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
64217,SRR14343411,SRX10697276,SRS8786690,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.,,,,HO 3,GSM5268475,,tissue:gonad|strain:TL|cell type:germ cell|genotype:foxl2l:egfp;foxl2l / |age:21 dpf,HO 3,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,GSM5268475,GSM5268475: HO 3; Danio rerio; RNA Seq,GSM5268475,,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:GSM5268475,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP316710,,,HO_3_run1.R1.fastq HO_3_run1.R2.fastq,fastq fastq,3534673132.0,24300429.0,GSM5268475 r1,0:72.72 1:72.74,A:983413722;C:772614472;G:797390978;T:980739251;N:514709,72,72,,,983413722,772614472,797390978,980739251,514709,SRX10697276,SRS8786690,SRA1224866,GEO,"Institute of Molecular Biology, Academia Sinica",2,0.92009,0.92081,0.07189,0.07113,0.66176,0.66502,0.48304,0.4818,76,76,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
64218,SRR14343412,SRX10697276,SRS8786690,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.,,,,HO 3,GSM5268475,,tissue:gonad|strain:TL|cell type:germ cell|genotype:foxl2l:egfp;foxl2l / |age:21 dpf,HO 3,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,GSM5268475,GSM5268475: HO 3; Danio rerio; RNA Seq,GSM5268475,,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:GSM5268475,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP316710,,,HO_3_run2.R1.fastq HO_3_run2.R2.fastq,fastq fastq,3789665865.0,25970236.0,GSM5268475 r2,0:72.95 1:72.97,A:1055034390;C:825452326;G:851854221;T:1054834294;N:2490634,72,72,,,1055034390,825452326,851854221,1054834294,2490634,SRX10697276,SRS8786690,SRA1224866,GEO,"Institute of Molecular Biology, Academia Sinica",2,0.92122,0.92134,0.07291,0.07232,0.66346,0.66649,0.48355,0.48092,74,74,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
64219,SRR14343409,SRX10697275,SRS8786689,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.,,,,HO 2,GSM5268474,,tissue:gonad|strain:TL|cell type:germ cell|genotype:foxl2l:egfp;foxl2l / |age:21 dpf,HO 2,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,GSM5268474,GSM5268474: HO 2; Danio rerio; RNA Seq,GSM5268474,,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:GSM5268474,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP316710,,,HO_2_run1.R1.fastq HO_2_run1.R2.fastq,fastq fastq,3972958992.0,27776809.0,GSM5268474 r1,0:71.50 1:71.53,A:1124808892;C:846395118;G:875350364;T:1125141364;N:1263254,71,71,,,1124808892,846395118,875350364,1125141364,1263254,SRX10697275,SRS8786689,SRA1224866,GEO,"Institute of Molecular Biology, Academia Sinica",2,0.89819,0.89964,0.11368,0.11314,0.65052,0.65387,0.49509,0.49244,76,76,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
64220,SRR14343410,SRX10697275,SRS8786689,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.,,,,HO 2,GSM5268474,,tissue:gonad|strain:TL|cell type:germ cell|genotype:foxl2l:egfp;foxl2l / |age:21 dpf,HO 2,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,GSM5268474,GSM5268474: HO 2; Danio rerio; RNA Seq,GSM5268474,,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:GSM5268474,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP316710,,,HO_2_run2.R2.fastq HO_2_run2.R1.fastq,fastq fastq,4396792493.0,30653836.0,GSM5268474 r2,0:71.70 1:71.73,A:1244672283;C:933954952;G:965736051;T:1248628688;N:3800519,71,71,,,1244672283,933954952,965736051,1248628688,3800519,SRX10697275,SRS8786689,SRA1224866,GEO,"Institute of Molecular Biology, Academia Sinica",2,0.89957,0.90042,0.11576,0.11485,0.64985,0.65348,0.48847,0.48933,76,76,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
64221,SRR14343407,SRX10697274,SRS8786688,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.,,,,HO 1,GSM5268473,,tissue:gonad|strain:TL|cell type:germ cell|genotype:foxl2l:egfp;foxl2l / |age:21 dpf,HO 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,GSM5268473,GSM5268473: HO 1; Danio rerio; RNA Seq,GSM5268473,,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:GSM5268473,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP316710,,,HO_1_run1.R1.fastq HO_1_run1.R2.fastq,fastq fastq,3833739891.0,26806927.0,GSM5268473 r1,0:71.49 1:71.52,A:1084861861;C:818381943;G:845191898;T:1084121864;N:1182325,71,71,,,1084861861,818381943,845191898,1084121864,1182325,SRX10697274,SRS8786688,SRA1224866,GEO,"Institute of Molecular Biology, Academia Sinica",2,0.90273,0.90247,0.09672,0.09556,0.6565,0.65932,0.48356,0.49197,74,75,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
64222,SRR14343408,SRX10697274,SRS8786688,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.,,,,HO 1,GSM5268473,,tissue:gonad|strain:TL|cell type:germ cell|genotype:foxl2l:egfp;foxl2l / |age:21 dpf,HO 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,GSM5268473,GSM5268473: HO 1; Danio rerio; RNA Seq,GSM5268473,,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:GSM5268473,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP316710,,,HO_1_run2.R2.fastq HO_1_run2.R1.fastq,fastq fastq,4251914417.0,29647144.0,GSM5268473 r2,0:71.69 1:71.72,A:1202985882;C:905068322;G:934722262;T:1205490290;N:3647661,71,71,,,1202985882,905068322,934722262,1205490290,3647661,SRX10697274,SRS8786688,SRA1224866,GEO,"Institute of Molecular Biology, Academia Sinica",2,0.90347,0.9046,0.09694,0.09634,0.65662,0.66131,0.49104,0.48825,76,76,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
64223,SRR14343405,SRX10697273,SRS8786687,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 3,GSM5268472,,tissue:gonad|strain:TL|cell type:germ cell|genotype:foxl2l:egfp;foxl2l+/+|age:21 dpf,WT 3,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,GSM5268472,GSM5268472: WT 3; Danio rerio; RNA Seq,GSM5268472,,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:GSM5268472,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP316710,,,WT_3_run1.R1.fastq WT_3_run1.R2.fastq,fastq fastq,3615402373.0,25312788.0,GSM5268472 r1,0:71.39 1:71.44,A:1078168256;C:699509937;G:739078497;T:1097303558;N:1342125,71,71,,,1078168256,699509937,739078497,1097303558,1342125,SRX10697273,SRS8786687,SRA1224866,GEO,"Institute of Molecular Biology, Academia Sinica",2,0.7144,0.71612,0.09852,0.09708,0.70027,0.70331,0.49157,0.49119,75,76,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
64224,SRR14343406,SRX10697273,SRS8786687,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 3,GSM5268472,,tissue:gonad|strain:TL|cell type:germ cell|genotype:foxl2l:egfp;foxl2l+/+|age:21 dpf,WT 3,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,GSM5268472,GSM5268472: WT 3; Danio rerio; RNA Seq,GSM5268472,,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:GSM5268472,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP316710,,,WT_3_run2.R1.fastq WT_3_run2.R2.fastq,fastq fastq,4010245556.0,27994253.0,GSM5268472 r2,0:71.60 1:71.65,A:1193569082;C:773024546;G:816013849;T:1223955095;N:3682984,71,71,,,1193569082,773024546,816013849,1223955095,3682984,SRX10697273,SRS8786687,SRA1224866,GEO,"Institute of Molecular Biology, Academia Sinica",2,0.71057,0.71162,0.09984,0.09845,0.70102,0.70435,0.4941,0.48909,74,75,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
64225,SRR14343403,SRX10697272,SRS8786686,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 2,GSM5268471,,tissue:gonad|strain:TL|cell type:germ cell|genotype:foxl2l:egfp;foxl2l+/+|age:21 dpf,WT 2,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,GSM5268471,GSM5268471: WT 2; Danio rerio; RNA Seq,GSM5268471,,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:GSM5268471,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP316710,,,WT_2_run1.R1.fastq WT_2_run1.R2.fastq,fastq fastq,4242860973.0,29911182.0,GSM5268471 r1,0:70.91 1:70.94,A:1225861906;C:877846427;G:910477747;T:1227170958;N:1503935,70,70,,,1225861906,877846427,910477747,1227170958,1503935,SRX10697272,SRS8786686,SRA1224866,GEO,"Institute of Molecular Biology, Academia Sinica",2,0.88249,0.8846,0.12426,0.12254,0.67568,0.67777,0.49104,0.49087,76,76,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
64226,SRR14343404,SRX10697272,SRS8786686,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 2,GSM5268471,,tissue:gonad|strain:TL|cell type:germ cell|genotype:foxl2l:egfp;foxl2l+/+|age:21 dpf,WT 2,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,GSM5268471,GSM5268471: WT 2; Danio rerio; RNA Seq,GSM5268471,,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:GSM5268471,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP316710,,,WT_2_run2.R2.fastq WT_2_run2.R1.fastq,fastq fastq,4702850600.0,33040042.0,GSM5268471 r2,0:71.15 1:71.19,A:1357977487;C:969603630;G:1005776160;T:1365277602;N:4215721,71,71,,,1357977487,969603630,1005776160,1365277602,4215721,SRX10697272,SRS8786686,SRA1224866,GEO,"Institute of Molecular Biology, Academia Sinica",2,0.88141,0.88412,0.12385,0.12227,0.67805,0.68156,0.48576,0.49354,76,76,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
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
64228,SRR14343402,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_run2.R2.fastq WT_1_run2.R1.fastq,fastq fastq,4100200544.0,28410131.0,GSM5268470 r2,0:72.15 1:72.17,A:1163123243;C:871020431;G:898995203;T:1163892058;N:3169609,72,72,,,1163123243,871020431,898995203,1163892058,3169609,SRX10697271,SRS8786685,SRA1224866,GEO,"Institute of Molecular Biology, Academia Sinica",2,0.90943,0.91044,0.10346,0.103,0.66914,0.67004,0.48705,0.49202,76,76,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
64467,SRR14703424,SRX11041446,SRS9110374,SRP322195,PRJNA734348,Methylome inheritance and enhancer dememorization construct an epigenetic gate safeguarding embryonic programs,GSE175951,Other,Unlike that of mammals  the total DNA methylome of many cold blooded vertebrates is globally inherited from gametes to early embryos. In zebrafish  this is however accompanied by sweeping “dememorization” of enhancers prior to fertilization for sperm and just post fertilization for oocyte  as they undergo full methylation and are not demethylated again until phylotypic stage. The significance of both global methylome inheritance and enhancer dememorization in early embryos remains largely unknown. Adding to the puzzles  the zygotic mutant zebrafish of dnmt1  the major DNA methylation maintenance methyltransferase  surprisingly can develop to term. To solve the role of DNA methylation in early development  we generated zebrafish embryos derived from dnmt1 knocking down oocytes using a recently developed method OMIS microinjection in situ  which successfully eliminated DNA methylation before zygotic genome activation. dnmt1 deficient embryos failed to initiate epiboly and died around gastrulation. This is in part caused by activation of immune response and p53 regulated apoptosis  likely triggered by the derepression of transposable elements. Single cell RNA seq further revealed defective differentiation in these mutants. DNA methylation is also required for the establishment of repressive histone marks H3K27me3 and H2AK119ub. Strikingly  the loss of DNA methylation leads to extensive derepression of somatic genes and enhancers  which acquire ectopic H3K27ac  accessible chromatin  and H3K4me3. These somatic enhancers are preferentially CG rich and are bound by CG containing TFs. By contrast  embryonic enhancers are generally CG poor  methylation insensitive  and are bound by CG less TFs. Hence  the global DNA methylome inheritance is essential for vertebrate early development  and enhancer dememorization resets an epigenetic gate that separates embryonic and somatic programs. Overall design: By employing MethylC seq  total RNA seq  scRNA seq  CUT&RUN  ChIP seq  and ATAC seq in control and dnmt1 mKD embryos at oocyte  256 cell  dome and shield stages in zebrafish  we interrogated the function of DNA methylome and its inheritance in early zebrafish development.,,pubmed:34936444,,Oocyte dnmt1 mKD total RNA seq rep2,GSM5351801,,source name:oocyte|strain:AB|genotype:WT|developmental stage:Oocyte|tissue:oocyte|treatment:microinjection with Rhodamine B and dnmt1 MO at oogenesis III stage GV,Oocyte dnmt1 mKD total RNA seq rep2,All STEM seq datasets were mapped to the danRer7 reference genome by Bismark Krueger and Andrews  2011. Reads were trimmed with cutadaptor Martin  2011 using parameters:   minimum length 20   pair filter=any. Alignments were performed with the following parameters:  N 1  X 600   score min L 0  0.6. Multi mapped reads and PCR duplicates were removed. bismark methylation extractor was used to calculate the DNA methylation level. Total RNA seq data were firstly processed using Trim Galore! with default parameters to trim the adapter containing and low quality reads. The filtered data were then mapped to the zebrafish reference genome danRer7 by STAR version: STAR 2.5.3a modified Dobin et al.  2013 with the following parameters:   outSAMstrandField intronMotif   outSAMattributes All   outSAMunmapped Within   outSAMattrIHstart 0   outWigStrand Stranded   outFilterMultimapNmax 20   twopassMode Basic. The gene expression level was normalized to fragments per kilobase of transcript per million mapped FPKM values using Cufflinks version 2.2.1 Trapnell et al.  2012. The scRNA seq data were processed with Cell Ranger 3.1 for genome alignment danRer10  transcript counting  and gene cell barcode matrix generation. Before the downstream analysis  cells with unique detected genes lower than <2 000 and higher than 6 000 genes were discarded  and cells with high percentage of mitochondrial genes >5% were removed too. Subtypes of cells were identified with Seurat 3.0 through the integrating of control and mKD embryos at dome and shield stages with setting control embryos as reference. To make the data comparable samples  we performed SCTransform normalization separately for each dataset. To further reduce the bais caused by sequencing depth of scRNA seq and percentage of mitochondrial genes  UMI variance and percent.mt were regressed out from SCTransform normalized data matrix by linear model with negative binomial distribution. All ChIP seq reads were aligned to the zebrafish reference genome danRer7 using Bowtie2 version 2.2.2 Langmead and Salzberg  2012 with the parameters –t –q –N 1 –L 25. All unmapped reads  non uniquely mapped reads and PCR duplicates were removed. For downstream analysis  the read counts were normalized by computing the numbers of reads per kilobase of bin per million of reads sequenced RPKM. To visualize the STAR ChIP seq signal in the UCSC genome browser  each read was extended by 250 bp and the coverage for each base was counted. Replicates of STAR ChIP seq were pooled for the downstream analysis. The ATAC seq data were mapped to the zebrafish reference genome danRer7 using Bowtie2 version 2.2.2 Langmead and Salzberg  2012 with the parameters –t –q –N 1 –L 25. All unmapped reads  non uniquely mapped reads and PCR duplicates were removed. For downstream analysis  the read counts were normalized by computing the numbers of reads per kilobase of bin per million of reads sequenced RPKM. To minimize the batch and cell type variation  RPKM values across whole genome were further Z score normalized. To visualize the CUT&RUN signals in the UCSC genome browser  each read was extended by 250 bp and the coverage for each base was counted. Genome build: danRer7 Supplementary files format and content: Matrix for scRNA seq data  gene expression table for total RNA seq data  Bigwig and narrowPeak for ChIP seq and ATAC seq data,oocyte,Briefly  on the first day of OMIS Wu et al.  2018b  adult females at 5 mpf 12 mpf were anesthetized in 550 µg/ml tricaine Sigma  Cat A5040 in a petri dish. Then the fish was placed on a damp sponge with specific buffer 5.4 mM KCl  136.8 mM NaCl  4.2 mM NaHCO3  0.44 mM KH2PO4  0.25 mM Na2HPO4  and 0.5% wt/vol BSA. A cut was made on one side of belly to expose the ovary. The diluted MOs were microinjected into each oocyte. Rhodamine B Sigma  Cat R8881 was co injected with MOs as a dye. post injection  the wound on the belly was sewed with a surgical sewing needle carefully and quickly. Once the operation was done  the female was transferred into fish water supplemented with 32 µg/ml tricaine  10 unit/ml penicillin and 10 µg/ml streptomycin HyClone  Cat SV30010. Then the fish was transferred to fish water containing gradually reduced concentrations of tricaine. In the evening of the second day  the female was paired with a wild type male. In the morning of the third day  the pair started to chase and lay fertilized eggs naturally. The injected oocyte derived embryos were identified by co injected dye rhodamine B at very early developmental stages. The injection doses of dnmt1 MO were 5 ng per oocyte in the same assay. MOs were dissolved in RNase free water  and heated to 65°C for 11 min before microinjection.,The oocytes were dechorionated manually by tweezers and transferred into 750 µl Trizol Invitrogen  Cat 15596018. About 10 fresh embryos were transferred into Trizol and vortexed until no visible particles. 150 µl chloroform Amresco  Cat 0757 was added and mixed thoroughly. The mixture was then transferred into phasemaker tube Invitrogen  Cat A33248 and spun at 14 000 rpm for 15 min. Next  the top phase was taken out from the tube  added 1 µl LPA Sigma  Cat 56575 and mixed well using pipettes. Then  RNA was precipitated by adding 750 µl isopropanol Sigma  Cat 59304 at  20℃ overnight. At next day  the tube was spun at 14 000 rpm for 30 min and supernatant was removed. The pellet was washed with freshly 70% ethanol  re suspend in 20 µl RNase free water and stored at  80℃ for later usage. NEBNext rRNA Depletion Kit NEB  Cat E6310S was used to deplete ribosomal RNA according to the manufacture’s instruction. Briefly  rRNA were hybridized with probes and digested with RNase H  then excess probes were digested with DNase I. post that  NEBNext RNA sample purification beads were used to purify rRNA depleted RNA. Purified RNA was fragmented before cDNA synthesis at 95℃ for 8 min. Double stranded cDNA was synthesized with NEB Next first strand NEB  Cat E7771S and second strand synthesis modules NEB  Cat E7550S  then purified with Ampure XP beads Beckman  Cat A63882. Synthesized cDNA was subjected to library preparation with NEBNext Ultr II DNA Library Prep Kit NEB  Cat E7645S. DNA was end repaired  adenylated  and ligated to TruSeq sequencing adaptors. DNA were amplified using KAPA HF HotStart ReadyMix KAPABiosystem  Cat RR2602. The amplified DNA was size selected using Ampure XP beads for 200 500 bp DNA fragments. All libraries were sequenced by Illumina Hi Seq 1500 or 2500 or XTen platform according to manufacturer’s instruction.,The wild type AB strain was used in the experiments. The females post OMIS were fed with live adult brine shrimp thrice a day. All embryos were raised in Holtfreter’s solution at 28.5C and staged as described previously Kimmel et al.  1995.,strain:AB|genotype:WT|developmental stage:Oocyte|tissue:oocyte|treatment:microinjection with Rhodamine B and dnmt1 MO at oogenesis III stage GV,GSM5351801,GSM5351801: Oocyte dnmt1 mKD total RNA seq rep2; Danio rerio; RNA Seq,GSM5351801,,1,The oocytes were dechorionated manually by tweezers and transferred into 750 µl Trizol Invitrogen  Cat 15596018. About 10 fresh embryos were transferred into Trizol and vortexed until no visible particles. 150 µl chloroform Amresco  Cat 0757 was added and mixed thoroughly. The mixture was then transferred into phasemaker tube Invitrogen  Cat A33248 and spun at 14 000 rpm for 15 min. Next  the top phase was taken out from the tube  added 1 µl LPA Sigma  Cat 56575 and mixed well using pipettes. Then  RNA was precipitated by adding 750 µl isopropanol Sigma  Cat 59304 at  20℃ overnight. At next day  the tube was spun at 14 000 rpm for 30 min and supernatant was removed. The pellet was washed with freshly 70% ethanol  re suspend in 20 µl RNase free water and stored at  80℃ for later usage. NEBNext rRNA Depletion Kit NEB  Cat E6310S was used to deplete ribosomal RNA according to the manufacture's instruction. Briefly  rRNA were hybridized with probes and digested with RNase H  then excess probes were digested with DNase I. post that  NEBNext RNA sample purification beads were used to purify rRNA depleted RNA. Purified RNA was fragmented before cDNA synthesis at 95℃ for 8 min. Double stranded cDNA was synthesized with NEB Next first strand NEB  Cat E7771S and second strand synthesis modules NEB  Cat E7550S  then purified with Ampure XP beads Beckman  Cat A63882. Synthesized cDNA was subjected to library preparation with NEBNext Ultr II DNA Library Prep Kit NEB  Cat E7645S. DNA was end repaired  adenylated  and ligated to TruSeq sequencing adaptors. DNA were amplified using KAPA HF HotStart ReadyMix KAPABiosystem  Cat RR2602. The amplified DNA was size selected using Ampure XP beads for 200 500 bp DNA fragments. All libraries were sequenced by Illumina Hi Seq 1500 or 2500 or XTen platform according to manufacturer's instruction.,GEO Accession:GSM5351801,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,,SRP322195,,loader:fastq load.py,Oocyte_dnmt1_mKD_total_RNA_seq_rep2_r1.fq.gz Oocyte_dnmt1_mKD_total_RNA_seq_rep2_r2.fq.gz,fastq fastq,16439504400.0,54798348.0,GSM5351801 r1,0:150 1:150,A:3396011593;C:4802098205;G:4970368429;T:3267104077;N:3922096,150,150,,,3396011593,4802098205,4970368429,3267104077,3922096,SRX11041446,SRS9110374,SRA1239365,GEO,"THU-PKU Center for Life Sciences, Tsinghua University",2,0.88579,0.90816,0.11025,0.11298,0.80095,0.80501,0.71771,0.73597,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,rrna_depletion,nebnext,sc_generic,single_cell_generic,generic-scrnaseq-only,,China,2021-06-01,Zygote,Embryo,Oocyte,Reproductive System
64468,SRR14703423,SRX11041445,SRS9110373,SRP322195,PRJNA734348,Methylome inheritance and enhancer dememorization construct an epigenetic gate safeguarding embryonic programs,GSE175951,Other,Unlike that of mammals  the total DNA methylome of many cold blooded vertebrates is globally inherited from gametes to early embryos. In zebrafish  this is however accompanied by sweeping “dememorization” of enhancers prior to fertilization for sperm and just post fertilization for oocyte  as they undergo full methylation and are not demethylated again until phylotypic stage. The significance of both global methylome inheritance and enhancer dememorization in early embryos remains largely unknown. Adding to the puzzles  the zygotic mutant zebrafish of dnmt1  the major DNA methylation maintenance methyltransferase  surprisingly can develop to term. To solve the role of DNA methylation in early development  we generated zebrafish embryos derived from dnmt1 knocking down oocytes using a recently developed method OMIS microinjection in situ  which successfully eliminated DNA methylation before zygotic genome activation. dnmt1 deficient embryos failed to initiate epiboly and died around gastrulation. This is in part caused by activation of immune response and p53 regulated apoptosis  likely triggered by the derepression of transposable elements. Single cell RNA seq further revealed defective differentiation in these mutants. DNA methylation is also required for the establishment of repressive histone marks H3K27me3 and H2AK119ub. Strikingly  the loss of DNA methylation leads to extensive derepression of somatic genes and enhancers  which acquire ectopic H3K27ac  accessible chromatin  and H3K4me3. These somatic enhancers are preferentially CG rich and are bound by CG containing TFs. By contrast  embryonic enhancers are generally CG poor  methylation insensitive  and are bound by CG less TFs. Hence  the global DNA methylome inheritance is essential for vertebrate early development  and enhancer dememorization resets an epigenetic gate that separates embryonic and somatic programs. Overall design: By employing MethylC seq  total RNA seq  scRNA seq  CUT&RUN  ChIP seq  and ATAC seq in control and dnmt1 mKD embryos at oocyte  256 cell  dome and shield stages in zebrafish  we interrogated the function of DNA methylome and its inheritance in early zebrafish development.,,pubmed:34936444,,Oocyte dnmt1 mKD total RNA seq rep1,GSM5351800,,source name:oocyte|strain:AB|genotype:WT|developmental stage:Oocyte|tissue:oocyte|treatment:microinjection with Rhodamine B and dnmt1 MO at oogenesis III stage GV,Oocyte dnmt1 mKD total RNA seq rep1,All STEM seq datasets were mapped to the danRer7 reference genome by Bismark Krueger and Andrews  2011. Reads were trimmed with cutadaptor Martin  2011 using parameters:   minimum length 20   pair filter=any. Alignments were performed with the following parameters:  N 1  X 600   score min L 0  0.6. Multi mapped reads and PCR duplicates were removed. bismark methylation extractor was used to calculate the DNA methylation level. Total RNA seq data were firstly processed using Trim Galore! with default parameters to trim the adapter containing and low quality reads. The filtered data were then mapped to the zebrafish reference genome danRer7 by STAR version: STAR 2.5.3a modified Dobin et al.  2013 with the following parameters:   outSAMstrandField intronMotif   outSAMattributes All   outSAMunmapped Within   outSAMattrIHstart 0   outWigStrand Stranded   outFilterMultimapNmax 20   twopassMode Basic. The gene expression level was normalized to fragments per kilobase of transcript per million mapped FPKM values using Cufflinks version 2.2.1 Trapnell et al.  2012. The scRNA seq data were processed with Cell Ranger 3.1 for genome alignment danRer10  transcript counting  and gene cell barcode matrix generation. Before the downstream analysis  cells with unique detected genes lower than <2 000 and higher than 6 000 genes were discarded  and cells with high percentage of mitochondrial genes >5% were removed too. Subtypes of cells were identified with Seurat 3.0 through the integrating of control and mKD embryos at dome and shield stages with setting control embryos as reference. To make the data comparable samples  we performed SCTransform normalization separately for each dataset. To further reduce the bais caused by sequencing depth of scRNA seq and percentage of mitochondrial genes  UMI variance and percent.mt were regressed out from SCTransform normalized data matrix by linear model with negative binomial distribution. All ChIP seq reads were aligned to the zebrafish reference genome danRer7 using Bowtie2 version 2.2.2 Langmead and Salzberg  2012 with the parameters –t –q –N 1 –L 25. All unmapped reads  non uniquely mapped reads and PCR duplicates were removed. For downstream analysis  the read counts were normalized by computing the numbers of reads per kilobase of bin per million of reads sequenced RPKM. To visualize the STAR ChIP seq signal in the UCSC genome browser  each read was extended by 250 bp and the coverage for each base was counted. Replicates of STAR ChIP seq were pooled for the downstream analysis. The ATAC seq data were mapped to the zebrafish reference genome danRer7 using Bowtie2 version 2.2.2 Langmead and Salzberg  2012 with the parameters –t –q –N 1 –L 25. All unmapped reads  non uniquely mapped reads and PCR duplicates were removed. For downstream analysis  the read counts were normalized by computing the numbers of reads per kilobase of bin per million of reads sequenced RPKM. To minimize the batch and cell type variation  RPKM values across whole genome were further Z score normalized. To visualize the CUT&RUN signals in the UCSC genome browser  each read was extended by 250 bp and the coverage for each base was counted. Genome build: danRer7 Supplementary files format and content: Matrix for scRNA seq data  gene expression table for total RNA seq data  Bigwig and narrowPeak for ChIP seq and ATAC seq data,oocyte,Briefly  on the first day of OMIS Wu et al.  2018b  adult females at 5 mpf 12 mpf were anesthetized in 550 µg/ml tricaine Sigma  Cat A5040 in a petri dish. Then the fish was placed on a damp sponge with specific buffer 5.4 mM KCl  136.8 mM NaCl  4.2 mM NaHCO3  0.44 mM KH2PO4  0.25 mM Na2HPO4  and 0.5% wt/vol BSA. A cut was made on one side of belly to expose the ovary. The diluted MOs were microinjected into each oocyte. Rhodamine B Sigma  Cat R8881 was co injected with MOs as a dye. post injection  the wound on the belly was sewed with a surgical sewing needle carefully and quickly. Once the operation was done  the female was transferred into fish water supplemented with 32 µg/ml tricaine  10 unit/ml penicillin and 10 µg/ml streptomycin HyClone  Cat SV30010. Then the fish was transferred to fish water containing gradually reduced concentrations of tricaine. In the evening of the second day  the female was paired with a wild type male. In the morning of the third day  the pair started to chase and lay fertilized eggs naturally. The injected oocyte derived embryos were identified by co injected dye rhodamine B at very early developmental stages. The injection doses of dnmt1 MO were 5 ng per oocyte in the same assay. MOs were dissolved in RNase free water  and heated to 65°C for 11 min before microinjection.,The oocytes were dechorionated manually by tweezers and transferred into 750 µl Trizol Invitrogen  Cat 15596018. About 10 fresh embryos were transferred into Trizol and vortexed until no visible particles. 150 µl chloroform Amresco  Cat 0757 was added and mixed thoroughly. The mixture was then transferred into phasemaker tube Invitrogen  Cat A33248 and spun at 14 000 rpm for 15 min. Next  the top phase was taken out from the tube  added 1 µl LPA Sigma  Cat 56575 and mixed well using pipettes. Then  RNA was precipitated by adding 750 µl isopropanol Sigma  Cat 59304 at  20℃ overnight. At next day  the tube was spun at 14 000 rpm for 30 min and supernatant was removed. The pellet was washed with freshly 70% ethanol  re suspend in 20 µl RNase free water and stored at  80℃ for later usage. NEBNext rRNA Depletion Kit NEB  Cat E6310S was used to deplete ribosomal RNA according to the manufacture’s instruction. Briefly  rRNA were hybridized with probes and digested with RNase H  then excess probes were digested with DNase I. post that  NEBNext RNA sample purification beads were used to purify rRNA depleted RNA. Purified RNA was fragmented before cDNA synthesis at 95℃ for 8 min. Double stranded cDNA was synthesized with NEB Next first strand NEB  Cat E7771S and second strand synthesis modules NEB  Cat E7550S  then purified with Ampure XP beads Beckman  Cat A63882. Synthesized cDNA was subjected to library preparation with NEBNext Ultr II DNA Library Prep Kit NEB  Cat E7645S. DNA was end repaired  adenylated  and ligated to TruSeq sequencing adaptors. DNA were amplified using KAPA HF HotStart ReadyMix KAPABiosystem  Cat RR2602. The amplified DNA was size selected using Ampure XP beads for 200 500 bp DNA fragments. All libraries were sequenced by Illumina Hi Seq 1500 or 2500 or XTen platform according to manufacturer’s instruction.,The wild type AB strain was used in the experiments. The females post OMIS were fed with live adult brine shrimp thrice a day. All embryos were raised in Holtfreter’s solution at 28.5C and staged as described previously Kimmel et al.  1995.,strain:AB|genotype:WT|developmental stage:Oocyte|tissue:oocyte|treatment:microinjection with Rhodamine B and dnmt1 MO at oogenesis III stage GV,GSM5351800,GSM5351800: Oocyte dnmt1 mKD total RNA seq rep1; Danio rerio; RNA Seq,GSM5351800,,1,The oocytes were dechorionated manually by tweezers and transferred into 750 µl Trizol Invitrogen  Cat 15596018. About 10 fresh embryos were transferred into Trizol and vortexed until no visible particles. 150 µl chloroform Amresco  Cat 0757 was added and mixed thoroughly. The mixture was then transferred into phasemaker tube Invitrogen  Cat A33248 and spun at 14 000 rpm for 15 min. Next  the top phase was taken out from the tube  added 1 µl LPA Sigma  Cat 56575 and mixed well using pipettes. Then  RNA was precipitated by adding 750 µl isopropanol Sigma  Cat 59304 at  20℃ overnight. At next day  the tube was spun at 14 000 rpm for 30 min and supernatant was removed. The pellet was washed with freshly 70% ethanol  re suspend in 20 µl RNase free water and stored at  80℃ for later usage. NEBNext rRNA Depletion Kit NEB  Cat E6310S was used to deplete ribosomal RNA according to the manufacture's instruction. Briefly  rRNA were hybridized with probes and digested with RNase H  then excess probes were digested with DNase I. post that  NEBNext RNA sample purification beads were used to purify rRNA depleted RNA. Purified RNA was fragmented before cDNA synthesis at 95℃ for 8 min. Double stranded cDNA was synthesized with NEB Next first strand NEB  Cat E7771S and second strand synthesis modules NEB  Cat E7550S  then purified with Ampure XP beads Beckman  Cat A63882. Synthesized cDNA was subjected to library preparation with NEBNext Ultr II DNA Library Prep Kit NEB  Cat E7645S. DNA was end repaired  adenylated  and ligated to TruSeq sequencing adaptors. DNA were amplified using KAPA HF HotStart ReadyMix KAPABiosystem  Cat RR2602. The amplified DNA was size selected using Ampure XP beads for 200 500 bp DNA fragments. All libraries were sequenced by Illumina Hi Seq 1500 or 2500 or XTen platform according to manufacturer's instruction.,GEO Accession:GSM5351800,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,,SRP322195,,loader:fastq load.py,Oocyte_dnmt1_mKD_total_RNA_seq_rep1_r1.fq.gz Oocyte_dnmt1_mKD_total_RNA_seq_rep1_r2.fq.gz,fastq fastq,14688433500.0,48961445.0,GSM5351800 r1,0:150 1:150,A:2682067386;C:4656142899;G:4847089762;T:2502503972;N:629481,150,150,,,2682067386,4656142899,4847089762,2502503972,629481,SRX11041445,SRS9110373,SRA1239365,GEO,"THU-PKU Center for Life Sciences, Tsinghua University",2,0.96866,0.97013,0.06205,0.06149,0.81138,0.81475,0.85317,0.85364,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,rrna_depletion,nebnext,sc_generic,single_cell_generic,generic-scrnaseq-only,,China,2021-06-01,Zygote,Embryo,Oocyte,Reproductive System
64469,SRR14703422,SRX11041444,SRS9110371,SRP322195,PRJNA734348,Methylome inheritance and enhancer dememorization construct an epigenetic gate safeguarding embryonic programs,GSE175951,Other,Unlike that of mammals  the total DNA methylome of many cold blooded vertebrates is globally inherited from gametes to early embryos. In zebrafish  this is however accompanied by sweeping “dememorization” of enhancers prior to fertilization for sperm and just post fertilization for oocyte  as they undergo full methylation and are not demethylated again until phylotypic stage. The significance of both global methylome inheritance and enhancer dememorization in early embryos remains largely unknown. Adding to the puzzles  the zygotic mutant zebrafish of dnmt1  the major DNA methylation maintenance methyltransferase  surprisingly can develop to term. To solve the role of DNA methylation in early development  we generated zebrafish embryos derived from dnmt1 knocking down oocytes using a recently developed method OMIS microinjection in situ  which successfully eliminated DNA methylation before zygotic genome activation. dnmt1 deficient embryos failed to initiate epiboly and died around gastrulation. This is in part caused by activation of immune response and p53 regulated apoptosis  likely triggered by the derepression of transposable elements. Single cell RNA seq further revealed defective differentiation in these mutants. DNA methylation is also required for the establishment of repressive histone marks H3K27me3 and H2AK119ub. Strikingly  the loss of DNA methylation leads to extensive derepression of somatic genes and enhancers  which acquire ectopic H3K27ac  accessible chromatin  and H3K4me3. These somatic enhancers are preferentially CG rich and are bound by CG containing TFs. By contrast  embryonic enhancers are generally CG poor  methylation insensitive  and are bound by CG less TFs. Hence  the global DNA methylome inheritance is essential for vertebrate early development  and enhancer dememorization resets an epigenetic gate that separates embryonic and somatic programs. Overall design: By employing MethylC seq  total RNA seq  scRNA seq  CUT&RUN  ChIP seq  and ATAC seq in control and dnmt1 mKD embryos at oocyte  256 cell  dome and shield stages in zebrafish  we interrogated the function of DNA methylome and its inheritance in early zebrafish development.,,pubmed:34936444,,Oocyte ctrl total RNA seq rep2,GSM5351799,,source name:oocyte|strain:AB|genotype:WT|developmental stage:Oocyte|tissue:oocyte|treatment:microinjection with Rhodamine B and control MO at oogenesis III stage GV,Oocyte ctrl total RNA seq rep2,All STEM seq datasets were mapped to the danRer7 reference genome by Bismark Krueger and Andrews  2011. Reads were trimmed with cutadaptor Martin  2011 using parameters:   minimum length 20   pair filter=any. Alignments were performed with the following parameters:  N 1  X 600   score min L 0  0.6. Multi mapped reads and PCR duplicates were removed. bismark methylation extractor was used to calculate the DNA methylation level. Total RNA seq data were firstly processed using Trim Galore! with default parameters to trim the adapter containing and low quality reads. The filtered data were then mapped to the zebrafish reference genome danRer7 by STAR version: STAR 2.5.3a modified Dobin et al.  2013 with the following parameters:   outSAMstrandField intronMotif   outSAMattributes All   outSAMunmapped Within   outSAMattrIHstart 0   outWigStrand Stranded   outFilterMultimapNmax 20   twopassMode Basic. The gene expression level was normalized to fragments per kilobase of transcript per million mapped FPKM values using Cufflinks version 2.2.1 Trapnell et al.  2012. The scRNA seq data were processed with Cell Ranger 3.1 for genome alignment danRer10  transcript counting  and gene cell barcode matrix generation. Before the downstream analysis  cells with unique detected genes lower than <2 000 and higher than 6 000 genes were discarded  and cells with high percentage of mitochondrial genes >5% were removed too. Subtypes of cells were identified with Seurat 3.0 through the integrating of control and mKD embryos at dome and shield stages with setting control embryos as reference. To make the data comparable samples  we performed SCTransform normalization separately for each dataset. To further reduce the bais caused by sequencing depth of scRNA seq and percentage of mitochondrial genes  UMI variance and percent.mt were regressed out from SCTransform normalized data matrix by linear model with negative binomial distribution. All ChIP seq reads were aligned to the zebrafish reference genome danRer7 using Bowtie2 version 2.2.2 Langmead and Salzberg  2012 with the parameters –t –q –N 1 –L 25. All unmapped reads  non uniquely mapped reads and PCR duplicates were removed. For downstream analysis  the read counts were normalized by computing the numbers of reads per kilobase of bin per million of reads sequenced RPKM. To visualize the STAR ChIP seq signal in the UCSC genome browser  each read was extended by 250 bp and the coverage for each base was counted. Replicates of STAR ChIP seq were pooled for the downstream analysis. The ATAC seq data were mapped to the zebrafish reference genome danRer7 using Bowtie2 version 2.2.2 Langmead and Salzberg  2012 with the parameters –t –q –N 1 –L 25. All unmapped reads  non uniquely mapped reads and PCR duplicates were removed. For downstream analysis  the read counts were normalized by computing the numbers of reads per kilobase of bin per million of reads sequenced RPKM. To minimize the batch and cell type variation  RPKM values across whole genome were further Z score normalized. To visualize the CUT&RUN signals in the UCSC genome browser  each read was extended by 250 bp and the coverage for each base was counted. Genome build: danRer7 Supplementary files format and content: Matrix for scRNA seq data  gene expression table for total RNA seq data  Bigwig and narrowPeak for ChIP seq and ATAC seq data,oocyte,Briefly  on the first day of OMIS Wu et al.  2018b  adult females at 5 mpf 12 mpf were anesthetized in 550 µg/ml tricaine Sigma  Cat A5040 in a petri dish. Then the fish was placed on a damp sponge with specific buffer 5.4 mM KCl  136.8 mM NaCl  4.2 mM NaHCO3  0.44 mM KH2PO4  0.25 mM Na2HPO4  and 0.5% wt/vol BSA. A cut was made on one side of belly to expose the ovary. The diluted MOs were microinjected into each oocyte. Rhodamine B Sigma  Cat R8881 was co injected with MOs as a dye. post injection  the wound on the belly was sewed with a surgical sewing needle carefully and quickly. Once the operation was done  the female was transferred into fish water supplemented with 32 µg/ml tricaine  10 unit/ml penicillin and 10 µg/ml streptomycin HyClone  Cat SV30010. Then the fish was transferred to fish water containing gradually reduced concentrations of tricaine. In the evening of the second day  the female was paired with a wild type male. In the morning of the third day  the pair started to chase and lay fertilized eggs naturally. The injected oocyte derived embryos were identified by co injected dye rhodamine B at very early developmental stages. The injection doses of standard control MO cMO were 5 ng per oocyte in the same assay. MOs were dissolved in RNase free water  and heated to 65°C for 10 min before microinjection.,The oocytes were dechorionated manually by tweezers and transferred into 750 µl Trizol Invitrogen  Cat 15596018. About 10 fresh embryos were transferred into Trizol and vortexed until no visible particles. 150 µl chloroform Amresco  Cat 0757 was added and mixed thoroughly. The mixture was then transferred into phasemaker tube Invitrogen  Cat A33248 and spun at 14 000 rpm for 15 min. Next  the top phase was taken out from the tube  added 1 µl LPA Sigma  Cat 56575 and mixed well using pipettes. Then  RNA was precipitated by adding 750 µl isopropanol Sigma  Cat 59304 at  20℃ overnight. At next day  the tube was spun at 14 000 rpm for 30 min and supernatant was removed. The pellet was washed with freshly 70% ethanol  re suspend in 20 µl RNase free water and stored at  80℃ for later usage. NEBNext rRNA Depletion Kit NEB  Cat E6310S was used to deplete ribosomal RNA according to the manufacture’s instruction. Briefly  rRNA were hybridized with probes and digested with RNase H  then excess probes were digested with DNase I. post that  NEBNext RNA sample purification beads were used to purify rRNA depleted RNA. Purified RNA was fragmented before cDNA synthesis at 95℃ for 8 min. Double stranded cDNA was synthesized with NEB Next first strand NEB  Cat E7771S and second strand synthesis modules NEB  Cat E7550S  then purified with Ampure XP beads Beckman  Cat A63882. Synthesized cDNA was subjected to library preparation with NEBNext Ultr II DNA Library Prep Kit NEB  Cat E7645S. DNA was end repaired  adenylated  and ligated to TruSeq sequencing adaptors. DNA were amplified using KAPA HF HotStart ReadyMix KAPABiosystem  Cat RR2602. The amplified DNA was size selected using Ampure XP beads for 200 500 bp DNA fragments. All libraries were sequenced by Illumina Hi Seq 1500 or 2500 or XTen platform according to manufacturer’s instruction.,The wild type AB strain was used in the experiments. The females post OMIS were fed with live adult brine shrimp thrice a day. All embryos were raised in Holtfreter’s solution at 28.5C and staged as described previously Kimmel et al.  1995.,strain:AB|genotype:WT|developmental stage:Oocyte|tissue:oocyte|treatment:microinjection with Rhodamine B and control MO at oogenesis III stage GV,GSM5351799,GSM5351799: Oocyte ctrl total RNA seq rep2; Danio rerio; RNA Seq,GSM5351799,,1,The oocytes were dechorionated manually by tweezers and transferred into 750 µl Trizol Invitrogen  Cat 15596018. About 10 fresh embryos were transferred into Trizol and vortexed until no visible particles. 150 µl chloroform Amresco  Cat 0757 was added and mixed thoroughly. The mixture was then transferred into phasemaker tube Invitrogen  Cat A33248 and spun at 14 000 rpm for 15 min. Next  the top phase was taken out from the tube  added 1 µl LPA Sigma  Cat 56575 and mixed well using pipettes. Then  RNA was precipitated by adding 750 µl isopropanol Sigma  Cat 59304 at  20℃ overnight. At next day  the tube was spun at 14 000 rpm for 30 min and supernatant was removed. The pellet was washed with freshly 70% ethanol  re suspend in 20 µl RNase free water and stored at  80℃ for later usage. NEBNext rRNA Depletion Kit NEB  Cat E6310S was used to deplete ribosomal RNA according to the manufacture's instruction. Briefly  rRNA were hybridized with probes and digested with RNase H  then excess probes were digested with DNase I. post that  NEBNext RNA sample purification beads were used to purify rRNA depleted RNA. Purified RNA was fragmented before cDNA synthesis at 95℃ for 8 min. Double stranded cDNA was synthesized with NEB Next first strand NEB  Cat E7771S and second strand synthesis modules NEB  Cat E7550S  then purified with Ampure XP beads Beckman  Cat A63882. Synthesized cDNA was subjected to library preparation with NEBNext Ultr II DNA Library Prep Kit NEB  Cat E7645S. DNA was end repaired  adenylated  and ligated to TruSeq sequencing adaptors. DNA were amplified using KAPA HF HotStart ReadyMix KAPABiosystem  Cat RR2602. The amplified DNA was size selected using Ampure XP beads for 200 500 bp DNA fragments. All libraries were sequenced by Illumina Hi Seq 1500 or 2500 or XTen platform according to manufacturer's instruction.,GEO Accession:GSM5351799,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,,SRP322195,,loader:fastq load.py,Oocyte_ctrl_total_RNA_seq_rep2_r1.fq.gz Oocyte_ctrl_total_RNA_seq_rep2_r2.fq.gz,fastq fastq,8180427000.0,27268090.0,GSM5351799 r1,0:150 1:150,A:1694775525;C:2388512701;G:2446021403;T:1649171179;N:1946192,150,150,,,1694775525,2388512701,2446021403,1649171179,1946192,SRX11041444,SRS9110371,SRA1239365,GEO,"THU-PKU Center for Life Sciences, Tsinghua University",2,0.95217,0.95176,0.08629,0.08619,0.79387,0.79778,0.76806,0.80396,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,rrna_depletion,nebnext,sc_generic,single_cell_generic,generic-scrnaseq-only,,China,2021-06-01,Zygote,Embryo,Oocyte,Reproductive System
64470,SRR14703421,SRX11041443,SRS9110372,SRP322195,PRJNA734348,Methylome inheritance and enhancer dememorization construct an epigenetic gate safeguarding embryonic programs,GSE175951,Other,Unlike that of mammals  the total DNA methylome of many cold blooded vertebrates is globally inherited from gametes to early embryos. In zebrafish  this is however accompanied by sweeping “dememorization” of enhancers prior to fertilization for sperm and just post fertilization for oocyte  as they undergo full methylation and are not demethylated again until phylotypic stage. The significance of both global methylome inheritance and enhancer dememorization in early embryos remains largely unknown. Adding to the puzzles  the zygotic mutant zebrafish of dnmt1  the major DNA methylation maintenance methyltransferase  surprisingly can develop to term. To solve the role of DNA methylation in early development  we generated zebrafish embryos derived from dnmt1 knocking down oocytes using a recently developed method OMIS microinjection in situ  which successfully eliminated DNA methylation before zygotic genome activation. dnmt1 deficient embryos failed to initiate epiboly and died around gastrulation. This is in part caused by activation of immune response and p53 regulated apoptosis  likely triggered by the derepression of transposable elements. Single cell RNA seq further revealed defective differentiation in these mutants. DNA methylation is also required for the establishment of repressive histone marks H3K27me3 and H2AK119ub. Strikingly  the loss of DNA methylation leads to extensive derepression of somatic genes and enhancers  which acquire ectopic H3K27ac  accessible chromatin  and H3K4me3. These somatic enhancers are preferentially CG rich and are bound by CG containing TFs. By contrast  embryonic enhancers are generally CG poor  methylation insensitive  and are bound by CG less TFs. Hence  the global DNA methylome inheritance is essential for vertebrate early development  and enhancer dememorization resets an epigenetic gate that separates embryonic and somatic programs. Overall design: By employing MethylC seq  total RNA seq  scRNA seq  CUT&RUN  ChIP seq  and ATAC seq in control and dnmt1 mKD embryos at oocyte  256 cell  dome and shield stages in zebrafish  we interrogated the function of DNA methylome and its inheritance in early zebrafish development.,,pubmed:34936444,,Oocyte ctrl total RNA seq rep1,GSM5351798,,source name:oocyte|strain:AB|genotype:WT|developmental stage:Oocyte|tissue:oocyte|treatment:microinjection with Rhodamine B and control MO at oogenesis III stage GV,Oocyte ctrl total RNA seq rep1,All STEM seq datasets were mapped to the danRer7 reference genome by Bismark Krueger and Andrews  2011. Reads were trimmed with cutadaptor Martin  2011 using parameters:   minimum length 20   pair filter=any. Alignments were performed with the following parameters:  N 1  X 600   score min L 0  0.6. Multi mapped reads and PCR duplicates were removed. bismark methylation extractor was used to calculate the DNA methylation level. Total RNA seq data were firstly processed using Trim Galore! with default parameters to trim the adapter containing and low quality reads. The filtered data were then mapped to the zebrafish reference genome danRer7 by STAR version: STAR 2.5.3a modified Dobin et al.  2013 with the following parameters:   outSAMstrandField intronMotif   outSAMattributes All   outSAMunmapped Within   outSAMattrIHstart 0   outWigStrand Stranded   outFilterMultimapNmax 20   twopassMode Basic. The gene expression level was normalized to fragments per kilobase of transcript per million mapped FPKM values using Cufflinks version 2.2.1 Trapnell et al.  2012. The scRNA seq data were processed with Cell Ranger 3.1 for genome alignment danRer10  transcript counting  and gene cell barcode matrix generation. Before the downstream analysis  cells with unique detected genes lower than <2 000 and higher than 6 000 genes were discarded  and cells with high percentage of mitochondrial genes >5% were removed too. Subtypes of cells were identified with Seurat 3.0 through the integrating of control and mKD embryos at dome and shield stages with setting control embryos as reference. To make the data comparable samples  we performed SCTransform normalization separately for each dataset. To further reduce the bais caused by sequencing depth of scRNA seq and percentage of mitochondrial genes  UMI variance and percent.mt were regressed out from SCTransform normalized data matrix by linear model with negative binomial distribution. All ChIP seq reads were aligned to the zebrafish reference genome danRer7 using Bowtie2 version 2.2.2 Langmead and Salzberg  2012 with the parameters –t –q –N 1 –L 25. All unmapped reads  non uniquely mapped reads and PCR duplicates were removed. For downstream analysis  the read counts were normalized by computing the numbers of reads per kilobase of bin per million of reads sequenced RPKM. To visualize the STAR ChIP seq signal in the UCSC genome browser  each read was extended by 250 bp and the coverage for each base was counted. Replicates of STAR ChIP seq were pooled for the downstream analysis. The ATAC seq data were mapped to the zebrafish reference genome danRer7 using Bowtie2 version 2.2.2 Langmead and Salzberg  2012 with the parameters –t –q –N 1 –L 25. All unmapped reads  non uniquely mapped reads and PCR duplicates were removed. For downstream analysis  the read counts were normalized by computing the numbers of reads per kilobase of bin per million of reads sequenced RPKM. To minimize the batch and cell type variation  RPKM values across whole genome were further Z score normalized. To visualize the CUT&RUN signals in the UCSC genome browser  each read was extended by 250 bp and the coverage for each base was counted. Genome build: danRer7 Supplementary files format and content: Matrix for scRNA seq data  gene expression table for total RNA seq data  Bigwig and narrowPeak for ChIP seq and ATAC seq data,oocyte,Briefly  on the first day of OMIS Wu et al.  2018b  adult females at 5 mpf 12 mpf were anesthetized in 550 µg/ml tricaine Sigma  Cat A5040 in a petri dish. Then the fish was placed on a damp sponge with specific buffer 5.4 mM KCl  136.8 mM NaCl  4.2 mM NaHCO3  0.44 mM KH2PO4  0.25 mM Na2HPO4  and 0.5% wt/vol BSA. A cut was made on one side of belly to expose the ovary. The diluted MOs were microinjected into each oocyte. Rhodamine B Sigma  Cat R8881 was co injected with MOs as a dye. post injection  the wound on the belly was sewed with a surgical sewing needle carefully and quickly. Once the operation was done  the female was transferred into fish water supplemented with 32 µg/ml tricaine  10 unit/ml penicillin and 10 µg/ml streptomycin HyClone  Cat SV30010. Then the fish was transferred to fish water containing gradually reduced concentrations of tricaine. In the evening of the second day  the female was paired with a wild type male. In the morning of the third day  the pair started to chase and lay fertilized eggs naturally. The injected oocyte derived embryos were identified by co injected dye rhodamine B at very early developmental stages. The injection doses of standard control MO cMO were 5 ng per oocyte in the same assay. MOs were dissolved in RNase free water  and heated to 65°C for 10 min before microinjection.,The oocytes were dechorionated manually by tweezers and transferred into 750 µl Trizol Invitrogen  Cat 15596018. About 10 fresh embryos were transferred into Trizol and vortexed until no visible particles. 150 µl chloroform Amresco  Cat 0757 was added and mixed thoroughly. The mixture was then transferred into phasemaker tube Invitrogen  Cat A33248 and spun at 14 000 rpm for 15 min. Next  the top phase was taken out from the tube  added 1 µl LPA Sigma  Cat 56575 and mixed well using pipettes. Then  RNA was precipitated by adding 750 µl isopropanol Sigma  Cat 59304 at  20℃ overnight. At next day  the tube was spun at 14 000 rpm for 30 min and supernatant was removed. The pellet was washed with freshly 70% ethanol  re suspend in 20 µl RNase free water and stored at  80℃ for later usage. NEBNext rRNA Depletion Kit NEB  Cat E6310S was used to deplete ribosomal RNA according to the manufacture’s instruction. Briefly  rRNA were hybridized with probes and digested with RNase H  then excess probes were digested with DNase I. post that  NEBNext RNA sample purification beads were used to purify rRNA depleted RNA. Purified RNA was fragmented before cDNA synthesis at 95℃ for 8 min. Double stranded cDNA was synthesized with NEB Next first strand NEB  Cat E7771S and second strand synthesis modules NEB  Cat E7550S  then purified with Ampure XP beads Beckman  Cat A63882. Synthesized cDNA was subjected to library preparation with NEBNext Ultr II DNA Library Prep Kit NEB  Cat E7645S. DNA was end repaired  adenylated  and ligated to TruSeq sequencing adaptors. DNA were amplified using KAPA HF HotStart ReadyMix KAPABiosystem  Cat RR2602. The amplified DNA was size selected using Ampure XP beads for 200 500 bp DNA fragments. All libraries were sequenced by Illumina Hi Seq 1500 or 2500 or XTen platform according to manufacturer’s instruction.,The wild type AB strain was used in the experiments. The females post OMIS were fed with live adult brine shrimp thrice a day. All embryos were raised in Holtfreter’s solution at 28.5C and staged as described previously Kimmel et al.  1995.,strain:AB|genotype:WT|developmental stage:Oocyte|tissue:oocyte|treatment:microinjection with Rhodamine B and control MO at oogenesis III stage GV,GSM5351798,GSM5351798: Oocyte ctrl total RNA seq rep1; Danio rerio; RNA Seq,GSM5351798,,1,The oocytes were dechorionated manually by tweezers and transferred into 750 µl Trizol Invitrogen  Cat 15596018. About 10 fresh embryos were transferred into Trizol and vortexed until no visible particles. 150 µl chloroform Amresco  Cat 0757 was added and mixed thoroughly. The mixture was then transferred into phasemaker tube Invitrogen  Cat A33248 and spun at 14 000 rpm for 15 min. Next  the top phase was taken out from the tube  added 1 µl LPA Sigma  Cat 56575 and mixed well using pipettes. Then  RNA was precipitated by adding 750 µl isopropanol Sigma  Cat 59304 at  20℃ overnight. At next day  the tube was spun at 14 000 rpm for 30 min and supernatant was removed. The pellet was washed with freshly 70% ethanol  re suspend in 20 µl RNase free water and stored at  80℃ for later usage. NEBNext rRNA Depletion Kit NEB  Cat E6310S was used to deplete ribosomal RNA according to the manufacture's instruction. Briefly  rRNA were hybridized with probes and digested with RNase H  then excess probes were digested with DNase I. post that  NEBNext RNA sample purification beads were used to purify rRNA depleted RNA. Purified RNA was fragmented before cDNA synthesis at 95℃ for 8 min. Double stranded cDNA was synthesized with NEB Next first strand NEB  Cat E7771S and second strand synthesis modules NEB  Cat E7550S  then purified with Ampure XP beads Beckman  Cat A63882. Synthesized cDNA was subjected to library preparation with NEBNext Ultr II DNA Library Prep Kit NEB  Cat E7645S. DNA was end repaired  adenylated  and ligated to TruSeq sequencing adaptors. DNA were amplified using KAPA HF HotStart ReadyMix KAPABiosystem  Cat RR2602. The amplified DNA was size selected using Ampure XP beads for 200 500 bp DNA fragments. All libraries were sequenced by Illumina Hi Seq 1500 or 2500 or XTen platform according to manufacturer's instruction.,GEO Accession:GSM5351798,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,,SRP322195,,loader:fastq load.py,Oocyte_ctrl_total_RNA_seq_rep1_r1.fq.gz Oocyte_ctrl_total_RNA_seq_rep1_r2.fq.gz,fastq fastq,14857394100.0,49524647.0,GSM5351798 r1,0:150 1:150,A:2831227396;C:4590477521;G:4795177217;T:2639889839;N:622127,150,150,,,2831227396,4590477521,4795177217,2639889839,622127,SRX11041443,SRS9110372,SRA1239365,GEO,"THU-PKU Center for Life Sciences, Tsinghua University",2,0.96771,0.96848,0.26114,0.26288,0.83968,0.84356,0.80056,0.84647,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,rrna_depletion,nebnext,sc_generic,single_cell_generic,generic-scrnaseq-only,,China,2021-06-01,Zygote,Embryo,Oocyte,Reproductive System