GSE232220", "Transcriptome Analysis", "Expression of zc3h12a encoding Mcpip1 is tightly controlled within first cell divisions of zebrafish. Overexpression of Mcpip1 leads to the profound transcriptomic changes in the developing embryos and impairs early embryonic development of zebrafish. Overall design: RNA seq was performed to analyse transcriptome of zebrafish embryos overexpressing Mcpip1 wild type and catalytically inactive mutant.", null, "pubmed:37805647", null, "Mcpip1 DN replicate3", "GSM7321058", null, "source name:embryo 6 hpf|tissue:embryo 6 hpf|genotype:AB/TL|treatment:microinjection with mRNA encoding zebrafish Mcpip1 D112N|geo loc name:missing|collection date:missing", "Mcpip1 DN replicate3", "Signal processing and basecalling was performed with Torrent Suite version 5.14.0. Raw reads were mapped to Danio rerio Ensembl genome version GRCz11 using STAR version 2.7.10a  PMID: 23104886 and bowtie2 version 2.4.4 PMID: 22388286 for unmapped reads. Gene counts were created with htseq count PMID: 25260700  using Ensembl gene model. Differential expression was tested with DESeq2 version version 1.40.1 PMID: 2551628 Assembly: Danio rerio Ensembl genome version GRCz11 Supplementary files format and content: DESeq2 normalized count", "embryo 6 hpf", "Zebrafish eggs at 1 cell stage were microinjected with mRNA using WPI Picopump PV820 microinjector.", "Zebrafish embryos were collected in Fenozol A&A Biotechnology  Gdansk  Polska and stored at  80\u00b0C  prior to analysis. For RNA isolation  the samples were homogenized in Fenozol using a tissue homogenizer OMNI International  Kennesaw  GA  USA. The poly A mRNA fraction from total RNA was isolated with Dynabeads\u00ae mRNA DIRECT\u2122 Micro Kit Thermo. The sequencing library for each RNA sample was prepared according to the protocol provided by the manufacturer using the Ion Total RNA Seq Kit v2 Thermo. The libraries were generated from 1 15 ng of mRNA by fragmenting the mRNA with RNaseIII  purifying the fragmented RNA  and hybridizing and ligating it with Ion adaptors. Subsequently  the RNA products were reverse transcribed and amplified to double stranded cDNA  and then purified using a magnetic bead based method. The molar concentration and size of each cDNA library was determined using the DNA HS Kit on Bioanalyzer 2100 Agilent. Each library was diluted to 53 pM concentration before template preparation. Up to three barcoded libraries were mixed in equal volume and used for automatic template preparation on the Ion Chef instrument Thermo using reagents from the Ion PI Hi Q 200 Kit Thermo and Ion PI v3 Proton Chip.", "AB/TL zebrafish were maintained in a continuous recirculating closed system aquarium with a light/dark cycle of 14/10 hours at 280C. Larvae were incubated in E3 medium at 28\u00b0C according to standard protocols.", "tissue:embryo 6 hpf|genotype:AB/TL|treatment:microinjection with mRNA encoding zebrafish Mcpip1 D112N", "GSM7321058", "GSM7321058: Mcpip1 DN replicate3; Danio rerio; RNA Seq", "GSM7321058 r1", "GSM7321058", "1", "Zebrafish embryos were collected in Fenozol A&A Biotechnology  Gdansk  Polska and stored at  80\u00b0C  prior to analysis. For RNA isolation  the samples were homogenized in Fenozol using a tissue homogenizer OMNI International  Kennesaw  GA  USA. The poly A mRNA fraction from total RNA was isolated with Dynabeads\u00ae mRNA DIRECT\u2122 Micro Kit Thermo. The sequencing library for each RNA sample was prepared according to the protocol provided by the manufacturer using the Ion Total RNA Seq Kit v2 Thermo. The libraries were generated from 1 15 ng of mRNA by fragmenting the mRNA with RNaseIII  purifying the fragmented RNA  and hybridizing and ligating it with Ion adaptors. Subsequently  the RNA products were reverse transcribed and amplified to double stranded cDNA  and then purified using a magnetic bead based method. The molar concentration and size of each cDNA library was determined using the DNA HS Kit on Bioanalyzer 2100 Agilent. Each library was diluted to 53 pM concentration before template preparation. Up to three barcoded libraries were mixed in equal volume and used for automatic template preparation on the Ion Chef instrument Thermo using reagents from the Ion PI Hi Q 200 Kit Thermo and Ion PI v3 Proton Chip.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP436940", null, null, "DN_C24.fastq.gz", "fastq", 4215951250.0, 27509986.0, "GSM7321058 r1", "0:153.25", "A:1174686445;C:999279135;G:1076390086;T:965595584;N:0", 153, null, null, null, 1174686445, 999279135, 1076390086, 965595584, 0, "SRX20282374", "SRS17609397", "SRA1636184", "Genetics, Maria Sklodowska-Curie National Research Institute of Oncology", "Genetics, Maria Sk\u0142odowska-Curie National Research Institute of Oncology", 1, 0.7271, null, 0.04079, null, 0.77583, null, 0.48331, null, 128, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "Poland", "2023-05-10", "Multi-stage", "Multi-stage", "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": ["75396"], "units": {}, "query_ms": 12.379804999000044}