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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
64472 SRR14710792 SRX11048791 SRS9116826 SRP322308 PRJNA734487 polyA+ RNA seq of zebrafish gonad at 25 dpf and 30dpf GSE175979 Transcriptome Analysis In this study we explored the biological process of zebrafish gonad differentiation through PolyA enriched RNA sequencing and found that the differences in the gonads differentiating towards testis or ovary were represented through types and expression levels of different genes. Using the GO enrichment classification it is found that in the differentiating ovary the differentially expressed genes are enriched in processes of material synthesis and metabolic pathway indicating that oocyte requires the accumulation of maternal RNA protein sugar lipids vitamins and other substances which is consistent with its basic function of providing primary materials for early development of fertilized embryo. In addition during ovarian differentiation the biological processes associated with the nucleus mitochondria and cytoplasmic particles are more active and the genes associated with sperm egg recognition are also expressed during this period. Unlike the differentiating ovary when the gonad differentiates into testis the differentially expressed genes are more enriched in biological regulation and development processes including morphogenesis cell proliferation etc.The cytometers adapted to these biological processes are associated with cell membrane such as membrane receptors extra cellular regions extra cellular matrix and cell connections and also associated with nuclear chromatin. In addition we enriched 14 signaling pathways involved in testis differentiation and showed the expression heat map of every differentially expressed gene of each pathway. Overall the study reveals the different biological processes existing in the differentiation of the zebrafish gonads into ovary or testis helping us to get a comprehensive understanding of the basis on biological events and molecules during this process. Overall design: Zebrafish larvae were anesthetized in 0.2 mg/mL MS 222 and disected to isolate gonads. Each gonad is placed under a microscope to identify either the testis or the ovary. Six 25 dpf and six 30 dpf undamaged gonads with sound integrity were choosen for PolyA+ RNA sequencing.   pubmed:36257818   30dpf testis rep2 GSM5352295   source name:Gonad|strain:AB|tissue:testis|age:post fertilization day 30|genotype:Tgpiwil1 egfp nos3UTRihb327Tg 30dpf testis rep2 High throughput sequencing raw image data files were converted to reads using fqtools plus analysis and using FastqC v0.11.8 and sequencing report tool of MultiQC v0.9to evaluate the raw read quality statistics. Reads were mapped to the corresponding reference genome Ensembl v96 with the parameters " dta x rna strandness RF" and " known spliceset infile" using Hisat2 v2.0.5 and gene annotation was performed in GTF format Ensembl 96. Hisat2 converts the data into BAM format sorted by Samtools v1.5 and removed duplicates using the Picard MarkDuplicates v2.18.15 tool. HTSeq v0.9.1 was used to read and count the parameter " t exon i gene id r pos s reverse". Genome build: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample Gonad   Gonads were removed and RNA was extracted using RNAprep pure Micro Kit TIANGEN. For each sample 5ul of RNA was used for synthesis and amplification of cDNA Discover sc WTA Kit N711 Vazyme and 5ng of amplified cDNA was used for construction of sequencing library using TruePrep DNA Library Prep Kit V2 for Illumina® Vazyme TD501/TD502. The zebrafish were maintained  raised  and staged according to zebrafish book. The rearing density is 50 larvae/L for age from 5 dpf to 15 dpf  20 fish/L for age 15 dpf to 1 mpf. strain:AB|tissue:testis|age:post fertilization day 30|genotype:Tgpiwil1 egfp nos3UTRihb327Tg GSM5352295 GSM5352295: 30dpf testis rep2; Danio rerio; RNA Seq GSM5352295   1 Gonads were removed and RNA was extracted using RNAprep pure Micro Kit TIANGEN. For each sample 5ul of RNA was used for synthesis and amplification of cDNA Discover sc WTA Kit N711 Vazyme and 5ng of amplified cDNA was used for construction of sequencing library using TruePrep DNA Library Prep Kit V2 for Illumina® Vazyme TD501/TD502. GEO Accession:GSM5352295 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP322308     30d_small_2_r1.fastq.gz 30d_small_2_r2.fastq.gz fastq fastq 6853411125.0 23219079.0 GSM5352295 r1 0:148.28 1:146.88 A:1858128706;C:1569075657;G:1580228791;T:1845965296;N:12675 148 146     1858128706 1569075657 1580228791 1845965296 12675 SRX11048791 SRS9116826 SRA1239593 GEO College of Life Science and Technology, Huazhong Agricultural University 2 0.93587 0.93627 0.05854 0.05886 0.68081 0.68337 0.49214 0.49713 150 149 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2021-06-02 Juvenile Juvenile Gonad Reproductive System