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 52242,SRR9047069,SRX5823596,SRS4751717,SRP198207,PRJNA542583,Migrasomes provide regional cues for organ morphogenesis during zebrafish gastrulation,PRJNA542583,Other,Our study shows that migrasomes are signaling organelles which provide specific biochemical information to coordinate organ morphogenesis.,,,,stdMO PBS,stdMO PBS,,strain:Tu|isolate:primary cell|dev stage:gastrulation|sex:not determined|tissue:embryo|collection date:2016 11 13|genotype:wild type|geo loc name:China: Beijing|sample type:embryos|BioSampleModel:Model organism or animal,,,,,,,,,tspan RNA seq,uniprot,uniprot,RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,BGISEQ,BGISEQ-500,,SRP198207,,,161214_I137_FCHF7TTBBXX_L2_WHFISclfRAAARAAPEI-203_1.fq.gz,fastq,633650654.0,12931646.0,161214 I137 FCHF7TTBBXX L2 WHFISclfRAAARAAPEI 203 1.fq.gz,0:49 1:0,A:165787428;C:152969494;G:145599180;T:169168973;N:125579,49,0,,,165787428,152969494,145599180,169168973,125579,SRX5823596,SRS4751717,SRA885639,Tsinghua University|School of Life Sciences,Tsinghua University,1,0.93004,,0.09559,,0.753,,0.47488,,49,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-05-30,Gastrula,Embryo,Embryo Imprecise,All anatomical structures 57168,SRR11237928,SRX7849591,SRS6259054,SRP251591,PRJNA610302,Transcriptome analysis of wild type and maternal zygotic double mutant of nup85;nup133 zebrafish embryos during early development,GSE146394,Transcriptome Analysis,To study the function of zebrafish nuclear pores during early embryogenesis we generated maternal zygotic double mutant of nup85;nup133 MZnup85;nup133 using CRISPR/Cas9 and report the transcriptome wide changes in comparison to wild type WT embryos. Our analysis reveals a dramatic delay of maternal mRNA degradation and zygotic genome activation in MZnup85;nup133 embryos during maternal to zygotic transition. Overall design: mRNA profile of zebrafish WT and MZnup85;nup133 embryos at 4.3 hpf or at stage with dome morphology,,,,MZ 7hpf Dome,GSM4379949,,source name:whole mount embryo|strain:AB|tissue:whole mount embryo|developmental stage:7 hpf nup85 / ;nup133 / ,MZ 7hpf Dome,BGISEQ 500 platform was used for base calling Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence on trimmomatic software v0.36 with paramwters ILLUMINACLIP:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50 then mapped to GRCz11 whole genome using Bowtie2 v2.2.5 with parameters q phred64 sensitive dpad 0 gbar 99999999 mp 1 1 np 1 score min L 0 0.1 p 16 k 200 Fragments Per Kilobase of exon per Megabase of library size FPKM were calculated using software RSEM v1.2.8 from Langmead B. et al. Nat. Methods 2012 and Li B. & Dewey C. N. BMC Bioinformatics 2011. Genome build: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample,whole mount embryo,,total RNAs were extracted from dechorionated whole embryos with RNeasy Mini Kit Qiagen RNA libraries were prepared for sequencing using standard protocols,,strain:AB|tissue:whole mount embryo|developmental stage:7 hpf nup85 / ;nup133 / ,GSM4379949,GSM4379949: MZ 7hpf Dome; Danio rerio; RNA Seq,GSM4379949,,1,total RNAs were extracted from dechorionated whole embryos with RNeasy Mini Kit Qiagen RNA libraries were prepared for sequencing using standard protocols,GEO Accession:GSM4379949,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP251591,,,MZ_7h_Dome_1.fq.gz,fastq,1065702100.0,21314042.0,GSM4379949 r1,0:50 1:0,A:283324952;C:247492025;G:242059243;T:291819466;N:1006414,50,0,,,283324952,247492025,242059243,291819466,1006414,SRX7849591,SRS6259054,SRA1051151,GEO,"School of life science, Tsinghua University",1,0.9445,,0.07752,,0.72565,,0.4828,,50,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2020-03-04,Gastrula,Embryo,Embryo Imprecise,All anatomical structures 57169,SRR11237927,SRX7849590,SRS6259053,SRP251591,PRJNA610302,Transcriptome analysis of wild type and maternal zygotic double mutant of nup85;nup133 zebrafish embryos during early development,GSE146394,Transcriptome Analysis,To study the function of zebrafish nuclear pores during early embryogenesis we generated maternal zygotic double mutant of nup85;nup133 MZnup85;nup133 using CRISPR/Cas9 and report the transcriptome wide changes in comparison to wild type WT embryos. Our analysis reveals a dramatic delay of maternal mRNA degradation and zygotic genome activation in MZnup85;nup133 embryos during maternal to zygotic transition. Overall design: mRNA profile of zebrafish WT and MZnup85;nup133 embryos at 4.3 hpf or at stage with dome morphology,,,,MZ 4.3hpf 1k,GSM4379948,,source name:whole mount embryo|strain:AB|tissue:whole mount embryo|developmental stage:4.3 hpf nup85 / ;nup133 / ,MZ 4.3hpf 1k,BGISEQ 500 platform was used for base calling Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence on trimmomatic software v0.36 with paramwters ILLUMINACLIP:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50 then mapped to GRCz11 whole genome using Bowtie2 v2.2.5 with parameters q phred64 sensitive dpad 0 gbar 99999999 mp 1 1 np 1 score min L 0 0.1 p 16 k 200 Fragments Per Kilobase of exon per Megabase of library size FPKM were calculated using software RSEM v1.2.8 from Langmead B. et al. Nat. Methods 2012 and Li B. & Dewey C. N. BMC Bioinformatics 2011. Genome build: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample,whole mount embryo,,total RNAs were extracted from dechorionated whole embryos with RNeasy Mini Kit Qiagen RNA libraries were prepared for sequencing using standard protocols,,strain:AB|tissue:whole mount embryo|developmental stage:4.3 hpf nup85 / ;nup133 / ,GSM4379948,GSM4379948: MZ 4.3hpf 1k; Danio rerio; RNA Seq,GSM4379948,,1,total RNAs were extracted from dechorionated whole embryos with RNeasy Mini Kit Qiagen RNA libraries were prepared for sequencing using standard protocols,GEO Accession:GSM4379948,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP251591,,,MZ_4.3h_1k_1.fq.gz,fastq,1059959500.0,21199190.0,GSM4379948 r1,0:50 1:0,A:278456455;C:249622199;G:244991579;T:285847713;N:1041554,50,0,,,278456455,249622199,244991579,285847713,1041554,SRX7849590,SRS6259053,SRA1051151,GEO,"School of life science, Tsinghua University",1,0.94882,,0.03659,,0.74361,,0.48435,,50,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2020-03-04,Blastula,Embryo,Embryo Imprecise,All anatomical structures 57170,SRR11237926,SRX7849589,SRS6259052,SRP251591,PRJNA610302,Transcriptome analysis of wild type and maternal zygotic double mutant of nup85;nup133 zebrafish embryos during early development,GSE146394,Transcriptome Analysis,To study the function of zebrafish nuclear pores during early embryogenesis we generated maternal zygotic double mutant of nup85;nup133 MZnup85;nup133 using CRISPR/Cas9 and report the transcriptome wide changes in comparison to wild type WT embryos. Our analysis reveals a dramatic delay of maternal mRNA degradation and zygotic genome activation in MZnup85;nup133 embryos during maternal to zygotic transition. Overall design: mRNA profile of zebrafish WT and MZnup85;nup133 embryos at 4.3 hpf or at stage with dome morphology,,,,WT 4.3hpf Dome,GSM4379947,,source name:whole mount embryo|strain:AB|tissue:whole mount embryo|developmental stage:4.3 hpf type,WT 4.3hpf Dome,BGISEQ 500 platform was used for base calling Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence on trimmomatic software v0.36 with paramwters ILLUMINACLIP:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50 then mapped to GRCz11 whole genome using Bowtie2 v2.2.5 with parameters q phred64 sensitive dpad 0 gbar 99999999 mp 1 1 np 1 score min L 0 0.1 p 16 k 200 Fragments Per Kilobase of exon per Megabase of library size FPKM were calculated using software RSEM v1.2.8 from Langmead B. et al. Nat. Methods 2012 and Li B. & Dewey C. N. BMC Bioinformatics 2011. Genome build: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample,whole mount embryo,,total RNAs were extracted from dechorionated whole embryos with RNeasy Mini Kit Qiagen RNA libraries were prepared for sequencing using standard protocols,,strain:AB|tissue:whole mount embryo|developmental stage:4.3 hpf type,GSM4379947,GSM4379947: WT 4.3hpf Dome; Danio rerio; RNA Seq,GSM4379947,,1,total RNAs were extracted from dechorionated whole embryos with RNeasy Mini Kit Qiagen RNA libraries were prepared for sequencing using standard protocols,GEO Accession:GSM4379947,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP251591,,,WT_4.3h_Dome_1.fq.gz,fastq,1058158950.0,21163179.0,GSM4379947 r1,0:50 1:0,A:279307143;C:247873321;G:244308380;T:285580565;N:1089541,50,0,,,279307143,247873321,244308380,285580565,1089541,SRX7849589,SRS6259052,SRA1051151,GEO,"School of life science, Tsinghua University",1,0.94374,,0.05294,,0.74164,,0.48705,,50,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2020-03-04,Blastula,Embryo,Embryo Imprecise,All anatomical structures 61503,SRR12780056,SRX9249644,SRS7482118,SRP286526,PRJNA667677,Bipartite histone H3 recognition by the PZP domain of PHF14 facilitates zygotic genome activation in zebrafish,GSE159087,Transcriptome Analysis,Standard and Phf14 MOs were injected into 1 cell stage embryos and when developed into sphere stage 4.7 hpf embryos were lysed for mRNA extraction for high through put sequencing based on BGISEQ in order to compare gene expression test at the whole genome level. Overall design: mRNA profiles of standard std MO 4.7h versus phf14 MO injected phf tMO 4.7h zebrash embryos at 4.7 hpf.,,,,phf tMO 4.7h,GSM4819005,,tissue:embryos|strain:Tuebingen|genotype/variation:phf14 MO injected|developmental stage:4.7 hpf|tissue/cell type:whole embryos,phf tMO 4.7h,Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to zv9 whole genome using SOAPaligner/soap2 Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from mortazavi et al. nature method 2008. Genome build: zv9 Supplementary files format and content: Excel files include RPKM values and read counts for each gene in the two samples,embryos,Embryos were injected with 5 ng standard or Phf14 morpholinos at xxx cell stage,Zebrafish embryos mRNA were extracted using Qiagen RNA extraction kit. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,Embryos were cultured in the holfretor water.,strain:Tuebingen|genotype/variation:phf14 MO injected|developmental stage:4.7 hpf|tissue/cell type:whole embryos,GSM4819005,GSM4819005: phf tMO 4.7h; Danio rerio; RNA Seq,GSM4819005,,1,Zebrafish embryos mRNA were extracted using Qiagen RNA extraction kit. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4819005,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP286526,,,phf_tMO_4.7h.fq.gz,fastq,1169147800.0,23382956.0,GSM4819005 r1,0:50,A:311605612;C:272452820;G:269040332;T:316049036;N:0,50,,,,311605612,272452820,269040332,316049036,0,SRX9249644,SRS7482118,SRA1139165,GEO,"Haitao Li, School of medicine, Tsinghua University",1,0.94966,,0.07252,,0.73651,,0.49931,,50,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,China,2020-10-06,Blastula,Embryo,Embryo Imprecise,All anatomical structures 61504,SRR12780055,SRX9249643,SRS7482117,SRP286526,PRJNA667677,Bipartite histone H3 recognition by the PZP domain of PHF14 facilitates zygotic genome activation in zebrafish,GSE159087,Transcriptome Analysis,Standard and Phf14 MOs were injected into 1 cell stage embryos and when developed into sphere stage 4.7 hpf embryos were lysed for mRNA extraction for high through put sequencing based on BGISEQ in order to compare gene expression test at the whole genome level. Overall design: mRNA profiles of standard std MO 4.7h versus phf14 MO injected phf tMO 4.7h zebrash embryos at 4.7 hpf.,,,,std MO 4.7h,GSM4819004,,tissue:embryos|strain:Tuebingen|genotype/variation:standard MO injected|developmental stage:4.7 hpf|tissue/cell type:whole embryos,std MO 4.7h,Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to zv9 whole genome using SOAPaligner/soap2 Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from mortazavi et al. nature method 2008. Genome build: zv9 Supplementary files format and content: Excel files include RPKM values and read counts for each gene in the two samples,embryos,Embryos were injected with 5 ng standard or Phf14 morpholinos at xxx cell stage,Zebrafish embryos mRNA were extracted using Qiagen RNA extraction kit. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,Embryos were cultured in the holfretor water.,strain:Tuebingen|genotype/variation:standard MO injected|developmental stage:4.7 hpf|tissue/cell type:whole embryos,GSM4819004,GSM4819004: std MO 4.7h; Danio rerio; RNA Seq,GSM4819004,,1,Zebrafish embryos mRNA were extracted using Qiagen RNA extraction kit. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4819004,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP286526,,,std_MO_4.7h.fq.gz,fastq,1169210150.0,23384203.0,GSM4819004 r1,0:50,A:311848924;C:271805947;G:268541126;T:317014153;N:0,50,,,,311848924,271805947,268541126,317014153,0,SRX9249643,SRS7482117,SRA1139165,GEO,"Haitao Li, School of medicine, Tsinghua University",1,0.94838,,0.07833,,0.74192,,0.48213,,50,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,China,2020-10-06,Blastula,Embryo,Embryo Imprecise,All anatomical structures 71312,SRR21487520,SRX17491012,SRS15043328,SRP396256,PRJNA878480,Effect of nuclear pore complex NPC blockage by WGA treatment on zygotic genome activation ZGA during zebrafish early development,GSE212929,Transcriptome Analysis,To investigate the function of nuclear pore complex NPC in the regulation of zygotic genome activation ZGA we microinjected medium dosage of WGA in zebrafish embryos at xxx cell stage to block NPC function. We then performed gene expression profiling analysis using data obtained from RNA seq of control or WGA treated embryo at comparable developmental time point 4.3 hpf or develomental stage dome. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish control embryo at 4.3 hpf of dome stage and WGA treated embryos at 4.3 hpf developmental time matched or 5 hpf dome like stage.,,pubmed:36493774,,zebrafish early embryos WGA treated 5 hpf dome like stage,GSM6562796,,source name:whole mount embryo|tissue:whole mount embryo|cell line:early embryo|cell type:embryonic cell|genotype:wildtype|treatment:0.65 ng WGA injected at 1 cell stage,zebrafish early embryos WGA treated 5 hpf dome like stage,BGISEQ 500 platform was used for base calling Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence on trimmomatic software v0.36 with paramwters ILLUMINACLIP:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50 then mapped to GRCz11 whole genome using Bowtie2 v2.2.5 with parameters q phred64 sensitive dpad 0 gbar 99999999 mp 1 1 np 1 score min L 0 0.1 p 16 k 200 Fragments Per Kilobase of exon per Megabase of library size FPKM were calculated using software RSEM v1.2.8 from Langmead B. et al. Nat. Methods 2012 and Li B. & Dewey C. N. BMC Bioinformatics 2011. Assembly: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample,whole mount embryo,1 nl WGA of 0.65 ng/nl dissolved in nuclease free water was microinjected into yolk of embryos at xxx cell stage.,total RNAs were extracted from dechorionated whole embryos with RNeasy Mini Kit Qiagen RNA libraries were prepared for sequencing using standard protocols,,tissue:whole mount embryo|cell line:early embryo|cell type:embryonic cell|genotype:wildtype|treatment:0.65 ng WGA injected at 1 cell stage,GSM6562796,GSM6562796: zebrafish early embryos WGA treated 5 hpf dome like stage; Danio rerio; RNA Seq,GSM6562796 r1,GSM6562796,1,total RNAs were extracted from dechorionated whole embryos with RNeasy Mini Kit Qiagen RNA libraries were prepared for sequencing using standard protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP396256,,,WGA_5h.fq.gz,fastq,1059386400.0,21187728.0,GSM6562796 r1,0:50 1:0,A:277040646;C:250203561;G:245816009;T:285209577;N:1116607,50,0,,,277040646,250203561,245816009,285209577,1116607,SRX17491012,SRS15043328,SRA1496611,"School of life science, Tsinghua University","School of life science, Tsinghua University",1,0.94419,,0.03669,,0.74919,,0.48293,,50,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2022-09-08,Blastula,Embryo,Embryo Imprecise,All anatomical structures 71313,SRR21487521,SRX17491011,SRS15043327,SRP396256,PRJNA878480,Effect of nuclear pore complex NPC blockage by WGA treatment on zygotic genome activation ZGA during zebrafish early development,GSE212929,Transcriptome Analysis,To investigate the function of nuclear pore complex NPC in the regulation of zygotic genome activation ZGA we microinjected medium dosage of WGA in zebrafish embryos at xxx cell stage to block NPC function. We then performed gene expression profiling analysis using data obtained from RNA seq of control or WGA treated embryo at comparable developmental time point 4.3 hpf or develomental stage dome. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish control embryo at 4.3 hpf of dome stage and WGA treated embryos at 4.3 hpf developmental time matched or 5 hpf dome like stage.,,pubmed:36493774,,zebrafish early embryos WGA treated 4.3 hpf,GSM6562795,,source name:whole mount embryo|tissue:whole mount embryo|cell line:early embryo|cell type:embryonic cell|genotype:wildtype|treatment:0.65 ng WGA injected at 1 cell stage,zebrafish early embryos WGA treated 4.3 hpf,BGISEQ 500 platform was used for base calling Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence on trimmomatic software v0.36 with paramwters ILLUMINACLIP:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50 then mapped to GRCz11 whole genome using Bowtie2 v2.2.5 with parameters q phred64 sensitive dpad 0 gbar 99999999 mp 1 1 np 1 score min L 0 0.1 p 16 k 200 Fragments Per Kilobase of exon per Megabase of library size FPKM were calculated using software RSEM v1.2.8 from Langmead B. et al. Nat. Methods 2012 and Li B. & Dewey C. N. BMC Bioinformatics 2011. Assembly: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample,whole mount embryo,1 nl WGA of 0.65 ng/nl dissolved in nuclease free water was microinjected into yolk of embryos at xxx cell stage.,total RNAs were extracted from dechorionated whole embryos with RNeasy Mini Kit Qiagen RNA libraries were prepared for sequencing using standard protocols,,tissue:whole mount embryo|cell line:early embryo|cell type:embryonic cell|genotype:wildtype|treatment:0.65 ng WGA injected at 1 cell stage,GSM6562795,GSM6562795: zebrafish early embryos WGA treated 4.3 hpf; Danio rerio; RNA Seq,GSM6562795 r1,GSM6562795,1,total RNAs were extracted from dechorionated whole embryos with RNeasy Mini Kit Qiagen RNA libraries were prepared for sequencing using standard protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP396256,,,WGA_4.3h.fq.gz,fastq,1062790650.0,21255813.0,GSM6562795 r1,0:50 1:0,A:277911032;C:251212426;G:246864055;T:285783146;N:1019991,50,0,,,277911032,251212426,246864055,285783146,1019991,SRX17491011,SRS15043327,SRA1496611,"School of life science, Tsinghua University","School of life science, Tsinghua University",1,0.94436,,0.0365,,0.7488,,0.47923,,50,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2022-09-08,Blastula,Embryo,Embryo Imprecise,All anatomical structures 71314,SRR21487522,SRX17491010,SRS15043326,SRP396256,PRJNA878480,Effect of nuclear pore complex NPC blockage by WGA treatment on zygotic genome activation ZGA during zebrafish early development,GSE212929,Transcriptome Analysis,To investigate the function of nuclear pore complex NPC in the regulation of zygotic genome activation ZGA we microinjected medium dosage of WGA in zebrafish embryos at xxx cell stage to block NPC function. We then performed gene expression profiling analysis using data obtained from RNA seq of control or WGA treated embryo at comparable developmental time point 4.3 hpf or develomental stage dome. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish control embryo at 4.3 hpf of dome stage and WGA treated embryos at 4.3 hpf developmental time matched or 5 hpf dome like stage.,,pubmed:36493774,,zebrafish early embryos wildtype 4.3 hpf dome stage,GSM6562794,,source name:whole mount embryo|tissue:whole mount embryo|cell line:early embryo|cell type:embryonic cell|genotype:wildtype|treatment:N/A,zebrafish early embryos wildtype 4.3 hpf dome stage,BGISEQ 500 platform was used for base calling Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence on trimmomatic software v0.36 with paramwters ILLUMINACLIP:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50 then mapped to GRCz11 whole genome using Bowtie2 v2.2.5 with parameters q phred64 sensitive dpad 0 gbar 99999999 mp 1 1 np 1 score min L 0 0.1 p 16 k 200 Fragments Per Kilobase of exon per Megabase of library size FPKM were calculated using software RSEM v1.2.8 from Langmead B. et al. Nat. Methods 2012 and Li B. & Dewey C. N. BMC Bioinformatics 2011. Assembly: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample,whole mount embryo,1 nl WGA of 0.65 ng/nl dissolved in nuclease free water was microinjected into yolk of embryos at xxx cell stage.,total RNAs were extracted from dechorionated whole embryos with RNeasy Mini Kit Qiagen RNA libraries were prepared for sequencing using standard protocols,,tissue:whole mount embryo|cell line:early embryo|cell type:embryonic cell|genotype:wildtype|treatment:N/A,GSM6562794,GSM6562794: zebrafish early embryos wildtype 4.3 hpf dome stage; Danio rerio; RNA Seq,GSM6562794 r1,GSM6562794,1,total RNAs were extracted from dechorionated whole embryos with RNeasy Mini Kit Qiagen RNA libraries were prepared for sequencing using standard protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP396256,,,WT_4.3h.fq.gz,fastq,1063999350.0,21279987.0,GSM6562794 r1,0:50 1:0,A:280657534;C:249334239;G:244705183;T:288194607;N:1107787,50,0,,,280657534,249334239,244705183,288194607,1107787,SRX17491010,SRS15043326,SRA1496611,"School of life science, Tsinghua University","School of life science, Tsinghua University",1,0.94283,,0.06247,,0.73474,,0.49113,,50,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2022-09-08,Blastula,Embryo,Embryo Imprecise,All anatomical structures