{"database": "metadata", "table": "run_metadata", "rows": [[42469, "SRR5605444", "SRX2858032", "SRS2228756", "SRP108050", "PRJNA388086", "Transcriptomic Analysis for Differentially Expressed Genes in Ovarian Follicle Activation and Puberty Onset in the Zebrafish", "GSE99308", "Transcriptome Analysis", "Puberty is a special transition period in sexual maturation  and it has been extensively studied in vertebrates in the past decades. In mammals  the initiation of puberty involves activation of numerous genes; however  there have been few comprehensive reports in small model teleosts such as the zebrafish. In the zebrafish  the onset of puberty in females is marked by the appearance of the first wave of pre vitellogenic PV follicles in the ovary during sexual maturation.  Using transcriptomics and real time qPCR  this study was undertaken to investigate temporal gene expression differences between the primary growth PG follicles and pre vitellogenic PV follicles  with particular emphasis on oocyte and follicular cell specific genes as well as several closely associated signaling pathways. Our results showed that totally 1082 genes were significantly upregulated and 530 evidently downregulated during the PG PV transition  and among them were some well recognized biomarkers such as cyp19a1a  fshr  inha and inhbaa and some novel genes like notch3  amh  gadd45ga and lpl.  Further gene ontology analysis showed that egg coat formation and steroid hormone mediated signaling pathway might be critical for follicle activation from PG to PV stage. In addition  KEGG identified several signaling pathways that might play pivotal roles in early folliculogenesis  including phosphatidylinositol signaling system  glycolsaminoglycan biosynthesis  RNA transport  and p53 signaling pathways. Overall  this study reported a comprehensive analysis for biomarker genes and potential pathways involved in PG PV transition or follicle activation  which also marks female puberty onset in the zebrafish when occurring for the first time in sexual maturation. Overall design: Examination of gene expression patterns in 2 different stage follicles PG and PV follicles", null, "pubmed:30364302", null, "PG WT2", "GSM2640956", null, "source name:PG WT2|strain:AB|tissue:follicle|developmental stage:primary growth|genotype:WT", "PG WT2", "Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Danio rerio genome version GRCz10 from Ensembl using Tophat2. Parameters:  p 6 StringTie and prepDE.py Python script provided with StringTie tool was used to assemble the alignments into transcripts and extract the raw read counts for reference genomic features respectively. The read count matrix was processed by DeSeq2 package for differential gene expression analysis. Genome build: GRCz10 Ensembl build 84 Supplementary files format and content: PG vs PV rawCounts.csv: Raw read counts for each sample. Supplementary files format and content: PG vs PV normCounts.tab: Normalized read counts for each sample.", "PG WT2", null, "Both PG and PV follicles were isolated and  followed by RNA extraction using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain:AB|tissue:follicle|developmental stage:primary growth|genotype:WT", "GSM2640956", "GSM2640956: PG WT2; Danio rerio; RNA Seq", "GSM2640956", null, "1", "Both PG and PV follicles were isolated and  followed by RNA extraction using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM2640956", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP108050", null, null, "PG_WT2_R1.fastq.gz PG_WT2_R2.fastq.gz", "fastq fastq", 3961495355.0, 20078542.0, "GSM2640956 r1", "0:98.66 1:98.64", "A:1001026721;C:972147725;G:960699221;T:1026249480;N:1372208", 98, 98, null, null, 1001026721, 972147725, 960699221, 1026249480, 1372208, "SRX2858032", "SRS2228756", "SRA566530", "GEO", "Genomics and Bioinformatics Core, Faculty of Health Sciences, University of Macau", 2, 0.93922, 0.94298, 0.01416, 0.01405, 0.77029, 0.77106, 0.46461, 0.46358, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "China", "2017-05-25", "Undetermined", "Undetermined", "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": ["42469"], "units": {}, "query_ms": 12.580753000293043}