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
25324,SRR25820349,SRX21542119,SRS18751470,SRP457651,PRJNA1010830,Identifying hand2 downstream targets in cardiomyocyte during early cardiogenesis,GSE241971,Other,hand2 reporter expressing cardiac cells fail to migrate to the midline.  To investigate the underlying molecular changes  we sequenced mRNA from 3900 and 3836 hand2 reporter expressing single cells from 24 hpf hand2 FLD /  and hand2 FLD+/? sibling embryos  respectively.  Furthermore  hand2 is broadly expressed within the LPM  which gives rise to various cell lineages and tissues including the cardiovascular system  blood  kidneys  mesothelium  and limb connective tissue.  To further investigate the requirement of Hand2 in the early events of cardiac lineage specification in zebrafish  we aim to characterize the early hand2 expressing cardiac precursors by using embryonic CM H3K27ac ChIP seq and ATAC seq data. Overall design: scRNA seq: WT: hand2 reporter expressing single cells from 24 hpf  hand2 FLD+/?  Embryos; mutants: hand2 reporter expressing single cells from 24 hpf hand2 FLD /  sibling embryos.  ATAC seq and CGIP seq: Comparing myl7:GFP+ CMs with  myl7:GFP  cells,,pubmed:39658721,,MUT  replicate1  scRNA,GSM7746945,,source name:whole embryo|tissue:whole embryo|cell type:hand2 reporter expressing single cells|genotype:hand2 mutants|geo loc name:missing|collection date:missing,MUT  replicate1  scRNA,demultiplexing star solo mapping: '  soloType CB UMI Simple   soloBarcodeReadLength 0   soloCellFilter EmptyDrops CR 5000 0.99 10 45000 90000 500 0.01 20000 0.01 10000' Assembly: danio rerio/101 Supplementary files format and content: 10x based mtx raw count matrix  barcodes and genes,whole embryo,,10xGenomics,,tissue:whole embryo|cell type:hand2 reporter expressing single cells|genotype:hand2 mutants,GSM7746945,GSM7746945: MUT  replicate1  scRNA; Danio rerio; RNA Seq,GSM7746945 r1,GSM7746945,1,10xGenomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP457651,,,Yanli_10x_Mut_24hpf_R2.fastq.gz Yanli_10x_Mut_24hpf_R1.fastq.gz,fastq fastq,12703207777.0,159786155.0,GSM7746945 r1,0:28 1:51.50,A:3417159154;C:2758515982;G:2823785724;T:3638099229;N:65647688,28,51,,,3417159154,2758515982,2823785724,3638099229,65647688,SRX21542119,SRS18751470,SRA1702565,Max Planck Institute for Heart and Lung Research,Max Planck Institute for Heart and Lung Research,2,0.00189,0.93843,0.0006,0.12822,0.99571,0.781,0.38429,0.49855,28,52,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_generic,generic-scrnaseq-only,,Germany,2023-08-30,Undetermined,Embryo,Whole Organism,All anatomical structures
25325,SRR25820350,SRX21542118,SRS18751469,SRP457651,PRJNA1010830,Identifying hand2 downstream targets in cardiomyocyte during early cardiogenesis,GSE241971,Other,hand2 reporter expressing cardiac cells fail to migrate to the midline.  To investigate the underlying molecular changes  we sequenced mRNA from 3900 and 3836 hand2 reporter expressing single cells from 24 hpf hand2 FLD /  and hand2 FLD+/? sibling embryos  respectively.  Furthermore  hand2 is broadly expressed within the LPM  which gives rise to various cell lineages and tissues including the cardiovascular system  blood  kidneys  mesothelium  and limb connective tissue.  To further investigate the requirement of Hand2 in the early events of cardiac lineage specification in zebrafish  we aim to characterize the early hand2 expressing cardiac precursors by using embryonic CM H3K27ac ChIP seq and ATAC seq data. Overall design: scRNA seq: WT: hand2 reporter expressing single cells from 24 hpf  hand2 FLD+/?  Embryos; mutants: hand2 reporter expressing single cells from 24 hpf hand2 FLD /  sibling embryos.  ATAC seq and CGIP seq: Comparing myl7:GFP+ CMs with  myl7:GFP  cells,,pubmed:39658721,,WT  replicate 1  scRNA,GSM7746944,,source name:whole embryo|tissue:whole embryo|cell type:hand2 reporter expressing single cells|genotype:WT|geo loc name:missing|collection date:missing,WT  replicate 1  scRNA,demultiplexing star solo mapping: '  soloType CB UMI Simple   soloBarcodeReadLength 0   soloCellFilter EmptyDrops CR 5000 0.99 10 45000 90000 500 0.01 20000 0.01 10000' Assembly: danio rerio/101 Supplementary files format and content: 10x based mtx raw count matrix  barcodes and genes,whole embryo,,10xGenomics,,tissue:whole embryo|cell type:hand2 reporter expressing single cells|genotype:WT,GSM7746944,GSM7746944: WT  replicate 1  scRNA; Danio rerio; RNA Seq,GSM7746944 r1,GSM7746944,1,10xGenomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP457651,,,Yanli_10x_WT_24hpf_R2.fastq.gz Yanli_10x_WT_24hpf_R1.fastq.gz,fastq fastq,9691697994.0,121912639.0,GSM7746944 r1,0:28 1:51.50,A:2617434834;C:2102210357;G:2159290265;T:2762773221;N:49989317,28,51,,,2617434834,2102210357,2159290265,2762773221,49989317,SRX21542118,SRS18751469,SRA1702565,Max Planck Institute for Heart and Lung Research,Max Planck Institute for Heart and Lung Research,2,0.00175,0.93872,0.00057,0.12715,0.99584,0.78713,0.40888,0.504,28,52,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_generic,generic-scrnaseq-only,,Germany,2023-08-30,Undetermined,Embryo,Whole Organism,All anatomical structures
28611,SRR26471890,SRX22175831,SRS19233331,SRP467949,PRJNA1031141,Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [bulkRNA Seq],GSE246037,Transcriptome Analysis,Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model  we have identified an eosinophil lineage specific marker  eslec. Using this marker we have established a Tgeslec:eGFP reporter line  which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells  tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis  in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment  differentiation  and maturation of the eosinophil lineage. In summary  this study characterized eosinophil development in multiple dimensions including spatial temporal patterns  expression profiles  and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For the RNA Seq analysis of eosinophils from different genotypes  eslec:eGFP+ eosinophils were sorted from whole larvae 7 dpf and lysed. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented  adpator tagged  and purified for further sequencing.,parent bioproject:PRJNA814534,pubmed:38280871,,cebpb mut eos 2,GSM7854238,,source name:eosinophils|strain:AB strain|tissue:whole larvae|genotype:cebpb / |transgene:Tgeslec:eGFP|geo loc name:missing|collection date:missing,cebpb mut eos 2,"Post quality control  the fastq files were mapped to the zebrafish genome with the ""STAR"" package. Mapped reads were annotated with the ""FeatureCounts"" package. Annotated reads were applied to the ""DESeq2"" package for differential expressed genes analysis. The sample to sample distance heatmaps were generated by ""pheatmap"" with the output of ""DESeq2"". The gene expression heatmaps were generated by ""pheatmap"" with the Z score of the TPM matrix. Assembly: GRCz11 Supplementary files format and content: Normalized matrix table with Transcripts Per Kilobase TPM for every gene and every sample",eosinophils,,Whole larvae were ground and digested into cell suspensions. The cell suspensions were then analyzed with FACS and the eGFP+ cells  500 cells for each sample were sorted into lysis buffer. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented  adpator tagged  and purified for further sequencing.,,strain:AB strain|tissue:whole larvae|genotype:cebpb / |transgene:Tgeslec:eGFP,GSM7854238,GSM7854238: cebpb mut eos 2; Danio rerio; RNA Seq,GSM7854238 r1,GSM7854238,1,Whole larvae were ground and digested into cell suspensions. The cell suspensions were then analyzed with FACS and the eGFP+ cells  500 cells for each sample were sorted into lysis buffer. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented  adpator tagged  and purified for further sequencing.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP467949,,loader:fastq load.py,F2_1.fq.gz F2_2.fq.gz,fastq fastq,6304806000.0,21016020.0,GSM7854238 r1,0:150 1:150,A:1797551316;C:1332146220;G:1348919312;T:1826125402;N:63750,150,150,,,1797551316,1332146220,1348919312,1826125402,63750,SRX22175831,SRS19233331,SRA1737851,South China University of Technology,South China University of Technology,2,0.90391,0.90473,0.3135,0.31222,0.83753,0.83613,0.53444,0.53443,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,China,2023-10-23,Larval,Larval,Whole Organism,All anatomical structures
28612,SRR26471891,SRX22175830,SRS19233328,SRP467949,PRJNA1031141,Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [bulkRNA Seq],GSE246037,Transcriptome Analysis,Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model  we have identified an eosinophil lineage specific marker  eslec. Using this marker we have established a Tgeslec:eGFP reporter line  which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells  tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis  in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment  differentiation  and maturation of the eosinophil lineage. In summary  this study characterized eosinophil development in multiple dimensions including spatial temporal patterns  expression profiles  and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For the RNA Seq analysis of eosinophils from different genotypes  eslec:eGFP+ eosinophils were sorted from whole larvae 7 dpf and lysed. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented  adpator tagged  and purified for further sequencing.,parent bioproject:PRJNA814534,pubmed:38280871,,cebpb wt eos 1,GSM7854239,,source name:eosinophils|strain:AB strain|tissue:whole larvae|genotype:wild type|transgene:Tgeslec:eGFP|geo loc name:missing|collection date:missing,cebpb wt eos 1,"Post quality control  the fastq files were mapped to the zebrafish genome with the ""STAR"" package. Mapped reads were annotated with the ""FeatureCounts"" package. Annotated reads were applied to the ""DESeq2"" package for differential expressed genes analysis. The sample to sample distance heatmaps were generated by ""pheatmap"" with the output of ""DESeq2"". The gene expression heatmaps were generated by ""pheatmap"" with the Z score of the TPM matrix. Assembly: GRCz11 Supplementary files format and content: Normalized matrix table with Transcripts Per Kilobase TPM for every gene and every sample",eosinophils,,Whole larvae were ground and digested into cell suspensions. The cell suspensions were then analyzed with FACS and the eGFP+ cells  500 cells for each sample were sorted into lysis buffer. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented  adpator tagged  and purified for further sequencing.,,strain:AB strain|tissue:whole larvae|genotype:wild type|transgene:Tgeslec:eGFP,GSM7854239,GSM7854239: cebpb wt eos 1; Danio rerio; RNA Seq,GSM7854239 r1,GSM7854239,1,Whole larvae were ground and digested into cell suspensions. The cell suspensions were then analyzed with FACS and the eGFP+ cells  500 cells for each sample were sorted into lysis buffer. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented  adpator tagged  and purified for further sequencing.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP467949,,loader:fastq load.py,Z1_1.fq.gz Z1_2.fq.gz,fastq fastq,6180805800.0,20602686.0,GSM7854239 r1,0:150 1:150,A:1699796929;C:1374020384;G:1377922189;T:1729003691;N:62607,150,150,,,1699796929,1374020384,1377922189,1729003691,62607,SRX22175830,SRS19233328,SRA1737851,South China University of Technology,South China University of Technology,2,0.91982,0.9224,0.18189,0.18148,0.82814,0.82672,0.51271,0.5152,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,China,2023-10-23,Larval,Larval,Whole Organism,All anatomical structures
28613,SRR26471892,SRX22175829,SRS19233330,SRP467949,PRJNA1031141,Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [bulkRNA Seq],GSE246037,Transcriptome Analysis,Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model  we have identified an eosinophil lineage specific marker  eslec. Using this marker we have established a Tgeslec:eGFP reporter line  which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells  tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis  in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment  differentiation  and maturation of the eosinophil lineage. In summary  this study characterized eosinophil development in multiple dimensions including spatial temporal patterns  expression profiles  and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For the RNA Seq analysis of eosinophils from different genotypes  eslec:eGFP+ eosinophils were sorted from whole larvae 7 dpf and lysed. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented  adpator tagged  and purified for further sequencing.,parent bioproject:PRJNA814534,pubmed:38280871,,cebpb wt eos 2,GSM7854240,,source name:eosinophils|strain:AB strain|tissue:whole larvae|genotype:wild type|transgene:Tgeslec:eGFP|geo loc name:missing|collection date:missing,cebpb wt eos 2,"Post quality control  the fastq files were mapped to the zebrafish genome with the ""STAR"" package. Mapped reads were annotated with the ""FeatureCounts"" package. Annotated reads were applied to the ""DESeq2"" package for differential expressed genes analysis. The sample to sample distance heatmaps were generated by ""pheatmap"" with the output of ""DESeq2"". The gene expression heatmaps were generated by ""pheatmap"" with the Z score of the TPM matrix. Assembly: GRCz11 Supplementary files format and content: Normalized matrix table with Transcripts Per Kilobase TPM for every gene and every sample",eosinophils,,Whole larvae were ground and digested into cell suspensions. The cell suspensions were then analyzed with FACS and the eGFP+ cells  500 cells for each sample were sorted into lysis buffer. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented  adpator tagged  and purified for further sequencing.,,strain:AB strain|tissue:whole larvae|genotype:wild type|transgene:Tgeslec:eGFP,GSM7854240,GSM7854240: cebpb wt eos 2; Danio rerio; RNA Seq,GSM7854240 r1,GSM7854240,1,Whole larvae were ground and digested into cell suspensions. The cell suspensions were then analyzed with FACS and the eGFP+ cells  500 cells for each sample were sorted into lysis buffer. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented  adpator tagged  and purified for further sequencing.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP467949,,loader:fastq load.py,Z2_1.fq.gz Z2_2.fq.gz,fastq fastq,6693470100.0,22311567.0,GSM7854240 r1,0:150 1:150,A:1840742978;C:1484923084;G:1499378237;T:1868364754;N:61047,150,150,,,1840742978,1484923084,1499378237,1868364754,61047,SRX22175829,SRS19233330,SRA1737851,South China University of Technology,South China University of Technology,2,0.92056,0.92353,0.18668,0.18721,0.82771,0.82696,0.53034,0.52277,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,China,2023-10-23,Larval,Larval,Whole Organism,All anatomical structures
28614,SRR26471893,SRX22175828,SRS19233332,SRP467949,PRJNA1031141,Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [bulkRNA Seq],GSE246037,Transcriptome Analysis,Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model  we have identified an eosinophil lineage specific marker  eslec. Using this marker we have established a Tgeslec:eGFP reporter line  which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells  tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis  in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment  differentiation  and maturation of the eosinophil lineage. In summary  this study characterized eosinophil development in multiple dimensions including spatial temporal patterns  expression profiles  and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For the RNA Seq analysis of eosinophils from different genotypes  eslec:eGFP+ eosinophils were sorted from whole larvae 7 dpf and lysed. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented  adpator tagged  and purified for further sequencing.,parent bioproject:PRJNA814534,pubmed:38280871,,cebpb mut eos 1,GSM7854237,,source name:eosinophils|strain:AB strain|tissue:whole larvae|genotype:cebpb / |transgene:Tgeslec:eGFP|geo loc name:missing|collection date:missing,cebpb mut eos 1,"Post quality control  the fastq files were mapped to the zebrafish genome with the ""STAR"" package. Mapped reads were annotated with the ""FeatureCounts"" package. Annotated reads were applied to the ""DESeq2"" package for differential expressed genes analysis. The sample to sample distance heatmaps were generated by ""pheatmap"" with the output of ""DESeq2"". The gene expression heatmaps were generated by ""pheatmap"" with the Z score of the TPM matrix. Assembly: GRCz11 Supplementary files format and content: Normalized matrix table with Transcripts Per Kilobase TPM for every gene and every sample",eosinophils,,Whole larvae were ground and digested into cell suspensions. The cell suspensions were then analyzed with FACS and the eGFP+ cells  500 cells for each sample were sorted into lysis buffer. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented  adpator tagged  and purified for further sequencing.,,strain:AB strain|tissue:whole larvae|genotype:cebpb / |transgene:Tgeslec:eGFP,GSM7854237,GSM7854237: cebpb mut eos 1; Danio rerio; RNA Seq,GSM7854237 r1,GSM7854237,1,Whole larvae were ground and digested into cell suspensions. The cell suspensions were then analyzed with FACS and the eGFP+ cells  500 cells for each sample were sorted into lysis buffer. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented  adpator tagged  and purified for further sequencing.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP467949,,loader:fastq load.py,F1_1.fq.gz F1_2.fq.gz,fastq fastq,7774783500.0,25915945.0,GSM7854237 r1,0:150 1:150,A:2205128515;C:1660071767;G:1677499789;T:2232048253;N:35176,150,150,,,2205128515,1660071767,1677499789,2232048253,35176,SRX22175828,SRS19233332,SRA1737851,South China University of Technology,South China University of Technology,2,0.90668,0.90886,0.34302,0.34395,0.81943,0.81937,0.5348,0.54523,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,China,2023-10-23,Larval,Larval,Whole Organism,All anatomical structures
28615,SRR26471894,SRX22175827,SRS19233329,SRP467949,PRJNA1031141,Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [bulkRNA Seq],GSE246037,Transcriptome Analysis,Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model  we have identified an eosinophil lineage specific marker  eslec. Using this marker we have established a Tgeslec:eGFP reporter line  which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells  tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis  in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment  differentiation  and maturation of the eosinophil lineage. In summary  this study characterized eosinophil development in multiple dimensions including spatial temporal patterns  expression profiles  and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For the RNA Seq analysis of eosinophils from different genotypes  eslec:eGFP+ eosinophils were sorted from whole larvae 7 dpf and lysed. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented  adpator tagged  and purified for further sequencing.,parent bioproject:PRJNA814534,pubmed:38280871,,cebp1 wt eos 2,GSM7854236,,source name:eosinophils|strain:AB strain|tissue:whole larvae|genotype:wild type|transgene:Tgeslec:eGFP|geo loc name:missing|collection date:missing,cebp1 wt eos 2,"Post quality control  the fastq files were mapped to the zebrafish genome with the ""STAR"" package. Mapped reads were annotated with the ""FeatureCounts"" package. Annotated reads were applied to the ""DESeq2"" package for differential expressed genes analysis. The sample to sample distance heatmaps were generated by ""pheatmap"" with the output of ""DESeq2"". The gene expression heatmaps were generated by ""pheatmap"" with the Z score of the TPM matrix. Assembly: GRCz11 Supplementary files format and content: Normalized matrix table with Transcripts Per Kilobase TPM for every gene and every sample",eosinophils,,Whole larvae were ground and digested into cell suspensions. The cell suspensions were then analyzed with FACS and the eGFP+ cells  500 cells for each sample were sorted into lysis buffer. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented  adpator tagged  and purified for further sequencing.,,strain:AB strain|tissue:whole larvae|genotype:wild type|transgene:Tgeslec:eGFP,GSM7854236,GSM7854236: cebp1 wt eos 2; Danio rerio; RNA Seq,GSM7854236 r1,GSM7854236,1,Whole larvae were ground and digested into cell suspensions. The cell suspensions were then analyzed with FACS and the eGFP+ cells  500 cells for each sample were sorted into lysis buffer. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented  adpator tagged  and purified for further sequencing.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP467949,,loader:fastq load.py,W2_1.fq.gz W2_2.fq.gz,fastq fastq,6478425300.0,21594751.0,GSM7854236 r1,0:150 1:150,A:2031706672;C:1135087913;G:1324534931;T:1987064653;N:31131,150,150,,,2031706672,1135087913,1324534931,1987064653,31131,SRX22175827,SRS19233329,SRA1737851,South China University of Technology,South China University of Technology,2,0.74912,0.74531,0.50454,0.49737,0.79255,0.78539,0.63484,0.64052,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,China,2023-10-23,Larval,Larval,Whole Organism,All anatomical structures
28616,SRR26471895,SRX22175826,SRS19233326,SRP467949,PRJNA1031141,Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [bulkRNA Seq],GSE246037,Transcriptome Analysis,Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model  we have identified an eosinophil lineage specific marker  eslec. Using this marker we have established a Tgeslec:eGFP reporter line  which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells  tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis  in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment  differentiation  and maturation of the eosinophil lineage. In summary  this study characterized eosinophil development in multiple dimensions including spatial temporal patterns  expression profiles  and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For the RNA Seq analysis of eosinophils from different genotypes  eslec:eGFP+ eosinophils were sorted from whole larvae 7 dpf and lysed. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented  adpator tagged  and purified for further sequencing.,parent bioproject:PRJNA814534,pubmed:38280871,,cebp1 wt eos 1,GSM7854235,,source name:eosinophils|strain:AB strain|tissue:whole larvae|genotype:wild type|transgene:Tgeslec:eGFP|geo loc name:missing|collection date:missing,cebp1 wt eos 1,"Post quality control  the fastq files were mapped to the zebrafish genome with the ""STAR"" package. Mapped reads were annotated with the ""FeatureCounts"" package. Annotated reads were applied to the ""DESeq2"" package for differential expressed genes analysis. The sample to sample distance heatmaps were generated by ""pheatmap"" with the output of ""DESeq2"". The gene expression heatmaps were generated by ""pheatmap"" with the Z score of the TPM matrix. Assembly: GRCz11 Supplementary files format and content: Normalized matrix table with Transcripts Per Kilobase TPM for every gene and every sample",eosinophils,,Whole larvae were ground and digested into cell suspensions. The cell suspensions were then analyzed with FACS and the eGFP+ cells  500 cells for each sample were sorted into lysis buffer. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented  adpator tagged  and purified for further sequencing.,,strain:AB strain|tissue:whole larvae|genotype:wild type|transgene:Tgeslec:eGFP,GSM7854235,GSM7854235: cebp1 wt eos 1; Danio rerio; RNA Seq,GSM7854235 r1,GSM7854235,1,Whole larvae were ground and digested into cell suspensions. The cell suspensions were then analyzed with FACS and the eGFP+ cells  500 cells for each sample were sorted into lysis buffer. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented  adpator tagged  and purified for further sequencing.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP467949,,loader:fastq load.py,W1_2.fq.gz W1_1.fq.gz,fastq fastq,6194437200.0,20648124.0,GSM7854235 r1,0:150 1:150,A:1953684038;C:1067667551;G:1247879965;T:1925172690;N:32956,150,150,,,1953684038,1067667551,1247879965,1925172690,32956,SRX22175826,SRS19233326,SRA1737851,South China University of Technology,South China University of Technology,2,0.76007,0.76295,0.54521,0.54298,0.78244,0.77281,0.62357,0.62562,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,China,2023-10-23,Larval,Larval,Whole Organism,All anatomical structures
28617,SRR26471896,SRX22175825,SRS19233327,SRP467949,PRJNA1031141,Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [bulkRNA Seq],GSE246037,Transcriptome Analysis,Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model  we have identified an eosinophil lineage specific marker  eslec. Using this marker we have established a Tgeslec:eGFP reporter line  which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells  tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis  in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment  differentiation  and maturation of the eosinophil lineage. In summary  this study characterized eosinophil development in multiple dimensions including spatial temporal patterns  expression profiles  and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For the RNA Seq analysis of eosinophils from different genotypes  eslec:eGFP+ eosinophils were sorted from whole larvae 7 dpf and lysed. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented  adpator tagged  and purified for further sequencing.,parent bioproject:PRJNA814534,pubmed:38280871,,cebp1 mut eos 2,GSM7854234,,source name:eosinophils|strain:AB strain|tissue:whole larvae|genotype:cebp1 / |transgene:Tgeslec:eGFP|geo loc name:missing|collection date:missing,cebp1 mut eos 2,"Post quality control  the fastq files were mapped to the zebrafish genome with the ""STAR"" package. Mapped reads were annotated with the ""FeatureCounts"" package. Annotated reads were applied to the ""DESeq2"" package for differential expressed genes analysis. The sample to sample distance heatmaps were generated by ""pheatmap"" with the output of ""DESeq2"". The gene expression heatmaps were generated by ""pheatmap"" with the Z score of the TPM matrix. Assembly: GRCz11 Supplementary files format and content: Normalized matrix table with Transcripts Per Kilobase TPM for every gene and every sample",eosinophils,,Whole larvae were ground and digested into cell suspensions. The cell suspensions were then analyzed with FACS and the eGFP+ cells  500 cells for each sample were sorted into lysis buffer. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented  adpator tagged  and purified for further sequencing.,,strain:AB strain|tissue:whole larvae|genotype:cebp1 / |transgene:Tgeslec:eGFP,GSM7854234,GSM7854234: cebp1 mut eos 2; Danio rerio; RNA Seq,GSM7854234 r1,GSM7854234,1,Whole larvae were ground and digested into cell suspensions. The cell suspensions were then analyzed with FACS and the eGFP+ cells  500 cells for each sample were sorted into lysis buffer. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented  adpator tagged  and purified for further sequencing.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP467949,,loader:fastq load.py,M2_2.fq.gz M2_1.fq.gz,fastq fastq,6104680800.0,20348936.0,GSM7854234 r1,0:150 1:150,A:1804058925;C:1198439018;G:1326225576;T:1775930488;N:26793,150,150,,,1804058925,1198439018,1326225576,1775930488,26793,SRX22175825,SRS19233327,SRA1737851,South China University of Technology,South China University of Technology,2,0.8123,0.81465,0.42735,0.42341,0.78171,0.77567,0.46764,0.65485,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,China,2023-10-23,Larval,Larval,Whole Organism,All anatomical structures
28618,SRR26471897,SRX22175824,SRS19233325,SRP467949,PRJNA1031141,Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [bulkRNA Seq],GSE246037,Transcriptome Analysis,Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model  we have identified an eosinophil lineage specific marker  eslec. Using this marker we have established a Tgeslec:eGFP reporter line  which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells  tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis  in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment  differentiation  and maturation of the eosinophil lineage. In summary  this study characterized eosinophil development in multiple dimensions including spatial temporal patterns  expression profiles  and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For the RNA Seq analysis of eosinophils from different genotypes  eslec:eGFP+ eosinophils were sorted from whole larvae 7 dpf and lysed. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented  adpator tagged  and purified for further sequencing.,parent bioproject:PRJNA814534,pubmed:38280871,,cebp1 mut eos 1,GSM7854233,,source name:eosinophils|strain:AB strain|tissue:whole larvae|genotype:cebp1 / |transgene:Tgeslec:eGFP|geo loc name:missing|collection date:missing,cebp1 mut eos 1,"Post quality control  the fastq files were mapped to the zebrafish genome with the ""STAR"" package. Mapped reads were annotated with the ""FeatureCounts"" package. Annotated reads were applied to the ""DESeq2"" package for differential expressed genes analysis. The sample to sample distance heatmaps were generated by ""pheatmap"" with the output of ""DESeq2"". The gene expression heatmaps were generated by ""pheatmap"" with the Z score of the TPM matrix. Assembly: GRCz11 Supplementary files format and content: Normalized matrix table with Transcripts Per Kilobase TPM for every gene and every sample",eosinophils,,Whole larvae were ground and digested into cell suspensions. The cell suspensions were then analyzed with FACS and the eGFP+ cells  500 cells for each sample were sorted into lysis buffer. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented  adpator tagged  and purified for further sequencing.,,strain:AB strain|tissue:whole larvae|genotype:cebp1 / |transgene:Tgeslec:eGFP,GSM7854233,GSM7854233: cebp1 mut eos 1; Danio rerio; RNA Seq,GSM7854233 r1,GSM7854233,1,Whole larvae were ground and digested into cell suspensions. The cell suspensions were then analyzed with FACS and the eGFP+ cells  500 cells for each sample were sorted into lysis buffer. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented  adpator tagged  and purified for further sequencing.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP467949,,loader:fastq load.py,M1_1.fq.gz M1_2.fq.gz,fastq fastq,6409092000.0,21363640.0,GSM7854233 r1,0:150 1:150,A:1887432519;C:1294546709;G:1354360945;T:1872720156;N:31671,150,150,,,1887432519,1294546709,1354360945,1872720156,31671,SRX22175824,SRS19233325,SRA1737851,South China University of Technology,South China University of Technology,2,0.84504,0.84611,0.39473,0.39207,0.76319,0.75767,0.63936,0.62743,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,China,2023-10-23,Larval,Larval,Whole Organism,All anatomical structures
44530,SRR7868772,SRX4707945,SRS3793646,SRP124607,PRJNA417594,From pioneer to repressor: Bimodal foxd3 activity dynamically remodels neural crest regulatory landscape in vivo,GSE106676,Other,The neural crest NC is a transient embryonic stem cell population characterised by its multipotency and broad developmental potential. Here  we perform NC specific transcriptional and epigenomic profiling of foxd3 mutant versus wild type cells in vivo to define the gene regulatory circuits controlling NC specification. Together with global binding analysis obtained by foxd3 biotin ChIP and single cell profiles of foxd3 expressing premigratory NC  our analysis shows that during early steps of NC formation  foxd3 acts globally as a pioneer factor to prime the onset of genes regulating NC specification and migration by re arranging the chromatin landscape  opening cis regulatory elements and reshuffling nucleosomes. Strikingly  foxd3 then gradually switches from an activator to its previously well described role as a transcriptional repressor. Taken together  these results demonstrate that foxd3 acts bimodally in the neural crest as a switch from 'permissive' to 'repressive' nucleosome/chromatin organisation to maintain multipotency and define cell fates. Overall design: Examination of RNA seq  ATAC seq  histone ChIP seq  Biotin ChIP seq in wild type and foxd3 mutant context at epib stages and in neural crest cells; single cell RNA seq,,pubmed:30513303;pubmed:33111104,,Cit cherry 8ss RNAseq,GSM3393490,,source name:Cit cherry 8ss RNAseq|strain:Gtfoxd3 Citrinect110a x Gtfoxd3 Cherryct110R|tissue:Embryo|development stage:8 somites|cell type:Neural crest foxd3 cells|isolation method:Dissociations and FACS|treatment:  |amplification:Illumina Nextera XT library preparation kit|assay:RNA seq,Cit cherry 8ss RNAseq,ChIP seq and ATAC seq reads were mapped using bowtie v.1.0.0 ChIP seq and ATAC seq: duplicates were removed using MarkDuplicates picard tools/1.83 Input reads were normalised to the same number of ChIP reads by random down sampling using samtools/1.1 ChIP peak calling was performed using Homer v.4.7 findPeaks script using  size 200 minDist 1500 parameters. ATAC seq: All samples were randomly down sampled to the lowest read containing sample 10 443 726 using samtools/1.1. ATAC seq: control tripilactes were merged and experimental triplicate BAM files were merged and sorted using samtools/1.1 ATAC seq:k means clustering of ATAC seq signal was carried out using SeqMINER software as described Ye et al.  2011  using 3.1 enhancer cluster ATAC seq peaks and all pulled foxd3 Biotin ChIP peaks as references for clustering. RNA seq reads were mapped using STAR v.2.4.2a Genome build: danRer10,Cit cherry 8ss RNAseq,,Illumina Nextera XT library preparation kit,,strain:Gtfoxd3 Citrinect110a x Gtfoxd3 Cherryct110R|tissue:Embryo|development stage:8 somites|cell type:Neural crest foxd3 cells|isolation method:Dissociations and FACS|treatment:  |amplification: Illumina Nextera XT library preparation kit|assay:RNA seq,GSM3393490,GSM3393490: Cit cherry 8ss RNAseq; Danio rerio; RNA Seq,GSM3393490,,1,Illumina Nextera XT library preparation kit,GEO Accession:GSM3393490,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP124607,,,WTCHG_116006_202_1.fastq.gz WTCHG_116006_202_2.fastq.gz,fastq fastq,5693168000.0,28465840.0,GSM3393490 r1,0:100 1:100,A:1555377665;C:1242066254;G:1291143037;T:1603783396;N:797648,100,100,,,1555377665,1242066254,1291143037,1603783396,797648,SRX4707945,SRS3793646,SRA629218,GEO,"Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine",2,0.94354,0.92073,0.14213,0.14162,0.74085,0.77181,0.53382,0.51129,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,United Kingdom,2018-09-18,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
44531,SRR7868771,SRX4707944,SRS3793647,SRP124607,PRJNA417594,From pioneer to repressor: Bimodal foxd3 activity dynamically remodels neural crest regulatory landscape in vivo,GSE106676,Other,The neural crest NC is a transient embryonic stem cell population characterised by its multipotency and broad developmental potential. Here  we perform NC specific transcriptional and epigenomic profiling of foxd3 mutant versus wild type cells in vivo to define the gene regulatory circuits controlling NC specification. Together with global binding analysis obtained by foxd3 biotin ChIP and single cell profiles of foxd3 expressing premigratory NC  our analysis shows that during early steps of NC formation  foxd3 acts globally as a pioneer factor to prime the onset of genes regulating NC specification and migration by re arranging the chromatin landscape  opening cis regulatory elements and reshuffling nucleosomes. Strikingly  foxd3 then gradually switches from an activator to its previously well described role as a transcriptional repressor. Taken together  these results demonstrate that foxd3 acts bimodally in the neural crest as a switch from 'permissive' to 'repressive' nucleosome/chromatin organisation to maintain multipotency and define cell fates. Overall design: Examination of RNA seq  ATAC seq  histone ChIP seq  Biotin ChIP seq in wild type and foxd3 mutant context at epib stages and in neural crest cells; single cell RNA seq,,pubmed:30513303;pubmed:33111104,,Cit 8ss RNAseq,GSM3393489,,source name:Cit 8ss RNAseq|strain:Gtfoxd3 Citrinect110a|tissue:Embryo|development stage:8 somites|cell type:Neural crest foxd3 cells|isolation method:Dissociations and FACS|treatment:  |amplification:Illumina Nextera XT library preparation kit|assay:RNA seq,Cit 8ss RNAseq,ChIP seq and ATAC seq reads were mapped using bowtie v.1.0.0 ChIP seq and ATAC seq: duplicates were removed using MarkDuplicates picard tools/1.83 Input reads were normalised to the same number of ChIP reads by random down sampling using samtools/1.1 ChIP peak calling was performed using Homer v.4.7 findPeaks script using  size 200 minDist 1500 parameters. ATAC seq: All samples were randomly down sampled to the lowest read containing sample 10 443 726 using samtools/1.1. ATAC seq: control tripilactes were merged and experimental triplicate BAM files were merged and sorted using samtools/1.1 ATAC seq:k means clustering of ATAC seq signal was carried out using SeqMINER software as described Ye et al.  2011  using 3.1 enhancer cluster ATAC seq peaks and all pulled foxd3 Biotin ChIP peaks as references for clustering. RNA seq reads were mapped using STAR v.2.4.2a Genome build: danRer10,Cit 8ss RNAseq,,Illumina Nextera XT library preparation kit,,strain:Gtfoxd3 Citrinect110a|tissue:Embryo|development stage:8 somites|cell type:Neural crest foxd3 cells|isolation method:Dissociations and FACS|treatment:  |amplification: Illumina Nextera XT library preparation kit|assay:RNA seq,GSM3393489,GSM3393489: Cit 8ss RNAseq; Danio rerio; RNA Seq,GSM3393489,,1,Illumina Nextera XT library preparation kit,GEO Accession:GSM3393489,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP124607,,,WTCHG_116006_201_1.fastq.gz WTCHG_116006_201_2.fastq.gz,fastq fastq,4981486000.0,24907430.0,GSM3393489 r1,0:100 1:100,A:1360272094;C:1090492330;G:1142929599;T:1387078225;N:713752,100,100,,,1360272094,1090492330,1142929599,1387078225,713752,SRX4707944,SRS3793647,SRA629218,GEO,"Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine",2,0.94827,0.92512,0.12816,0.13505,0.74554,0.77613,0.51991,0.49505,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc_generic,single_cell_generic,generic-scrnaseq-only,,United Kingdom,2018-09-18,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
60875,SRR12623500,SRX9106225,SRS7349642,SRP282042,PRJNA662909,Nanoplastics and sunscreens contained in personal care products induce neurotoxicity in early zebrafish embryos,GSE157816,Transcriptome Analysis,Nanoplastics with small particle size and high surface area/volume ratio make them easy to absorb environmental pollutants and affect their bioavailability. In this study  polystyrene nanoplastic beads PS NPBs with a particle size of 100nm and sunscreen butyl methoxydibenzoylmethane BMDBM contained in personal care products were chosen as target pollutants to study their developmental toxicity and interactive effects on zebrafish embryo. The exposure period was 2 hpf 12 hpf. The BMDBM and PS NPBs significantly upregulated the genes related to antioxidant enzymes and downregulated the gene expression of aromatase and DNA methyltransferases  but the influenced genes were not exactly the same  and the combined exposure reduced the adverse effects on the expression of all genes. With the help of single cell RNA sequencing technology  the neural mid cells were identified as the target cells of both pollutants  and brain development  head development and notch signaling pathway were the functions they commonly altered. The key genes and functions that are specifically affected by BMDBM and/or PS NPBs were identified. The BMDBM mainly affect the differentiation and fate of neurons in central nervous system through the regulation of her5  her6  her11  lfng  pax2a and fgfr4. The PS NPBs regulated the expression of olig2  foxg1a  fzd8b  six3a  rx1  lhx2b  nkx2.1a and sfrp5 to alter nervous system development  retinal development  and stem cell differentiation. The phenotypic responses of zebrafish larvae at 120 hpf were tested  and significant inhibition of locomotor activity was found  indicating that early disrupting effect on central nervous system would have a sustained impact on the behavior of zebrafish. Overall design: mRNA profiles of 12 hpf wild type zebrafish embryos,,,,BMDBM+MPs,GSM4775402,,tissue:emberyo|treatment:exposed to BMDBM and MPs|age:12 hpf|genotype:wild type,BMDBM+MPs,Seurat package in R version 3.5.2 was used to analyze the sequenced reads. Principal component analysis PCA was used for dimensionality reduction and a graph based clustering was applied to cluster in PCA space. UMAP was used for the visualization of the clusters. The marker genes of each cluster were identified by FindMarkers function in the Seurat package. The clusters were annotated to a known cell type according to the Zebrafish Information Network ZFIN database and current literature Genome build: mm10 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell,emberyo,,post exposure  forty embryos collected from each group were transferred to 1 mL phosphate buffer saline PBS with 1% bovine serum albumin BSA. post incubated in 0.5 mL Hank's balanced salt solution HBSS containing 0.6 U/mL of dispase Yuanye Biotechnology  Shanghai  China at 37 °C for 5 min  100 µL of fetal bovine serum FBS was added to stop digestion. The cell suspension was filtered through a 40 µm filter and washed by 1% BSA HBSS. The cells were finally transferred to 1 mL PBS in preparation for single cell sequencing. The obtained cells were loaded on a GemCode Single Cell Instrument 10× Genomics  Pleasanton  USA to generate single cell gel beads in the emulsion. ScRNA seq libraries were prepared using the GemCode Single Cell 3′ Gel Bead  Chip and Library Kits 10× Genomics  Pleasanton  USA.,,treatment:exposed to BMDBM and MPs|age:12 hpf|genotype:wild type,GSM4775402,GSM4775402: BMDBM+MPs; Danio rerio; RNA Seq,GSM4775402,,1,post exposure  forty embryos collected from each group were transferred to 1 mL phosphate buffer saline PBS with 1% bovine serum albumin BSA. post incubated in 0.5 mL Hank's balanced salt solution HBSS containing 0.6 U/mL of dispase Yuanye Biotechnology  Shanghai  China at 37 °C for 5 min  100 µL of fetal bovine serum FBS was added to stop digestion. The cell suspension was filtered through a 40 µm filter and washed by 1% BSA HBSS. The cells were finally transferred to 1 mL PBS in preparation for single cell sequencing. The obtained cells were loaded on a GemCode Single Cell Instrument 10× Genomics  Pleasanton  USA to generate single cell gel beads in the emulsion. ScRNA seq libraries were prepared using the GemCode Single Cell 3′ Gel Bead  Chip and Library Kits 10× Genomics  Pleasanton  USA.,GEO Accession:GSM4775402,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP282042,,,BMDBM_MPs_S3_L007_I1_001.fastq.gz,fastq,3620111768.0,452513971.0,GSM4775402 r1,0:8 1:0,A:924051959;C:918558406;G:941209576;T:833464242;N:2827585,8,0,,,924051959,918558406,941209576,833464242,2827585,SRX9106225,SRS7349642,SRA1123780,GEO,HOHAI,1,0.0,,0.0,,1.0,,,,8,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,China,2020-09-11,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
60876,SRR12623501,SRX9106225,SRS7349642,SRP282042,PRJNA662909,Nanoplastics and sunscreens contained in personal care products induce neurotoxicity in early zebrafish embryos,GSE157816,Transcriptome Analysis,Nanoplastics with small particle size and high surface area/volume ratio make them easy to absorb environmental pollutants and affect their bioavailability. In this study  polystyrene nanoplastic beads PS NPBs with a particle size of 100nm and sunscreen butyl methoxydibenzoylmethane BMDBM contained in personal care products were chosen as target pollutants to study their developmental toxicity and interactive effects on zebrafish embryo. The exposure period was 2 hpf 12 hpf. The BMDBM and PS NPBs significantly upregulated the genes related to antioxidant enzymes and downregulated the gene expression of aromatase and DNA methyltransferases  but the influenced genes were not exactly the same  and the combined exposure reduced the adverse effects on the expression of all genes. With the help of single cell RNA sequencing technology  the neural mid cells were identified as the target cells of both pollutants  and brain development  head development and notch signaling pathway were the functions they commonly altered. The key genes and functions that are specifically affected by BMDBM and/or PS NPBs were identified. The BMDBM mainly affect the differentiation and fate of neurons in central nervous system through the regulation of her5  her6  her11  lfng  pax2a and fgfr4. The PS NPBs regulated the expression of olig2  foxg1a  fzd8b  six3a  rx1  lhx2b  nkx2.1a and sfrp5 to alter nervous system development  retinal development  and stem cell differentiation. The phenotypic responses of zebrafish larvae at 120 hpf were tested  and significant inhibition of locomotor activity was found  indicating that early disrupting effect on central nervous system would have a sustained impact on the behavior of zebrafish. Overall design: mRNA profiles of 12 hpf wild type zebrafish embryos,,,,BMDBM+MPs,GSM4775402,,tissue:emberyo|treatment:exposed to BMDBM and MPs|age:12 hpf|genotype:wild type,BMDBM+MPs,Seurat package in R version 3.5.2 was used to analyze the sequenced reads. Principal component analysis PCA was used for dimensionality reduction and a graph based clustering was applied to cluster in PCA space. UMAP was used for the visualization of the clusters. The marker genes of each cluster were identified by FindMarkers function in the Seurat package. The clusters were annotated to a known cell type according to the Zebrafish Information Network ZFIN database and current literature Genome build: mm10 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell,emberyo,,post exposure  forty embryos collected from each group were transferred to 1 mL phosphate buffer saline PBS with 1% bovine serum albumin BSA. post incubated in 0.5 mL Hank's balanced salt solution HBSS containing 0.6 U/mL of dispase Yuanye Biotechnology  Shanghai  China at 37 °C for 5 min  100 µL of fetal bovine serum FBS was added to stop digestion. The cell suspension was filtered through a 40 µm filter and washed by 1% BSA HBSS. The cells were finally transferred to 1 mL PBS in preparation for single cell sequencing. The obtained cells were loaded on a GemCode Single Cell Instrument 10× Genomics  Pleasanton  USA to generate single cell gel beads in the emulsion. ScRNA seq libraries were prepared using the GemCode Single Cell 3′ Gel Bead  Chip and Library Kits 10× Genomics  Pleasanton  USA.,,treatment:exposed to BMDBM and MPs|age:12 hpf|genotype:wild type,GSM4775402,GSM4775402: BMDBM+MPs; Danio rerio; RNA Seq,GSM4775402,,1,post exposure  forty embryos collected from each group were transferred to 1 mL phosphate buffer saline PBS with 1% bovine serum albumin BSA. post incubated in 0.5 mL Hank's balanced salt solution HBSS containing 0.6 U/mL of dispase Yuanye Biotechnology  Shanghai  China at 37 °C for 5 min  100 µL of fetal bovine serum FBS was added to stop digestion. The cell suspension was filtered through a 40 µm filter and washed by 1% BSA HBSS. The cells were finally transferred to 1 mL PBS in preparation for single cell sequencing. The obtained cells were loaded on a GemCode Single Cell Instrument 10× Genomics  Pleasanton  USA to generate single cell gel beads in the emulsion. ScRNA seq libraries were prepared using the GemCode Single Cell 3′ Gel Bead  Chip and Library Kits 10× Genomics  Pleasanton  USA.,GEO Accession:GSM4775402,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP282042,,,BMDBM_MPs_S3_L007_R1_001.fastq.gz,fastq,68329609621.0,452513971.0,GSM4775402 r2,0:151 1:0,A:15968867427;C:10386534473;G:9436335438;T:32534409412;N:3462871,151,0,,,15968867427,10386534473,9436335438,32534409412,3462871,SRX9106225,SRS7349642,SRA1123780,GEO,HOHAI,1,0.10852,,0.01154,,0.96708,,0.50742,,151,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,China,2020-09-11,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
60877,SRR12623502,SRX9106225,SRS7349642,SRP282042,PRJNA662909,Nanoplastics and sunscreens contained in personal care products induce neurotoxicity in early zebrafish embryos,GSE157816,Transcriptome Analysis,Nanoplastics with small particle size and high surface area/volume ratio make them easy to absorb environmental pollutants and affect their bioavailability. In this study  polystyrene nanoplastic beads PS NPBs with a particle size of 100nm and sunscreen butyl methoxydibenzoylmethane BMDBM contained in personal care products were chosen as target pollutants to study their developmental toxicity and interactive effects on zebrafish embryo. The exposure period was 2 hpf 12 hpf. The BMDBM and PS NPBs significantly upregulated the genes related to antioxidant enzymes and downregulated the gene expression of aromatase and DNA methyltransferases  but the influenced genes were not exactly the same  and the combined exposure reduced the adverse effects on the expression of all genes. With the help of single cell RNA sequencing technology  the neural mid cells were identified as the target cells of both pollutants  and brain development  head development and notch signaling pathway were the functions they commonly altered. The key genes and functions that are specifically affected by BMDBM and/or PS NPBs were identified. The BMDBM mainly affect the differentiation and fate of neurons in central nervous system through the regulation of her5  her6  her11  lfng  pax2a and fgfr4. The PS NPBs regulated the expression of olig2  foxg1a  fzd8b  six3a  rx1  lhx2b  nkx2.1a and sfrp5 to alter nervous system development  retinal development  and stem cell differentiation. The phenotypic responses of zebrafish larvae at 120 hpf were tested  and significant inhibition of locomotor activity was found  indicating that early disrupting effect on central nervous system would have a sustained impact on the behavior of zebrafish. Overall design: mRNA profiles of 12 hpf wild type zebrafish embryos,,,,BMDBM+MPs,GSM4775402,,tissue:emberyo|treatment:exposed to BMDBM and MPs|age:12 hpf|genotype:wild type,BMDBM+MPs,Seurat package in R version 3.5.2 was used to analyze the sequenced reads. Principal component analysis PCA was used for dimensionality reduction and a graph based clustering was applied to cluster in PCA space. UMAP was used for the visualization of the clusters. The marker genes of each cluster were identified by FindMarkers function in the Seurat package. The clusters were annotated to a known cell type according to the Zebrafish Information Network ZFIN database and current literature Genome build: mm10 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell,emberyo,,post exposure  forty embryos collected from each group were transferred to 1 mL phosphate buffer saline PBS with 1% bovine serum albumin BSA. post incubated in 0.5 mL Hank's balanced salt solution HBSS containing 0.6 U/mL of dispase Yuanye Biotechnology  Shanghai  China at 37 °C for 5 min  100 µL of fetal bovine serum FBS was added to stop digestion. The cell suspension was filtered through a 40 µm filter and washed by 1% BSA HBSS. The cells were finally transferred to 1 mL PBS in preparation for single cell sequencing. The obtained cells were loaded on a GemCode Single Cell Instrument 10× Genomics  Pleasanton  USA to generate single cell gel beads in the emulsion. ScRNA seq libraries were prepared using the GemCode Single Cell 3′ Gel Bead  Chip and Library Kits 10× Genomics  Pleasanton  USA.,,treatment:exposed to BMDBM and MPs|age:12 hpf|genotype:wild type,GSM4775402,GSM4775402: BMDBM+MPs; Danio rerio; RNA Seq,GSM4775402,,1,post exposure  forty embryos collected from each group were transferred to 1 mL phosphate buffer saline PBS with 1% bovine serum albumin BSA. post incubated in 0.5 mL Hank's balanced salt solution HBSS containing 0.6 U/mL of dispase Yuanye Biotechnology  Shanghai  China at 37 °C for 5 min  100 µL of fetal bovine serum FBS was added to stop digestion. The cell suspension was filtered through a 40 µm filter and washed by 1% BSA HBSS. The cells were finally transferred to 1 mL PBS in preparation for single cell sequencing. The obtained cells were loaded on a GemCode Single Cell Instrument 10× Genomics  Pleasanton  USA to generate single cell gel beads in the emulsion. ScRNA seq libraries were prepared using the GemCode Single Cell 3′ Gel Bead  Chip and Library Kits 10× Genomics  Pleasanton  USA.,GEO Accession:GSM4775402,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP282042,,,BMDBM_MPs_S3_L007_R2_001.fastq.gz,fastq,68329609621.0,452513971.0,GSM4775402 r3,0:0 1:151,A:19536873897;C:13980215147;G:15484746923;T:19320520134;N:7253520,0,151,,,19536873897,13980215147,15484746923,19320520134,7253520,SRX9106225,SRS7349642,SRA1123780,GEO,HOHAI,1,0.91212,,0.13005,,0.7892,,0.5032,,151,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,China,2020-09-11,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
60878,SRR12623497,SRX9106224,SRS7349641,SRP282042,PRJNA662909,Nanoplastics and sunscreens contained in personal care products induce neurotoxicity in early zebrafish embryos,GSE157816,Transcriptome Analysis,Nanoplastics with small particle size and high surface area/volume ratio make them easy to absorb environmental pollutants and affect their bioavailability. In this study  polystyrene nanoplastic beads PS NPBs with a particle size of 100nm and sunscreen butyl methoxydibenzoylmethane BMDBM contained in personal care products were chosen as target pollutants to study their developmental toxicity and interactive effects on zebrafish embryo. The exposure period was 2 hpf 12 hpf. The BMDBM and PS NPBs significantly upregulated the genes related to antioxidant enzymes and downregulated the gene expression of aromatase and DNA methyltransferases  but the influenced genes were not exactly the same  and the combined exposure reduced the adverse effects on the expression of all genes. With the help of single cell RNA sequencing technology  the neural mid cells were identified as the target cells of both pollutants  and brain development  head development and notch signaling pathway were the functions they commonly altered. The key genes and functions that are specifically affected by BMDBM and/or PS NPBs were identified. The BMDBM mainly affect the differentiation and fate of neurons in central nervous system through the regulation of her5  her6  her11  lfng  pax2a and fgfr4. The PS NPBs regulated the expression of olig2  foxg1a  fzd8b  six3a  rx1  lhx2b  nkx2.1a and sfrp5 to alter nervous system development  retinal development  and stem cell differentiation. The phenotypic responses of zebrafish larvae at 120 hpf were tested  and significant inhibition of locomotor activity was found  indicating that early disrupting effect on central nervous system would have a sustained impact on the behavior of zebrafish. Overall design: mRNA profiles of 12 hpf wild type zebrafish embryos,,,,MPs,GSM4775401,,tissue:emberyo|treatment:exposed to MPs|age:12 hpf|genotype:wild type,MPs,Seurat package in R version 3.5.2 was used to analyze the sequenced reads. Principal component analysis PCA was used for dimensionality reduction and a graph based clustering was applied to cluster in PCA space. UMAP was used for the visualization of the clusters. The marker genes of each cluster were identified by FindMarkers function in the Seurat package. The clusters were annotated to a known cell type according to the Zebrafish Information Network ZFIN database and current literature Genome build: mm10 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell,emberyo,,post exposure  forty embryos collected from each group were transferred to 1 mL phosphate buffer saline PBS with 1% bovine serum albumin BSA. post incubated in 0.5 mL Hank's balanced salt solution HBSS containing 0.6 U/mL of dispase Yuanye Biotechnology  Shanghai  China at 37 °C for 5 min  100 µL of fetal bovine serum FBS was added to stop digestion. The cell suspension was filtered through a 40 µm filter and washed by 1% BSA HBSS. The cells were finally transferred to 1 mL PBS in preparation for single cell sequencing. The obtained cells were loaded on a GemCode Single Cell Instrument 10× Genomics  Pleasanton  USA to generate single cell gel beads in the emulsion. ScRNA seq libraries were prepared using the GemCode Single Cell 3′ Gel Bead  Chip and Library Kits 10× Genomics  Pleasanton  USA.,,treatment:exposed to MPs|age:12 hpf|genotype:wild type,GSM4775401,GSM4775401: MPs; Danio rerio; RNA Seq,GSM4775401,,1,post exposure  forty embryos collected from each group were transferred to 1 mL phosphate buffer saline PBS with 1% bovine serum albumin BSA. post incubated in 0.5 mL Hank's balanced salt solution HBSS containing 0.6 U/mL of dispase Yuanye Biotechnology  Shanghai  China at 37 °C for 5 min  100 µL of fetal bovine serum FBS was added to stop digestion. The cell suspension was filtered through a 40 µm filter and washed by 1% BSA HBSS. The cells were finally transferred to 1 mL PBS in preparation for single cell sequencing. The obtained cells were loaded on a GemCode Single Cell Instrument 10× Genomics  Pleasanton  USA to generate single cell gel beads in the emulsion. ScRNA seq libraries were prepared using the GemCode Single Cell 3′ Gel Bead  Chip and Library Kits 10× Genomics  Pleasanton  USA.,GEO Accession:GSM4775401,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP282042,,,MPs_S2_L006_I1_001.fastq.gz,fastq,3659913904.0,457489238.0,GSM4775401 r1,0:8 1:0,A:886140861;C:1122590125;G:954712949;T:692928663;N:3541306,8,0,,,886140861,1122590125,954712949,692928663,3541306,SRX9106224,SRS7349641,SRA1123780,GEO,HOHAI,1,0.0,,0.0,,1.0,,,,8,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,China,2020-09-11,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
60879,SRR12623498,SRX9106224,SRS7349641,SRP282042,PRJNA662909,Nanoplastics and sunscreens contained in personal care products induce neurotoxicity in early zebrafish embryos,GSE157816,Transcriptome Analysis,Nanoplastics with small particle size and high surface area/volume ratio make them easy to absorb environmental pollutants and affect their bioavailability. In this study  polystyrene nanoplastic beads PS NPBs with a particle size of 100nm and sunscreen butyl methoxydibenzoylmethane BMDBM contained in personal care products were chosen as target pollutants to study their developmental toxicity and interactive effects on zebrafish embryo. The exposure period was 2 hpf 12 hpf. The BMDBM and PS NPBs significantly upregulated the genes related to antioxidant enzymes and downregulated the gene expression of aromatase and DNA methyltransferases  but the influenced genes were not exactly the same  and the combined exposure reduced the adverse effects on the expression of all genes. With the help of single cell RNA sequencing technology  the neural mid cells were identified as the target cells of both pollutants  and brain development  head development and notch signaling pathway were the functions they commonly altered. The key genes and functions that are specifically affected by BMDBM and/or PS NPBs were identified. The BMDBM mainly affect the differentiation and fate of neurons in central nervous system through the regulation of her5  her6  her11  lfng  pax2a and fgfr4. The PS NPBs regulated the expression of olig2  foxg1a  fzd8b  six3a  rx1  lhx2b  nkx2.1a and sfrp5 to alter nervous system development  retinal development  and stem cell differentiation. The phenotypic responses of zebrafish larvae at 120 hpf were tested  and significant inhibition of locomotor activity was found  indicating that early disrupting effect on central nervous system would have a sustained impact on the behavior of zebrafish. Overall design: mRNA profiles of 12 hpf wild type zebrafish embryos,,,,MPs,GSM4775401,,tissue:emberyo|treatment:exposed to MPs|age:12 hpf|genotype:wild type,MPs,Seurat package in R version 3.5.2 was used to analyze the sequenced reads. Principal component analysis PCA was used for dimensionality reduction and a graph based clustering was applied to cluster in PCA space. UMAP was used for the visualization of the clusters. The marker genes of each cluster were identified by FindMarkers function in the Seurat package. The clusters were annotated to a known cell type according to the Zebrafish Information Network ZFIN database and current literature Genome build: mm10 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell,emberyo,,post exposure  forty embryos collected from each group were transferred to 1 mL phosphate buffer saline PBS with 1% bovine serum albumin BSA. post incubated in 0.5 mL Hank's balanced salt solution HBSS containing 0.6 U/mL of dispase Yuanye Biotechnology  Shanghai  China at 37 °C for 5 min  100 µL of fetal bovine serum FBS was added to stop digestion. The cell suspension was filtered through a 40 µm filter and washed by 1% BSA HBSS. The cells were finally transferred to 1 mL PBS in preparation for single cell sequencing. The obtained cells were loaded on a GemCode Single Cell Instrument 10× Genomics  Pleasanton  USA to generate single cell gel beads in the emulsion. ScRNA seq libraries were prepared using the GemCode Single Cell 3′ Gel Bead  Chip and Library Kits 10× Genomics  Pleasanton  USA.,,treatment:exposed to MPs|age:12 hpf|genotype:wild type,GSM4775401,GSM4775401: MPs; Danio rerio; RNA Seq,GSM4775401,,1,post exposure  forty embryos collected from each group were transferred to 1 mL phosphate buffer saline PBS with 1% bovine serum albumin BSA. post incubated in 0.5 mL Hank's balanced salt solution HBSS containing 0.6 U/mL of dispase Yuanye Biotechnology  Shanghai  China at 37 °C for 5 min  100 µL of fetal bovine serum FBS was added to stop digestion. The cell suspension was filtered through a 40 µm filter and washed by 1% BSA HBSS. The cells were finally transferred to 1 mL PBS in preparation for single cell sequencing. The obtained cells were loaded on a GemCode Single Cell Instrument 10× Genomics  Pleasanton  USA to generate single cell gel beads in the emulsion. ScRNA seq libraries were prepared using the GemCode Single Cell 3′ Gel Bead  Chip and Library Kits 10× Genomics  Pleasanton  USA.,GEO Accession:GSM4775401,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP282042,,,MPs_S2_L006_R1_001.fastq.gz,fastq,69080874938.0,457489238.0,GSM4775401 r2,0:151 1:0,A:16058446984;C:10537982472;G:9566377499;T:32913863031;N:4204952,151,0,,,16058446984,10537982472,9566377499,32913863031,4204952,SRX9106224,SRS7349641,SRA1123780,GEO,HOHAI,1,0.10674,,0.01242,,0.96621,,0.50529,,151,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,China,2020-09-11,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
60880,SRR12623499,SRX9106224,SRS7349641,SRP282042,PRJNA662909,Nanoplastics and sunscreens contained in personal care products induce neurotoxicity in early zebrafish embryos,GSE157816,Transcriptome Analysis,Nanoplastics with small particle size and high surface area/volume ratio make them easy to absorb environmental pollutants and affect their bioavailability. In this study  polystyrene nanoplastic beads PS NPBs with a particle size of 100nm and sunscreen butyl methoxydibenzoylmethane BMDBM contained in personal care products were chosen as target pollutants to study their developmental toxicity and interactive effects on zebrafish embryo. The exposure period was 2 hpf 12 hpf. The BMDBM and PS NPBs significantly upregulated the genes related to antioxidant enzymes and downregulated the gene expression of aromatase and DNA methyltransferases  but the influenced genes were not exactly the same  and the combined exposure reduced the adverse effects on the expression of all genes. With the help of single cell RNA sequencing technology  the neural mid cells were identified as the target cells of both pollutants  and brain development  head development and notch signaling pathway were the functions they commonly altered. The key genes and functions that are specifically affected by BMDBM and/or PS NPBs were identified. The BMDBM mainly affect the differentiation and fate of neurons in central nervous system through the regulation of her5  her6  her11  lfng  pax2a and fgfr4. The PS NPBs regulated the expression of olig2  foxg1a  fzd8b  six3a  rx1  lhx2b  nkx2.1a and sfrp5 to alter nervous system development  retinal development  and stem cell differentiation. The phenotypic responses of zebrafish larvae at 120 hpf were tested  and significant inhibition of locomotor activity was found  indicating that early disrupting effect on central nervous system would have a sustained impact on the behavior of zebrafish. Overall design: mRNA profiles of 12 hpf wild type zebrafish embryos,,,,MPs,GSM4775401,,tissue:emberyo|treatment:exposed to MPs|age:12 hpf|genotype:wild type,MPs,Seurat package in R version 3.5.2 was used to analyze the sequenced reads. Principal component analysis PCA was used for dimensionality reduction and a graph based clustering was applied to cluster in PCA space. UMAP was used for the visualization of the clusters. The marker genes of each cluster were identified by FindMarkers function in the Seurat package. The clusters were annotated to a known cell type according to the Zebrafish Information Network ZFIN database and current literature Genome build: mm10 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell,emberyo,,post exposure  forty embryos collected from each group were transferred to 1 mL phosphate buffer saline PBS with 1% bovine serum albumin BSA. post incubated in 0.5 mL Hank's balanced salt solution HBSS containing 0.6 U/mL of dispase Yuanye Biotechnology  Shanghai  China at 37 °C for 5 min  100 µL of fetal bovine serum FBS was added to stop digestion. The cell suspension was filtered through a 40 µm filter and washed by 1% BSA HBSS. The cells were finally transferred to 1 mL PBS in preparation for single cell sequencing. The obtained cells were loaded on a GemCode Single Cell Instrument 10× Genomics  Pleasanton  USA to generate single cell gel beads in the emulsion. ScRNA seq libraries were prepared using the GemCode Single Cell 3′ Gel Bead  Chip and Library Kits 10× Genomics  Pleasanton  USA.,,treatment:exposed to MPs|age:12 hpf|genotype:wild type,GSM4775401,GSM4775401: MPs; Danio rerio; RNA Seq,GSM4775401,,1,post exposure  forty embryos collected from each group were transferred to 1 mL phosphate buffer saline PBS with 1% bovine serum albumin BSA. post incubated in 0.5 mL Hank's balanced salt solution HBSS containing 0.6 U/mL of dispase Yuanye Biotechnology  Shanghai  China at 37 °C for 5 min  100 µL of fetal bovine serum FBS was added to stop digestion. The cell suspension was filtered through a 40 µm filter and washed by 1% BSA HBSS. The cells were finally transferred to 1 mL PBS in preparation for single cell sequencing. The obtained cells were loaded on a GemCode Single Cell Instrument 10× Genomics  Pleasanton  USA to generate single cell gel beads in the emulsion. ScRNA seq libraries were prepared using the GemCode Single Cell 3′ Gel Bead  Chip and Library Kits 10× Genomics  Pleasanton  USA.,GEO Accession:GSM4775401,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP282042,,,MPs_S2_L006_R2_001.fastq.gz,fastq,69080874938.0,457489238.0,GSM4775401 r3,0:0 1:151,A:19750564621;C:14246380787;G:15737229467;T:19336788954;N:9911109,0,151,,,19750564621,14246380787,15737229467,19336788954,9911109,SRX9106224,SRS7349641,SRA1123780,GEO,HOHAI,1,0.91283,,0.12317,,0.78709,,0.50722,,151,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,China,2020-09-11,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
60881,SRR12623494,SRX9106223,SRS7349639,SRP282042,PRJNA662909,Nanoplastics and sunscreens contained in personal care products induce neurotoxicity in early zebrafish embryos,GSE157816,Transcriptome Analysis,Nanoplastics with small particle size and high surface area/volume ratio make them easy to absorb environmental pollutants and affect their bioavailability. In this study  polystyrene nanoplastic beads PS NPBs with a particle size of 100nm and sunscreen butyl methoxydibenzoylmethane BMDBM contained in personal care products were chosen as target pollutants to study their developmental toxicity and interactive effects on zebrafish embryo. The exposure period was 2 hpf 12 hpf. The BMDBM and PS NPBs significantly upregulated the genes related to antioxidant enzymes and downregulated the gene expression of aromatase and DNA methyltransferases  but the influenced genes were not exactly the same  and the combined exposure reduced the adverse effects on the expression of all genes. With the help of single cell RNA sequencing technology  the neural mid cells were identified as the target cells of both pollutants  and brain development  head development and notch signaling pathway were the functions they commonly altered. The key genes and functions that are specifically affected by BMDBM and/or PS NPBs were identified. The BMDBM mainly affect the differentiation and fate of neurons in central nervous system through the regulation of her5  her6  her11  lfng  pax2a and fgfr4. The PS NPBs regulated the expression of olig2  foxg1a  fzd8b  six3a  rx1  lhx2b  nkx2.1a and sfrp5 to alter nervous system development  retinal development  and stem cell differentiation. The phenotypic responses of zebrafish larvae at 120 hpf were tested  and significant inhibition of locomotor activity was found  indicating that early disrupting effect on central nervous system would have a sustained impact on the behavior of zebrafish. Overall design: mRNA profiles of 12 hpf wild type zebrafish embryos,,,,BMDBM,GSM4775400,,tissue:emberyo|treatment:exposed to BMDBM|age:12 hpf|genotype:wild type,BMDBM,Seurat package in R version 3.5.2 was used to analyze the sequenced reads. Principal component analysis PCA was used for dimensionality reduction and a graph based clustering was applied to cluster in PCA space. UMAP was used for the visualization of the clusters. The marker genes of each cluster were identified by FindMarkers function in the Seurat package. The clusters were annotated to a known cell type according to the Zebrafish Information Network ZFIN database and current literature Genome build: mm10 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell,emberyo,,post exposure  forty embryos collected from each group were transferred to 1 mL phosphate buffer saline PBS with 1% bovine serum albumin BSA. post incubated in 0.5 mL Hank's balanced salt solution HBSS containing 0.6 U/mL of dispase Yuanye Biotechnology  Shanghai  China at 37 °C for 5 min  100 µL of fetal bovine serum FBS was added to stop digestion. The cell suspension was filtered through a 40 µm filter and washed by 1% BSA HBSS. The cells were finally transferred to 1 mL PBS in preparation for single cell sequencing. The obtained cells were loaded on a GemCode Single Cell Instrument 10× Genomics  Pleasanton  USA to generate single cell gel beads in the emulsion. ScRNA seq libraries were prepared using the GemCode Single Cell 3′ Gel Bead  Chip and Library Kits 10× Genomics  Pleasanton  USA.,,treatment:exposed to BMDBM|age:12 hpf|genotype:wild type,GSM4775400,GSM4775400: BMDBM; Danio rerio; RNA Seq,GSM4775400,,1,post exposure  forty embryos collected from each group were transferred to 1 mL phosphate buffer saline PBS with 1% bovine serum albumin BSA. post incubated in 0.5 mL Hank's balanced salt solution HBSS containing 0.6 U/mL of dispase Yuanye Biotechnology  Shanghai  China at 37 °C for 5 min  100 µL of fetal bovine serum FBS was added to stop digestion. The cell suspension was filtered through a 40 µm filter and washed by 1% BSA HBSS. The cells were finally transferred to 1 mL PBS in preparation for single cell sequencing. The obtained cells were loaded on a GemCode Single Cell Instrument 10× Genomics  Pleasanton  USA to generate single cell gel beads in the emulsion. ScRNA seq libraries were prepared using the GemCode Single Cell 3′ Gel Bead  Chip and Library Kits 10× Genomics  Pleasanton  USA.,GEO Accession:GSM4775400,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP282042,,,BMDBM_S1_L005_I1_001.fastq.gz,fastq,3694225840.0,461778230.0,GSM4775400 r1,0:8 1:0,A:935556783;C:904215986;G:936380692;T:913315503;N:4756876,8,0,,,935556783,904215986,936380692,913315503,4756876,SRX9106223,SRS7349639,SRA1123780,GEO,HOHAI,1,0.0,,0.0,,1.0,,,,8,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,China,2020-09-11,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
60882,SRR12623495,SRX9106223,SRS7349639,SRP282042,PRJNA662909,Nanoplastics and sunscreens contained in personal care products induce neurotoxicity in early zebrafish embryos,GSE157816,Transcriptome Analysis,Nanoplastics with small particle size and high surface area/volume ratio make them easy to absorb environmental pollutants and affect their bioavailability. In this study  polystyrene nanoplastic beads PS NPBs with a particle size of 100nm and sunscreen butyl methoxydibenzoylmethane BMDBM contained in personal care products were chosen as target pollutants to study their developmental toxicity and interactive effects on zebrafish embryo. The exposure period was 2 hpf 12 hpf. The BMDBM and PS NPBs significantly upregulated the genes related to antioxidant enzymes and downregulated the gene expression of aromatase and DNA methyltransferases  but the influenced genes were not exactly the same  and the combined exposure reduced the adverse effects on the expression of all genes. With the help of single cell RNA sequencing technology  the neural mid cells were identified as the target cells of both pollutants  and brain development  head development and notch signaling pathway were the functions they commonly altered. The key genes and functions that are specifically affected by BMDBM and/or PS NPBs were identified. The BMDBM mainly affect the differentiation and fate of neurons in central nervous system through the regulation of her5  her6  her11  lfng  pax2a and fgfr4. The PS NPBs regulated the expression of olig2  foxg1a  fzd8b  six3a  rx1  lhx2b  nkx2.1a and sfrp5 to alter nervous system development  retinal development  and stem cell differentiation. The phenotypic responses of zebrafish larvae at 120 hpf were tested  and significant inhibition of locomotor activity was found  indicating that early disrupting effect on central nervous system would have a sustained impact on the behavior of zebrafish. Overall design: mRNA profiles of 12 hpf wild type zebrafish embryos,,,,BMDBM,GSM4775400,,tissue:emberyo|treatment:exposed to BMDBM|age:12 hpf|genotype:wild type,BMDBM,Seurat package in R version 3.5.2 was used to analyze the sequenced reads. Principal component analysis PCA was used for dimensionality reduction and a graph based clustering was applied to cluster in PCA space. UMAP was used for the visualization of the clusters. The marker genes of each cluster were identified by FindMarkers function in the Seurat package. The clusters were annotated to a known cell type according to the Zebrafish Information Network ZFIN database and current literature Genome build: mm10 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell,emberyo,,post exposure  forty embryos collected from each group were transferred to 1 mL phosphate buffer saline PBS with 1% bovine serum albumin BSA. post incubated in 0.5 mL Hank's balanced salt solution HBSS containing 0.6 U/mL of dispase Yuanye Biotechnology  Shanghai  China at 37 °C for 5 min  100 µL of fetal bovine serum FBS was added to stop digestion. The cell suspension was filtered through a 40 µm filter and washed by 1% BSA HBSS. The cells were finally transferred to 1 mL PBS in preparation for single cell sequencing. The obtained cells were loaded on a GemCode Single Cell Instrument 10× Genomics  Pleasanton  USA to generate single cell gel beads in the emulsion. ScRNA seq libraries were prepared using the GemCode Single Cell 3′ Gel Bead  Chip and Library Kits 10× Genomics  Pleasanton  USA.,,treatment:exposed to BMDBM|age:12 hpf|genotype:wild type,GSM4775400,GSM4775400: BMDBM; Danio rerio; RNA Seq,GSM4775400,,1,post exposure  forty embryos collected from each group were transferred to 1 mL phosphate buffer saline PBS with 1% bovine serum albumin BSA. post incubated in 0.5 mL Hank's balanced salt solution HBSS containing 0.6 U/mL of dispase Yuanye Biotechnology  Shanghai  China at 37 °C for 5 min  100 µL of fetal bovine serum FBS was added to stop digestion. The cell suspension was filtered through a 40 µm filter and washed by 1% BSA HBSS. The cells were finally transferred to 1 mL PBS in preparation for single cell sequencing. The obtained cells were loaded on a GemCode Single Cell Instrument 10× Genomics  Pleasanton  USA to generate single cell gel beads in the emulsion. ScRNA seq libraries were prepared using the GemCode Single Cell 3′ Gel Bead  Chip and Library Kits 10× Genomics  Pleasanton  USA.,GEO Accession:GSM4775400,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP282042,,,BMDBM_S1_L005_R1_001.fastq.gz,fastq,69728512730.0,461778230.0,GSM4775400 r2,0:151 1:0,A:15960469244;C:10192809811;G:9259621013;T:34312311107;N:3301555,151,0,,,15960469244,10192809811,9259621013,34312311107,3301555,SRX9106223,SRS7349639,SRA1123780,GEO,HOHAI,1,0.09757,,0.01318,,0.97027,,0.50451,,151,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,China,2020-09-11,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
60883,SRR12623496,SRX9106223,SRS7349639,SRP282042,PRJNA662909,Nanoplastics and sunscreens contained in personal care products induce neurotoxicity in early zebrafish embryos,GSE157816,Transcriptome Analysis,Nanoplastics with small particle size and high surface area/volume ratio make them easy to absorb environmental pollutants and affect their bioavailability. In this study  polystyrene nanoplastic beads PS NPBs with a particle size of 100nm and sunscreen butyl methoxydibenzoylmethane BMDBM contained in personal care products were chosen as target pollutants to study their developmental toxicity and interactive effects on zebrafish embryo. The exposure period was 2 hpf 12 hpf. The BMDBM and PS NPBs significantly upregulated the genes related to antioxidant enzymes and downregulated the gene expression of aromatase and DNA methyltransferases  but the influenced genes were not exactly the same  and the combined exposure reduced the adverse effects on the expression of all genes. With the help of single cell RNA sequencing technology  the neural mid cells were identified as the target cells of both pollutants  and brain development  head development and notch signaling pathway were the functions they commonly altered. The key genes and functions that are specifically affected by BMDBM and/or PS NPBs were identified. The BMDBM mainly affect the differentiation and fate of neurons in central nervous system through the regulation of her5  her6  her11  lfng  pax2a and fgfr4. The PS NPBs regulated the expression of olig2  foxg1a  fzd8b  six3a  rx1  lhx2b  nkx2.1a and sfrp5 to alter nervous system development  retinal development  and stem cell differentiation. The phenotypic responses of zebrafish larvae at 120 hpf were tested  and significant inhibition of locomotor activity was found  indicating that early disrupting effect on central nervous system would have a sustained impact on the behavior of zebrafish. Overall design: mRNA profiles of 12 hpf wild type zebrafish embryos,,,,BMDBM,GSM4775400,,tissue:emberyo|treatment:exposed to BMDBM|age:12 hpf|genotype:wild type,BMDBM,Seurat package in R version 3.5.2 was used to analyze the sequenced reads. Principal component analysis PCA was used for dimensionality reduction and a graph based clustering was applied to cluster in PCA space. UMAP was used for the visualization of the clusters. The marker genes of each cluster were identified by FindMarkers function in the Seurat package. The clusters were annotated to a known cell type according to the Zebrafish Information Network ZFIN database and current literature Genome build: mm10 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell,emberyo,,post exposure  forty embryos collected from each group were transferred to 1 mL phosphate buffer saline PBS with 1% bovine serum albumin BSA. post incubated in 0.5 mL Hank's balanced salt solution HBSS containing 0.6 U/mL of dispase Yuanye Biotechnology  Shanghai  China at 37 °C for 5 min  100 µL of fetal bovine serum FBS was added to stop digestion. The cell suspension was filtered through a 40 µm filter and washed by 1% BSA HBSS. The cells were finally transferred to 1 mL PBS in preparation for single cell sequencing. The obtained cells were loaded on a GemCode Single Cell Instrument 10× Genomics  Pleasanton  USA to generate single cell gel beads in the emulsion. ScRNA seq libraries were prepared using the GemCode Single Cell 3′ Gel Bead  Chip and Library Kits 10× Genomics  Pleasanton  USA.,,treatment:exposed to BMDBM|age:12 hpf|genotype:wild type,GSM4775400,GSM4775400: BMDBM; Danio rerio; RNA Seq,GSM4775400,,1,post exposure  forty embryos collected from each group were transferred to 1 mL phosphate buffer saline PBS with 1% bovine serum albumin BSA. post incubated in 0.5 mL Hank's balanced salt solution HBSS containing 0.6 U/mL of dispase Yuanye Biotechnology  Shanghai  China at 37 °C for 5 min  100 µL of fetal bovine serum FBS was added to stop digestion. The cell suspension was filtered through a 40 µm filter and washed by 1% BSA HBSS. The cells were finally transferred to 1 mL PBS in preparation for single cell sequencing. The obtained cells were loaded on a GemCode Single Cell Instrument 10× Genomics  Pleasanton  USA to generate single cell gel beads in the emulsion. ScRNA seq libraries were prepared using the GemCode Single Cell 3′ Gel Bead  Chip and Library Kits 10× Genomics  Pleasanton  USA.,GEO Accession:GSM4775400,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP282042,,,BMDBM_S1_L005_R2_001.fastq.gz,fastq,69728512730.0,461778230.0,GSM4775400 r3,0:0 1:151,A:19980383167;C:14335137303;G:15821349675;T:19587033197;N:4609388,0,151,,,19980383167,14335137303,15821349675,19587033197,4609388,SRX9106223,SRS7349639,SRA1123780,GEO,HOHAI,1,0.9141,,0.12738,,0.79036,,0.49919,,151,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,China,2020-09-11,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
60884,SRR12623491,SRX9106222,SRS7349638,SRP282042,PRJNA662909,Nanoplastics and sunscreens contained in personal care products induce neurotoxicity in early zebrafish embryos,GSE157816,Transcriptome Analysis,Nanoplastics with small particle size and high surface area/volume ratio make them easy to absorb environmental pollutants and affect their bioavailability. In this study  polystyrene nanoplastic beads PS NPBs with a particle size of 100nm and sunscreen butyl methoxydibenzoylmethane BMDBM contained in personal care products were chosen as target pollutants to study their developmental toxicity and interactive effects on zebrafish embryo. The exposure period was 2 hpf 12 hpf. The BMDBM and PS NPBs significantly upregulated the genes related to antioxidant enzymes and downregulated the gene expression of aromatase and DNA methyltransferases  but the influenced genes were not exactly the same  and the combined exposure reduced the adverse effects on the expression of all genes. With the help of single cell RNA sequencing technology  the neural mid cells were identified as the target cells of both pollutants  and brain development  head development and notch signaling pathway were the functions they commonly altered. The key genes and functions that are specifically affected by BMDBM and/or PS NPBs were identified. The BMDBM mainly affect the differentiation and fate of neurons in central nervous system through the regulation of her5  her6  her11  lfng  pax2a and fgfr4. The PS NPBs regulated the expression of olig2  foxg1a  fzd8b  six3a  rx1  lhx2b  nkx2.1a and sfrp5 to alter nervous system development  retinal development  and stem cell differentiation. The phenotypic responses of zebrafish larvae at 120 hpf were tested  and significant inhibition of locomotor activity was found  indicating that early disrupting effect on central nervous system would have a sustained impact on the behavior of zebrafish. Overall design: mRNA profiles of 12 hpf wild type zebrafish embryos,,,,control,GSM4775399,,tissue:emberyo|treatment:untreated|age:12 hpf|genotype:wild type,control,Seurat package in R version 3.5.2 was used to analyze the sequenced reads. Principal component analysis PCA was used for dimensionality reduction and a graph based clustering was applied to cluster in PCA space. UMAP was used for the visualization of the clusters. The marker genes of each cluster were identified by FindMarkers function in the Seurat package. The clusters were annotated to a known cell type according to the Zebrafish Information Network ZFIN database and current literature Genome build: mm10 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell,emberyo,,post exposure  forty embryos collected from each group were transferred to 1 mL phosphate buffer saline PBS with 1% bovine serum albumin BSA. post incubated in 0.5 mL Hank's balanced salt solution HBSS containing 0.6 U/mL of dispase Yuanye Biotechnology  Shanghai  China at 37 °C for 5 min  100 µL of fetal bovine serum FBS was added to stop digestion. The cell suspension was filtered through a 40 µm filter and washed by 1% BSA HBSS. The cells were finally transferred to 1 mL PBS in preparation for single cell sequencing. The obtained cells were loaded on a GemCode Single Cell Instrument 10× Genomics  Pleasanton  USA to generate single cell gel beads in the emulsion. ScRNA seq libraries were prepared using the GemCode Single Cell 3′ Gel Bead  Chip and Library Kits 10× Genomics  Pleasanton  USA.,,treatment:untreated|age:12 hpf|genotype:wild type,GSM4775399,GSM4775399: control; Danio rerio; RNA Seq,GSM4775399,,1,post exposure  forty embryos collected from each group were transferred to 1 mL phosphate buffer saline PBS with 1% bovine serum albumin BSA. post incubated in 0.5 mL Hank's balanced salt solution HBSS containing 0.6 U/mL of dispase Yuanye Biotechnology  Shanghai  China at 37 °C for 5 min  100 µL of fetal bovine serum FBS was added to stop digestion. The cell suspension was filtered through a 40 µm filter and washed by 1% BSA HBSS. The cells were finally transferred to 1 mL PBS in preparation for single cell sequencing. The obtained cells were loaded on a GemCode Single Cell Instrument 10× Genomics  Pleasanton  USA to generate single cell gel beads in the emulsion. ScRNA seq libraries were prepared using the GemCode Single Cell 3′ Gel Bead  Chip and Library Kits 10× Genomics  Pleasanton  USA.,GEO Accession:GSM4775399,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP282042,,,Control_S4_L008_I1_001.fastq.gz,fastq,3625394648.0,453174331.0,GSM4775399 r1,0:8 1:0,A:929536518;C:904453181;G:887748830;T:900577332;N:3078787,8,0,,,929536518,904453181,887748830,900577332,3078787,SRX9106222,SRS7349638,SRA1123780,GEO,HOHAI,1,0.0,,0.0,,1.0,,,,8,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,China,2020-09-11,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
60885,SRR12623492,SRX9106222,SRS7349638,SRP282042,PRJNA662909,Nanoplastics and sunscreens contained in personal care products induce neurotoxicity in early zebrafish embryos,GSE157816,Transcriptome Analysis,Nanoplastics with small particle size and high surface area/volume ratio make them easy to absorb environmental pollutants and affect their bioavailability. In this study  polystyrene nanoplastic beads PS NPBs with a particle size of 100nm and sunscreen butyl methoxydibenzoylmethane BMDBM contained in personal care products were chosen as target pollutants to study their developmental toxicity and interactive effects on zebrafish embryo. The exposure period was 2 hpf 12 hpf. The BMDBM and PS NPBs significantly upregulated the genes related to antioxidant enzymes and downregulated the gene expression of aromatase and DNA methyltransferases  but the influenced genes were not exactly the same  and the combined exposure reduced the adverse effects on the expression of all genes. With the help of single cell RNA sequencing technology  the neural mid cells were identified as the target cells of both pollutants  and brain development  head development and notch signaling pathway were the functions they commonly altered. The key genes and functions that are specifically affected by BMDBM and/or PS NPBs were identified. The BMDBM mainly affect the differentiation and fate of neurons in central nervous system through the regulation of her5  her6  her11  lfng  pax2a and fgfr4. The PS NPBs regulated the expression of olig2  foxg1a  fzd8b  six3a  rx1  lhx2b  nkx2.1a and sfrp5 to alter nervous system development  retinal development  and stem cell differentiation. The phenotypic responses of zebrafish larvae at 120 hpf were tested  and significant inhibition of locomotor activity was found  indicating that early disrupting effect on central nervous system would have a sustained impact on the behavior of zebrafish. Overall design: mRNA profiles of 12 hpf wild type zebrafish embryos,,,,control,GSM4775399,,tissue:emberyo|treatment:untreated|age:12 hpf|genotype:wild type,control,Seurat package in R version 3.5.2 was used to analyze the sequenced reads. Principal component analysis PCA was used for dimensionality reduction and a graph based clustering was applied to cluster in PCA space. UMAP was used for the visualization of the clusters. The marker genes of each cluster were identified by FindMarkers function in the Seurat package. The clusters were annotated to a known cell type according to the Zebrafish Information Network ZFIN database and current literature Genome build: mm10 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell,emberyo,,post exposure  forty embryos collected from each group were transferred to 1 mL phosphate buffer saline PBS with 1% bovine serum albumin BSA. post incubated in 0.5 mL Hank's balanced salt solution HBSS containing 0.6 U/mL of dispase Yuanye Biotechnology  Shanghai  China at 37 °C for 5 min  100 µL of fetal bovine serum FBS was added to stop digestion. The cell suspension was filtered through a 40 µm filter and washed by 1% BSA HBSS. The cells were finally transferred to 1 mL PBS in preparation for single cell sequencing. The obtained cells were loaded on a GemCode Single Cell Instrument 10× Genomics  Pleasanton  USA to generate single cell gel beads in the emulsion. ScRNA seq libraries were prepared using the GemCode Single Cell 3′ Gel Bead  Chip and Library Kits 10× Genomics  Pleasanton  USA.,,treatment:untreated|age:12 hpf|genotype:wild type,GSM4775399,GSM4775399: control; Danio rerio; RNA Seq,GSM4775399,,1,post exposure  forty embryos collected from each group were transferred to 1 mL phosphate buffer saline PBS with 1% bovine serum albumin BSA. post incubated in 0.5 mL Hank's balanced salt solution HBSS containing 0.6 U/mL of dispase Yuanye Biotechnology  Shanghai  China at 37 °C for 5 min  100 µL of fetal bovine serum FBS was added to stop digestion. The cell suspension was filtered through a 40 µm filter and washed by 1% BSA HBSS. The cells were finally transferred to 1 mL PBS in preparation for single cell sequencing. The obtained cells were loaded on a GemCode Single Cell Instrument 10× Genomics  Pleasanton  USA to generate single cell gel beads in the emulsion. ScRNA seq libraries were prepared using the GemCode Single Cell 3′ Gel Bead  Chip and Library Kits 10× Genomics  Pleasanton  USA.,GEO Accession:GSM4775399,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP282042,,,Control_S4_L008_R1_001.fastq.gz,fastq,68429323981.0,453174331.0,GSM4775399 r2,0:151 1:0,A:15754477093;C:10050345557;G:9186011628;T:33434210009;N:4279694,151,0,,,15754477093,10050345557,9186011628,33434210009,4279694,SRX9106222,SRS7349638,SRA1123780,GEO,HOHAI,1,0.09756,,0.01164,,0.97218,,0.51238,,151,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,China,2020-09-11,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
60886,SRR12623493,SRX9106222,SRS7349638,SRP282042,PRJNA662909,Nanoplastics and sunscreens contained in personal care products induce neurotoxicity in early zebrafish embryos,GSE157816,Transcriptome Analysis,Nanoplastics with small particle size and high surface area/volume ratio make them easy to absorb environmental pollutants and affect their bioavailability. In this study  polystyrene nanoplastic beads PS NPBs with a particle size of 100nm and sunscreen butyl methoxydibenzoylmethane BMDBM contained in personal care products were chosen as target pollutants to study their developmental toxicity and interactive effects on zebrafish embryo. The exposure period was 2 hpf 12 hpf. The BMDBM and PS NPBs significantly upregulated the genes related to antioxidant enzymes and downregulated the gene expression of aromatase and DNA methyltransferases  but the influenced genes were not exactly the same  and the combined exposure reduced the adverse effects on the expression of all genes. With the help of single cell RNA sequencing technology  the neural mid cells were identified as the target cells of both pollutants  and brain development  head development and notch signaling pathway were the functions they commonly altered. The key genes and functions that are specifically affected by BMDBM and/or PS NPBs were identified. The BMDBM mainly affect the differentiation and fate of neurons in central nervous system through the regulation of her5  her6  her11  lfng  pax2a and fgfr4. The PS NPBs regulated the expression of olig2  foxg1a  fzd8b  six3a  rx1  lhx2b  nkx2.1a and sfrp5 to alter nervous system development  retinal development  and stem cell differentiation. The phenotypic responses of zebrafish larvae at 120 hpf were tested  and significant inhibition of locomotor activity was found  indicating that early disrupting effect on central nervous system would have a sustained impact on the behavior of zebrafish. Overall design: mRNA profiles of 12 hpf wild type zebrafish embryos,,,,control,GSM4775399,,tissue:emberyo|treatment:untreated|age:12 hpf|genotype:wild type,control,Seurat package in R version 3.5.2 was used to analyze the sequenced reads. Principal component analysis PCA was used for dimensionality reduction and a graph based clustering was applied to cluster in PCA space. UMAP was used for the visualization of the clusters. The marker genes of each cluster were identified by FindMarkers function in the Seurat package. The clusters were annotated to a known cell type according to the Zebrafish Information Network ZFIN database and current literature Genome build: mm10 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell,emberyo,,post exposure  forty embryos collected from each group were transferred to 1 mL phosphate buffer saline PBS with 1% bovine serum albumin BSA. post incubated in 0.5 mL Hank's balanced salt solution HBSS containing 0.6 U/mL of dispase Yuanye Biotechnology  Shanghai  China at 37 °C for 5 min  100 µL of fetal bovine serum FBS was added to stop digestion. The cell suspension was filtered through a 40 µm filter and washed by 1% BSA HBSS. The cells were finally transferred to 1 mL PBS in preparation for single cell sequencing. The obtained cells were loaded on a GemCode Single Cell Instrument 10× Genomics  Pleasanton  USA to generate single cell gel beads in the emulsion. ScRNA seq libraries were prepared using the GemCode Single Cell 3′ Gel Bead  Chip and Library Kits 10× Genomics  Pleasanton  USA.,,treatment:untreated|age:12 hpf|genotype:wild type,GSM4775399,GSM4775399: control; Danio rerio; RNA Seq,GSM4775399,,1,post exposure  forty embryos collected from each group were transferred to 1 mL phosphate buffer saline PBS with 1% bovine serum albumin BSA. post incubated in 0.5 mL Hank's balanced salt solution HBSS containing 0.6 U/mL of dispase Yuanye Biotechnology  Shanghai  China at 37 °C for 5 min  100 µL of fetal bovine serum FBS was added to stop digestion. The cell suspension was filtered through a 40 µm filter and washed by 1% BSA HBSS. The cells were finally transferred to 1 mL PBS in preparation for single cell sequencing. The obtained cells were loaded on a GemCode Single Cell Instrument 10× Genomics  Pleasanton  USA to generate single cell gel beads in the emulsion. ScRNA seq libraries were prepared using the GemCode Single Cell 3′ Gel Bead  Chip and Library Kits 10× Genomics  Pleasanton  USA.,GEO Accession:GSM4775399,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP282042,,,Control_S4_L008_R2_001.fastq.gz,fastq,68429323981.0,453174331.0,GSM4775399 r3,0:0 1:151,A:19629507419;C:13923809144;G:15473487376;T:19395858693;N:6661349,0,151,,,19629507419,13923809144,15473487376,19395858693,6661349,SRX9106222,SRS7349638,SRA1123780,GEO,HOHAI,1,0.90437,,0.12406,,0.79076,,0.50621,,151,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,China,2020-09-11,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
64455,SRR14703436,SRX11041458,SRS9110385,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,,Shield dnmt1 mKD total RNA seq rep2,GSM5351813,,source name:embryo|strain:AB|genotype:WT|developmental stage:Shield|tissue:embryo|treatment:microinjection with Rhodamine B and dnmt1 MO at oogenesis III stage GV,Shield 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,embryo,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 embryos 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:Shield|tissue:embryo|treatment:microinjection with Rhodamine B and dnmt1 MO at oogenesis III stage GV,GSM5351813,GSM5351813: Shield dnmt1 mKD total RNA seq rep2; Danio rerio; RNA Seq,GSM5351813,,1,The embryos 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:GSM5351813,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,,SRP322195,,loader:fastq load.py,Shield_dnmt1_mKD_total_RNA_seq_rep2_r1.fq.gz Shield_dnmt1_mKD_total_RNA_seq_rep2_r2.fq.gz,fastq fastq,26909768700.0,89699229.0,GSM5351813 r1,0:150 1:150,A:4548192039;C:8603854547;G:9492577543;T:4264608573;N:535998,150,150,,,4548192039,8603854547,9492577543,4264608573,535998,SRX11041458,SRS9110385,SRA1239365,GEO,"THU-PKU Center for Life Sciences, Tsinghua University",2,0.96382,0.95515,0.08353,0.08101,0.85466,0.85587,0.88024,0.92689,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,rrna_depletion,nebnext,sc_generic,single_cell_generic,generic-scrnaseq-only,,China,2021-06-01,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
64456,SRR14703435,SRX11041457,SRS9110386,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,,Shield dnmt1 mKD total RNA seq rep1,GSM5351812,,source name:embryo|strain:AB|genotype:WT|developmental stage:Shield|tissue:embryo|treatment:microinjection with Rhodamine B and dnmt1 MO at oogenesis III stage GV,Shield 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,embryo,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 embryos 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:Shield|tissue:embryo|treatment:microinjection with Rhodamine B and dnmt1 MO at oogenesis III stage GV,GSM5351812,GSM5351812: Shield dnmt1 mKD total RNA seq rep1; Danio rerio; RNA Seq,GSM5351812,,1,The embryos 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:GSM5351812,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,,SRP322195,,loader:fastq load.py,Shield_dnmt1_mKD_total_RNA_seq_rep1_r1.fq.gz Shield_dnmt1_mKD_total_RNA_seq_rep1_r2.fq.gz,fastq fastq,3563831100.0,11879437.0,GSM5351812 r1,0:150 1:150,A:703591136;C:1071626098;G:1077809090;T:710675047;N:129729,150,150,,,703591136,1071626098,1077809090,710675047,129729,SRX11041457,SRS9110386,SRA1239365,GEO,"THU-PKU Center for Life Sciences, Tsinghua University",2,0.93843,0.94627,0.17226,0.15591,0.84336,0.85569,0.86129,0.88342,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,rrna_depletion,nebnext,sc_generic,single_cell_generic,generic-scrnaseq-only,,China,2021-06-01,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
64457,SRR14703434,SRX11041456,SRS9110384,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,,Shield ctrl total RNA seq rep2,GSM5351811,,source name:embryo|strain:AB|genotype:WT|developmental stage:Shield|tissue:embryo|treatment:microinjection with Rhodamine B and control MO at oogenesis III stage GV,Shield 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,embryo,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 embryos 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:Shield|tissue:embryo|treatment:microinjection with Rhodamine B and control MO at oogenesis III stage GV,GSM5351811,GSM5351811: Shield ctrl total RNA seq rep2; Danio rerio; RNA Seq,GSM5351811,,1,The embryos 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:GSM5351811,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,,SRP322195,,loader:fastq load.py,Shield_ctrl_total_RNA_seq_rep2_r1.fq.gz Shield_ctrl_total_RNA_seq_rep2_r2.fq.gz,fastq fastq,21074509800.0,70248366.0,GSM5351811 r1,0:150 1:150,A:4067157835;C:6122340804;G:7071532505;T:3813060334;N:418322,150,150,,,4067157835,6122340804,7071532505,3813060334,418322,SRX11041456,SRS9110384,SRA1239365,GEO,"THU-PKU Center for Life Sciences, Tsinghua University",2,0.87376,0.88111,0.26582,0.26674,0.86697,0.86742,0.86575,0.83545,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,rrna_depletion,nebnext,sc_generic,single_cell_generic,generic-scrnaseq-only,,China,2021-06-01,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
64458,SRR14703433,SRX11041455,SRS9110383,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,,Shield ctrl total RNA seq rep1,GSM5351810,,source name:embryo|strain:AB|genotype:WT|developmental stage:Shield|tissue:embryo|treatment:microinjection with Rhodamine B and control MO at oogenesis III stage GV,Shield 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,embryo,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 embryos 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:Shield|tissue:embryo|treatment:microinjection with Rhodamine B and control MO at oogenesis III stage GV,GSM5351810,GSM5351810: Shield ctrl total RNA seq rep1; Danio rerio; RNA Seq,GSM5351810,,1,The embryos 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:GSM5351810,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,,SRP322195,,loader:fastq load.py,Shield_ctrl_total_RNA_seq_rep1_r1.fq.gz Shield_ctrl_total_RNA_seq_rep1_r2.fq.gz,fastq fastq,1745258700.0,5817529.0,GSM5351810 r1,0:150 1:150,A:344351011;C:524534205;G:528698402;T:347611625;N:63457,150,150,,,344351011,524534205,528698402,347611625,63457,SRX11041455,SRS9110383,SRA1239365,GEO,"THU-PKU Center for Life Sciences, Tsinghua University",2,0.9215,0.94202,0.19896,0.18582,0.85029,0.85717,0.8101,0.8693,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,rrna_depletion,nebnext,sc_generic,single_cell_generic,generic-scrnaseq-only,,China,2021-06-01,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
64459,SRR14703432,SRX11041454,SRS9110382,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,,Dome dnmt1 mKD total RNA seq rep2,GSM5351809,,source name:embryo|strain:AB|genotype:WT|developmental stage:Dome|tissue:embryo|treatment:microinjection with Rhodamine B and dnmt1 MO at oogenesis III stage GV,Dome 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,embryo,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 embryos 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:Dome|tissue:embryo|treatment:microinjection with Rhodamine B and dnmt1 MO at oogenesis III stage GV,GSM5351809,GSM5351809: Dome dnmt1 mKD total RNA seq rep2; Danio rerio; RNA Seq,GSM5351809,,1,The embryos 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:GSM5351809,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,,SRP322195,,loader:fastq load.py,Dome_dnmt1_mKD_total_RNA_seq_rep2_r1.fq.gz Dome_dnmt1_mKD_total_RNA_seq_rep2_r2.fq.gz,fastq fastq,12542379300.0,41807931.0,GSM5351809 r1,0:150 1:150,A:3294568365;C:2579704130;G:3156773841;T:3510995787;N:337177,150,150,,,3294568365,2579704130,3156773841,3510995787,337177,SRX11041454,SRS9110382,SRA1239365,GEO,"THU-PKU Center for Life Sciences, Tsinghua University",2,0.82428,0.61631,0.13953,0.12414,0.74604,0.83226,0.46496,0.46485,150,150,B,B,mate2-mate1 similar by mapping diff,illumina,hiseq_era,unknown,rrna_depletion,nebnext,sc_generic,single_cell_generic,generic-scrnaseq-only,,China,2021-06-01,Blastula,Embryo,Embryo Imprecise,All anatomical structures
64460,SRR14703431,SRX11041453,SRS9110381,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,,Dome dnmt1 mKD total RNA seq rep1,GSM5351808,,source name:embryo|strain:AB|genotype:WT|developmental stage:Dome|tissue:embryo|treatment:microinjection with Rhodamine B and dnmt1 MO at oogenesis III stage GV,Dome 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,embryo,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 embryos 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:Dome|tissue:embryo|treatment:microinjection with Rhodamine B and dnmt1 MO at oogenesis III stage GV,GSM5351808,GSM5351808: Dome dnmt1 mKD total RNA seq rep1; Danio rerio; RNA Seq,GSM5351808,,1,The embryos 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:GSM5351808,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,,SRP322195,,loader:fastq load.py,Dome_dnmt1_mKD_total_RNA_seq_rep1_r1.fq.gz Dome_dnmt1_mKD_total_RNA_seq_rep1_r2.fq.gz,fastq fastq,13994434500.0,46648115.0,GSM5351808 r1,0:150 1:150,A:3803938174;C:2618240373;G:3360449717;T:4211342983;N:463253,150,150,,,3803938174,2618240373,3360449717,4211342983,463253,SRX11041453,SRS9110381,SRA1239365,GEO,"THU-PKU Center for Life Sciences, Tsinghua University",2,0.795,0.47894,0.1317,0.08944,0.75284,0.84471,0.47102,0.46153,150,150,B,B,mate2-mate1 similar by mapping diff,illumina,hiseq_era,unknown,rrna_depletion,nebnext,sc_generic,single_cell_generic,generic-scrnaseq-only,,China,2021-06-01,Blastula,Embryo,Embryo Imprecise,All anatomical structures
64461,SRR14703430,SRX11041452,SRS9110380,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,,Dome ctrl total RNA seq rep2,GSM5351807,,source name:embryo|strain:AB|genotype:WT|developmental stage:Dome|tissue:embryo|treatment:microinjection with Rhodamine B and control MO at oogenesis III stage GV,Dome 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,embryo,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 embryos 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:Dome|tissue:embryo|treatment:microinjection with Rhodamine B and control MO at oogenesis III stage GV,GSM5351807,GSM5351807: Dome ctrl total RNA seq rep2; Danio rerio; RNA Seq,GSM5351807,,1,The embryos 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:GSM5351807,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP322195,,loader:fastq load.py,Dome_ctrl_total_RNA_seq_rep2_r1.fq.gz Dome_ctrl_total_RNA_seq_rep2_r2.fq.gz,fastq fastq,12671756400.0,42239188.0,GSM5351807 r1,0:150 1:150,A:3423269098;C:2581499456;G:3112756356;T:3553888309;N:343181,150,150,,,3423269098,2581499456,3112756356,3553888309,343181,SRX11041452,SRS9110380,SRA1239365,GEO,"THU-PKU Center for Life Sciences, Tsinghua University",2,0.82802,0.63774,0.15332,0.13097,0.75278,0.8269,0.46199,0.46075,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,rrna_depletion,nebnext,sc_generic,single_cell_generic,generic-scrnaseq-only,,China,2021-06-01,Blastula,Embryo,Embryo Imprecise,All anatomical structures
64462,SRR14703429,SRX11041451,SRS9110379,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,,Dome ctrl total RNA seq rep1,GSM5351806,,source name:embryo|strain:AB|genotype:WT|developmental stage:Dome|tissue:embryo|treatment:microinjection with Rhodamine B and control MO at oogenesis III stage GV,Dome 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,embryo,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 embryos 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:Dome|tissue:embryo|treatment:microinjection with Rhodamine B and control MO at oogenesis III stage GV,GSM5351806,GSM5351806: Dome ctrl total RNA seq rep1; Danio rerio; RNA Seq,GSM5351806,,1,The embryos 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:GSM5351806,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP322195,,loader:fastq load.py,Dome_ctrl_total_RNA_seq_rep1_r1.fq.gz Dome_ctrl_total_RNA_seq_rep1_r2.fq.gz,fastq fastq,14091428400.0,46971428.0,GSM5351806 r1,0:150 1:150,A:4018054419;C:2522984249;G:3207217323;T:4342734285;N:438124,150,150,,,4018054419,2522984249,3207217323,4342734285,438124,SRX11041451,SRS9110379,SRA1239365,GEO,"THU-PKU Center for Life Sciences, Tsinghua University",2,0.75859,0.42979,0.1223,0.07655,0.75816,0.84293,0.47333,0.47506,150,150,B,B,mate2-mate1 similar by mapping diff,illumina,hiseq_era,unknown,rrna_depletion,nebnext,sc_generic,single_cell_generic,generic-scrnaseq-only,,China,2021-06-01,Blastula,Embryo,Embryo Imprecise,All anatomical structures
64463,SRR14703428,SRX11041450,SRS9110378,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,,256 cell dnmt1 mKD total RNA seq rep2,GSM5351805,,source name:embryo|strain:AB|genotype:WT|developmental stage:256 cell|tissue:embryo|treatment:microinjection with Rhodamine B and dnmt1 MO at oogenesis III stage GV,256 cell 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,embryo,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 embryos 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:256 cell|tissue:embryo|treatment:microinjection with Rhodamine B and dnmt1 MO at oogenesis III stage GV,GSM5351805,GSM5351805: 256 cell dnmt1 mKD total RNA seq rep2; Danio rerio; RNA Seq,GSM5351805,,1,The embryos 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:GSM5351805,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,,SRP322195,,loader:fastq load.py,256_cell_dnmt1_mKD_total_RNA_seq_rep2_r1.fq.gz 256_cell_dnmt1_mKD_total_RNA_seq_rep2_r2.fq.gz,fastq fastq,1872530700.0,6241769.0,GSM5351805 r1,0:150 1:150,A:359970717;C:575390795;G:588093584;T:348986747;N:88857,150,150,,,359970717,575390795,588093584,348986747,88857,SRX11041450,SRS9110378,SRA1239365,GEO,"THU-PKU Center for Life Sciences, Tsinghua University",2,0.98109,0.98288,0.25725,0.26026,0.8367,0.84376,0.83625,0.88456,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,rrna_depletion,nebnext,sc_generic,single_cell_generic,generic-scrnaseq-only,,China,2021-06-01,Blastula,Embryo,Embryo Imprecise,All anatomical structures
64464,SRR14703427,SRX11041449,SRS9110377,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,,256 cell dnmt1 mKD total RNA seq rep1,GSM5351804,,source name:embryo|strain:AB|genotype:WT|developmental stage:256 cell|tissue:embryo|treatment:microinjection with Rhodamine B and dnmt1 MO at oogenesis III stage GV,256 cell 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,embryo,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 embryos 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:256 cell|tissue:embryo|treatment:microinjection with Rhodamine B and dnmt1 MO at oogenesis III stage GV,GSM5351804,GSM5351804: 256 cell dnmt1 mKD total RNA seq rep1; Danio rerio; RNA Seq,GSM5351804,,1,The embryos 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:GSM5351804,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,,SRP322195,,loader:fastq load.py,256_cell_dnmt1_mKD_total_RNA_seq_rep1_r1.fq.gz 256_cell_dnmt1_mKD_total_RNA_seq_rep1_r2.fq.gz,fastq fastq,3502818900.0,11676063.0,GSM5351804 r1,0:150 1:150,A:657618236;C:1085606230;G:1093022247;T:666443716;N:128471,150,150,,,657618236,1085606230,1093022247,666443716,128471,SRX11041449,SRS9110377,SRA1239365,GEO,"THU-PKU Center for Life Sciences, Tsinghua University",2,0.96154,0.96561,0.03783,0.03582,0.8196,0.82542,0.80623,0.76284,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,rrna_depletion,nebnext,sc_generic,single_cell_generic,generic-scrnaseq-only,,China,2021-06-01,Blastula,Embryo,Embryo Imprecise,All anatomical structures
64465,SRR14703426,SRX11041448,SRS9110376,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,,256 cell ctrl total RNA seq rep2,GSM5351803,,source name:embryo|strain:AB|genotype:WT|developmental stage:256 cell|tissue:embryo|treatment:microinjection with Rhodamine B and control MO at oogenesis III stage GV,256 cell 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,embryo,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 embryos 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:256 cell|tissue:embryo|treatment:microinjection with Rhodamine B and control MO at oogenesis III stage GV,GSM5351803,GSM5351803: 256 cell ctrl total RNA seq rep2; Danio rerio; RNA Seq,GSM5351803,,1,The embryos 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:GSM5351803,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,,SRP322195,,loader:fastq load.py,256_cell_ctrl_total_RNA_seq_rep2_r1.fq.gz 256_cell_ctrl_total_RNA_seq_rep2_r2.fq.gz,fastq fastq,1605083700.0,5350279.0,GSM5351803 r1,0:150 1:150,A:307781523;C:495294154;G:510998289;T:290935069;N:74665,150,150,,,307781523,495294154,510998289,290935069,74665,SRX11041448,SRS9110376,SRA1239365,GEO,"THU-PKU Center for Life Sciences, Tsinghua University",2,0.97836,0.98077,0.26741,0.2707,0.85318,0.85865,0.89211,0.9035,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,rrna_depletion,nebnext,sc_generic,single_cell_generic,generic-scrnaseq-only,,China,2021-06-01,Blastula,Embryo,Embryo Imprecise,All anatomical structures
64466,SRR14703425,SRX11041447,SRS9110375,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,,256 cell ctrl total RNA seq rep1,GSM5351802,,source name:embryo|strain:AB|genotype:WT|developmental stage:256 cell|tissue:embryo|treatment:microinjection with Rhodamine B and control MO at oogenesis III stage GV,256 cell 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,embryo,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 embryos 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:256 cell|tissue:embryo|treatment:microinjection with Rhodamine B and control MO at oogenesis III stage GV,GSM5351802,GSM5351802: 256 cell ctrl total RNA seq rep1; Danio rerio; RNA Seq,GSM5351802,,1,The embryos 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:GSM5351802,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,,SRP322195,,loader:fastq load.py,256_cell_ctrl_total_RNA_seq_rep1_r1.fq.gz 256_cell_ctrl_total_RNA_seq_rep1_r2.fq.gz,fastq fastq,2420361900.0,8067873.0,GSM5351802 r1,0:150 1:150,A:454557501;C:749692029;G:757871245;T:458161398;N:79727,150,150,,,454557501,749692029,757871245,458161398,79727,SRX11041447,SRS9110375,SRA1239365,GEO,"THU-PKU Center for Life Sciences, Tsinghua University",2,0.96133,0.96753,0.07785,0.07288,0.83205,0.84315,0.79113,0.84498,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,rrna_depletion,nebnext,sc_generic,single_cell_generic,generic-scrnaseq-only,,China,2021-06-01,Blastula,Embryo,Embryo Imprecise,All anatomical structures
73913,SRR23284054,SRX19227385,SRS16633552,SRP420237,PRJNA929924,A single cell map of maternal and zygotic mRNA dynamics during cell type specification in zebrafish embryos [SLAM seq],GSE224113,Other,During early embryogenesis  embryos undergo a massive degradation of maternally inherited mRNAs and produce new zygotic transcripts. This maternal to zygotic transition requires a tight interplay of mRNA transcription and degradation  but distinguishing their unique contributions remains a challenge. Here  we dissect gene regulation during the zebrafish maternal to zygotic transition by combining single cell RNA sequencing with RNA metabolic labeling and nucleotide conversion within zebrafish embryos. We decompose single cell transcriptomes into their new zygotic and old maternal mRNA components  and elicit critical information on gene regulation as it unfolds over both time and space. We show that most cell type restricted expression arises by zygotic transcription  but distinguish a specific role for maternal transcripts in defining germ cell and enveloping layer identity  two earliest specified cell identities. We recover the underlying replacement between maternal and zygotic copies of embryonic genes with a relatively constant overall mRNA level  and associate a fast replacement with genes that has a restricted zygotic expression in either cell type or time. Our study provides a valuable resource to investigate maternal and zygotic transcriptomes and reveals post transcriptional events that control gene regulation during early embryogenesis. Overall design: SLAM seq  zebrafish embryos  1hpf and 6hpf  2 technical replicates,parent bioproject:PRJNA933118,pubmed:37131717;pubmed:38600066,,zebrafish embryo  6hpf  rep2,GSM7012036,,source name:whole embryo|tissue:whole embryo|genotype:AB/TL|treatment:4sU injection|time:6hpf|geo loc name:missing|collection date:missing,zebrafish embryo  6hpf  rep2,Sequence reads were trimmed for adaptor sequence using cutadapt Trimmed sequence reads were mapped to GRCz11 using STAR Read count extraction and NTR calculation were performed using GRAND SLAM Assembly: GRCz11/102 Supplementary files format and content: tab delimited text file includes readcount and NTR %new RNA for each Sample Library strategy: SLAM seq,whole embryo,20mM 4sU injection at 1 cell stage RNA was treated with Iodoacetamide to induce T to C conversions,Total RNA was isolated using tri reagent Sigma T9424 and quantified using nanodrop polyA+RNA: Indexed RNA Seq libraries were prepared from 500 ng total RNA using the KAPA Stranded mRNA Seq Kit Kapa Biosystems  Inc. according to the manufacturer’s protocol. Libraries were size selected with SPRI beads and quantified by QuBIT Life Technologies. Average size of 300 bp was determined by TapeStation Agilent Technologies  USA. Libraries are then sequenced using an Illumina Nextseq500 sequencer. total RNA: indexed RNA Seq libraries for each sample were generated from total RNA using the Illumina RiboZeroHuman/Mouse/Rat kit following the manufacturer’s instructions. Libraries were size selected with SPRI beads and quantified by QuBIT Life Technologies. Libraries are then sequenced using an Illumina Novaseq sequencer.,,tissue:whole embryo|genotype:AB/TL|treatment:4sU injection|time:6hpf,GSM7012036,GSM7012036: zebrafish embryo  6hpf  rep2; Danio rerio; RNA Seq,GSM7012036 r1,GSM7012036,1,Total RNA was isolated using tri reagent Sigma T9424 and quantified using nanodrop polyA+RNA: Indexed RNA Seq libraries were prepared from 500 ng total RNA using the KAPA Stranded mRNA Seq Kit Kapa Biosystems  Inc. according to the manufacturer's protocol. Libraries were size selected with SPRI beads and quantified by QuBIT Life Technologies. Average size of 300 bp was determined by TapeStation Agilent Technologies  USA. Libraries are then sequenced using an Illumina Nextseq500 sequencer. total RNA: indexed RNA Seq libraries for each sample were generated from total RNA using the Illumina RiboZeroHuman/Mouse/Rat kit following the manufacturer's instructions. Libraries were size selected with SPRI beads and quantified by QuBIT Life Technologies. Libraries are then sequenced using an Illumina Novaseq sequencer.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP420237,,loader:fastq load.py,nextseq_20220515_slam_120122_6hr_S20_R1_001.fastq.gz,fastq,1231038044.0,16197869.0,GSM7012036 r1,0:76,A:287858332;C:300689662;G:294179125;T:348288250;N:22675,76,,,,287858332,300689662,294179125,348288250,22675,SRX19227385,SRS16633552,SRA1587567,Hebrew University of Jerusalem,Hebrew University of Jerusalem,1,0.91125,,0.06969,,0.75538,,0.55355,,76,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,ribozero,sc_generic,single_cell_generic,generic-scrnaseq-only,,Israel,2023-01-31,Gastrula,Embryo,Whole Organism,All anatomical structures
73914,SRR23284055,SRX19227384,SRS16633551,SRP420237,PRJNA929924,A single cell map of maternal and zygotic mRNA dynamics during cell type specification in zebrafish embryos [SLAM seq],GSE224113,Other,During early embryogenesis  embryos undergo a massive degradation of maternally inherited mRNAs and produce new zygotic transcripts. This maternal to zygotic transition requires a tight interplay of mRNA transcription and degradation  but distinguishing their unique contributions remains a challenge. Here  we dissect gene regulation during the zebrafish maternal to zygotic transition by combining single cell RNA sequencing with RNA metabolic labeling and nucleotide conversion within zebrafish embryos. We decompose single cell transcriptomes into their new zygotic and old maternal mRNA components  and elicit critical information on gene regulation as it unfolds over both time and space. We show that most cell type restricted expression arises by zygotic transcription  but distinguish a specific role for maternal transcripts in defining germ cell and enveloping layer identity  two earliest specified cell identities. We recover the underlying replacement between maternal and zygotic copies of embryonic genes with a relatively constant overall mRNA level  and associate a fast replacement with genes that has a restricted zygotic expression in either cell type or time. Our study provides a valuable resource to investigate maternal and zygotic transcriptomes and reveals post transcriptional events that control gene regulation during early embryogenesis. Overall design: SLAM seq  zebrafish embryos  1hpf and 6hpf  2 technical replicates,parent bioproject:PRJNA933118,pubmed:37131717;pubmed:38600066,,zebrafish embryo  1hpf  rep2,GSM7012035,,source name:whole embryo|tissue:whole embryo|genotype:AB/TL|treatment:4sU injection|time:1hpf|geo loc name:missing|collection date:missing,zebrafish embryo  1hpf  rep2,Sequence reads were trimmed for adaptor sequence using cutadapt Trimmed sequence reads were mapped to GRCz11 using STAR Read count extraction and NTR calculation were performed using GRAND SLAM Assembly: GRCz11/102 Supplementary files format and content: tab delimited text file includes readcount and NTR %new RNA for each Sample Library strategy: SLAM seq,whole embryo,20mM 4sU injection at 1 cell stage RNA was treated with Iodoacetamide to induce T to C conversions,Total RNA was isolated using tri reagent Sigma T9424 and quantified using nanodrop polyA+RNA: Indexed RNA Seq libraries were prepared from 500 ng total RNA using the KAPA Stranded mRNA Seq Kit Kapa Biosystems  Inc. according to the manufacturer’s protocol. Libraries were size selected with SPRI beads and quantified by QuBIT Life Technologies. Average size of 300 bp was determined by TapeStation Agilent Technologies  USA. Libraries are then sequenced using an Illumina Nextseq500 sequencer. total RNA: indexed RNA Seq libraries for each sample were generated from total RNA using the Illumina RiboZeroHuman/Mouse/Rat kit following the manufacturer’s instructions. Libraries were size selected with SPRI beads and quantified by QuBIT Life Technologies. Libraries are then sequenced using an Illumina Novaseq sequencer.,,tissue:whole embryo|genotype:AB/TL|treatment:4sU injection|time:1hpf,GSM7012035,GSM7012035: zebrafish embryo  1hpf  rep2; Danio rerio; RNA Seq,GSM7012035 r1,GSM7012035,1,Total RNA was isolated using tri reagent Sigma T9424 and quantified using nanodrop polyA+RNA: Indexed RNA Seq libraries were prepared from 500 ng total RNA using the KAPA Stranded mRNA Seq Kit Kapa Biosystems  Inc. according to the manufacturer's protocol. Libraries were size selected with SPRI beads and quantified by QuBIT Life Technologies. Average size of 300 bp was determined by TapeStation Agilent Technologies  USA. Libraries are then sequenced using an Illumina Nextseq500 sequencer. total RNA: indexed RNA Seq libraries for each sample were generated from total RNA using the Illumina RiboZeroHuman/Mouse/Rat kit following the manufacturer's instructions. Libraries were size selected with SPRI beads and quantified by QuBIT Life Technologies. Libraries are then sequenced using an Illumina Novaseq sequencer.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP420237,,loader:fastq load.py,nextseq_20220515_slam_120122_1hr_S19_R1_001.fastq.gz,fastq,988543704.0,13007154.0,GSM7012035 r1,0:76,A:237897735;C:241764496;G:233504938;T:275357752;N:18783,76,,,,237897735,241764496,233504938,275357752,18783,SRX19227384,SRS16633551,SRA1587567,Hebrew University of Jerusalem,Hebrew University of Jerusalem,1,0.93827,,0.03581,,0.78027,,0.53364,,76,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,ribozero,sc_generic,single_cell_generic,generic-scrnaseq-only,,Israel,2023-01-31,Cleavage,Embryo,Whole Organism,All anatomical structures
73915,SRR23284056,SRX19227383,SRS16633550,SRP420237,PRJNA929924,A single cell map of maternal and zygotic mRNA dynamics during cell type specification in zebrafish embryos [SLAM seq],GSE224113,Other,During early embryogenesis  embryos undergo a massive degradation of maternally inherited mRNAs and produce new zygotic transcripts. This maternal to zygotic transition requires a tight interplay of mRNA transcription and degradation  but distinguishing their unique contributions remains a challenge. Here  we dissect gene regulation during the zebrafish maternal to zygotic transition by combining single cell RNA sequencing with RNA metabolic labeling and nucleotide conversion within zebrafish embryos. We decompose single cell transcriptomes into their new zygotic and old maternal mRNA components  and elicit critical information on gene regulation as it unfolds over both time and space. We show that most cell type restricted expression arises by zygotic transcription  but distinguish a specific role for maternal transcripts in defining germ cell and enveloping layer identity  two earliest specified cell identities. We recover the underlying replacement between maternal and zygotic copies of embryonic genes with a relatively constant overall mRNA level  and associate a fast replacement with genes that has a restricted zygotic expression in either cell type or time. Our study provides a valuable resource to investigate maternal and zygotic transcriptomes and reveals post transcriptional events that control gene regulation during early embryogenesis. Overall design: SLAM seq  zebrafish embryos  1hpf and 6hpf  2 technical replicates,parent bioproject:PRJNA933118,pubmed:37131717;pubmed:38600066,,zebrafish embryo  6hpf  rep1,GSM7012034,,source name:whole embryo|tissue:whole embryo|genotype:AB/TL|treatment:4sU injection|time:6hpf|geo loc name:missing|collection date:missing,zebrafish embryo  6hpf  rep1,Sequence reads were trimmed for adaptor sequence using cutadapt Trimmed sequence reads were mapped to GRCz11 using STAR Read count extraction and NTR calculation were performed using GRAND SLAM Assembly: GRCz11/102 Supplementary files format and content: tab delimited text file includes readcount and NTR %new RNA for each Sample Library strategy: SLAM seq,whole embryo,20mM 4sU injection at 1 cell stage RNA was treated with Iodoacetamide to induce T to C conversions,Total RNA was isolated using tri reagent Sigma T9424 and quantified using nanodrop polyA+RNA: Indexed RNA Seq libraries were prepared from 500 ng total RNA using the KAPA Stranded mRNA Seq Kit Kapa Biosystems  Inc. according to the manufacturer’s protocol. Libraries were size selected with SPRI beads and quantified by QuBIT Life Technologies. Average size of 300 bp was determined by TapeStation Agilent Technologies  USA. Libraries are then sequenced using an Illumina Nextseq500 sequencer. total RNA: indexed RNA Seq libraries for each sample were generated from total RNA using the Illumina RiboZeroHuman/Mouse/Rat kit following the manufacturer’s instructions. Libraries were size selected with SPRI beads and quantified by QuBIT Life Technologies. Libraries are then sequenced using an Illumina Novaseq sequencer.,,tissue:whole embryo|genotype:AB/TL|treatment:4sU injection|time:6hpf,GSM7012034,GSM7012034: zebrafish embryo  6hpf  rep1; Danio rerio; RNA Seq,GSM7012034 r1,GSM7012034,1,Total RNA was isolated using tri reagent Sigma T9424 and quantified using nanodrop polyA+RNA: Indexed RNA Seq libraries were prepared from 500 ng total RNA using the KAPA Stranded mRNA Seq Kit Kapa Biosystems  Inc. according to the manufacturer's protocol. Libraries were size selected with SPRI beads and quantified by QuBIT Life Technologies. Average size of 300 bp was determined by TapeStation Agilent Technologies  USA. Libraries are then sequenced using an Illumina Nextseq500 sequencer. total RNA: indexed RNA Seq libraries for each sample were generated from total RNA using the Illumina RiboZeroHuman/Mouse/Rat kit following the manufacturer's instructions. Libraries were size selected with SPRI beads and quantified by QuBIT Life Technologies. Libraries are then sequenced using an Illumina Novaseq sequencer.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP420237,,loader:fastq load.py,novaseq_20220630_slam_120122_6h_1.fastq.gz novaseq_20220630_slam_120122_6h_2.fastq.gz,fastq fastq,7578082116.0,37515258.0,GSM7012034 r1,0:101 1:101,A:1938942537;C:1836634013;G:1866966085;T:1935520946;N:18535,101,101,,,1938942537,1836634013,1866966085,1935520946,18535,SRX19227383,SRS16633550,SRA1587567,Hebrew University of Jerusalem,Hebrew University of Jerusalem,2,0.86852,0.87284,0.11981,0.11692,0.7571,0.75702,0.63941,0.63601,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,ribozero,sc_generic,single_cell_generic,generic-scrnaseq-only,,Israel,2023-01-31,Gastrula,Embryo,Whole Organism,All anatomical structures
73916,SRR23284057,SRX19227382,SRS16633549,SRP420237,PRJNA929924,A single cell map of maternal and zygotic mRNA dynamics during cell type specification in zebrafish embryos [SLAM seq],GSE224113,Other,During early embryogenesis  embryos undergo a massive degradation of maternally inherited mRNAs and produce new zygotic transcripts. This maternal to zygotic transition requires a tight interplay of mRNA transcription and degradation  but distinguishing their unique contributions remains a challenge. Here  we dissect gene regulation during the zebrafish maternal to zygotic transition by combining single cell RNA sequencing with RNA metabolic labeling and nucleotide conversion within zebrafish embryos. We decompose single cell transcriptomes into their new zygotic and old maternal mRNA components  and elicit critical information on gene regulation as it unfolds over both time and space. We show that most cell type restricted expression arises by zygotic transcription  but distinguish a specific role for maternal transcripts in defining germ cell and enveloping layer identity  two earliest specified cell identities. We recover the underlying replacement between maternal and zygotic copies of embryonic genes with a relatively constant overall mRNA level  and associate a fast replacement with genes that has a restricted zygotic expression in either cell type or time. Our study provides a valuable resource to investigate maternal and zygotic transcriptomes and reveals post transcriptional events that control gene regulation during early embryogenesis. Overall design: SLAM seq  zebrafish embryos  1hpf and 6hpf  2 technical replicates,parent bioproject:PRJNA933118,pubmed:37131717;pubmed:38600066,,zebrafish embryo  1hpf  rep1,GSM7012033,,source name:whole embryo|tissue:whole embryo|genotype:AB/TL|treatment:4sU injection|time:1hpf|geo loc name:missing|collection date:missing,zebrafish embryo  1hpf  rep1,Sequence reads were trimmed for adaptor sequence using cutadapt Trimmed sequence reads were mapped to GRCz11 using STAR Read count extraction and NTR calculation were performed using GRAND SLAM Assembly: GRCz11/102 Supplementary files format and content: tab delimited text file includes readcount and NTR %new RNA for each Sample Library strategy: SLAM seq,whole embryo,20mM 4sU injection at 1 cell stage RNA was treated with Iodoacetamide to induce T to C conversions,Total RNA was isolated using tri reagent Sigma T9424 and quantified using nanodrop polyA+RNA: Indexed RNA Seq libraries were prepared from 500 ng total RNA using the KAPA Stranded mRNA Seq Kit Kapa Biosystems  Inc. according to the manufacturer’s protocol. Libraries were size selected with SPRI beads and quantified by QuBIT Life Technologies. Average size of 300 bp was determined by TapeStation Agilent Technologies  USA. Libraries are then sequenced using an Illumina Nextseq500 sequencer. total RNA: indexed RNA Seq libraries for each sample were generated from total RNA using the Illumina RiboZeroHuman/Mouse/Rat kit following the manufacturer’s instructions. Libraries were size selected with SPRI beads and quantified by QuBIT Life Technologies. Libraries are then sequenced using an Illumina Novaseq sequencer.,,tissue:whole embryo|genotype:AB/TL|treatment:4sU injection|time:1hpf,GSM7012033,GSM7012033: zebrafish embryo  1hpf  rep1; Danio rerio; RNA Seq,GSM7012033 r1,GSM7012033,1,Total RNA was isolated using tri reagent Sigma T9424 and quantified using nanodrop polyA+RNA: Indexed RNA Seq libraries were prepared from 500 ng total RNA using the KAPA Stranded mRNA Seq Kit Kapa Biosystems  Inc. according to the manufacturer's protocol. Libraries were size selected with SPRI beads and quantified by QuBIT Life Technologies. Average size of 300 bp was determined by TapeStation Agilent Technologies  USA. Libraries are then sequenced using an Illumina Nextseq500 sequencer. total RNA: indexed RNA Seq libraries for each sample were generated from total RNA using the Illumina RiboZeroHuman/Mouse/Rat kit following the manufacturer's instructions. Libraries were size selected with SPRI beads and quantified by QuBIT Life Technologies. Libraries are then sequenced using an Illumina Novaseq sequencer.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP420237,,loader:fastq load.py,novaseq_20220630_slam_120122_1h_1.fastq.gz novaseq_20220630_slam_120122_1h_2.fastq.gz,fastq fastq,7422864306.0,36746853.0,GSM7012033 r1,0:101 1:101,A:1927554601;C:1775023714;G:1801237102;T:1919030393;N:18496,101,101,,,1927554601,1775023714,1801237102,1919030393,18496,SRX19227382,SRS16633549,SRA1587567,Hebrew University of Jerusalem,Hebrew University of Jerusalem,2,0.91995,0.92316,0.05523,0.05324,0.7595,0.75897,0.57483,0.57891,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,ribozero,sc_generic,single_cell_generic,generic-scrnaseq-only,,Israel,2023-01-31,Cleavage,Embryo,Whole Organism,All anatomical structures
74361,SRR30639559,SRX26061375,SRS22630890,SRP425398,PRJNA940501,Zebrahub: Multimodal Zebrafish Developmental Atlas,PRJNA940501,Other,A single embryo single cell RNA seq developmental atlas of Zebrafish.,,,,TDR110,TDR110 30sinternew EKW NA none 10x,,strain:EKW|isolate:single embryo|breed:siblings per timepoint|cultivar:not applicable|ecotype:not applicable|age:24 hpf|collection date:2022 11 30|geo loc name:USA: California  San Francisco|sex:not determined|tissue:Whole embryo|replicate:4|BioSampleModel:Model organism or animal,,,,,,,,,TDR110,TDR110 30sinternew EKW NA none 10x,TDR110 30sinternew EKW NA none 10x,single embryo dissociation,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP425398,,,TDR110_30sinternew_EKW_NA_none_10x_S8_L001_I1_001.fastq.gz TDR110_30sinternew_EKW_NA_none_10x_S8_L001_I2_001.fastq.gz TDR110_30sinternew_EKW_NA_none_10x_S8_L001_R1_001.fastq.gz TDR110_30sinternew_EKW_NA_none_10x_S8_L001_R2_001.fastq.gz TDR110_30sinternew_EKW_NA_none_10x_S8_L002_I1_001.fastq.gz TDR110_30sinternew_EKW_NA_none_10x_S8_L002_I2_001.fastq.gz TDR110_30sinternew_EKW_NA_none_10x_S8_L002_R1_001.fastq.gz TDR110_30sinternew_EKW_NA_none_10x_S8_L002_R2_001.fastq.gz TDR110_30sinternew_EKW_NA_none_10x_S8_L003_I1_001.fastq.gz TDR110_30sinternew_EKW_NA_none_10x_S8_L003_I2_001.fastq.gz TDR110_30sinternew_EKW_NA_none_10x_S8_L003_R1_001.fastq.gz TDR110_30sinternew_EKW_NA_none_10x_S8_L003_R2_001.fastq.gz TDR110_30sinternew_EKW_NA_none_10x_S8_L004_I1_001.fastq.gz TDR110_30sinternew_EKW_NA_none_10x_S8_L004_I2_001.fastq.gz TDR110_30sinternew_EKW_NA_none_10x_S8_L004_R1_001.fastq.gz TDR110_30sinternew_EKW_NA_none_10x_S8_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,,,TDR110 30sinternew EKW NA none 10x S8 L001 I1 001.fastq.gz,,,,,,,,,,,,SRX26061375,,SRA1969971,Chan Zuckerberg Biohub|Quantitative Cell Science,Chan Zuckerberg Biohub,,,,,,,,,,,,,,,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2024-09-11,Pharyngula,Embryo,Whole Organism,All anatomical structures
74362,SRR30639560,SRX26061374,SRS22630889,SRP425398,PRJNA940501,Zebrahub: Multimodal Zebrafish Developmental Atlas,PRJNA940501,Other,A single embryo single cell RNA seq developmental atlas of Zebrafish.,,,,TDR108,TDR108 30sinternew EKW NA none 10x,,strain:EKW|isolate:single embryo|breed:siblings per timepoint|cultivar:not applicable|ecotype:not applicable|age:24 hpf|collection date:2022 11 30|geo loc name:USA: California  San Francisco|sex:not determined|tissue:Whole embryo|replicate:3|BioSampleModel:Model organism or animal,,,,,,,,,TDR108,TDR108 30sinternew EKW NA none 10x,TDR108 30sinternew EKW NA none 10x,single embryo dissociation,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP425398,,,TDR108_30sinternew_EKW_NA_none_10x_S7_L001_I1_001.fastq.gz TDR108_30sinternew_EKW_NA_none_10x_S7_L001_I2_001.fastq.gz TDR108_30sinternew_EKW_NA_none_10x_S7_L001_R1_001.fastq.gz TDR108_30sinternew_EKW_NA_none_10x_S7_L001_R2_001.fastq.gz TDR108_30sinternew_EKW_NA_none_10x_S7_L002_I1_001.fastq.gz TDR108_30sinternew_EKW_NA_none_10x_S7_L002_I2_001.fastq.gz TDR108_30sinternew_EKW_NA_none_10x_S7_L002_R1_001.fastq.gz TDR108_30sinternew_EKW_NA_none_10x_S7_L002_R2_001.fastq.gz TDR108_30sinternew_EKW_NA_none_10x_S7_L003_I1_001.fastq.gz TDR108_30sinternew_EKW_NA_none_10x_S7_L003_I2_001.fastq.gz TDR108_30sinternew_EKW_NA_none_10x_S7_L003_R1_001.fastq.gz TDR108_30sinternew_EKW_NA_none_10x_S7_L003_R2_001.fastq.gz TDR108_30sinternew_EKW_NA_none_10x_S7_L004_I1_001.fastq.gz TDR108_30sinternew_EKW_NA_none_10x_S7_L004_I2_001.fastq.gz TDR108_30sinternew_EKW_NA_none_10x_S7_L004_R1_001.fastq.gz TDR108_30sinternew_EKW_NA_none_10x_S7_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,,,TDR108 30sinternew EKW NA none 10x S7 L001 I1 001.fastq.gz,,,,,,,,,,,,SRX26061374,,SRA1969971,Chan Zuckerberg Biohub|Quantitative Cell Science,Chan Zuckerberg Biohub,,,,,,,,,,,,,,,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2024-09-11,Pharyngula,Embryo,Whole Organism,All anatomical structures
74363,SRR30639561,SRX26061373,SRS22630888,SRP425398,PRJNA940501,Zebrahub: Multimodal Zebrafish Developmental Atlas,PRJNA940501,Other,A single embryo single cell RNA seq developmental atlas of Zebrafish.,,,,TDR107,TDR107 30sinternew EKW NA none 10x,,strain:EKW|isolate:single embryo|breed:siblings per timepoint|cultivar:not applicable|ecotype:not applicable|age:24 hpf|collection date:2022 11 30|geo loc name:USA: California  San Francisco|sex:not determined|tissue:Whole embryo|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,TDR107,TDR107 30sinternew EKW NA none 10x,TDR107 30sinternew EKW NA none 10x,single embryo dissociation,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP425398,,,TDR107_30sinternew_EKW_NA_none_10x_S6_L001_I1_001.fastq.gz TDR107_30sinternew_EKW_NA_none_10x_S6_L001_I2_001.fastq.gz TDR107_30sinternew_EKW_NA_none_10x_S6_L001_R1_001.fastq.gz TDR107_30sinternew_EKW_NA_none_10x_S6_L001_R2_001.fastq.gz TDR107_30sinternew_EKW_NA_none_10x_S6_L002_I1_001.fastq.gz TDR107_30sinternew_EKW_NA_none_10x_S6_L002_I2_001.fastq.gz TDR107_30sinternew_EKW_NA_none_10x_S6_L002_R1_001.fastq.gz TDR107_30sinternew_EKW_NA_none_10x_S6_L002_R2_001.fastq.gz TDR107_30sinternew_EKW_NA_none_10x_S6_L003_I1_001.fastq.gz TDR107_30sinternew_EKW_NA_none_10x_S6_L003_I2_001.fastq.gz TDR107_30sinternew_EKW_NA_none_10x_S6_L003_R1_001.fastq.gz TDR107_30sinternew_EKW_NA_none_10x_S6_L003_R2_001.fastq.gz TDR107_30sinternew_EKW_NA_none_10x_S6_L004_I1_001.fastq.gz TDR107_30sinternew_EKW_NA_none_10x_S6_L004_I2_001.fastq.gz TDR107_30sinternew_EKW_NA_none_10x_S6_L004_R1_001.fastq.gz TDR107_30sinternew_EKW_NA_none_10x_S6_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,,,TDR107 30sinternew EKW NA none 10x S6 L001 I1 001.fastq.gz,,,,,,,,,,,,SRX26061373,,SRA1969971,Chan Zuckerberg Biohub|Quantitative Cell Science,Chan Zuckerberg Biohub,,,,,,,,,,,,,,,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2024-09-11,Pharyngula,Embryo,Whole Organism,All anatomical structures
74364,SRR30639562,SRX26061372,SRS22630887,SRP425398,PRJNA940501,Zebrahub: Multimodal Zebrafish Developmental Atlas,PRJNA940501,Other,A single embryo single cell RNA seq developmental atlas of Zebrafish.,,,,TDR106,TDR106 30sinternew EKW NA none 10x,,strain:EKW|isolate:single embryo|breed:siblings per timepoint|cultivar:not applicable|ecotype:not applicable|age:24 hpf|collection date:2022 11 30|geo loc name:USA: California  San Francisco|sex:not determined|tissue:Whole embryo|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,TDR106,TDR106 30sinternew EKW NA none 10x,TDR106 30sinternew EKW NA none 10x,single embryo dissociation,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP425398,,,TDR106_30sinternew_EKW_NA_none_10x_S5_L001_I1_001.fastq.gz TDR106_30sinternew_EKW_NA_none_10x_S5_L001_I2_001.fastq.gz TDR106_30sinternew_EKW_NA_none_10x_S5_L001_R1_001.fastq.gz TDR106_30sinternew_EKW_NA_none_10x_S5_L001_R2_001.fastq.gz TDR106_30sinternew_EKW_NA_none_10x_S5_L002_I1_001.fastq.gz TDR106_30sinternew_EKW_NA_none_10x_S5_L002_I2_001.fastq.gz TDR106_30sinternew_EKW_NA_none_10x_S5_L002_R1_001.fastq.gz TDR106_30sinternew_EKW_NA_none_10x_S5_L002_R2_001.fastq.gz TDR106_30sinternew_EKW_NA_none_10x_S5_L003_I1_001.fastq.gz TDR106_30sinternew_EKW_NA_none_10x_S5_L003_I2_001.fastq.gz TDR106_30sinternew_EKW_NA_none_10x_S5_L003_R1_001.fastq.gz TDR106_30sinternew_EKW_NA_none_10x_S5_L003_R2_001.fastq.gz TDR106_30sinternew_EKW_NA_none_10x_S5_L004_I1_001.fastq.gz TDR106_30sinternew_EKW_NA_none_10x_S5_L004_I2_001.fastq.gz TDR106_30sinternew_EKW_NA_none_10x_S5_L004_R1_001.fastq.gz TDR106_30sinternew_EKW_NA_none_10x_S5_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,,,TDR106 30sinternew EKW NA none 10x S5 L001 I1 001.fastq.gz,,,,,,,,,,,,SRX26061372,,SRA1969971,Chan Zuckerberg Biohub|Quantitative Cell Science,Chan Zuckerberg Biohub,,,,,,,,,,,,,,,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2024-09-11,Pharyngula,Embryo,Whole Organism,All anatomical structures
74365,SRR23691708,SRX19554131,SRS16938876,SRP425398,PRJNA940501,Zebrahub: Multimodal Zebrafish Developmental Atlas,PRJNA940501,Other,A single embryo single cell RNA seq developmental atlas of Zebrafish.,,,,TDR69,TDR69 3dpf EKW NA none 10x,,strain:EKW|isolate:single embryo|breed:siblings per timepoint|cultivar:not applicable|ecotype:not applicable|age:3 dpf|sex:not determined|tissue:Whole embryo|replicate:rep3|BioSampleModel:Model organism or animal,,,,,,,,,TDR69,TDR69 3dpf EKW NA none 10x,TDR69 3dpf EKW NA none 10x,single embryo dissociation,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP425398,,,TDR69_3dpf_EKW_NA_none_10x_S7_L001_I1_001.fastq.gz TDR69_3dpf_EKW_NA_none_10x_S7_L001_I2_001.fastq.gz TDR69_3dpf_EKW_NA_none_10x_S7_L001_R1_001.fastq.gz TDR69_3dpf_EKW_NA_none_10x_S7_L001_R2_001.fastq.gz TDR69_3dpf_EKW_NA_none_10x_S7_L002_I1_001.fastq.gz TDR69_3dpf_EKW_NA_none_10x_S7_L002_I2_001.fastq.gz TDR69_3dpf_EKW_NA_none_10x_S7_L002_R1_001.fastq.gz TDR69_3dpf_EKW_NA_none_10x_S7_L002_R2_001.fastq.gz TDR69_3dpf_EKW_NA_none_10x_S7_L003_I1_001.fastq.gz TDR69_3dpf_EKW_NA_none_10x_S7_L003_I2_001.fastq.gz TDR69_3dpf_EKW_NA_none_10x_S7_L003_R1_001.fastq.gz TDR69_3dpf_EKW_NA_none_10x_S7_L003_R2_001.fastq.gz TDR69_3dpf_EKW_NA_none_10x_S7_L004_I1_001.fastq.gz TDR69_3dpf_EKW_NA_none_10x_S7_L004_I2_001.fastq.gz TDR69_3dpf_EKW_NA_none_10x_S7_L004_R1_001.fastq.gz TDR69_3dpf_EKW_NA_none_10x_S7_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,141857572788.0,1027953426.0,TDR69 3dpf EKW NA none 10x S7 L001 I1 001.fastq.gz,0:10 1:10 2:28 3:90,A:28328864562;C:19239372522;G:21305538387;T:23641635703;N:397166,10,10,28,90,28328864562,19239372522,21305538387,23641635703,397166,SRX19554131,SRS16938876,SRA1598656,Chan Zuckerberg Biohub|Quantitative Cell Science,Chan Zuckerberg Biohub,1,0.88204,,0.16198,,0.75755,,0.60319,,90,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2023-03-03,Larval,Larval,Whole Organism,All anatomical structures
74366,SRR23691680,SRX19554130,SRS16938877,SRP425398,PRJNA940501,Zebrahub: Multimodal Zebrafish Developmental Atlas,PRJNA940501,Other,A single embryo single cell RNA seq developmental atlas of Zebrafish.,,,,TDR68,TDR68 3dpf EKW NA none 10x,,strain:EKW|isolate:single embryo|breed:siblings per timepoint|cultivar:not applicable|ecotype:not applicable|age:3 dpf|sex:not determined|tissue:Whole embryo|replicate:rep2|BioSampleModel:Model organism or animal,,,,,,,,,TDR68,TDR68 3dpf EKW NA none 10x,TDR68 3dpf EKW NA none 10x,single embryo dissociation,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP425398,,,TDR68_3dpf_EKW_NA_none_10x_S6_L001_I1_001.fastq.gz TDR68_3dpf_EKW_NA_none_10x_S6_L001_I2_001.fastq.gz TDR68_3dpf_EKW_NA_none_10x_S6_L001_R1_001.fastq.gz TDR68_3dpf_EKW_NA_none_10x_S6_L001_R2_001.fastq.gz TDR68_3dpf_EKW_NA_none_10x_S6_L002_I1_001.fastq.gz TDR68_3dpf_EKW_NA_none_10x_S6_L002_I2_001.fastq.gz TDR68_3dpf_EKW_NA_none_10x_S6_L002_R1_001.fastq.gz TDR68_3dpf_EKW_NA_none_10x_S6_L002_R2_001.fastq.gz TDR68_3dpf_EKW_NA_none_10x_S6_L003_I1_001.fastq.gz TDR68_3dpf_EKW_NA_none_10x_S6_L003_I2_001.fastq.gz TDR68_3dpf_EKW_NA_none_10x_S6_L003_R1_001.fastq.gz TDR68_3dpf_EKW_NA_none_10x_S6_L003_R2_001.fastq.gz TDR68_3dpf_EKW_NA_none_10x_S6_L004_I1_001.fastq.gz TDR68_3dpf_EKW_NA_none_10x_S6_L004_I2_001.fastq.gz TDR68_3dpf_EKW_NA_none_10x_S6_L004_R1_001.fastq.gz TDR68_3dpf_EKW_NA_none_10x_S6_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,110769022074.0,802674073.0,TDR68 3dpf EKW NA none 10x S6 L001 I1 001.fastq.gz,0:10 1:10 2:28 3:90,A:22289181655;C:15092942636;G:16399615434;T:18458614634;N:312211,10,10,28,90,22289181655,15092942636,16399615434,18458614634,312211,SRX19554130,SRS16938877,SRA1598656,Chan Zuckerberg Biohub|Quantitative Cell Science,Chan Zuckerberg Biohub,1,0.8863,,0.13277,,0.7763,,0.63421,,90,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2023-03-03,Larval,Larval,Whole Organism,All anatomical structures
74367,SRR23691681,SRX19554129,SRS16938875,SRP425398,PRJNA940501,Zebrahub: Multimodal Zebrafish Developmental Atlas,PRJNA940501,Other,A single embryo single cell RNA seq developmental atlas of Zebrafish.,,,,TDR67,TDR67 3dpf EKW NA none 10x,,strain:EKW|isolate:single embryo|breed:siblings per timepoint|cultivar:not applicable|ecotype:not applicable|age:3 dpf|sex:not determined|tissue:Whole embryo|replicate:rep1|BioSampleModel:Model organism or animal,,,,,,,,,TDR67,TDR67 3dpf EKW NA none 10x,TDR67 3dpf EKW NA none 10x,single embryo dissociation,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP425398,,,TDR67_3dpf_EKW_NA_none_10x_S5_L001_I1_001.fastq.gz TDR67_3dpf_EKW_NA_none_10x_S5_L001_I2_001.fastq.gz TDR67_3dpf_EKW_NA_none_10x_S5_L001_R1_001.fastq.gz TDR67_3dpf_EKW_NA_none_10x_S5_L001_R2_001.fastq.gz TDR67_3dpf_EKW_NA_none_10x_S5_L002_I1_001.fastq.gz TDR67_3dpf_EKW_NA_none_10x_S5_L002_I2_001.fastq.gz TDR67_3dpf_EKW_NA_none_10x_S5_L002_R1_001.fastq.gz TDR67_3dpf_EKW_NA_none_10x_S5_L002_R2_001.fastq.gz TDR67_3dpf_EKW_NA_none_10x_S5_L003_I1_001.fastq.gz TDR67_3dpf_EKW_NA_none_10x_S5_L003_I2_001.fastq.gz TDR67_3dpf_EKW_NA_none_10x_S5_L003_R1_001.fastq.gz TDR67_3dpf_EKW_NA_none_10x_S5_L003_R2_001.fastq.gz TDR67_3dpf_EKW_NA_none_10x_S5_L004_I1_001.fastq.gz TDR67_3dpf_EKW_NA_none_10x_S5_L004_I2_001.fastq.gz TDR67_3dpf_EKW_NA_none_10x_S5_L004_R1_001.fastq.gz TDR67_3dpf_EKW_NA_none_10x_S5_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,119516314086.0,866060247.0,TDR67 3dpf EKW NA none 10x S5 L001 I1 001.fastq.gz,0:10 1:10 2:28 3:90,A:24193630011;C:16247091070;G:17646962144;T:19857399932;N:339073,10,10,28,90,24193630011,16247091070,17646962144,19857399932,339073,SRX19554129,SRS16938875,SRA1598656,Chan Zuckerberg Biohub|Quantitative Cell Science,Chan Zuckerberg Biohub,1,0.88156,,0.15085,,0.77735,,0.65657,,90,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2023-03-03,Larval,Larval,Whole Organism,All anatomical structures
74368,SRR23691682,SRX19554128,SRS16938874,SRP425398,PRJNA940501,Zebrahub: Multimodal Zebrafish Developmental Atlas,PRJNA940501,Other,A single embryo single cell RNA seq developmental atlas of Zebrafish.,,,,TDR54,TDR54 5dpf EKW NA none 10x,,strain:EKW|isolate:single embryo|breed:siblings per timepoint|cultivar:not applicable|ecotype:not applicable|age:5 dpf|sex:not determined|tissue:Whole embryo|replicate:rep4|BioSampleModel:Model organism or animal,,,,,,,,,TDR54,TDR54 5dpf EKW NA none 10x,TDR54 5dpf EKW NA none 10x,single embryo dissociation,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP425398,,,TDR54_5dpf_EKW_NA_none_10x_S8_L001_I1_001.fastq.gz TDR54_5dpf_EKW_NA_none_10x_S8_L001_I2_001.fastq.gz TDR54_5dpf_EKW_NA_none_10x_S8_L001_R1_001.fastq.gz TDR54_5dpf_EKW_NA_none_10x_S8_L001_R2_001.fastq.gz TDR54_5dpf_EKW_NA_none_10x_S8_L002_I1_001.fastq.gz TDR54_5dpf_EKW_NA_none_10x_S8_L002_I2_001.fastq.gz TDR54_5dpf_EKW_NA_none_10x_S8_L002_R1_001.fastq.gz TDR54_5dpf_EKW_NA_none_10x_S8_L002_R2_001.fastq.gz TDR54_5dpf_EKW_NA_none_10x_S8_L003_I1_001.fastq.gz TDR54_5dpf_EKW_NA_none_10x_S8_L003_I2_001.fastq.gz TDR54_5dpf_EKW_NA_none_10x_S8_L003_R1_001.fastq.gz TDR54_5dpf_EKW_NA_none_10x_S8_L003_R2_001.fastq.gz TDR54_5dpf_EKW_NA_none_10x_S8_L004_I1_001.fastq.gz TDR54_5dpf_EKW_NA_none_10x_S8_L004_I2_001.fastq.gz TDR54_5dpf_EKW_NA_none_10x_S8_L004_R1_001.fastq.gz TDR54_5dpf_EKW_NA_none_10x_S8_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,102943738698.0,745969121.0,TDR54 5dpf EKW NA none 10x S8 L001 I1 001.fastq.gz,0:10 1:10 2:28 3:90,A:18441288819;C:15293958091;G:17147898256;T:16254015416;N:60308,10,10,28,90,18441288819,15293958091,17147898256,16254015416,60308,SRX19554128,SRS16938874,SRA1598656,Chan Zuckerberg Biohub|Quantitative Cell Science,Chan Zuckerberg Biohub,1,0.90349,,0.2328,,0.78865,,0.64502,,90,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2023-03-03,Larval,Larval,Whole Organism,All anatomical structures
74369,SRR23691683,SRX19554127,SRS16938873,SRP425398,PRJNA940501,Zebrahub: Multimodal Zebrafish Developmental Atlas,PRJNA940501,Other,A single embryo single cell RNA seq developmental atlas of Zebrafish.,,,,TDR22,TDR22 10somite EKW NA none 10x,,strain:EKW|isolate:single embryo|breed:siblings per timepoint|cultivar:not applicable|ecotype:not applicable|age:14 hpf|sex:not determined|tissue:Whole embryo|replicate:rep4|BioSampleModel:Model organism or animal,,,,,,,,,TDR22,TDR22 10somite EKW NA none 10x,TDR22 10somite EKW NA none 10x,single embryo dissociation,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP425398,,,TDR22_10somite_EKW_NA_none_10x_S4_L001_I1_001.fastq.gz TDR22_10somite_EKW_NA_none_10x_S4_L001_R1_001.fastq.gz TDR22_10somite_EKW_NA_none_10x_S4_L001_R2_001.fastq.gz TDR22_10somite_EKW_NA_none_10x_S4_L002_I1_001.fastq.gz TDR22_10somite_EKW_NA_none_10x_S4_L002_R1_001.fastq.gz TDR22_10somite_EKW_NA_none_10x_S4_L002_R2_001.fastq.gz TDR22_10somite_EKW_NA_none_10x_S4_L003_I1_001.fastq.gz TDR22_10somite_EKW_NA_none_10x_S4_L003_R1_001.fastq.gz TDR22_10somite_EKW_NA_none_10x_S4_L003_R2_001.fastq.gz TDR22_10somite_EKW_NA_none_10x_S4_L004_I1_001.fastq.gz TDR22_10somite_EKW_NA_none_10x_S4_L004_R1_001.fastq.gz TDR22_10somite_EKW_NA_none_10x_S4_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,,,TDR22 10somite EKW NA none 10x S4 L001 I1 001.fastq.gz,,,,,,,,,,,,SRX19554127,,SRA1598656,Chan Zuckerberg Biohub|Quantitative Cell Science,Chan Zuckerberg Biohub,,,,,,,,,,,,,,,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2023-03-02,Segmentation,Embryo,Whole Organism,All anatomical structures
74370,SRR23691685,SRX19554126,SRS16938872,SRP425398,PRJNA940501,Zebrahub: Multimodal Zebrafish Developmental Atlas,PRJNA940501,Other,A single embryo single cell RNA seq developmental atlas of Zebrafish.,,,,TDR52,TDR52 5dpf EKW NA none 10x,,strain:EKW|isolate:single embryo|breed:siblings per timepoint|cultivar:not applicable|ecotype:not applicable|age:5 dpf|sex:not determined|tissue:Whole embryo|replicate:rep2|BioSampleModel:Model organism or animal,,,,,,,,,TDR52,TDR52 5dpf EKW NA none 10x,TDR52 5dpf EKW NA none 10x,single embryo dissociation,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP425398,,,TDR52_5dpf_EKW_NA_none_10x_S6_L001_I1_001.fastq.gz TDR52_5dpf_EKW_NA_none_10x_S6_L001_I2_001.fastq.gz TDR52_5dpf_EKW_NA_none_10x_S6_L001_R1_001.fastq.gz TDR52_5dpf_EKW_NA_none_10x_S6_L001_R2_001.fastq.gz TDR52_5dpf_EKW_NA_none_10x_S6_L002_I1_001.fastq.gz TDR52_5dpf_EKW_NA_none_10x_S6_L002_I2_001.fastq.gz TDR52_5dpf_EKW_NA_none_10x_S6_L002_R1_001.fastq.gz TDR52_5dpf_EKW_NA_none_10x_S6_L002_R2_001.fastq.gz TDR52_5dpf_EKW_NA_none_10x_S6_L003_I1_001.fastq.gz TDR52_5dpf_EKW_NA_none_10x_S6_L003_I2_001.fastq.gz TDR52_5dpf_EKW_NA_none_10x_S6_L003_R1_001.fastq.gz TDR52_5dpf_EKW_NA_none_10x_S6_L003_R2_001.fastq.gz TDR52_5dpf_EKW_NA_none_10x_S6_L004_I1_001.fastq.gz TDR52_5dpf_EKW_NA_none_10x_S6_L004_I2_001.fastq.gz TDR52_5dpf_EKW_NA_none_10x_S6_L004_R1_001.fastq.gz TDR52_5dpf_EKW_NA_none_10x_S6_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,101121414750.0,732763875.0,TDR52 5dpf EKW NA none 10x S6 L001 I1 001.fastq.gz,0:10 1:10 2:28 3:90,A:18381382068;C:14949962451;G:16391823629;T:16225521055;N:59547,10,10,28,90,18381382068,14949962451,16391823629,16225521055,59547,SRX19554126,SRS16938872,SRA1598656,Chan Zuckerberg Biohub|Quantitative Cell Science,Chan Zuckerberg Biohub,1,0.92316,,0.19197,,0.77337,,0.62427,,90,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2023-03-03,Larval,Larval,Whole Organism,All anatomical structures
74371,SRR23691702,SRX19554125,SRS16938871,SRP425398,PRJNA940501,Zebrahub: Multimodal Zebrafish Developmental Atlas,PRJNA940501,Other,A single embryo single cell RNA seq developmental atlas of Zebrafish.,,,,TDR24,TDR24 budstage EKW NA none 10x,,strain:EKW|isolate:single embryo|breed:siblings per timepoint|cultivar:not applicable|ecotype:not applicable|age:10 hpf|sex:not determined|tissue:Whole embryo|replicate:rep2|BioSampleModel:Model organism or animal,,,,,,,,,TDR24,TDR24 budstage EKW NA none 10x,TDR24 budstage EKW NA none 10x,single embryo dissociation,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP425398,,,TDR24_budstage_EKW_NA_none_10x_S2_L001_I1_001.fastq.gz TDR24_budstage_EKW_NA_none_10x_S2_L001_R1_001.fastq.gz TDR24_budstage_EKW_NA_none_10x_S2_L001_R2_001.fastq.gz TDR24_budstage_EKW_NA_none_10x_S2_L002_I1_001.fastq.gz TDR24_budstage_EKW_NA_none_10x_S2_L002_R1_001.fastq.gz TDR24_budstage_EKW_NA_none_10x_S2_L002_R2_001.fastq.gz TDR24_budstage_EKW_NA_none_10x_S2_L003_I1_001.fastq.gz TDR24_budstage_EKW_NA_none_10x_S2_L003_R1_001.fastq.gz TDR24_budstage_EKW_NA_none_10x_S2_L003_R2_001.fastq.gz TDR24_budstage_EKW_NA_none_10x_S2_L004_I1_001.fastq.gz TDR24_budstage_EKW_NA_none_10x_S2_L004_R1_001.fastq.gz TDR24_budstage_EKW_NA_none_10x_S2_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,,,TDR24 budstage EKW NA none 10x S2 L001 I1 001.fastq.gz,,,,,,,,,,,,SRX19554125,,SRA1598656,Chan Zuckerberg Biohub|Quantitative Cell Science,Chan Zuckerberg Biohub,,,,,,,,,,,,,,,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2023-03-02,Gastrula,Embryo,Whole Organism,All anatomical structures
74372,SRR23691684,SRX19554124,SRS16938870,SRP425398,PRJNA940501,Zebrahub: Multimodal Zebrafish Developmental Atlas,PRJNA940501,Other,A single embryo single cell RNA seq developmental atlas of Zebrafish.,,,,TDR53,TDR53 5dpf EKW NA none 10x,,strain:EKW|isolate:single embryo|breed:siblings per timepoint|cultivar:not applicable|ecotype:not applicable|age:5 dpf|sex:not determined|tissue:Whole embryo|replicate:rep3|BioSampleModel:Model organism or animal,,,,,,,,,TDR53,TDR53 5dpf EKW NA none 10x,TDR53 5dpf EKW NA none 10x,single embryo dissociation,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP425398,,,TDR53_5dpf_EKW_NA_none_10x_S7_L001_I1_001.fastq.gz TDR53_5dpf_EKW_NA_none_10x_S7_L001_I2_001.fastq.gz TDR53_5dpf_EKW_NA_none_10x_S7_L001_R1_001.fastq.gz TDR53_5dpf_EKW_NA_none_10x_S7_L001_R2_001.fastq.gz TDR53_5dpf_EKW_NA_none_10x_S7_L002_I1_001.fastq.gz TDR53_5dpf_EKW_NA_none_10x_S7_L002_I2_001.fastq.gz TDR53_5dpf_EKW_NA_none_10x_S7_L002_R1_001.fastq.gz TDR53_5dpf_EKW_NA_none_10x_S7_L002_R2_001.fastq.gz TDR53_5dpf_EKW_NA_none_10x_S7_L003_I1_001.fastq.gz TDR53_5dpf_EKW_NA_none_10x_S7_L003_I2_001.fastq.gz TDR53_5dpf_EKW_NA_none_10x_S7_L003_R1_001.fastq.gz TDR53_5dpf_EKW_NA_none_10x_S7_L003_R2_001.fastq.gz TDR53_5dpf_EKW_NA_none_10x_S7_L004_I1_001.fastq.gz TDR53_5dpf_EKW_NA_none_10x_S7_L004_I2_001.fastq.gz TDR53_5dpf_EKW_NA_none_10x_S7_L004_R1_001.fastq.gz TDR53_5dpf_EKW_NA_none_10x_S7_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,67168978188.0,486731726.0,TDR53 5dpf EKW NA none 10x S7 L001 I1 001.fastq.gz,0:10 1:10 2:28 3:90,A:12286816007;C:9835631121;G:10821946765;T:10861420866;N:40581,10,10,28,90,12286816007,9835631121,10821946765,10861420866,40581,SRX19554124,SRS16938870,SRA1598656,Chan Zuckerberg Biohub|Quantitative Cell Science,Chan Zuckerberg Biohub,1,0.92074,,0.21231,,0.77488,,0.65154,,90,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2023-03-03,Larval,Larval,Whole Organism,All anatomical structures
74373,SRR23691686,SRX19554123,SRS16938869,SRP425398,PRJNA940501,Zebrahub: Multimodal Zebrafish Developmental Atlas,PRJNA940501,Other,A single embryo single cell RNA seq developmental atlas of Zebrafish.,,,,TDR51,TDR51 5dpf EKW NA none 10x,,strain:EKW|isolate:single embryo|breed:siblings per timepoint|cultivar:not applicable|ecotype:not applicable|age:5 dpf|sex:not determined|tissue:Whole embryo|replicate:rep1|BioSampleModel:Model organism or animal,,,,,,,,,TDR51,TDR51 5dpf EKW NA none 10x,TDR51 5dpf EKW NA none 10x,single embryo dissociation,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP425398,,,TDR51_5dpf_EKW_NA_none_10x_S5_L001_I1_001.fastq.gz TDR51_5dpf_EKW_NA_none_10x_S5_L001_I2_001.fastq.gz TDR51_5dpf_EKW_NA_none_10x_S5_L001_R1_001.fastq.gz TDR51_5dpf_EKW_NA_none_10x_S5_L001_R2_001.fastq.gz TDR51_5dpf_EKW_NA_none_10x_S5_L002_I1_001.fastq.gz TDR51_5dpf_EKW_NA_none_10x_S5_L002_I2_001.fastq.gz TDR51_5dpf_EKW_NA_none_10x_S5_L002_R1_001.fastq.gz TDR51_5dpf_EKW_NA_none_10x_S5_L002_R2_001.fastq.gz TDR51_5dpf_EKW_NA_none_10x_S5_L003_I1_001.fastq.gz TDR51_5dpf_EKW_NA_none_10x_S5_L003_I2_001.fastq.gz TDR51_5dpf_EKW_NA_none_10x_S5_L003_R1_001.fastq.gz TDR51_5dpf_EKW_NA_none_10x_S5_L003_R2_001.fastq.gz TDR51_5dpf_EKW_NA_none_10x_S5_L004_I1_001.fastq.gz TDR51_5dpf_EKW_NA_none_10x_S5_L004_I2_001.fastq.gz TDR51_5dpf_EKW_NA_none_10x_S5_L004_R1_001.fastq.gz TDR51_5dpf_EKW_NA_none_10x_S5_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,107234170842.0,777059209.0,TDR51 5dpf EKW NA none 10x S5 L001 I1 001.fastq.gz,0:10 1:10 2:28 3:90,A:19755252329;C:15612604707;G:17171775681;T:17395631095;N:64998,10,10,28,90,19755252329,15612604707,17171775681,17395631095,64998,SRX19554123,SRS16938869,SRA1598656,Chan Zuckerberg Biohub|Quantitative Cell Science,Chan Zuckerberg Biohub,1,0.90333,,0.21644,,0.76706,,0.65091,,90,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2023-03-03,Larval,Larval,Whole Organism,All anatomical structures
74374,SRR23691687,SRX19554122,SRS16938868,SRP425398,PRJNA940501,Zebrahub: Multimodal Zebrafish Developmental Atlas,PRJNA940501,Other,A single embryo single cell RNA seq developmental atlas of Zebrafish.,,,,TDR50,TDR50 2dpf EKW NA none 10x,,strain:EKW|isolate:single embryo|breed:siblings per timepoint|cultivar:not applicable|ecotype:not applicable|age:2 dpf|sex:not determined|tissue:Whole embryo|replicate:rep4|BioSampleModel:Model organism or animal,,,,,,,,,TDR50,TDR50 2dpf EKW NA none 10x,TDR50 2dpf EKW NA none 10x,single embryo dissociation,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP425398,,,TDR50_2dpf_EKW_NA_none_10x_S4_L001_I1_001.fastq.gz TDR50_2dpf_EKW_NA_none_10x_S4_L001_I2_001.fastq.gz TDR50_2dpf_EKW_NA_none_10x_S4_L001_R1_001.fastq.gz TDR50_2dpf_EKW_NA_none_10x_S4_L001_R2_001.fastq.gz TDR50_2dpf_EKW_NA_none_10x_S4_L002_I1_001.fastq.gz TDR50_2dpf_EKW_NA_none_10x_S4_L002_I2_001.fastq.gz TDR50_2dpf_EKW_NA_none_10x_S4_L002_R1_001.fastq.gz TDR50_2dpf_EKW_NA_none_10x_S4_L002_R2_001.fastq.gz TDR50_2dpf_EKW_NA_none_10x_S4_L003_I1_001.fastq.gz TDR50_2dpf_EKW_NA_none_10x_S4_L003_I2_001.fastq.gz TDR50_2dpf_EKW_NA_none_10x_S4_L003_R1_001.fastq.gz TDR50_2dpf_EKW_NA_none_10x_S4_L003_R2_001.fastq.gz TDR50_2dpf_EKW_NA_none_10x_S4_L004_I1_001.fastq.gz TDR50_2dpf_EKW_NA_none_10x_S4_L004_I2_001.fastq.gz TDR50_2dpf_EKW_NA_none_10x_S4_L004_R1_001.fastq.gz TDR50_2dpf_EKW_NA_none_10x_S4_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,110075703450.0,797650025.0,TDR50 2dpf EKW NA none 10x S4 L001 I1 001.fastq.gz,0:10 1:10 2:28 3:90,A:19338422691;C:16766252744;G:19693997103;T:15989765605;N:64107,10,10,28,90,19338422691,16766252744,19693997103,15989765605,64107,SRX19554122,SRS16938868,SRA1598656,Chan Zuckerberg Biohub|Quantitative Cell Science,Chan Zuckerberg Biohub,1,0.87838,,0.18625,,0.8355,,0.58184,,90,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2023-03-03,Hatching,Embryo,Whole Organism,All anatomical structures
74375,SRR23691717,SRX19554121,SRS16938867,SRP425398,PRJNA940501,Zebrahub: Multimodal Zebrafish Developmental Atlas,PRJNA940501,Other,A single embryo single cell RNA seq developmental atlas of Zebrafish.,,,,TDR41,TDR41 15somite EKW NA none 10x,,strain:EKW|isolate:single embryo|breed:siblings per timepoint|cultivar:not applicable|ecotype:not applicable|age:16 hpf|sex:not determined|tissue:Whole embryo|replicate:rep3|BioSampleModel:Model organism or animal,,,,,,,,,TDR41,TDR41 15somite EKW NA none 10x,TDR41 15somite EKW NA none 10x,single embryo dissociation,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP425398,,,TDR41_15somite_EKW_NA_none_10x_S7_L001_I1_001.fastq.gz TDR41_15somite_EKW_NA_none_10x_S7_L001_I2_001.fastq.gz TDR41_15somite_EKW_NA_none_10x_S7_L001_R1_001.fastq.gz TDR41_15somite_EKW_NA_none_10x_S7_L001_R2_001.fastq.gz TDR41_15somite_EKW_NA_none_10x_S7_L002_I1_001.fastq.gz TDR41_15somite_EKW_NA_none_10x_S7_L002_I2_001.fastq.gz TDR41_15somite_EKW_NA_none_10x_S7_L002_R1_001.fastq.gz TDR41_15somite_EKW_NA_none_10x_S7_L002_R2_001.fastq.gz TDR41_15somite_EKW_NA_none_10x_S7_L003_I1_001.fastq.gz TDR41_15somite_EKW_NA_none_10x_S7_L003_I2_001.fastq.gz TDR41_15somite_EKW_NA_none_10x_S7_L003_R1_001.fastq.gz TDR41_15somite_EKW_NA_none_10x_S7_L003_R2_001.fastq.gz TDR41_15somite_EKW_NA_none_10x_S7_L004_I1_001.fastq.gz TDR41_15somite_EKW_NA_none_10x_S7_L004_I2_001.fastq.gz TDR41_15somite_EKW_NA_none_10x_S7_L004_R1_001.fastq.gz TDR41_15somite_EKW_NA_none_10x_S7_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,93499956408.0,677535916.0,TDR41 15somite EKW NA none 10x S7 L001 I1 001.fastq.gz,0:10 1:10 2:28 3:90,A:17289943134;C:13691132218;G:15290920650;T:14706171425;N:65013,10,10,28,90,17289943134,13691132218,15290920650,14706171425,65013,SRX19554121,SRS16938867,SRA1598656,Chan Zuckerberg Biohub|Quantitative Cell Science,Chan Zuckerberg Biohub,1,0.94201,,0.12543,,0.80129,,0.52789,,90,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2023-03-03,Segmentation,Embryo,Whole Organism,All anatomical structures
74376,SRR23691689,SRX19554120,SRS16938866,SRP425398,PRJNA940501,Zebrahub: Multimodal Zebrafish Developmental Atlas,PRJNA940501,Other,A single embryo single cell RNA seq developmental atlas of Zebrafish.,,,,TDR40,TDR40 15somite EKW NA none 10x,,strain:EKW|isolate:single embryo|breed:siblings per timepoint|cultivar:not applicable|ecotype:not applicable|age:16 hpf|sex:not determined|tissue:Whole embryo|replicate:rep2|BioSampleModel:Model organism or animal,,,,,,,,,TDR40,TDR40 15somite EKW NA none 10x,TDR40 15somite EKW NA none 10x,single embryo dissociation,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP425398,,,TDR40_15somite_EKW_NA_none_10x_S6_L001_I1_001.fastq.gz TDR40_15somite_EKW_NA_none_10x_S6_L001_I2_001.fastq.gz TDR40_15somite_EKW_NA_none_10x_S6_L001_R1_001.fastq.gz TDR40_15somite_EKW_NA_none_10x_S6_L001_R2_001.fastq.gz TDR40_15somite_EKW_NA_none_10x_S6_L002_I1_001.fastq.gz TDR40_15somite_EKW_NA_none_10x_S6_L002_I2_001.fastq.gz TDR40_15somite_EKW_NA_none_10x_S6_L002_R1_001.fastq.gz TDR40_15somite_EKW_NA_none_10x_S6_L002_R2_001.fastq.gz TDR40_15somite_EKW_NA_none_10x_S6_L003_I1_001.fastq.gz TDR40_15somite_EKW_NA_none_10x_S6_L003_I2_001.fastq.gz TDR40_15somite_EKW_NA_none_10x_S6_L003_R1_001.fastq.gz TDR40_15somite_EKW_NA_none_10x_S6_L003_R2_001.fastq.gz TDR40_15somite_EKW_NA_none_10x_S6_L004_I1_001.fastq.gz TDR40_15somite_EKW_NA_none_10x_S6_L004_I2_001.fastq.gz TDR40_15somite_EKW_NA_none_10x_S6_L004_R1_001.fastq.gz TDR40_15somite_EKW_NA_none_10x_S6_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,94772546316.0,686757582.0,TDR40 15somite EKW NA none 10x S6 L001 I1 001.fastq.gz,0:10 1:10 2:28 3:90,A:17499834278;C:13832305488;G:15425748483;T:15050229511;N:64620,10,10,28,90,17499834278,13832305488,15425748483,15050229511,64620,SRX19554120,SRS16938866,SRA1598656,Chan Zuckerberg Biohub|Quantitative Cell Science,Chan Zuckerberg Biohub,1,0.93907,,0.13477,,0.79143,,0.5485,,90,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2023-03-03,Segmentation,Embryo,Whole Organism,All anatomical structures
74377,SRR23691690,SRX19554119,SRS16938865,SRP425398,PRJNA940501,Zebrahub: Multimodal Zebrafish Developmental Atlas,PRJNA940501,Other,A single embryo single cell RNA seq developmental atlas of Zebrafish.,,,,TDR39,TDR39 15somite EKW NA none 10x,,strain:EKW|isolate:single embryo|breed:siblings per timepoint|cultivar:not applicable|ecotype:not applicable|age:16 hpf|sex:not determined|tissue:Whole embryo|replicate:rep1|BioSampleModel:Model organism or animal,,,,,,,,,TDR39,TDR39 15somite EKW NA none 10x,TDR39 15somite EKW NA none 10x,single embryo dissociation,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP425398,,,TDR39_15somite_EKW_NA_none_10x_S5_L001_I1_001.fastq.gz TDR39_15somite_EKW_NA_none_10x_S5_L001_I2_001.fastq.gz TDR39_15somite_EKW_NA_none_10x_S5_L001_R1_001.fastq.gz TDR39_15somite_EKW_NA_none_10x_S5_L001_R2_001.fastq.gz TDR39_15somite_EKW_NA_none_10x_S5_L002_I1_001.fastq.gz TDR39_15somite_EKW_NA_none_10x_S5_L002_I2_001.fastq.gz TDR39_15somite_EKW_NA_none_10x_S5_L002_R1_001.fastq.gz TDR39_15somite_EKW_NA_none_10x_S5_L002_R2_001.fastq.gz TDR39_15somite_EKW_NA_none_10x_S5_L003_I1_001.fastq.gz TDR39_15somite_EKW_NA_none_10x_S5_L003_I2_001.fastq.gz TDR39_15somite_EKW_NA_none_10x_S5_L003_R1_001.fastq.gz TDR39_15somite_EKW_NA_none_10x_S5_L003_R2_001.fastq.gz TDR39_15somite_EKW_NA_none_10x_S5_L004_I1_001.fastq.gz TDR39_15somite_EKW_NA_none_10x_S5_L004_I2_001.fastq.gz TDR39_15somite_EKW_NA_none_10x_S5_L004_R1_001.fastq.gz TDR39_15somite_EKW_NA_none_10x_S5_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,134364525240.0,973655980.0,TDR39 15somite EKW NA none 10x S5 L001 I1 001.fastq.gz,0:10 1:10 2:28 3:90,A:25028565859;C:19549118640;G:21889948945;T:21161311123;N:93633,10,10,28,90,25028565859,19549118640,21889948945,21161311123,93633,SRX19554119,SRS16938865,SRA1598656,Chan Zuckerberg Biohub|Quantitative Cell Science,Chan Zuckerberg Biohub,1,0.93786,,0.13635,,0.79817,,0.5526,,90,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2023-03-03,Segmentation,Embryo,Whole Organism,All anatomical structures
74378,SRR23691691,SRX19554118,SRS16938864,SRP425398,PRJNA940501,Zebrahub: Multimodal Zebrafish Developmental Atlas,PRJNA940501,Other,A single embryo single cell RNA seq developmental atlas of Zebrafish.,,,,TDR38,TDR38 5somite EKW NA none 10x,,strain:EKW|isolate:single embryo|breed:siblings per timepoint|cultivar:not applicable|ecotype:not applicable|age:12 hpf|sex:not determined|tissue:Whole embryo|replicate:rep4|BioSampleModel:Model organism or animal,,,,,,,,,TDR38,TDR38 5somite EKW NA none 10x,TDR38 5somite EKW NA none 10x,single embryo dissociation,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP425398,,,TDR38_5somite_EKW_NA_none_10x_S4_L001_I1_001.fastq.gz TDR38_5somite_EKW_NA_none_10x_S4_L001_I2_001.fastq.gz TDR38_5somite_EKW_NA_none_10x_S4_L001_R1_001.fastq.gz TDR38_5somite_EKW_NA_none_10x_S4_L001_R2_001.fastq.gz TDR38_5somite_EKW_NA_none_10x_S4_L002_I1_001.fastq.gz TDR38_5somite_EKW_NA_none_10x_S4_L002_I2_001.fastq.gz TDR38_5somite_EKW_NA_none_10x_S4_L002_R1_001.fastq.gz TDR38_5somite_EKW_NA_none_10x_S4_L002_R2_001.fastq.gz TDR38_5somite_EKW_NA_none_10x_S4_L003_I1_001.fastq.gz TDR38_5somite_EKW_NA_none_10x_S4_L003_I2_001.fastq.gz TDR38_5somite_EKW_NA_none_10x_S4_L003_R1_001.fastq.gz TDR38_5somite_EKW_NA_none_10x_S4_L003_R2_001.fastq.gz TDR38_5somite_EKW_NA_none_10x_S4_L004_I1_001.fastq.gz TDR38_5somite_EKW_NA_none_10x_S4_L004_I2_001.fastq.gz TDR38_5somite_EKW_NA_none_10x_S4_L004_R1_001.fastq.gz TDR38_5somite_EKW_NA_none_10x_S4_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,109163562504.0,791040308.0,TDR38 5somite EKW NA none 10x S4 L001 I1 001.fastq.gz,0:10 1:10 2:28 3:90,A:20296889655;C:15295509612;G:16665411100;T:18935743224;N:74129,10,10,28,90,20296889655,15295509612,16665411100,18935743224,74129,SRX19554118,SRS16938864,SRA1598656,Chan Zuckerberg Biohub|Quantitative Cell Science,Chan Zuckerberg Biohub,1,0.94177,,0.14801,,0.79078,,0.51715,,90,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2023-03-03,Segmentation,Embryo,Whole Organism,All anatomical structures
74379,SRR23691692,SRX19554117,SRS16938863,SRP425398,PRJNA940501,Zebrahub: Multimodal Zebrafish Developmental Atlas,PRJNA940501,Other,A single embryo single cell RNA seq developmental atlas of Zebrafish.,,,,TDR37,TDR37 5somite EKW NA none 10x,,strain:EKW|isolate:single embryo|breed:siblings per timepoint|cultivar:not applicable|ecotype:not applicable|age:12 hpf|sex:not determined|tissue:Whole embryo|replicate:rep3|BioSampleModel:Model organism or animal,,,,,,,,,TDR37,TDR37 5somite EKW NA none 10x,TDR37 5somite EKW NA none 10x,single embryo dissociation,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP425398,,,TDR37_5somite_EKW_NA_none_10x_S3_L001_I1_001.fastq.gz TDR37_5somite_EKW_NA_none_10x_S3_L001_I2_001.fastq.gz TDR37_5somite_EKW_NA_none_10x_S3_L001_R1_001.fastq.gz TDR37_5somite_EKW_NA_none_10x_S3_L001_R2_001.fastq.gz TDR37_5somite_EKW_NA_none_10x_S3_L002_I1_001.fastq.gz TDR37_5somite_EKW_NA_none_10x_S3_L002_I2_001.fastq.gz TDR37_5somite_EKW_NA_none_10x_S3_L002_R1_001.fastq.gz TDR37_5somite_EKW_NA_none_10x_S3_L002_R2_001.fastq.gz TDR37_5somite_EKW_NA_none_10x_S3_L003_I1_001.fastq.gz TDR37_5somite_EKW_NA_none_10x_S3_L003_I2_001.fastq.gz TDR37_5somite_EKW_NA_none_10x_S3_L003_R1_001.fastq.gz TDR37_5somite_EKW_NA_none_10x_S3_L003_R2_001.fastq.gz TDR37_5somite_EKW_NA_none_10x_S3_L004_I1_001.fastq.gz TDR37_5somite_EKW_NA_none_10x_S3_L004_I2_001.fastq.gz TDR37_5somite_EKW_NA_none_10x_S3_L004_R1_001.fastq.gz TDR37_5somite_EKW_NA_none_10x_S3_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,86186871072.0,624542544.0,TDR37 5somite EKW NA none 10x S3 L001 I1 001.fastq.gz,0:10 1:10 2:28 3:90,A:16098325109;C:11599595645;G:12688698356;T:15822148067;N:61783,10,10,28,90,16098325109,11599595645,12688698356,15822148067,61783,SRX19554117,SRS16938863,SRA1598656,Chan Zuckerberg Biohub|Quantitative Cell Science,Chan Zuckerberg Biohub,1,0.93181,,0.14342,,0.78293,,0.50708,,90,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2023-03-03,Segmentation,Embryo,Whole Organism,All anatomical structures
74380,SRR23691693,SRX19554116,SRS16938862,SRP425398,PRJNA940501,Zebrahub: Multimodal Zebrafish Developmental Atlas,PRJNA940501,Other,A single embryo single cell RNA seq developmental atlas of Zebrafish.,,,,TDR36,TDR36 5somite EKW NA none 10x,,strain:EKW|isolate:single embryo|breed:siblings per timepoint|cultivar:not applicable|ecotype:not applicable|age:12 hpf|sex:not determined|tissue:Whole embryo|replicate:rep2|BioSampleModel:Model organism or animal,,,,,,,,,TDR36,TDR36 5somite EKW NA none 10x,TDR36 5somite EKW NA none 10x,single embryo dissociation,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP425398,,,TDR36_5somite_EKW_NA_none_10x_S2_L001_I1_001.fastq.gz TDR36_5somite_EKW_NA_none_10x_S2_L001_I2_001.fastq.gz TDR36_5somite_EKW_NA_none_10x_S2_L001_R1_001.fastq.gz TDR36_5somite_EKW_NA_none_10x_S2_L001_R2_001.fastq.gz TDR36_5somite_EKW_NA_none_10x_S2_L002_I1_001.fastq.gz TDR36_5somite_EKW_NA_none_10x_S2_L002_I2_001.fastq.gz TDR36_5somite_EKW_NA_none_10x_S2_L002_R1_001.fastq.gz TDR36_5somite_EKW_NA_none_10x_S2_L002_R2_001.fastq.gz TDR36_5somite_EKW_NA_none_10x_S2_L003_I1_001.fastq.gz TDR36_5somite_EKW_NA_none_10x_S2_L003_I2_001.fastq.gz TDR36_5somite_EKW_NA_none_10x_S2_L003_R1_001.fastq.gz TDR36_5somite_EKW_NA_none_10x_S2_L003_R2_001.fastq.gz TDR36_5somite_EKW_NA_none_10x_S2_L004_I1_001.fastq.gz TDR36_5somite_EKW_NA_none_10x_S2_L004_I2_001.fastq.gz TDR36_5somite_EKW_NA_none_10x_S2_L004_R1_001.fastq.gz TDR36_5somite_EKW_NA_none_10x_S2_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,135123329832.0,979154564.0,TDR36 5somite EKW NA none 10x S2 L001 I1 001.fastq.gz,0:10 1:10 2:28 3:90,A:25030401855;C:19108313489;G:21135503897;T:22849597141;N:94378,10,10,28,90,25030401855,19108313489,21135503897,22849597141,94378,SRX19554116,SRS16938862,SRA1598656,Chan Zuckerberg Biohub|Quantitative Cell Science,Chan Zuckerberg Biohub,1,0.93706,,0.13959,,0.79322,,0.53064,,90,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2023-03-03,Segmentation,Embryo,Whole Organism,All anatomical structures
74381,SRR23691715,SRX19554115,SRS16938861,SRP425398,PRJNA940501,Zebrahub: Multimodal Zebrafish Developmental Atlas,PRJNA940501,Other,A single embryo single cell RNA seq developmental atlas of Zebrafish.,,,,TDR43,TDR43 30somite EKW NA none 10x,,strain:EKW|isolate:single embryo|breed:siblings per timepoint|cultivar:not applicable|ecotype:not applicable|age:24 hpf|sex:not determined|tissue:Whole embryo|replicate:rep1|BioSampleModel:Model organism or animal,,,,,,,,,TDR43,TDR43 30somite EKW NA none 10x,TDR43 30somite EKW NA none 10x,single embryo dissociation,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP425398,,,TDR43_30somite_EKW_NA_none_10x_S9_L001_I1_001.fastq.gz TDR43_30somite_EKW_NA_none_10x_S9_L001_I2_001.fastq.gz TDR43_30somite_EKW_NA_none_10x_S9_L001_R1_001.fastq.gz TDR43_30somite_EKW_NA_none_10x_S9_L001_R2_001.fastq.gz TDR43_30somite_EKW_NA_none_10x_S9_L002_I1_001.fastq.gz TDR43_30somite_EKW_NA_none_10x_S9_L002_I2_001.fastq.gz TDR43_30somite_EKW_NA_none_10x_S9_L002_R1_001.fastq.gz TDR43_30somite_EKW_NA_none_10x_S9_L002_R2_001.fastq.gz TDR43_30somite_EKW_NA_none_10x_S9_L003_I1_001.fastq.gz TDR43_30somite_EKW_NA_none_10x_S9_L003_I2_001.fastq.gz TDR43_30somite_EKW_NA_none_10x_S9_L003_R1_001.fastq.gz TDR43_30somite_EKW_NA_none_10x_S9_L003_R2_001.fastq.gz TDR43_30somite_EKW_NA_none_10x_S9_L004_I1_001.fastq.gz TDR43_30somite_EKW_NA_none_10x_S9_L004_I2_001.fastq.gz TDR43_30somite_EKW_NA_none_10x_S9_L004_R1_001.fastq.gz TDR43_30somite_EKW_NA_none_10x_S9_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,149387152524.0,1082515598.0,TDR43 30somite EKW NA none 10x S9 L001 I1 001.fastq.gz,0:10 1:10 2:28 3:90,A:27335818210;C:22229444114;G:24395538574;T:23465497486;N:105436,10,10,28,90,27335818210,22229444114,24395538574,23465497486,105436,SRX19554115,SRS16938861,SRA1598656,Chan Zuckerberg Biohub|Quantitative Cell Science,Chan Zuckerberg Biohub,1,0.93754,,0.11997,,0.79695,,0.50775,,90,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2023-03-03,Pharyngula,Embryo,Whole Organism,All anatomical structures
74382,SRR23691694,SRX19554114,SRS16938860,SRP425398,PRJNA940501,Zebrahub: Multimodal Zebrafish Developmental Atlas,PRJNA940501,Other,A single embryo single cell RNA seq developmental atlas of Zebrafish.,,,,TDR35,TDR35 5somite EKW NA none 10x,,strain:EKW|isolate:single embryo|breed:siblings per timepoint|cultivar:not applicable|ecotype:not applicable|age:12 hpf|sex:not determined|tissue:Whole embryo|replicate:rep1|BioSampleModel:Model organism or animal,,,,,,,,,TDR35,TDR35 5somite EKW NA none 10x,TDR35 5somite EKW NA none 10x,single embryo dissociation,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP425398,,,TDR35_5somite_EKW_NA_none_10x_S1_L001_I1_001.fastq.gz TDR35_5somite_EKW_NA_none_10x_S1_L001_I2_001.fastq.gz TDR35_5somite_EKW_NA_none_10x_S1_L001_R1_001.fastq.gz TDR35_5somite_EKW_NA_none_10x_S1_L001_R2_001.fastq.gz TDR35_5somite_EKW_NA_none_10x_S1_L002_I1_001.fastq.gz TDR35_5somite_EKW_NA_none_10x_S1_L002_I2_001.fastq.gz TDR35_5somite_EKW_NA_none_10x_S1_L002_R1_001.fastq.gz TDR35_5somite_EKW_NA_none_10x_S1_L002_R2_001.fastq.gz TDR35_5somite_EKW_NA_none_10x_S1_L003_I1_001.fastq.gz TDR35_5somite_EKW_NA_none_10x_S1_L003_I2_001.fastq.gz TDR35_5somite_EKW_NA_none_10x_S1_L003_R1_001.fastq.gz TDR35_5somite_EKW_NA_none_10x_S1_L003_R2_001.fastq.gz TDR35_5somite_EKW_NA_none_10x_S1_L004_I1_001.fastq.gz TDR35_5somite_EKW_NA_none_10x_S1_L004_I2_001.fastq.gz TDR35_5somite_EKW_NA_none_10x_S1_L004_R1_001.fastq.gz TDR35_5somite_EKW_NA_none_10x_S1_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,,,TDR35 5somite EKW NA none 10x S1 L001 I1 001.fastq.gz,,,,,,,,,,,,SRX19554114,,SRA1598656,Chan Zuckerberg Biohub|Quantitative Cell Science,Chan Zuckerberg Biohub,,,,,,,,,,,,,,,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2023-03-02,Segmentation,Embryo,Whole Organism,All anatomical structures
74383,SRR23691695,SRX19554113,SRS16938859,SRP425398,PRJNA940501,Zebrahub: Multimodal Zebrafish Developmental Atlas,PRJNA940501,Other,A single embryo single cell RNA seq developmental atlas of Zebrafish.,,,,TDR30,TDR30 20somite EKW NA none 10x,,strain:EKW|isolate:single embryo|breed:siblings per timepoint|cultivar:not applicable|ecotype:not applicable|age:19 hpf|sex:not determined|tissue:Whole embryo|replicate:rep4|BioSampleModel:Model organism or animal,,,,,,,,,TDR30,TDR30 20somite EKW NA none 10x,TDR30 20somite EKW NA none 10x,single embryo dissociation,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP425398,,,TDR30_20somite_EKW_NA_none_10x_S4_L001_I1_001.fastq.gz TDR30_20somite_EKW_NA_none_10x_S4_L001_I2_001.fastq.gz TDR30_20somite_EKW_NA_none_10x_S4_L001_R1_001.fastq.gz TDR30_20somite_EKW_NA_none_10x_S4_L001_R2_001.fastq.gz TDR30_20somite_EKW_NA_none_10x_S4_L002_I1_001.fastq.gz TDR30_20somite_EKW_NA_none_10x_S4_L002_I2_001.fastq.gz TDR30_20somite_EKW_NA_none_10x_S4_L002_R1_001.fastq.gz TDR30_20somite_EKW_NA_none_10x_S4_L002_R2_001.fastq.gz TDR30_20somite_EKW_NA_none_10x_S4_L003_I1_001.fastq.gz TDR30_20somite_EKW_NA_none_10x_S4_L003_I2_001.fastq.gz TDR30_20somite_EKW_NA_none_10x_S4_L003_R1_001.fastq.gz TDR30_20somite_EKW_NA_none_10x_S4_L003_R2_001.fastq.gz TDR30_20somite_EKW_NA_none_10x_S4_L004_I1_001.fastq.gz TDR30_20somite_EKW_NA_none_10x_S4_L004_I2_001.fastq.gz TDR30_20somite_EKW_NA_none_10x_S4_L004_R1_001.fastq.gz TDR30_20somite_EKW_NA_none_10x_S4_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,126551285262.0,917038299.0,TDR30 20somite EKW NA none 10x S4 L001 I1 001.fastq.gz,0:10 1:10 2:28 3:90,A:22992867453;C:19066092511;G:21900344853;T:18572896783;N:1245310,10,10,28,90,22992867453,19066092511,21900344853,18572896783,1245310,SRX19554113,SRS16938859,SRA1598656,Chan Zuckerberg Biohub|Quantitative Cell Science,Chan Zuckerberg Biohub,1,0.90514,,0.17664,,0.81921,,0.58589,,90,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2023-03-03,Segmentation,Embryo,Whole Organism,All anatomical structures
74384,SRR23691696,SRX19554112,SRS16938858,SRP425398,PRJNA940501,Zebrahub: Multimodal Zebrafish Developmental Atlas,PRJNA940501,Other,A single embryo single cell RNA seq developmental atlas of Zebrafish.,,,,TDR29,TDR29 20somite EKW NA none 10x,,strain:EKW|isolate:single embryo|breed:siblings per timepoint|cultivar:not applicable|ecotype:not applicable|age:19 hpf|sex:not determined|tissue:Whole embryo|replicate:rep3|BioSampleModel:Model organism or animal,,,,,,,,,TDR29,TDR29 20somite EKW NA none 10x,TDR29 20somite EKW NA none 10x,single embryo dissociation,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP425398,,,TDR29_20somite_EKW_NA_none_10x_S3_L001_I1_001.fastq.gz TDR29_20somite_EKW_NA_none_10x_S3_L001_I2_001.fastq.gz TDR29_20somite_EKW_NA_none_10x_S3_L001_R1_001.fastq.gz TDR29_20somite_EKW_NA_none_10x_S3_L001_R2_001.fastq.gz TDR29_20somite_EKW_NA_none_10x_S3_L002_I1_001.fastq.gz TDR29_20somite_EKW_NA_none_10x_S3_L002_I2_001.fastq.gz TDR29_20somite_EKW_NA_none_10x_S3_L002_R1_001.fastq.gz TDR29_20somite_EKW_NA_none_10x_S3_L002_R2_001.fastq.gz TDR29_20somite_EKW_NA_none_10x_S3_L003_I1_001.fastq.gz TDR29_20somite_EKW_NA_none_10x_S3_L003_I2_001.fastq.gz TDR29_20somite_EKW_NA_none_10x_S3_L003_R1_001.fastq.gz TDR29_20somite_EKW_NA_none_10x_S3_L003_R2_001.fastq.gz TDR29_20somite_EKW_NA_none_10x_S3_L004_I1_001.fastq.gz TDR29_20somite_EKW_NA_none_10x_S3_L004_I2_001.fastq.gz TDR29_20somite_EKW_NA_none_10x_S3_L004_R1_001.fastq.gz TDR29_20somite_EKW_NA_none_10x_S3_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,,,TDR29 20somite EKW NA none 10x S3 L001 I1 001.fastq.gz,,,,,,,,,,,,SRX19554112,,SRA1598656,Chan Zuckerberg Biohub|Quantitative Cell Science,Chan Zuckerberg Biohub,,,,,,,,,,,,,,,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2023-03-02,Segmentation,Embryo,Whole Organism,All anatomical structures
74385,SRR23691697,SRX19554111,SRS16938857,SRP425398,PRJNA940501,Zebrahub: Multimodal Zebrafish Developmental Atlas,PRJNA940501,Other,A single embryo single cell RNA seq developmental atlas of Zebrafish.,,,,TDR27,TDR27 20somite EKW NA none 10x,,strain:EKW|isolate:single embryo|breed:siblings per timepoint|cultivar:not applicable|ecotype:not applicable|age:19 hpf|sex:not determined|tissue:Whole embryo|replicate:rep1|BioSampleModel:Model organism or animal,,,,,,,,,TDR27,TDR27 20somite EKW NA none 10x,TDR27 20somite EKW NA none 10x,single embryo dissociation,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP425398,,,TDR27_20somite_EKW_NA_none_10x_S1_L001_I1_001.fastq.gz TDR27_20somite_EKW_NA_none_10x_S1_L001_I2_001.fastq.gz TDR27_20somite_EKW_NA_none_10x_S1_L001_R1_001.fastq.gz TDR27_20somite_EKW_NA_none_10x_S1_L001_R2_001.fastq.gz TDR27_20somite_EKW_NA_none_10x_S1_L002_I1_001.fastq.gz TDR27_20somite_EKW_NA_none_10x_S1_L002_I2_001.fastq.gz TDR27_20somite_EKW_NA_none_10x_S1_L002_R1_001.fastq.gz TDR27_20somite_EKW_NA_none_10x_S1_L002_R2_001.fastq.gz TDR27_20somite_EKW_NA_none_10x_S1_L003_I1_001.fastq.gz TDR27_20somite_EKW_NA_none_10x_S1_L003_I2_001.fastq.gz TDR27_20somite_EKW_NA_none_10x_S1_L003_R1_001.fastq.gz TDR27_20somite_EKW_NA_none_10x_S1_L003_R2_001.fastq.gz TDR27_20somite_EKW_NA_none_10x_S1_L004_I1_001.fastq.gz TDR27_20somite_EKW_NA_none_10x_S1_L004_I2_001.fastq.gz TDR27_20somite_EKW_NA_none_10x_S1_L004_R1_001.fastq.gz TDR27_20somite_EKW_NA_none_10x_S1_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,,,TDR27 20somite EKW NA none 10x S1 L001 I1 001.fastq.gz,,,,,,,,,,,,SRX19554111,,SRA1598656,Chan Zuckerberg Biohub|Quantitative Cell Science,Chan Zuckerberg Biohub,,,,,,,,,,,,,,,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2023-03-02,Segmentation,Embryo,Whole Organism,All anatomical structures
74386,SRR23691699,SRX19554110,SRS16938856,SRP425398,PRJNA940501,Zebrahub: Multimodal Zebrafish Developmental Atlas,PRJNA940501,Other,A single embryo single cell RNA seq developmental atlas of Zebrafish.,,,,TDR25,TDR25 budstage EKW NA none 10x,,strain:EKW|isolate:single embryo|breed:siblings per timepoint|cultivar:not applicable|ecotype:not applicable|age:10 hpf|sex:not determined|tissue:Whole embryo|replicate:rep3|BioSampleModel:Model organism or animal,,,,,,,,,TDR25,TDR25 budstage EKW NA none 10x,TDR25 budstage EKW NA none 10x,single embryo dissociation,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP425398,,,TDR25_budstage_EKW_NA_none_10x_S3_L001_I1_001.fastq.gz TDR25_budstage_EKW_NA_none_10x_S3_L001_R1_001.fastq.gz TDR25_budstage_EKW_NA_none_10x_S3_L001_R2_001.fastq.gz TDR25_budstage_EKW_NA_none_10x_S3_L002_I1_001.fastq.gz TDR25_budstage_EKW_NA_none_10x_S3_L002_R1_001.fastq.gz TDR25_budstage_EKW_NA_none_10x_S3_L002_R2_001.fastq.gz TDR25_budstage_EKW_NA_none_10x_S3_L003_I1_001.fastq.gz TDR25_budstage_EKW_NA_none_10x_S3_L003_R1_001.fastq.gz TDR25_budstage_EKW_NA_none_10x_S3_L003_R2_001.fastq.gz TDR25_budstage_EKW_NA_none_10x_S3_L004_I1_001.fastq.gz TDR25_budstage_EKW_NA_none_10x_S3_L004_R1_001.fastq.gz TDR25_budstage_EKW_NA_none_10x_S3_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,,,TDR25 budstage EKW NA none 10x S3 L001 I1 001.fastq.gz,,,,,,,,,,,,SRX19554110,,SRA1598656,Chan Zuckerberg Biohub|Quantitative Cell Science,Chan Zuckerberg Biohub,,,,,,,,,,,,,,,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2023-03-02,Gastrula,Embryo,Whole Organism,All anatomical structures
74387,SRR23691701,SRX19554109,SRS16938855,SRP425398,PRJNA940501,Zebrahub: Multimodal Zebrafish Developmental Atlas,PRJNA940501,Other,A single embryo single cell RNA seq developmental atlas of Zebrafish.,,,,TDR23,TDR23 budstage EKW NA none 10x,,strain:EKW|isolate:single embryo|breed:siblings per timepoint|cultivar:not applicable|ecotype:not applicable|age:10 hpf|sex:not determined|tissue:Whole embryo|replicate:rep1|BioSampleModel:Model organism or animal,,,,,,,,,TDR23,TDR23 budstage EKW NA none 10x,TDR23 budstage EKW NA none 10x,single embryo dissociation,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP425398,,,TDR23_budstage_EKW_NA_none_10x_S1_L001_I1_001.fastq.gz TDR23_budstage_EKW_NA_none_10x_S1_L001_R1_001.fastq.gz TDR23_budstage_EKW_NA_none_10x_S1_L001_R2_001.fastq.gz TDR23_budstage_EKW_NA_none_10x_S1_L002_I1_001.fastq.gz TDR23_budstage_EKW_NA_none_10x_S1_L002_R1_001.fastq.gz TDR23_budstage_EKW_NA_none_10x_S1_L002_R2_001.fastq.gz TDR23_budstage_EKW_NA_none_10x_S1_L003_I1_001.fastq.gz TDR23_budstage_EKW_NA_none_10x_S1_L003_R1_001.fastq.gz TDR23_budstage_EKW_NA_none_10x_S1_L003_R2_001.fastq.gz TDR23_budstage_EKW_NA_none_10x_S1_L004_I1_001.fastq.gz TDR23_budstage_EKW_NA_none_10x_S1_L004_R1_001.fastq.gz TDR23_budstage_EKW_NA_none_10x_S1_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,,,TDR23 budstage EKW NA none 10x S1 L001 I1 001.fastq.gz,,,,,,,,,,,,SRX19554109,,SRA1598656,Chan Zuckerberg Biohub|Quantitative Cell Science,Chan Zuckerberg Biohub,,,,,,,,,,,,,,,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2023-03-02,Gastrula,Embryo,Whole Organism,All anatomical structures
74388,SRR23691703,SRX19554108,SRS16938854,SRP425398,PRJNA940501,Zebrahub: Multimodal Zebrafish Developmental Atlas,PRJNA940501,Other,A single embryo single cell RNA seq developmental atlas of Zebrafish.,,,,TDR74,TDR74 10dpf EKW NA none 10x,,strain:EKW|isolate:single embryo|breed:siblings per timepoint|cultivar:not applicable|ecotype:not applicable|age:10 dpf|sex:not determined|tissue:Whole embryo|replicate:rep4|BioSampleModel:Model organism or animal,,,,,,,,,TDR74,TDR74 10dpf EKW NA none 10x,TDR74 10dpf EKW NA none 10x,single embryo dissociation,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP425398,,,TDR74_10dpf_EKW_NA_none_10x_S12_L001_I1_001.fastq.gz TDR74_10dpf_EKW_NA_none_10x_S12_L001_I2_001.fastq.gz TDR74_10dpf_EKW_NA_none_10x_S12_L001_R1_001.fastq.gz TDR74_10dpf_EKW_NA_none_10x_S12_L001_R2_001.fastq.gz TDR74_10dpf_EKW_NA_none_10x_S12_L002_I1_001.fastq.gz TDR74_10dpf_EKW_NA_none_10x_S12_L002_I2_001.fastq.gz TDR74_10dpf_EKW_NA_none_10x_S12_L002_R1_001.fastq.gz TDR74_10dpf_EKW_NA_none_10x_S12_L002_R2_001.fastq.gz TDR74_10dpf_EKW_NA_none_10x_S12_L003_I1_001.fastq.gz TDR74_10dpf_EKW_NA_none_10x_S12_L003_I2_001.fastq.gz TDR74_10dpf_EKW_NA_none_10x_S12_L003_R1_001.fastq.gz TDR74_10dpf_EKW_NA_none_10x_S12_L003_R2_001.fastq.gz TDR74_10dpf_EKW_NA_none_10x_S12_L004_I1_001.fastq.gz TDR74_10dpf_EKW_NA_none_10x_S12_L004_I2_001.fastq.gz TDR74_10dpf_EKW_NA_none_10x_S12_L004_R1_001.fastq.gz TDR74_10dpf_EKW_NA_none_10x_S12_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,127541718162.0,924215349.0,TDR74 10dpf EKW NA none 10x S12 L001 I1 001.fastq.gz,0:10 1:10 2:28 3:90,A:25488649266;C:17959072964;G:19518445217;T:20212853491;N:360472,10,10,28,90,25488649266,17959072964,19518445217,20212853491,360472,SRX19554108,SRS16938854,SRA1598656,Chan Zuckerberg Biohub|Quantitative Cell Science,Chan Zuckerberg Biohub,1,0.89605,,0.11636,,0.80359,,0.67034,,90,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2023-03-03,Larval,Larval,Whole Organism,All anatomical structures
74389,SRR23691704,SRX19554107,SRS16938853,SRP425398,PRJNA940501,Zebrahub: Multimodal Zebrafish Developmental Atlas,PRJNA940501,Other,A single embryo single cell RNA seq developmental atlas of Zebrafish.,,,,TDR73,TDR73 10dpf EKW NA none 10x,,strain:EKW|isolate:single embryo|breed:siblings per timepoint|cultivar:not applicable|ecotype:not applicable|age:10 dpf|sex:not determined|tissue:Whole embryo|replicate:rep3|BioSampleModel:Model organism or animal,,,,,,,,,TDR73,TDR73 10dpf EKW NA none 10x,TDR73 10dpf EKW NA none 10x,single embryo dissociation,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP425398,,,TDR73_10dpf_EKW_NA_none_10x_S11_L001_I1_001.fastq.gz TDR73_10dpf_EKW_NA_none_10x_S11_L001_I2_001.fastq.gz TDR73_10dpf_EKW_NA_none_10x_S11_L001_R1_001.fastq.gz TDR73_10dpf_EKW_NA_none_10x_S11_L001_R2_001.fastq.gz TDR73_10dpf_EKW_NA_none_10x_S11_L002_I1_001.fastq.gz TDR73_10dpf_EKW_NA_none_10x_S11_L002_I2_001.fastq.gz TDR73_10dpf_EKW_NA_none_10x_S11_L002_R1_001.fastq.gz TDR73_10dpf_EKW_NA_none_10x_S11_L002_R2_001.fastq.gz TDR73_10dpf_EKW_NA_none_10x_S11_L003_I1_001.fastq.gz TDR73_10dpf_EKW_NA_none_10x_S11_L003_I2_001.fastq.gz TDR73_10dpf_EKW_NA_none_10x_S11_L003_R1_001.fastq.gz TDR73_10dpf_EKW_NA_none_10x_S11_L003_R2_001.fastq.gz TDR73_10dpf_EKW_NA_none_10x_S11_L004_I1_001.fastq.gz TDR73_10dpf_EKW_NA_none_10x_S11_L004_I2_001.fastq.gz TDR73_10dpf_EKW_NA_none_10x_S11_L004_R1_001.fastq.gz TDR73_10dpf_EKW_NA_none_10x_S11_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,114302302866.0,828277557.0,TDR73 10dpf EKW NA none 10x S11 L001 I1 001.fastq.gz,0:10 1:10 2:28 3:90,A:22714080081;C:16064432542;G:17485020946;T:18281123311;N:323250,10,10,28,90,22714080081,16064432542,17485020946,18281123311,323250,SRX19554107,SRS16938853,SRA1598656,Chan Zuckerberg Biohub|Quantitative Cell Science,Chan Zuckerberg Biohub,1,0.89363,,0.11601,,0.81264,,0.66087,,90,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2023-03-03,Larval,Larval,Whole Organism,All anatomical structures
74390,SRR23691705,SRX19554106,SRS16938852,SRP425398,PRJNA940501,Zebrahub: Multimodal Zebrafish Developmental Atlas,PRJNA940501,Other,A single embryo single cell RNA seq developmental atlas of Zebrafish.,,,,TDR72,TDR72 10dpf EKW NA none 10x,,strain:EKW|isolate:single embryo|breed:siblings per timepoint|cultivar:not applicable|ecotype:not applicable|age:10 dpf|sex:not determined|tissue:Whole embryo|replicate:rep2|BioSampleModel:Model organism or animal,,,,,,,,,TDR72,TDR72 10dpf EKW NA none 10x,TDR72 10dpf EKW NA none 10x,single embryo dissociation,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP425398,,,TDR72_10dpf_EKW_NA_none_10x_S10_L001_I1_001.fastq.gz TDR72_10dpf_EKW_NA_none_10x_S10_L001_I2_001.fastq.gz TDR72_10dpf_EKW_NA_none_10x_S10_L001_R1_001.fastq.gz TDR72_10dpf_EKW_NA_none_10x_S10_L001_R2_001.fastq.gz TDR72_10dpf_EKW_NA_none_10x_S10_L002_I1_001.fastq.gz TDR72_10dpf_EKW_NA_none_10x_S10_L002_I2_001.fastq.gz TDR72_10dpf_EKW_NA_none_10x_S10_L002_R1_001.fastq.gz TDR72_10dpf_EKW_NA_none_10x_S10_L002_R2_001.fastq.gz TDR72_10dpf_EKW_NA_none_10x_S10_L003_I1_001.fastq.gz TDR72_10dpf_EKW_NA_none_10x_S10_L003_I2_001.fastq.gz TDR72_10dpf_EKW_NA_none_10x_S10_L003_R1_001.fastq.gz TDR72_10dpf_EKW_NA_none_10x_S10_L003_R2_001.fastq.gz TDR72_10dpf_EKW_NA_none_10x_S10_L004_I1_001.fastq.gz TDR72_10dpf_EKW_NA_none_10x_S10_L004_I2_001.fastq.gz TDR72_10dpf_EKW_NA_none_10x_S10_L004_R1_001.fastq.gz TDR72_10dpf_EKW_NA_none_10x_S10_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,121568547690.0,880931505.0,TDR72 10dpf EKW NA none 10x S10 L001 I1 001.fastq.gz,0:10 1:10 2:28 3:90,A:24679161080;C:16685502546;G:18726693111;T:19192140433;N:338280,10,10,28,90,24679161080,16685502546,18726693111,19192140433,338280,SRX19554106,SRS16938852,SRA1598656,Chan Zuckerberg Biohub|Quantitative Cell Science,Chan Zuckerberg Biohub,1,0.85476,,0.12578,,0.80906,,0.6567,,90,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2023-03-03,Larval,Larval,Whole Organism,All anatomical structures
74391,SRR23691706,SRX19554105,SRS16938851,SRP425398,PRJNA940501,Zebrahub: Multimodal Zebrafish Developmental Atlas,PRJNA940501,Other,A single embryo single cell RNA seq developmental atlas of Zebrafish.,,,,TDR71,TDR71 10dpf EKW NA none 10x,,strain:EKW|isolate:single embryo|breed:siblings per timepoint|cultivar:not applicable|ecotype:not applicable|age:10 dpf|sex:not determined|tissue:Whole embryo|replicate:rep1|BioSampleModel:Model organism or animal,,,,,,,,,TDR71,TDR71 10dpf EKW NA none 10x,TDR71 10dpf EKW NA none 10x,single embryo dissociation,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP425398,,,TDR71_10dpf_EKW_NA_none_10x_S9_L001_I1_001.fastq.gz TDR71_10dpf_EKW_NA_none_10x_S9_L001_I2_001.fastq.gz TDR71_10dpf_EKW_NA_none_10x_S9_L001_R1_001.fastq.gz TDR71_10dpf_EKW_NA_none_10x_S9_L001_R2_001.fastq.gz TDR71_10dpf_EKW_NA_none_10x_S9_L002_I1_001.fastq.gz TDR71_10dpf_EKW_NA_none_10x_S9_L002_I2_001.fastq.gz TDR71_10dpf_EKW_NA_none_10x_S9_L002_R1_001.fastq.gz TDR71_10dpf_EKW_NA_none_10x_S9_L002_R2_001.fastq.gz TDR71_10dpf_EKW_NA_none_10x_S9_L003_I1_001.fastq.gz TDR71_10dpf_EKW_NA_none_10x_S9_L003_I2_001.fastq.gz TDR71_10dpf_EKW_NA_none_10x_S9_L003_R1_001.fastq.gz TDR71_10dpf_EKW_NA_none_10x_S9_L003_R2_001.fastq.gz TDR71_10dpf_EKW_NA_none_10x_S9_L004_I1_001.fastq.gz TDR71_10dpf_EKW_NA_none_10x_S9_L004_I2_001.fastq.gz TDR71_10dpf_EKW_NA_none_10x_S9_L004_R1_001.fastq.gz TDR71_10dpf_EKW_NA_none_10x_S9_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,124544763606.0,902498287.0,TDR71 10dpf EKW NA none 10x S9 L001 I1 001.fastq.gz,0:10 1:10 2:28 3:90,A:24670559612;C:17725900620;G:19044403365;T:19783628987;N:353246,10,10,28,90,24670559612,17725900620,19044403365,19783628987,353246,SRX19554105,SRS16938851,SRA1598656,Chan Zuckerberg Biohub|Quantitative Cell Science,Chan Zuckerberg Biohub,1,0.90676,,0.09847,,0.81475,,0.67323,,90,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2023-03-03,Larval,Larval,Whole Organism,All anatomical structures
74392,SRR23691679,SRX19554104,SRS16938850,SRP425398,PRJNA940501,Zebrahub: Multimodal Zebrafish Developmental Atlas,PRJNA940501,Other,A single embryo single cell RNA seq developmental atlas of Zebrafish.,,,,TDR28,TDR28 20somite EKW NA none 10x,,strain:EKW|isolate:single embryo|breed:siblings per timepoint|cultivar:not applicable|ecotype:not applicable|age:19 hpf|sex:not determined|tissue:Whole embryo|replicate:rep2|BioSampleModel:Model organism or animal,,,,,,,,,TDR28,TDR28 20somite EKW NA none 10x,TDR28 20somite EKW NA none 10x,single embryo dissociation,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP425398,,,TDR28_20somite_EKW_NA_none_10x_S2_L001_I1_001.fastq.gz TDR28_20somite_EKW_NA_none_10x_S2_L001_I2_001.fastq.gz TDR28_20somite_EKW_NA_none_10x_S2_L001_R1_001.fastq.gz TDR28_20somite_EKW_NA_none_10x_S2_L001_R2_001.fastq.gz TDR28_20somite_EKW_NA_none_10x_S2_L002_I1_001.fastq.gz TDR28_20somite_EKW_NA_none_10x_S2_L002_I2_001.fastq.gz TDR28_20somite_EKW_NA_none_10x_S2_L002_R1_001.fastq.gz TDR28_20somite_EKW_NA_none_10x_S2_L002_R2_001.fastq.gz TDR28_20somite_EKW_NA_none_10x_S2_L003_I1_001.fastq.gz TDR28_20somite_EKW_NA_none_10x_S2_L003_I2_001.fastq.gz TDR28_20somite_EKW_NA_none_10x_S2_L003_R1_001.fastq.gz TDR28_20somite_EKW_NA_none_10x_S2_L003_R2_001.fastq.gz TDR28_20somite_EKW_NA_none_10x_S2_L004_I1_001.fastq.gz TDR28_20somite_EKW_NA_none_10x_S2_L004_I2_001.fastq.gz TDR28_20somite_EKW_NA_none_10x_S2_L004_R1_001.fastq.gz TDR28_20somite_EKW_NA_none_10x_S2_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,,,TDR28 20somite EKW NA none 10x S2 L001 I1 001.fastq.gz,,,,,,,,,,,,SRX19554104,,SRA1598656,Chan Zuckerberg Biohub|Quantitative Cell Science,Chan Zuckerberg Biohub,,,,,,,,,,,,,,,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2023-03-02,Segmentation,Embryo,Whole Organism,All anatomical structures
74393,SRR23691707,SRX19554103,SRS16938849,SRP425398,PRJNA940501,Zebrahub: Multimodal Zebrafish Developmental Atlas,PRJNA940501,Other,A single embryo single cell RNA seq developmental atlas of Zebrafish.,,,,TDR70,TDR70 3dpf EKW NA none 10x,,strain:EKW|isolate:single embryo|breed:siblings per timepoint|cultivar:not applicable|ecotype:not applicable|age:3 dpf|sex:not determined|tissue:Whole embryo|replicate:rep4|BioSampleModel:Model organism or animal,,,,,,,,,TDR70,TDR70 3dpf EKW NA none 10x,TDR70 3dpf EKW NA none 10x,single embryo dissociation,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP425398,,,TDR70_3dpf_EKW_NA_none_10x_S8_L001_I1_001.fastq.gz TDR70_3dpf_EKW_NA_none_10x_S8_L001_I2_001.fastq.gz TDR70_3dpf_EKW_NA_none_10x_S8_L001_R1_001.fastq.gz TDR70_3dpf_EKW_NA_none_10x_S8_L001_R2_001.fastq.gz TDR70_3dpf_EKW_NA_none_10x_S8_L002_I1_001.fastq.gz TDR70_3dpf_EKW_NA_none_10x_S8_L002_I2_001.fastq.gz TDR70_3dpf_EKW_NA_none_10x_S8_L002_R1_001.fastq.gz TDR70_3dpf_EKW_NA_none_10x_S8_L002_R2_001.fastq.gz TDR70_3dpf_EKW_NA_none_10x_S8_L003_I1_001.fastq.gz TDR70_3dpf_EKW_NA_none_10x_S8_L003_I2_001.fastq.gz TDR70_3dpf_EKW_NA_none_10x_S8_L003_R1_001.fastq.gz TDR70_3dpf_EKW_NA_none_10x_S8_L003_R2_001.fastq.gz TDR70_3dpf_EKW_NA_none_10x_S8_L004_I1_001.fastq.gz TDR70_3dpf_EKW_NA_none_10x_S8_L004_I2_001.fastq.gz TDR70_3dpf_EKW_NA_none_10x_S8_L004_R1_001.fastq.gz TDR70_3dpf_EKW_NA_none_10x_S8_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,105158760966.0,762020007.0,TDR70 3dpf EKW NA none 10x S8 L001 I1 001.fastq.gz,0:10 1:10 2:28 3:90,A:21281448836;C:14331451262;G:15718459674;T:17250143686;N:297172,10,10,28,90,21281448836,14331451262,15718459674,17250143686,297172,SRX19554103,SRS16938849,SRA1598656,Chan Zuckerberg Biohub|Quantitative Cell Science,Chan Zuckerberg Biohub,1,0.87781,,0.14577,,0.77595,,0.64139,,90,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2023-03-03,Larval,Larval,Whole Organism,All anatomical structures
74394,SRR23691688,SRX19554102,SRS16938848,SRP425398,PRJNA940501,Zebrahub: Multimodal Zebrafish Developmental Atlas,PRJNA940501,Other,A single embryo single cell RNA seq developmental atlas of Zebrafish.,,,,TDR49,TDR49 2dpf EKW NA none 10x,,strain:EKW|isolate:single embryo|breed:siblings per timepoint|cultivar:not applicable|ecotype:not applicable|age:2 dpf|sex:not determined|tissue:Whole embryo|replicate:rep3|BioSampleModel:Model organism or animal,,,,,,,,,TDR49,TDR49 2dpf EKW NA none 10x,TDR49 2dpf EKW NA none 10x,single embryo dissociation,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP425398,,,TDR49_2dpf_EKW_NA_none_10x_S3_L001_I1_001.fastq.gz TDR49_2dpf_EKW_NA_none_10x_S3_L001_I2_001.fastq.gz TDR49_2dpf_EKW_NA_none_10x_S3_L001_R1_001.fastq.gz TDR49_2dpf_EKW_NA_none_10x_S3_L001_R2_001.fastq.gz TDR49_2dpf_EKW_NA_none_10x_S3_L002_I1_001.fastq.gz TDR49_2dpf_EKW_NA_none_10x_S3_L002_I2_001.fastq.gz TDR49_2dpf_EKW_NA_none_10x_S3_L002_R1_001.fastq.gz TDR49_2dpf_EKW_NA_none_10x_S3_L002_R2_001.fastq.gz TDR49_2dpf_EKW_NA_none_10x_S3_L003_I1_001.fastq.gz TDR49_2dpf_EKW_NA_none_10x_S3_L003_I2_001.fastq.gz TDR49_2dpf_EKW_NA_none_10x_S3_L003_R1_001.fastq.gz TDR49_2dpf_EKW_NA_none_10x_S3_L003_R2_001.fastq.gz TDR49_2dpf_EKW_NA_none_10x_S3_L004_I1_001.fastq.gz TDR49_2dpf_EKW_NA_none_10x_S3_L004_I2_001.fastq.gz TDR49_2dpf_EKW_NA_none_10x_S3_L004_R1_001.fastq.gz TDR49_2dpf_EKW_NA_none_10x_S3_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,118537620432.0,858968264.0,TDR49 2dpf EKW NA none 10x S3 L001 I1 001.fastq.gz,0:10 1:10 2:28 3:90,A:19359775172;C:19118553633;G:22580874113;T:16247869796;N:71046,10,10,28,90,19359775172,19118553633,22580874113,16247869796,71046,SRX19554102,SRS16938848,SRA1598656,Chan Zuckerberg Biohub|Quantitative Cell Science,Chan Zuckerberg Biohub,1,0.86228,,0.22633,,0.87436,,0.68374,,90,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2023-03-03,Hatching,Embryo,Whole Organism,All anatomical structures
74395,SRR23691709,SRX19554101,SRS16938847,SRP425398,PRJNA940501,Zebrahub: Multimodal Zebrafish Developmental Atlas,PRJNA940501,Other,A single embryo single cell RNA seq developmental atlas of Zebrafish.,,,,TDR48,TDR48 2dpf EKW NA none 10x,,strain:EKW|isolate:single embryo|breed:siblings per timepoint|cultivar:not applicable|ecotype:not applicable|age:2 dpf|sex:not determined|tissue:Whole embryo|replicate:rep2|BioSampleModel:Model organism or animal,,,,,,,,,TDR48,TDR48 2dpf EKW NA none 10x,TDR48 2dpf EKW NA none 10x,single embryo dissociation,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP425398,,,TDR48_2dpf_EKW_NA_none_10x_S2_L001_I1_001.fastq.gz TDR48_2dpf_EKW_NA_none_10x_S2_L001_I2_001.fastq.gz TDR48_2dpf_EKW_NA_none_10x_S2_L001_R1_001.fastq.gz TDR48_2dpf_EKW_NA_none_10x_S2_L001_R2_001.fastq.gz TDR48_2dpf_EKW_NA_none_10x_S2_L002_I1_001.fastq.gz TDR48_2dpf_EKW_NA_none_10x_S2_L002_I2_001.fastq.gz TDR48_2dpf_EKW_NA_none_10x_S2_L002_R1_001.fastq.gz TDR48_2dpf_EKW_NA_none_10x_S2_L002_R2_001.fastq.gz TDR48_2dpf_EKW_NA_none_10x_S2_L003_I1_001.fastq.gz TDR48_2dpf_EKW_NA_none_10x_S2_L003_I2_001.fastq.gz TDR48_2dpf_EKW_NA_none_10x_S2_L003_R1_001.fastq.gz TDR48_2dpf_EKW_NA_none_10x_S2_L003_R2_001.fastq.gz TDR48_2dpf_EKW_NA_none_10x_S2_L004_I1_001.fastq.gz TDR48_2dpf_EKW_NA_none_10x_S2_L004_I2_001.fastq.gz TDR48_2dpf_EKW_NA_none_10x_S2_L004_R1_001.fastq.gz TDR48_2dpf_EKW_NA_none_10x_S2_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,130790722266.0,947758857.0,TDR48 2dpf EKW NA none 10x S2 L001 I1 001.fastq.gz,0:10 1:10 2:28 3:90,A:22786070358;C:19996387148;G:23390030207;T:19125732270;N:77147,10,10,28,90,22786070358,19996387148,23390030207,19125732270,77147,SRX19554101,SRS16938847,SRA1598656,Chan Zuckerberg Biohub|Quantitative Cell Science,Chan Zuckerberg Biohub,1,0.86692,,0.1987,,0.82856,,0.62968,,90,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2023-03-03,Hatching,Embryo,Whole Organism,All anatomical structures
74396,SRR23691710,SRX19554100,SRS16938845,SRP425398,PRJNA940501,Zebrahub: Multimodal Zebrafish Developmental Atlas,PRJNA940501,Other,A single embryo single cell RNA seq developmental atlas of Zebrafish.,,,,TDR47,TDR47 2dpf EKW NA none 10x,,strain:EKW|isolate:single embryo|breed:siblings per timepoint|cultivar:not applicable|ecotype:not applicable|age:2 dpf|sex:not determined|tissue:Whole embryo|replicate:rep1|BioSampleModel:Model organism or animal,,,,,,,,,TDR47,TDR47 2dpf EKW NA none 10x,TDR47 2dpf EKW NA none 10x,single embryo dissociation,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP425398,,,TDR47_2dpf_EKW_NA_none_10x_S1_L001_I1_001.fastq.gz TDR47_2dpf_EKW_NA_none_10x_S1_L001_I2_001.fastq.gz TDR47_2dpf_EKW_NA_none_10x_S1_L001_R1_001.fastq.gz TDR47_2dpf_EKW_NA_none_10x_S1_L001_R2_001.fastq.gz TDR47_2dpf_EKW_NA_none_10x_S1_L002_I1_001.fastq.gz TDR47_2dpf_EKW_NA_none_10x_S1_L002_I2_001.fastq.gz TDR47_2dpf_EKW_NA_none_10x_S1_L002_R1_001.fastq.gz TDR47_2dpf_EKW_NA_none_10x_S1_L002_R2_001.fastq.gz TDR47_2dpf_EKW_NA_none_10x_S1_L003_I1_001.fastq.gz TDR47_2dpf_EKW_NA_none_10x_S1_L003_I2_001.fastq.gz TDR47_2dpf_EKW_NA_none_10x_S1_L003_R1_001.fastq.gz TDR47_2dpf_EKW_NA_none_10x_S1_L003_R2_001.fastq.gz TDR47_2dpf_EKW_NA_none_10x_S1_L004_I1_001.fastq.gz TDR47_2dpf_EKW_NA_none_10x_S1_L004_I2_001.fastq.gz TDR47_2dpf_EKW_NA_none_10x_S1_L004_R1_001.fastq.gz TDR47_2dpf_EKW_NA_none_10x_S1_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,131472152880.0,952696760.0,TDR47 2dpf EKW NA none 10x S1 L001 I1 001.fastq.gz,0:10 1:10 2:28 3:90,A:23266007781;C:19700328945;G:22763807680;T:20012485432;N:78562,10,10,28,90,23266007781,19700328945,22763807680,20012485432,78562,SRX19554100,SRS16938845,SRA1598656,Chan Zuckerberg Biohub|Quantitative Cell Science,Chan Zuckerberg Biohub,1,0.88128,,0.22898,,0.80665,,0.64263,,90,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2023-03-03,Hatching,Embryo,Whole Organism,All anatomical structures
74397,SRR23691711,SRX19554099,SRS16938846,SRP425398,PRJNA940501,Zebrahub: Multimodal Zebrafish Developmental Atlas,PRJNA940501,Other,A single embryo single cell RNA seq developmental atlas of Zebrafish.,,,,TDR46,TDR46 30somite EKW NA none 10x,,strain:EKW|isolate:single embryo|breed:siblings per timepoint|cultivar:not applicable|ecotype:not applicable|age:24 hpf|sex:not determined|tissue:Whole embryo|replicate:rep4|BioSampleModel:Model organism or animal,,,,,,,,,TDR46,TDR46 30somite EKW NA none 10x,TDR46 30somite EKW NA none 10x,single embryo dissociation,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP425398,,,TDR46_30somite_EKW_NA_none_10x_S12_L001_I1_001.fastq.gz TDR46_30somite_EKW_NA_none_10x_S12_L001_I2_001.fastq.gz TDR46_30somite_EKW_NA_none_10x_S12_L001_R1_001.fastq.gz TDR46_30somite_EKW_NA_none_10x_S12_L001_R2_001.fastq.gz TDR46_30somite_EKW_NA_none_10x_S12_L002_I1_001.fastq.gz TDR46_30somite_EKW_NA_none_10x_S12_L002_I2_001.fastq.gz TDR46_30somite_EKW_NA_none_10x_S12_L002_R1_001.fastq.gz TDR46_30somite_EKW_NA_none_10x_S12_L002_R2_001.fastq.gz TDR46_30somite_EKW_NA_none_10x_S12_L003_I1_001.fastq.gz TDR46_30somite_EKW_NA_none_10x_S12_L003_I2_001.fastq.gz TDR46_30somite_EKW_NA_none_10x_S12_L003_R1_001.fastq.gz TDR46_30somite_EKW_NA_none_10x_S12_L003_R2_001.fastq.gz TDR46_30somite_EKW_NA_none_10x_S12_L004_I1_001.fastq.gz TDR46_30somite_EKW_NA_none_10x_S12_L004_I2_001.fastq.gz TDR46_30somite_EKW_NA_none_10x_S12_L004_R1_001.fastq.gz TDR46_30somite_EKW_NA_none_10x_S12_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,113538856782.0,822745339.0,TDR46 30somite EKW NA none 10x S12 L001 I1 001.fastq.gz,0:10 1:10 2:28 3:90,A:21088382542;C:16482826983;G:18272838919;T:18202952478;N:79588,10,10,28,90,21088382542,16482826983,18272838919,18202952478,79588,SRX19554099,SRS16938846,SRA1598656,Chan Zuckerberg Biohub|Quantitative Cell Science,Chan Zuckerberg Biohub,1,0.92485,,0.12469,,0.78441,,0.51979,,90,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2023-03-03,Pharyngula,Embryo,Whole Organism,All anatomical structures
74398,SRR23691712,SRX19554098,SRS16938844,SRP425398,PRJNA940501,Zebrahub: Multimodal Zebrafish Developmental Atlas,PRJNA940501,Other,A single embryo single cell RNA seq developmental atlas of Zebrafish.,,,,TDR45,TDR45 30somite EKW NA none 10x,,strain:EKW|isolate:single embryo|breed:siblings per timepoint|cultivar:not applicable|ecotype:not applicable|age:24 hpf|sex:not determined|tissue:Whole embryo|replicate:rep3|BioSampleModel:Model organism or animal,,,,,,,,,TDR45,TDR45 30somite EKW NA none 10x,TDR45 30somite EKW NA none 10x,single embryo dissociation,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP425398,,,TDR45_30somite_EKW_NA_none_10x_S11_L001_I1_001.fastq.gz TDR45_30somite_EKW_NA_none_10x_S11_L001_I2_001.fastq.gz TDR45_30somite_EKW_NA_none_10x_S11_L001_R1_001.fastq.gz TDR45_30somite_EKW_NA_none_10x_S11_L001_R2_001.fastq.gz TDR45_30somite_EKW_NA_none_10x_S11_L002_I1_001.fastq.gz TDR45_30somite_EKW_NA_none_10x_S11_L002_I2_001.fastq.gz TDR45_30somite_EKW_NA_none_10x_S11_L002_R1_001.fastq.gz TDR45_30somite_EKW_NA_none_10x_S11_L002_R2_001.fastq.gz TDR45_30somite_EKW_NA_none_10x_S11_L003_I1_001.fastq.gz TDR45_30somite_EKW_NA_none_10x_S11_L003_I2_001.fastq.gz TDR45_30somite_EKW_NA_none_10x_S11_L003_R1_001.fastq.gz TDR45_30somite_EKW_NA_none_10x_S11_L003_R2_001.fastq.gz TDR45_30somite_EKW_NA_none_10x_S11_L004_I1_001.fastq.gz TDR45_30somite_EKW_NA_none_10x_S11_L004_I2_001.fastq.gz TDR45_30somite_EKW_NA_none_10x_S11_L004_R1_001.fastq.gz TDR45_30somite_EKW_NA_none_10x_S11_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,151741402440.0,1099575380.0,TDR45 30somite EKW NA none 10x S11 L001 I1 001.fastq.gz,0:10 1:10 2:28 3:90,A:28305264381;C:22203945096;G:24554199279;T:23898269926;N:105518,10,10,28,90,28305264381,22203945096,24554199279,23898269926,105518,SRX19554098,SRS16938844,SRA1598656,Chan Zuckerberg Biohub|Quantitative Cell Science,Chan Zuckerberg Biohub,1,0.92131,,0.13041,,0.78409,,0.52692,,90,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2023-03-03,Pharyngula,Embryo,Whole Organism,All anatomical structures
74399,SRR23691713,SRX19554097,SRS16938843,SRP425398,PRJNA940501,Zebrahub: Multimodal Zebrafish Developmental Atlas,PRJNA940501,Other,A single embryo single cell RNA seq developmental atlas of Zebrafish.,,,,TDR44,TDR44 30somite EKW NA none 10x,,strain:EKW|isolate:single embryo|breed:siblings per timepoint|cultivar:not applicable|ecotype:not applicable|age:24 hpf|sex:not determined|tissue:Whole embryo|replicate:rep2|BioSampleModel:Model organism or animal,,,,,,,,,TDR44,TDR44 30somite EKW NA none 10x,TDR44 30somite EKW NA none 10x,single embryo dissociation,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP425398,,,TDR44_30somite_EKW_NA_none_10x_S10_L001_I1_001.fastq.gz TDR44_30somite_EKW_NA_none_10x_S10_L001_I2_001.fastq.gz TDR44_30somite_EKW_NA_none_10x_S10_L001_R1_001.fastq.gz TDR44_30somite_EKW_NA_none_10x_S10_L001_R2_001.fastq.gz TDR44_30somite_EKW_NA_none_10x_S10_L002_I1_001.fastq.gz TDR44_30somite_EKW_NA_none_10x_S10_L002_I2_001.fastq.gz TDR44_30somite_EKW_NA_none_10x_S10_L002_R1_001.fastq.gz TDR44_30somite_EKW_NA_none_10x_S10_L002_R2_001.fastq.gz TDR44_30somite_EKW_NA_none_10x_S10_L003_I1_001.fastq.gz TDR44_30somite_EKW_NA_none_10x_S10_L003_I2_001.fastq.gz TDR44_30somite_EKW_NA_none_10x_S10_L003_R1_001.fastq.gz TDR44_30somite_EKW_NA_none_10x_S10_L003_R2_001.fastq.gz TDR44_30somite_EKW_NA_none_10x_S10_L004_I1_001.fastq.gz TDR44_30somite_EKW_NA_none_10x_S10_L004_I2_001.fastq.gz TDR44_30somite_EKW_NA_none_10x_S10_L004_R1_001.fastq.gz TDR44_30somite_EKW_NA_none_10x_S10_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,,,TDR44 30somite EKW NA none 10x S10 L001 I1 001.fastq.gz,,,,,,,,,,,,SRX19554097,,SRA1598656,Chan Zuckerberg Biohub|Quantitative Cell Science,Chan Zuckerberg Biohub,,,,,,,,,,,,,,,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2023-03-02,Pharyngula,Embryo,Whole Organism,All anatomical structures
74400,SRR23691714,SRX19554096,SRS16938842,SRP425398,PRJNA940501,Zebrahub: Multimodal Zebrafish Developmental Atlas,PRJNA940501,Other,A single embryo single cell RNA seq developmental atlas of Zebrafish.,,,,TDR21,TDR21 10somite EKW NA none 10x,,strain:EKW|isolate:single embryo|breed:siblings per timepoint|cultivar:not applicable|ecotype:not applicable|age:14 hpf|sex:not determined|tissue:Whole embryo|replicate:rep3|BioSampleModel:Model organism or animal,,,,,,,,,TDR21,TDR21 10somite EKW NA none 10x,TDR21 10somite EKW NA none 10x,single embryo dissociation,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP425398,,,TDR21_10somite_EKW_NA_none_10x_S3_L001_I1_001.fastq.gz TDR21_10somite_EKW_NA_none_10x_S3_L001_R1_001.fastq.gz TDR21_10somite_EKW_NA_none_10x_S3_L001_R2_001.fastq.gz TDR21_10somite_EKW_NA_none_10x_S3_L002_I1_001.fastq.gz TDR21_10somite_EKW_NA_none_10x_S3_L002_R1_001.fastq.gz TDR21_10somite_EKW_NA_none_10x_S3_L002_R2_001.fastq.gz TDR21_10somite_EKW_NA_none_10x_S3_L003_I1_001.fastq.gz TDR21_10somite_EKW_NA_none_10x_S3_L003_R1_001.fastq.gz TDR21_10somite_EKW_NA_none_10x_S3_L003_R2_001.fastq.gz TDR21_10somite_EKW_NA_none_10x_S3_L004_I1_001.fastq.gz TDR21_10somite_EKW_NA_none_10x_S3_L004_R1_001.fastq.gz TDR21_10somite_EKW_NA_none_10x_S3_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,,,TDR21 10somite EKW NA none 10x S3 L001 I1 001.fastq.gz,,,,,,,,,,,,SRX19554096,,SRA1598656,Chan Zuckerberg Biohub|Quantitative Cell Science,Chan Zuckerberg Biohub,,,,,,,,,,,,,,,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2023-03-02,Segmentation,Embryo,Whole Organism,All anatomical structures
74401,SRR23691716,SRX19554095,SRS16938841,SRP425398,PRJNA940501,Zebrahub: Multimodal Zebrafish Developmental Atlas,PRJNA940501,Other,A single embryo single cell RNA seq developmental atlas of Zebrafish.,,,,TDR42,TDR42 15somite EKW NA none 10x,,strain:EKW|isolate:single embryo|breed:siblings per timepoint|cultivar:not applicable|ecotype:not applicable|age:16 hpf|sex:not determined|tissue:Whole embryo|replicate:rep4|BioSampleModel:Model organism or animal,,,,,,,,,TDR42,TDR42 15somite EKW NA none 10x,TDR42 15somite EKW NA none 10x,single embryo dissociation,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP425398,,,TDR42_15somite_EKW_NA_none_10x_S8_L001_I1_001.fastq.gz TDR42_15somite_EKW_NA_none_10x_S8_L001_I2_001.fastq.gz TDR42_15somite_EKW_NA_none_10x_S8_L001_R1_001.fastq.gz TDR42_15somite_EKW_NA_none_10x_S8_L001_R2_001.fastq.gz TDR42_15somite_EKW_NA_none_10x_S8_L002_I1_001.fastq.gz TDR42_15somite_EKW_NA_none_10x_S8_L002_I2_001.fastq.gz TDR42_15somite_EKW_NA_none_10x_S8_L002_R1_001.fastq.gz TDR42_15somite_EKW_NA_none_10x_S8_L002_R2_001.fastq.gz TDR42_15somite_EKW_NA_none_10x_S8_L003_I1_001.fastq.gz TDR42_15somite_EKW_NA_none_10x_S8_L003_I2_001.fastq.gz TDR42_15somite_EKW_NA_none_10x_S8_L003_R1_001.fastq.gz TDR42_15somite_EKW_NA_none_10x_S8_L003_R2_001.fastq.gz TDR42_15somite_EKW_NA_none_10x_S8_L004_I1_001.fastq.gz TDR42_15somite_EKW_NA_none_10x_S8_L004_I2_001.fastq.gz TDR42_15somite_EKW_NA_none_10x_S8_L004_R1_001.fastq.gz TDR42_15somite_EKW_NA_none_10x_S8_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,104417359968.0,756647536.0,TDR42 15somite EKW NA none 10x S8 L001 I1 001.fastq.gz,0:10 1:10 2:28 3:90,A:19133695070;C:15471236758;G:17206957805;T:16286315487;N:73120,10,10,28,90,19133695070,15471236758,17206957805,16286315487,73120,SRX19554095,SRS16938841,SRA1598656,Chan Zuckerberg Biohub|Quantitative Cell Science,Chan Zuckerberg Biohub,1,0.94293,,0.12989,,0.80614,,0.55582,,90,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2023-03-03,Segmentation,Embryo,Whole Organism,All anatomical structures
74402,SRR23691700,SRX19554094,SRS16938840,SRP425398,PRJNA940501,Zebrahub: Multimodal Zebrafish Developmental Atlas,PRJNA940501,Other,A single embryo single cell RNA seq developmental atlas of Zebrafish.,,,,TDR26,TDR26 budstage EKW NA none 10x,,strain:EKW|isolate:single embryo|breed:siblings per timepoint|cultivar:not applicable|ecotype:not applicable|age:10 hpf|sex:not determined|tissue:Whole embryo|replicate:rep4|BioSampleModel:Model organism or animal,,,,,,,,,TDR26,TDR26 budstage EKW NA none 10x,TDR26 budstage EKW NA none 10x,single embryo dissociation,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP425398,,,TDR26_budstage_EKW_NA_none_10x_S4_L001_I1_001.fastq.gz TDR26_budstage_EKW_NA_none_10x_S4_L001_R1_001.fastq.gz TDR26_budstage_EKW_NA_none_10x_S4_L001_R2_001.fastq.gz TDR26_budstage_EKW_NA_none_10x_S4_L002_I1_001.fastq.gz TDR26_budstage_EKW_NA_none_10x_S4_L002_R1_001.fastq.gz TDR26_budstage_EKW_NA_none_10x_S4_L002_R2_001.fastq.gz TDR26_budstage_EKW_NA_none_10x_S4_L003_I1_001.fastq.gz TDR26_budstage_EKW_NA_none_10x_S4_L003_R1_001.fastq.gz TDR26_budstage_EKW_NA_none_10x_S4_L003_R2_001.fastq.gz TDR26_budstage_EKW_NA_none_10x_S4_L004_I1_001.fastq.gz TDR26_budstage_EKW_NA_none_10x_S4_L004_R1_001.fastq.gz TDR26_budstage_EKW_NA_none_10x_S4_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,,,TDR26 budstage EKW NA none 10x S4 L001 I1 001.fastq.gz,,,,,,,,,,,,SRX19554094,,SRA1598656,Chan Zuckerberg Biohub|Quantitative Cell Science,Chan Zuckerberg Biohub,,,,,,,,,,,,,,,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2023-03-02,Gastrula,Embryo,Whole Organism,All anatomical structures
74403,SRR23691698,SRX19554093,SRS16938839,SRP425398,PRJNA940501,Zebrahub: Multimodal Zebrafish Developmental Atlas,PRJNA940501,Other,A single embryo single cell RNA seq developmental atlas of Zebrafish.,,,,TDR19,TDR19 10somite EKW NA none 10x,,strain:EKW|isolate:single embryo|breed:siblings per timepoint|cultivar:not applicable|ecotype:not applicable|age:14 hpf|sex:not determined|tissue:Whole embryo|replicate:rep2|BioSampleModel:Model organism or animal,,,,,,,,,TDR19,TDR19 10somite EKW NA none 10x,TDR19 10somite EKW NA none 10x,single embryo dissociation,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP425398,,,TDR19_10somite_EKW_NA_none_10x_S2_L004_R2_001.fastq.gz TDR19_10somite_EKW_NA_none_10x_S2_L004_R1_001.fastq.gz TDR19_10somite_EKW_NA_none_10x_S2_L004_I1_001.fastq.gz TDR19_10somite_EKW_NA_none_10x_S2_L003_R2_001.fastq.gz TDR19_10somite_EKW_NA_none_10x_S2_L003_R1_001.fastq.gz TDR19_10somite_EKW_NA_none_10x_S2_L003_I1_001.fastq.gz TDR19_10somite_EKW_NA_none_10x_S2_L002_R2_001.fastq.gz TDR19_10somite_EKW_NA_none_10x_S2_L002_R1_001.fastq.gz TDR19_10somite_EKW_NA_none_10x_S2_L002_I1_001.fastq.gz TDR19_10somite_EKW_NA_none_10x_S2_L001_R2_001.fastq.gz TDR19_10somite_EKW_NA_none_10x_S2_L001_R1_001.fastq.gz TDR19_10somite_EKW_NA_none_10x_S2_L001_I1_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,,,TDR19 10somite EKW NA none 10x S2 L001 I1 001.fastq.gz,,,,,,,,,,,,SRX19554093,,SRA1598656,Chan Zuckerberg Biohub|Quantitative Cell Science,Chan Zuckerberg Biohub,,,,,,,,,,,,,,,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2023-03-02,Segmentation,Embryo,Whole Organism,All anatomical structures
74404,SRR23691718,SRX19554092,SRS16939474,SRP425398,PRJNA940501,Zebrahub: Multimodal Zebrafish Developmental Atlas,PRJNA940501,Other,A single embryo single cell RNA seq developmental atlas of Zebrafish.,,,,TDR18,TDR18 10somite EKW NA none 10x,,strain:EKW|isolate:single embryo|breed:siblings per timepoint|cultivar:not applicable|ecotype:not applicable|age:14 hpf|sex:not determined|tissue:Whole embryo|replicate:rep1|BioSampleModel:Model organism or animal,,,,,,,,,TDR18,TDR18 10somite EKW NA none 10x,TDR18 10somite EKW NA none 10x,single embryo dissociation,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP425398,,,TDR18_10somite_EKW_NA_none_10x_S1_L001_I1_001.fastq.gz TDR18_10somite_EKW_NA_none_10x_S1_L001_R1_001.fastq.gz TDR18_10somite_EKW_NA_none_10x_S1_L001_R2_001.fastq.gz TDR18_10somite_EKW_NA_none_10x_S1_L002_I1_001.fastq.gz TDR18_10somite_EKW_NA_none_10x_S1_L002_R1_001.fastq.gz TDR18_10somite_EKW_NA_none_10x_S1_L002_R2_001.fastq.gz TDR18_10somite_EKW_NA_none_10x_S1_L003_I1_001.fastq.gz TDR18_10somite_EKW_NA_none_10x_S1_L003_R1_001.fastq.gz TDR18_10somite_EKW_NA_none_10x_S1_L003_R2_001.fastq.gz TDR18_10somite_EKW_NA_none_10x_S1_L004_I1_001.fastq.gz TDR18_10somite_EKW_NA_none_10x_S1_L004_R1_001.fastq.gz TDR18_10somite_EKW_NA_none_10x_S1_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,,,TDR18 10somite EKW NA none 10x S1 L001 I1 001.fastq.gz,,,,,,,,,,,,SRX19554092,,SRA1598656,Chan Zuckerberg Biohub|Quantitative Cell Science,Chan Zuckerberg Biohub,,,,,,,,,,,,,,,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2023-03-02,Segmentation,Embryo,Whole Organism,All anatomical structures
76532,SRR25081951,SRX20835391,SRS18112575,SRP446710,PRJNA987386,Single nucleus chromatin landscapes during zebrafish early embryogenesis,PRJNA987386,Other,Vertebrate embryogenesis is a remarkable process  during which numerous cell types of different lineages arise within a short time frame. An overwhelming challenge to understand this process is the lack of dynamic chromatin accessibility information to correlate cis regulatory elements CREs and gene expression within the hierarchy of cell fate decisions. Here  we employed single nucleus ATAC seq to generate a chromatin accessibility dataset on the first day of zebrafish embryogenesis  including 3.3 hpf  5.25 hpf  6 hpf  10 hpf  12 hpf  18 hpf and 24 hpf  obtained 51 620 high quality nuclei and 23 clusters. Furthermore  by integrating snATAC seq data with single cell RNA seq data  we described the dynamics of chromatin accessibility and gene expression across developmental time points  which validates the accuracy of the chromatin landscape data. Together  our data could serve as a fundamental resource for revealing the epigenetic regulatory mechanisms of zebrafish embryogenesis.,,,,6 hpf embryos,scRNA zf6hpf 2,,strain:AB/Wild type|isolate:scRNA zf6hpf 2|breed:not collected|cultivar:not collected|ecotype:not determined|age:embryo|dev stage:6 hpf|collection date:2021 08 08|geo loc name:China: Wuhan|sex:not determined|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,scRNA 6 hpf,scRNA 6 hpf rep2 oligo,scRNA 6 hpf rep2 oligo,scRNA seq of 6 hpf embryos,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP446710,,CNGB Experiment ID:CNX0591993,DP8450003515BR_L01_5_1.fq.gz DP8450003515BR_L01_5_2.fq.gz,fastq fastq,14588474300.0,291769486.0,DP8450003515BR L01 5 1.fq.gz,0:20 1:30,A:3813233297;C:3660627848;G:3388591530;T:3724524333;N:1497292,20,30,,,3813233297,3660627848,3388591530,3724524333,1497292,SRX20835391,SRS18112575,SRA1664681,"BGI Research, Shenzhen","BGI Research, Shenzhen CNGB Nucleotide Sequence Archive (CNSA) BGI-Shenzhen",2,0.00464,0.0003,0.00396,0.00028,0.9978,0.99995,0.39694,0.5,20,30,T,T,mates < 9% mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,China,2023-06-30,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
76533,SRR25081952,SRX20835390,SRS18112575,SRP446710,PRJNA987386,Single nucleus chromatin landscapes during zebrafish early embryogenesis,PRJNA987386,Other,Vertebrate embryogenesis is a remarkable process  during which numerous cell types of different lineages arise within a short time frame. An overwhelming challenge to understand this process is the lack of dynamic chromatin accessibility information to correlate cis regulatory elements CREs and gene expression within the hierarchy of cell fate decisions. Here  we employed single nucleus ATAC seq to generate a chromatin accessibility dataset on the first day of zebrafish embryogenesis  including 3.3 hpf  5.25 hpf  6 hpf  10 hpf  12 hpf  18 hpf and 24 hpf  obtained 51 620 high quality nuclei and 23 clusters. Furthermore  by integrating snATAC seq data with single cell RNA seq data  we described the dynamics of chromatin accessibility and gene expression across developmental time points  which validates the accuracy of the chromatin landscape data. Together  our data could serve as a fundamental resource for revealing the epigenetic regulatory mechanisms of zebrafish embryogenesis.,,,,6 hpf embryos,scRNA zf6hpf 2,,strain:AB/Wild type|isolate:scRNA zf6hpf 2|breed:not collected|cultivar:not collected|ecotype:not determined|age:embryo|dev stage:6 hpf|collection date:2021 08 08|geo loc name:China: Wuhan|sex:not determined|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,scRNA 6 hpf,scRNA 6 hpf rep2 cDNA,scRNA 6 hpf rep2 cDNA,scRNA seq of 6 hpf embryos,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP446710,,CNGB Experiment ID:CNX0591991,E100036348_L01_5_1.fq.gz E100036348_L01_5_2.fq.gz,fastq fastq,55097250780.0,423825006.0,E100036348 L01 5 1.fq.gz,0:30 1:100,A:16194629059;C:11467532715;G:12387290556;T:15046756280;N:1042170,30,100,,,16194629059,11467532715,12387290556,15046756280,1042170,SRX20835390,SRS18112575,SRA1664681,"BGI Research, Shenzhen","BGI Research, Shenzhen CNGB Nucleotide Sequence Archive (CNSA) BGI-Shenzhen",2,0.00035,0.58961,0.00033,0.06118,0.99993,0.82564,0.33333,0.62483,30,100,T,B,mate1 technical by mapping diff,bgi,bgi,unknown,cdna_unspecified,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,China,2023-06-30,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
76534,SRR25081953,SRX20835389,SRS18112574,SRP446710,PRJNA987386,Single nucleus chromatin landscapes during zebrafish early embryogenesis,PRJNA987386,Other,Vertebrate embryogenesis is a remarkable process  during which numerous cell types of different lineages arise within a short time frame. An overwhelming challenge to understand this process is the lack of dynamic chromatin accessibility information to correlate cis regulatory elements CREs and gene expression within the hierarchy of cell fate decisions. Here  we employed single nucleus ATAC seq to generate a chromatin accessibility dataset on the first day of zebrafish embryogenesis  including 3.3 hpf  5.25 hpf  6 hpf  10 hpf  12 hpf  18 hpf and 24 hpf  obtained 51 620 high quality nuclei and 23 clusters. Furthermore  by integrating snATAC seq data with single cell RNA seq data  we described the dynamics of chromatin accessibility and gene expression across developmental time points  which validates the accuracy of the chromatin landscape data. Together  our data could serve as a fundamental resource for revealing the epigenetic regulatory mechanisms of zebrafish embryogenesis.,,,,6 hpf embryos,scRNA zf6hpf 1,,strain:AB/Wild type|isolate:scRNA zf6hpf 1|breed:not collected|cultivar:not collected|ecotype:not determined|age:embryo|dev stage:6 hpf|collection date:2021 08 08|geo loc name:China: Wuhan|sex:not determined|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,scRNA 6 hpf,scRNA 6 hpf rep1 oligo,scRNA 6 hpf rep1 oligo,scRNA seq of 6 hpf embryos,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP446710,,CNGB Experiment ID:CNX0591992,DP8450003515BR_L01_4_2.fq.gz DP8450003515BR_L01_4_1.fq.gz,fastq fastq,11338346750.0,226766935.0,DP8450003515BR L01 4 1.fq.gz,0:20 1:30,A:2978703558;C:2824119061;G:2623216087;T:2911128054;N:1179990,20,30,,,2978703558,2824119061,2623216087,2911128054,1179990,SRX20835389,SRS18112574,SRA1664681,"BGI Research, Shenzhen","BGI Research, Shenzhen CNGB Nucleotide Sequence Archive (CNSA) BGI-Shenzhen",2,0.00475,0.00048,0.0041,0.00042,0.99799,0.99979,0.472,0.4,20,30,T,T,mates < 9% mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,China,2023-06-30,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
76535,SRR25081954,SRX20835388,SRS18112574,SRP446710,PRJNA987386,Single nucleus chromatin landscapes during zebrafish early embryogenesis,PRJNA987386,Other,Vertebrate embryogenesis is a remarkable process  during which numerous cell types of different lineages arise within a short time frame. An overwhelming challenge to understand this process is the lack of dynamic chromatin accessibility information to correlate cis regulatory elements CREs and gene expression within the hierarchy of cell fate decisions. Here  we employed single nucleus ATAC seq to generate a chromatin accessibility dataset on the first day of zebrafish embryogenesis  including 3.3 hpf  5.25 hpf  6 hpf  10 hpf  12 hpf  18 hpf and 24 hpf  obtained 51 620 high quality nuclei and 23 clusters. Furthermore  by integrating snATAC seq data with single cell RNA seq data  we described the dynamics of chromatin accessibility and gene expression across developmental time points  which validates the accuracy of the chromatin landscape data. Together  our data could serve as a fundamental resource for revealing the epigenetic regulatory mechanisms of zebrafish embryogenesis.,,,,6 hpf embryos,scRNA zf6hpf 1,,strain:AB/Wild type|isolate:scRNA zf6hpf 1|breed:not collected|cultivar:not collected|ecotype:not determined|age:embryo|dev stage:6 hpf|collection date:2021 08 08|geo loc name:China: Wuhan|sex:not determined|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,scRNA 6 hpf,scRNA 6 hpf rep1 cDNA,scRNA 6 hpf rep1 cDNA,scRNA seq of 6 hpf embryos,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP446710,,CNGB Experiment ID:CNX0591990,E100036348_L01_6_1.fq.gz E100036348_L01_6_2.fq.gz,fastq fastq,28127062860.0,216362022.0,E100036348 L01 6 1.fq.gz,0:30 1:100,A:8147068380;C:5889045118;G:6317467122;T:7772966880;N:515360,30,100,,,8147068380,5889045118,6317467122,7772966880,515360,SRX20835388,SRS18112574,SRA1664681,"BGI Research, Shenzhen","BGI Research, Shenzhen CNGB Nucleotide Sequence Archive (CNSA) BGI-Shenzhen",2,0.00014,0.82035,0.00012,0.07422,0.99995,0.81412,1.0,0.68234,30,100,T,B,mate1 technical by mapping diff,bgi,bgi,unknown,cdna_unspecified,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,China,2023-06-30,Gastrula,Embryo,Embryo Imprecise,All anatomical structures