{"database": "metadata", "table": "run_metadata", "rows": [[62961, "SRR13520380", "SRX9931398", "SRS8106883", "SRP303129", "PRJNA694577", "Next Generation Sequencing Facilitates Quantitative Analysis of different developmental stage pEGFP N1 injected zebrafish embryos and untreated group transcriptomes", "GSE165422", "Transcriptome Analysis", "Purpose: Next generation sequencing NGS has revolutionized systems based analysis of cellular pathways. The goals of this study are to compare the early stage of pEGFP N1 injected zebrafish embros transcriptome profiling RNA seq to microarray and quantitative reverse transcription polymerase chain reaction qRT\u2013PCR methods and to evaluate protocols for optimal high throughput data analysis Methods: we injected the plasmid pEGFP N1 into zebrafish zygotes by microinjection  and then when the embryos to develop ttwo xxx hpf  6 hpf and 12 hpf  these groups was collected respectively by deep sequencing  in triplicate  using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows\u2013Wheeler Aligner BWA followed by ANOVA ANOVA and TopHat followed by Cufflinks. qRT\u2013PCR validation was performed using TaqMan and SYBR Green assays Results: Bioinformatics analysis of the transcriptome sequencing found that the expression levels of genes related to the apoptosis process Fig.1A  endogenous immune response and tumor necrosis factor mediated signaling pathways were abnormal up regulation  mainly including isg15  foxo3b  phlda3  cdkn1a  zgc:136826  and si:dkey 204l11.1  compared with the non injected group at xxxhpf. These genes are found in somatic cells to deal with foreign plasmids invasion. Overall design: Zebrafish embryos in 1hpf  6hpf and 12hpf mRNA profiles of pEGFP N1 injected and untreated group", null, "pubmed:35690839", null, "G8 1: pEGFP N1 injected at 1hpf", "GSM5033115", null, "source name:zebrafish embryos|strain:TU|developmental stage:1hpf|tissue:embryo", "G8 1: pEGFP N1 injected at 1hpf", "Reads filtering under criteria removing reads with 20% of the base quality lower than 13 Clean Reads mapped to GRCz10  genome using Mapsplice v2.1.8 with  parameters  s 22  p 15   ins 6   del 6   non canonical   bam  o count counting Genome build: GRCz10 Supplementary files format and content: TXT file contain counts for each sample", "zebrafish embryos", "In the 1 cell stage of zebrafish embryos  8ng/\u03bcL pEGFP N1 was injected  and the embryos of the injected group and the non injected group were collected when the embryos developed ttwo xxxhpf  6hpf and 12hpf. Add 1mL TRIzol Invitrogen  USA  store at  80\u2103", "RNA was harvested using Trizol reagent Invitrogen. RNA library using standard Ion proton RNA Seq Kit v2.0 protocol", null, "strain:TU|developmental stage:1hpf|tissue:embryo", "GSM5033115", "GSM5033115: G8 1: pEGFP N1 injected at 1hpf; Danio rerio; RNA Seq", "GSM5033115", null, "1", "RNA was harvested using Trizol reagent Invitrogen. RNA library using standard Ion proton RNA Seq Kit v2.0 protocol", "GEO Accession:GSM5033115", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP303129", null, null, "G8-1.fastq.gz", "fastq", 2029634086.0, 12394054.0, "GSM5033115 r1", "0:163.76", "A:548662597;C:501840467;G:525047427;T:454083595;N:0", 163, null, null, null, 548662597, 501840467, 525047427, 454083595, 0, "SRX9931398", "SRS8106883", "SRA1187495", "GEO", "Qingshun Zhao", 1, 0.81344, null, 0.01015, null, 0.78058, null, 0.48067, null, 90, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2021-01-25", "Cleavage", "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": ["62961"], "units": {}, "query_ms": 9.977244000765495}