run_metadata: 31498

This data as json

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
31498	SRR28376594	SRX23981566	SRS20779633	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.				zebrafish sperm biological repeat 4	GSM8152760		tissue:sperm\|cell type:sperm\|genotype:wildtype\|geo loc name:missing\|collection date:missing	zebrafish sperm biological repeat 4	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		Sperm samples were collected from five zebrafish three GSCT zebrafish and five wild type grass carps. 0.5 μL sperm from each fish was diluted into 20 μL Hank’s buffer. For one sample 1μL 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.		cell type:sperm\|genotype:wildtype	GSM8152760	GSM8152760: zebrafish sperm biological repeat 4; Danio rerio; RNA Seq	GSM8152760 r1	GSM8152760	1	Sperm samples were collected from five zebrafish three GSCT zebrafish and five wild type grass carps. 0.5 μL sperm from each fish was diluted into 20 μL Hank's buffer. For one sample 1μL 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.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP496164		loader:fastq load.py	z_4_R2.fastq.gz z_4_R1.fastq.gz	fastq fastq	6599629800.0	21998766.0	GSM8152760 r1	0:150 1:150	A:1931341078;C:1360012552;G:1372884703;T:1935376140;N:15327	150	150			1931341078	1360012552	1372884703	1935376140	15327	SRX23981566	SRS20779633	SRA1827922	ChenLab, Lion Rock Street 1, Huazhong agricultural university	ChenLab, College of Life Science and Technology, Huazhong agricultural university	2	0.83841	0.85766	0.42253	0.44132	0.83025	0.81274	0.75221	0.7614	150	150	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	unknown	bulk	unknown	unknown		China	2024-03-18	Zygote	Embryo	Oocyte	Reproductive System