metadata: run_metadata: 30 rows where experiment.library_source = "TRANSCRIPTOMIC", technology = "generic-scrnaseq-only" and tissue

30 rows where experiment.library_source = "TRANSCRIPTOMIC", technology = "generic-scrnaseq-only" and tissue_curation = "Embryo Imprecise"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.title	sample.alias	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.study_ref	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.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	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
44530	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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 oocyt…	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 L…	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	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 oocyt…	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 L…	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	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 oocyt…	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 L…	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	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 oocyt…	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 L…	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	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 oocyt…	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 L…	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	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 oocyt…	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 L…	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	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 oocyt…	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 L…	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	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 oocyt…	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 L…	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	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 oocyt…	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 L…	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	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 oocyt…	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 L…	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	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 oocyt…	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 L…	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	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 oocyt…	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 L…	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
76532	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	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	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	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

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;