{"database": "metadata", "table": "run_metadata", "rows": [[25270, "SRR25744345", "SRX21467659", "SRS18702378", "SRP456724", "PRJNA1008624", "RNA seq of female gonads isolated from juvenile eif4e1b mutant and wild type zebrafish", "GSE241537", "Transcriptome Analysis", "The mRNA cap binding protein eIF4E1b is critical for female germline development in zebrafish. To study the effect of eIF4E1b loss in zebrafish  we isolated gonads with a high expression of ziwi:GFP female germline marker from wild type and eif4e1b mutant juveniles and performed RNA seq. Overall design: We performed differential expression gene analyses of wild type and eif4e1b mutant gonads n = 3 biological replicates containing 3 gonads each", null, "pubmed:38177902", null, "Gonad WT 3", "GSM7730279", null, "source name:Ovary|tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP  eif4e1b +/+|geo loc name:missing|collection date:missing", "Gonad WT 3", "RNA seq reads were trimmed using trim galore v0.5.0  and reads mapping to abundant sequences Dr mitochondrial chromosome  SILVA Dr ribosomal RNA  phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts  subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts", "Ovary", null, "RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero", null, "tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP  eif4e1b +/+", "GSM7730279", "GSM7730279: Gonad WT 3; Danio rerio; ssRNA seq", "GSM7730279 r1", "GSM7730279", "1", "RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP456724", null, "loader:fastq load.py", "Ovary_WT3_1.fastq.gz Ovary_WT3_2.fastq.gz", "fastq fastq", 3674041448.0, 18188324.0, "GSM7730279 r1", "0:101 1:101", "A:910831144;C:876967044;G:953299105;T:932928913;N:15242", 101, 101, null, null, 910831144, 876967044, 953299105, 932928913, 15242, "SRX21467659", "SRS18702378", "SRA1698764", "IMP", "IMP", 2, 0.89093, 0.89038, 0.09253, 0.09348, 0.73892, 0.73858, 0.47115, 0.47218, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "Austria", "2023-08-23", "Undetermined", "Juvenile", "Gonad", "Reproductive System"]], "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": ["25270"], "units": {}, "query_ms": 11.076265000156127}