run_metadata: 64227

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
64227	SRR14343401	SRX10697271	SRS8786685	SRP316710	PRJNA725806	foxl2l regulates female meiotic entry during juvenile gonadal development in zebrafish	GSE173480	Transcriptome Analysis	Sex determination is distinct from development of other organs for its diversity among species. In zebrafish the sex determination in juvenile stage could be hermaphroditic or gonochoristic. However the detail mechanism is still unclear. Here in this study we found that the transcription factor that belongs to forkhead box family Foxl2l is required for determination of female fate in zebrafish. Foxl2l was expressed from larva stage and became female bias in juvenile stage. The expression was restricted in pre meiotic germ cells. Disruption of Foxl2l function by CRISPR/Cas9 system resulted in all male phenotype in the mutant. Germ cells in foxl2l mutant were arrested in pre meiotic stage at 21 dpf the critical period for female meiotic entry. To further verify the downstream mechanism of Foxl2l on female sex determination wildtype or foxl2l mutant germ cells labeled by foxl2l:egfp at 21 dpf dpf and germ cells labeled by ziwi:egfp at 26 dpf were analyzed by RNA seq and single cell RNA seq respectively Overall design: Trunks of foxl2l:egfp;foxl2l / or foxl2l:egfp;foxl2l+/+ containing gonad were dissociated by 0.2% collagenase and 0.25% trypsin at 21 dpf. Around 300 EGFP+ germ cells of each genotype were sorted by fluorescence activated cell sorter. cDNA was synthesized by SMART Seq HT kit seq Takara Bio cDNA library was constructed by Nextera XT DNA Library Prep Kit Illumina Inc. and RNA sequencing was performed by Illumina NextSeq 500. Each genotype contained triple samples.				WT 1	GSM5268470		tissue:gonad\|strain:TL\|cell type:germ cell\|genotype:foxl2l:egfp;foxl2l+/+\|age:21 dpf	WT 1	Sequenced data was analyzed by NextSeq Control Software 2.2.0 The de multiplexing adaptor removal and FASTQ file transformation were performed by bcl2fastq Conversion Software 2.17 Illumina Inc. The FASTQ files were imported into CLC Genomics Workbench v.11.0.1 QIAGEN to remove low quality reads including reads with lengths less than 30 nucleotides or with Phred quality score lower than 20 The trimmed reads were mapped to zebrafish genome GRCz11 and TPM were calculated by CLC Genomics Workbench v.11.0.1 QIAGEN Genome build: GRCz11 Supplementary files format and content: txt files contain expression data for all cells	gonad		Trunks of foxl2l:egfp;foxl2l / or foxl2l:egfp;foxl2l+/+ containing gonad were dissociated by 0.2% collagenase and 0.25% trypsin at 21 dpf. Around 300 EGFP+ germ cells of each genotype were sorted by fluorescence activated cell sorter. cDNA was synthesized by SMART Seq HT kit seq Takara Bio. cDNA library was constructed by Nextera XT DNA Library Prep Kit Illumina Inc. following the manufacturer's protocols.		strain:TL\|cell type:germ cell\|genotype:foxl2l:egfp;foxl2l+/+\|age:21 dpf	GSM5268470	GSM5268470: WT 1; Danio rerio; RNA Seq	GSM5268470		1	Trunks of foxl2l:egfp;foxl2l / or foxl2l:egfp;foxl2l+/+ containing gonad were dissociated by 0.2% collagenase and 0.25% trypsin at 21 dpf. Around 300 EGFP+ germ cells of each genotype were sorted by fluorescence activated cell sorter. cDNA was synthesized by SMART Seq HT kit seq Takara Bio. cDNA library was constructed by Nextera XT DNA Library Prep Kit Illumina Inc. following the manufacturer's protocols.	GEO Accession:GSM5268470	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP316710			WT_1_run1.R2.fastq WT_1_run1.R1.fastq	fastq fastq	3768759279.0	26193297.0	GSM5268470 r1	0:71.93 1:71.95	A:1068721513;C:803440242;G:829244956;T:1066480466;N:872102	71	71			1068721513	803440242	829244956	1066480466	872102	SRX10697271	SRS8786685	SRA1224866	GEO	Institute of Molecular Biology, Academia Sinica	2	0.90907	0.91124	0.10338	0.1029	0.67054	0.67343	0.48963	0.49025	75	75	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only		Taiwan	2021-04-28	Larval	Larval	Gonad	Reproductive System