{"database": "metadata", "table": "run_metadata", "rows": [[31497, "SRR28376593", "SRX23981567", "SRS20779635", "SRP496164", "PRJNA1089179", "Super fast generation of all X sperm grass carp by female germline stem cell transplantation", "GSE261835", "Other", "Grass carp Ctenopharyngodon idellus  the world's largest aquaculture fish species  exhibits superior growth in females compared to males. However  the lengthy sexual maturation period of four to five years poses a significant obstacle to the genetic reproduction and breeding of grass carp. Consequently  classical methods such as gonadogenesis or sex reversal through steroid treatment  employed for breeding all female grass carp  demand considerable time and effort. In this study  we developed an super fast breeding strategy for generating all female grass carp in a total of half a year  using a surrogate production method. We first characterized grass carp female germline stem cells GSCs from genetic female juveniles at three mpf. The female GSCs with XX chromosomes were then transplanted into germ cell depleted zebrafish larvae at five dpf. The transplanted grass carp XX germ cells underwent rapid spermatogenesis in the zebrafish recipient. At three months post transplantation  all zebrafish recipients had developed into males capable of producing the all X sperm of the grass carp. By using these sperm to fertilize wildtype grass carp eggs  we successfully produced an all female grass carp offspring. This groundbreaking achievement highlights the potential of surrogate production in the genetic breeding of valuable fish species  and opens a new avenue for advancing genetic breeding in aquaculture. Overall design: The GSCT Germline stem cell transplantation  grass carp and zebrafish sperm were applied to RNA seq analysis to further examine the genetic consistency among them.", null, null, null, "zebrafish sperm  biological repeat 5", "GSM8152761", null, "tissue:sperm|cell type:sperm|genotype:wildtype|geo loc name:missing|collection date:missing", "zebrafish sperm  biological repeat  5", "Illumina Casava software used for basecalling. FastQC was used to check the quality of the raw sequence fastq files. High quality pruning was performed using fastp. Paired end reads were mapped to the reference genome of NCBI HZGC01 using HISAT2. And SAMtools is used to sort and index aligned BAM files. Reads were counted using the featureCounts program in the Subread. Assembly: HZGC01 Supplementary files format and content: counts", "sperm", null, "Sperm samples were collected from five zebrafish  three GSCT zebrafish and five wild type grass carps. 0.5 \u03bcL sperm from each fish was diluted into 20 \u03bcL Hank\u2019s buffer. For one sample  1\u03bcL of diluted sperm was used to extract RNA and synthetize cDNA in one reaction using the single cell full length mRNA amplification kit N712  Vazyme following manufacturer's protocols. cDNA was used to prepare DNA library for sequencing using the DNA Library Prep Kit for Illumina TD504  Vazyme following manufacturer's protocols.", null, "cell type:sperm|genotype:wildtype", "GSM8152761", "GSM8152761: zebrafish sperm  biological repeat  5; Danio rerio; RNA Seq", "GSM8152761 r1", "GSM8152761", "1", "Sperm samples were collected from five zebrafish  three GSCT zebrafish and five wild type grass carps. 0.5 \u03bcL sperm from each fish was diluted into 20 \u03bcL Hank's buffer. For one sample  1\u03bcL of diluted sperm was used to extract RNA and synthetize cDNA in one reaction using the single cell full length mRNA amplification kit N712  Vazyme following manufacturer's protocols. cDNA was used to prepare DNA library for sequencing using the DNA Library Prep Kit for Illumina TD504  Vazyme following manufacturer's protocols.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP496164", null, "loader:fastq load.py", "z_5_R2.fastq.gz z_5_R1.fastq.gz", "fastq fastq", 14998736400.0, 49995788.0, "GSM8152761 r1", "0:150 1:150", "A:4353574493;C:3164509159;G:3155567016;T:4325031916;N:53816", 150, 150, null, null, 4353574493, 3164509159, 3155567016, 4325031916, 53816, "SRX23981567", "SRS20779635", "SRA1827922", "ChenLab, Lion Rock Street 1, Huazhong agricultural university", "ChenLab, College of Life Science and Technology, Huazhong agricultural university", 2, 0.8449, 0.85198, 0.3975, 0.40011, 0.82785, 0.8243, 0.80796, 0.80275, 150, 150, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-03-18", "Zygote", "Embryo", "Oocyte", "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": ["31497"], "units": {}, "query_ms": 8.460488999844529}