metadata: run_metadata: 81 rows where devstage_curation = "Gastrula" and technology = "10x"

81 rows where devstage_curation = "Gastrula" and technology = "10x"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	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.r3_length	run.r4_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
29445	29445	SRR27352062	SRX23028823	SRS19990706	SRP480147	PRJNA1057153	Gene module reconstruction elucidates cellular differentiation processes and the regulatory logic of specialized secretion	GSE252032	Transcriptome Analysis	During differentiation cells become structurally and functionally specialized but comprehensive views of the underlying remodeling processes are elusive. Here we leverage scRNA seq developmental trajectories to reconstruct differentiation using two secretory tissues as a model system – the zebrafish notochord and hatch gland. First we present an approach MIMIR to integrate expression and functional similarities for gene module identification revealing dozens of gene modules representing known and newly associated differentiation processes and their temporal ordering. Second we focused on the unfolded protein response UPR transducer module to study how general versus cell type specific secretory functions are regulated. By profiling loss and gain of function embryos we found that the UPR transcription factors creb3l1 creb3l2 and xbp1 are master regulators of a general secretion program. creb3l1/creb3l2 additionally activate an extracellular matrix secretion program while xbp1 partners with bhlha15 to activate a gland specific secretion program. Our study offers an integrated approach for functional gene module identification and illustrates how transcription factors confer general and specialized cellular functions. Overall design: scRNA seq experiments were conducted to study the regulatory roles of the unfolded protein response UPR pathway transcription factors TFs during zebrafish embryogenesis. We focused on the four UPR TFs xbp1 atf6 creb3l1 and creb3l2 that are expressed during the early differentiation of the notochord and/or the hatch gland. We hypothesized that the UPR TFs regulate the secretory machinery genes in these two cell types. To identify the endogenous target genes of the UPR TFs we performed scRNA seq of UPR TF loss of function embryos at 12 hpf when UPR TFs and secretory pathway genes are normally highly expressed in the notochord and hatch gland. Loss of function embryos were generated by CRISPR mediated mutagenesis. Crispants were created by injecting Cas9 protein and guide …		pubmed:38234833;pubmed:39591963	xbp1 s+bhlha15 me batch C	GSM7992600	source name:Whole embryo\|tissue:Whole embryo\|strain:TL/AB\|developmental stage:8 hpf\|genotype:xbp1 s+bhlha15 co mis expression in xbp1+atf6 double crispant\|geo loc name:missing\|collection date:missing	xbp1 s+bhlha15 me batch C	The cellranger command line tool was used to map reads in the fastq files to reference transcriptomes with the "cellranger count" command For libraries that include xbp1 s misexpression ME E 5 to ME E 8 the reference transcriptome was modified: the mis expressed codon optimized xbp1 s sequence was appended to the reference transcriptome. Assembly: dr99 Supplementary files format and content: All processed data are output from the "cellranger count" command. barcodes.tsv.gz features.tsv.gz and matrix.mtx.gz can be collectively input into third party packages to allow users to wrangle the barcode feature matrix. The matrix contains only detected cell associated barcodes. Each element of the matrix is the number of UMIs associated with a feature row and a barcode column. The filtered feature bc matrix.h5 files contain the same detected cell associated feature and barcode information in HDF5 format.	Whole embryo	1 cell stage embryos were either injected with Cas9 and gRNA injected with mRNA or uninjected according to experimental conditions.	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer’s solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	Zebrafish embryos were collected at 1 cell stage and cultured in standard E3 medium in a 27°C incubator until desired stages.	tissue:Whole embryo\|strain:TL/AB\|developmental stage:8 hpf\|genotype:xbp1 s+bhlha15 co mis expression in xbp1+atf6 double crispant	GSM7992600	GSM7992600: xbp1 s+bhlha15 me batch C; Danio rerio; RNA Seq	GSM7992600 r1	GSM7992600	1	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer's solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP480147	loader:fastq load.py	ME_E_8_S5_L001_I1_001.fastq.gz ME_E_8_S5_L001_I2_001.fastq.gz ME_E_8_S5_L001_R1_001.fastq.gz ME_E_8_S5_L001_R2_001.fastq.gz	fastq fastq fastq fastq	5181513462.0	37547199.0	GSM7992600 r1	0:10 1:10 2:28 3:90	A:956100499;C:718374108;G:793571214;T:911118244;N:83845	10	10	28	90	956100499	718374108	793571214	911118244	83845	SRX23028823	SRS19990706	SRA1775820	Schier Lab, Harvard University	Schier Lab, Harvard University	1	0.93072		0.1664		0.79411		0.55992		90		B		usable mapping rate	illumina	novaseq_era	full_length	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-12-26	Gastrula	Embryo	Whole Organism	All anatomical structures
29446	29446	SRR27352063	SRX23028823	SRS19990706	SRP480147	PRJNA1057153	Gene module reconstruction elucidates cellular differentiation processes and the regulatory logic of specialized secretion	GSE252032	Transcriptome Analysis	During differentiation cells become structurally and functionally specialized but comprehensive views of the underlying remodeling processes are elusive. Here we leverage scRNA seq developmental trajectories to reconstruct differentiation using two secretory tissues as a model system – the zebrafish notochord and hatch gland. First we present an approach MIMIR to integrate expression and functional similarities for gene module identification revealing dozens of gene modules representing known and newly associated differentiation processes and their temporal ordering. Second we focused on the unfolded protein response UPR transducer module to study how general versus cell type specific secretory functions are regulated. By profiling loss and gain of function embryos we found that the UPR transcription factors creb3l1 creb3l2 and xbp1 are master regulators of a general secretion program. creb3l1/creb3l2 additionally activate an extracellular matrix secretion program while xbp1 partners with bhlha15 to activate a gland specific secretion program. Our study offers an integrated approach for functional gene module identification and illustrates how transcription factors confer general and specialized cellular functions. Overall design: scRNA seq experiments were conducted to study the regulatory roles of the unfolded protein response UPR pathway transcription factors TFs during zebrafish embryogenesis. We focused on the four UPR TFs xbp1 atf6 creb3l1 and creb3l2 that are expressed during the early differentiation of the notochord and/or the hatch gland. We hypothesized that the UPR TFs regulate the secretory machinery genes in these two cell types. To identify the endogenous target genes of the UPR TFs we performed scRNA seq of UPR TF loss of function embryos at 12 hpf when UPR TFs and secretory pathway genes are normally highly expressed in the notochord and hatch gland. Loss of function embryos were generated by CRISPR mediated mutagenesis. Crispants were created by injecting Cas9 protein and guide …		pubmed:38234833;pubmed:39591963	xbp1 s+bhlha15 me batch C	GSM7992600	source name:Whole embryo\|tissue:Whole embryo\|strain:TL/AB\|developmental stage:8 hpf\|genotype:xbp1 s+bhlha15 co mis expression in xbp1+atf6 double crispant\|geo loc name:missing\|collection date:missing	xbp1 s+bhlha15 me batch C	The cellranger command line tool was used to map reads in the fastq files to reference transcriptomes with the "cellranger count" command For libraries that include xbp1 s misexpression ME E 5 to ME E 8 the reference transcriptome was modified: the mis expressed codon optimized xbp1 s sequence was appended to the reference transcriptome. Assembly: dr99 Supplementary files format and content: All processed data are output from the "cellranger count" command. barcodes.tsv.gz features.tsv.gz and matrix.mtx.gz can be collectively input into third party packages to allow users to wrangle the barcode feature matrix. The matrix contains only detected cell associated barcodes. Each element of the matrix is the number of UMIs associated with a feature row and a barcode column. The filtered feature bc matrix.h5 files contain the same detected cell associated feature and barcode information in HDF5 format.	Whole embryo	1 cell stage embryos were either injected with Cas9 and gRNA injected with mRNA or uninjected according to experimental conditions.	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer’s solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	Zebrafish embryos were collected at 1 cell stage and cultured in standard E3 medium in a 27°C incubator until desired stages.	tissue:Whole embryo\|strain:TL/AB\|developmental stage:8 hpf\|genotype:xbp1 s+bhlha15 co mis expression in xbp1+atf6 double crispant	GSM7992600	GSM7992600: xbp1 s+bhlha15 me batch C; Danio rerio; RNA Seq	GSM7992600 r1	GSM7992600	1	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer's solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP480147	loader:fastq load.py	ME_E_8_S5_L002_I1_001.fastq.gz ME_E_8_S5_L002_I2_001.fastq.gz ME_E_8_S5_L002_R1_001.fastq.gz ME_E_8_S5_L002_R2_001.fastq.gz	fastq fastq fastq fastq	5260063890.0	38116405.0	GSM7992600 r2	0:10 1:10 2:28 3:90	A:971301150;C:729023972;G:805112224;T:924994096;N:45008	10	10	28	90	971301150	729023972	805112224	924994096	45008	SRX23028823	SRS19990706	SRA1775820	Schier Lab, Harvard University	Schier Lab, Harvard University	1	0.92931		0.16683		0.79456		0.55431		90		B		usable mapping rate	illumina	novaseq_era	full_length	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-12-26	Gastrula	Embryo	Whole Organism	All anatomical structures
29447	29447	SRR27352064	SRX23028822	SRS19990705	SRP480147	PRJNA1057153	Gene module reconstruction elucidates cellular differentiation processes and the regulatory logic of specialized secretion	GSE252032	Transcriptome Analysis	During differentiation cells become structurally and functionally specialized but comprehensive views of the underlying remodeling processes are elusive. Here we leverage scRNA seq developmental trajectories to reconstruct differentiation using two secretory tissues as a model system – the zebrafish notochord and hatch gland. First we present an approach MIMIR to integrate expression and functional similarities for gene module identification revealing dozens of gene modules representing known and newly associated differentiation processes and their temporal ordering. Second we focused on the unfolded protein response UPR transducer module to study how general versus cell type specific secretory functions are regulated. By profiling loss and gain of function embryos we found that the UPR transcription factors creb3l1 creb3l2 and xbp1 are master regulators of a general secretion program. creb3l1/creb3l2 additionally activate an extracellular matrix secretion program while xbp1 partners with bhlha15 to activate a gland specific secretion program. Our study offers an integrated approach for functional gene module identification and illustrates how transcription factors confer general and specialized cellular functions. Overall design: scRNA seq experiments were conducted to study the regulatory roles of the unfolded protein response UPR pathway transcription factors TFs during zebrafish embryogenesis. We focused on the four UPR TFs xbp1 atf6 creb3l1 and creb3l2 that are expressed during the early differentiation of the notochord and/or the hatch gland. We hypothesized that the UPR TFs regulate the secretory machinery genes in these two cell types. To identify the endogenous target genes of the UPR TFs we performed scRNA seq of UPR TF loss of function embryos at 12 hpf when UPR TFs and secretory pathway genes are normally highly expressed in the notochord and hatch gland. Loss of function embryos were generated by CRISPR mediated mutagenesis. Crispants were created by injecting Cas9 protein and guide …		pubmed:38234833;pubmed:39591963	bhlha15 me batch C 50pg	GSM7992599	source name:Whole embryo\|tissue:Whole embryo\|strain:TL/AB\|developmental stage:8 hpf\|genotype:bhlha15 mis expression in xbp1+atf6 double crispant\|geo loc name:missing\|collection date:missing	bhlha15 me batch C 50pg	The cellranger command line tool was used to map reads in the fastq files to reference transcriptomes with the "cellranger count" command For libraries that include xbp1 s misexpression ME E 5 to ME E 8 the reference transcriptome was modified: the mis expressed codon optimized xbp1 s sequence was appended to the reference transcriptome. Assembly: dr99 Supplementary files format and content: All processed data are output from the "cellranger count" command. barcodes.tsv.gz features.tsv.gz and matrix.mtx.gz can be collectively input into third party packages to allow users to wrangle the barcode feature matrix. The matrix contains only detected cell associated barcodes. Each element of the matrix is the number of UMIs associated with a feature row and a barcode column. The filtered feature bc matrix.h5 files contain the same detected cell associated feature and barcode information in HDF5 format.	Whole embryo	1 cell stage embryos were either injected with Cas9 and gRNA injected with mRNA or uninjected according to experimental conditions.	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer’s solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	Zebrafish embryos were collected at 1 cell stage and cultured in standard E3 medium in a 27°C incubator until desired stages.	tissue:Whole embryo\|strain:TL/AB\|developmental stage:8 hpf\|genotype:bhlha15 mis expression in xbp1+atf6 double crispant	GSM7992599	GSM7992599: bhlha15 me batch C 50pg; Danio rerio; RNA Seq	GSM7992599 r1	GSM7992599	1	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer's solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP480147	loader:fastq load.py	ME_E_7_S6_L001_R2_001.fastq.gz ME_E_7_S6_L001_R1_001.fastq.gz ME_E_7_S6_L001_I2_001.fastq.gz ME_E_7_S6_L001_I1_001.fastq.gz	fastq fastq fastq fastq	6938831682.0	50281389.0	GSM7992599 r1	0:10 1:10 2:28 3:90	A:1306218371;C:953247355;G:1099874957;T:1165870220;N:114107	10	10	28	90	1306218371	953247355	1099874957	1165870220	114107	SRX23028822	SRS19990705	SRA1775820	Schier Lab, Harvard University	Schier Lab, Harvard University	1	0.9066		0.1671		0.81174		0.54662		90		B		usable mapping rate	illumina	novaseq_era	full_length	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-12-26	Gastrula	Embryo	Whole Organism	All anatomical structures
29448	29448	SRR27352065	SRX23028822	SRS19990705	SRP480147	PRJNA1057153	Gene module reconstruction elucidates cellular differentiation processes and the regulatory logic of specialized secretion	GSE252032	Transcriptome Analysis	During differentiation cells become structurally and functionally specialized but comprehensive views of the underlying remodeling processes are elusive. Here we leverage scRNA seq developmental trajectories to reconstruct differentiation using two secretory tissues as a model system – the zebrafish notochord and hatch gland. First we present an approach MIMIR to integrate expression and functional similarities for gene module identification revealing dozens of gene modules representing known and newly associated differentiation processes and their temporal ordering. Second we focused on the unfolded protein response UPR transducer module to study how general versus cell type specific secretory functions are regulated. By profiling loss and gain of function embryos we found that the UPR transcription factors creb3l1 creb3l2 and xbp1 are master regulators of a general secretion program. creb3l1/creb3l2 additionally activate an extracellular matrix secretion program while xbp1 partners with bhlha15 to activate a gland specific secretion program. Our study offers an integrated approach for functional gene module identification and illustrates how transcription factors confer general and specialized cellular functions. Overall design: scRNA seq experiments were conducted to study the regulatory roles of the unfolded protein response UPR pathway transcription factors TFs during zebrafish embryogenesis. We focused on the four UPR TFs xbp1 atf6 creb3l1 and creb3l2 that are expressed during the early differentiation of the notochord and/or the hatch gland. We hypothesized that the UPR TFs regulate the secretory machinery genes in these two cell types. To identify the endogenous target genes of the UPR TFs we performed scRNA seq of UPR TF loss of function embryos at 12 hpf when UPR TFs and secretory pathway genes are normally highly expressed in the notochord and hatch gland. Loss of function embryos were generated by CRISPR mediated mutagenesis. Crispants were created by injecting Cas9 protein and guide …		pubmed:38234833;pubmed:39591963	bhlha15 me batch C 50pg	GSM7992599	source name:Whole embryo\|tissue:Whole embryo\|strain:TL/AB\|developmental stage:8 hpf\|genotype:bhlha15 mis expression in xbp1+atf6 double crispant\|geo loc name:missing\|collection date:missing	bhlha15 me batch C 50pg	The cellranger command line tool was used to map reads in the fastq files to reference transcriptomes with the "cellranger count" command For libraries that include xbp1 s misexpression ME E 5 to ME E 8 the reference transcriptome was modified: the mis expressed codon optimized xbp1 s sequence was appended to the reference transcriptome. Assembly: dr99 Supplementary files format and content: All processed data are output from the "cellranger count" command. barcodes.tsv.gz features.tsv.gz and matrix.mtx.gz can be collectively input into third party packages to allow users to wrangle the barcode feature matrix. The matrix contains only detected cell associated barcodes. Each element of the matrix is the number of UMIs associated with a feature row and a barcode column. The filtered feature bc matrix.h5 files contain the same detected cell associated feature and barcode information in HDF5 format.	Whole embryo	1 cell stage embryos were either injected with Cas9 and gRNA injected with mRNA or uninjected according to experimental conditions.	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer’s solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	Zebrafish embryos were collected at 1 cell stage and cultured in standard E3 medium in a 27°C incubator until desired stages.	tissue:Whole embryo\|strain:TL/AB\|developmental stage:8 hpf\|genotype:bhlha15 mis expression in xbp1+atf6 double crispant	GSM7992599	GSM7992599: bhlha15 me batch C 50pg; Danio rerio; RNA Seq	GSM7992599 r1	GSM7992599	1	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer's solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP480147	loader:fastq load.py	ME_E_7_S6_L002_R2_001.fastq.gz ME_E_7_S6_L002_R1_001.fastq.gz ME_E_7_S6_L002_I2_001.fastq.gz ME_E_7_S6_L002_I1_001.fastq.gz	fastq fastq fastq fastq	7064201370.0	51189865.0	GSM7992599 r2	0:10 1:10 2:28 3:90	A:1330402466;C:970104628;G:1119275399;T:1187243465;N:61892	10	10	28	90	1330402466	970104628	1119275399	1187243465	61892	SRX23028822	SRS19990705	SRA1775820	Schier Lab, Harvard University	Schier Lab, Harvard University	1	0.90484		0.16778		0.81061		0.523		90		B		usable mapping rate	illumina	novaseq_era	full_length	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-12-26	Gastrula	Embryo	Whole Organism	All anatomical structures
29449	29449	SRR27352066	SRX23028821	SRS19990704	SRP480147	PRJNA1057153	Gene module reconstruction elucidates cellular differentiation processes and the regulatory logic of specialized secretion	GSE252032	Transcriptome Analysis	During differentiation cells become structurally and functionally specialized but comprehensive views of the underlying remodeling processes are elusive. Here we leverage scRNA seq developmental trajectories to reconstruct differentiation using two secretory tissues as a model system – the zebrafish notochord and hatch gland. First we present an approach MIMIR to integrate expression and functional similarities for gene module identification revealing dozens of gene modules representing known and newly associated differentiation processes and their temporal ordering. Second we focused on the unfolded protein response UPR transducer module to study how general versus cell type specific secretory functions are regulated. By profiling loss and gain of function embryos we found that the UPR transcription factors creb3l1 creb3l2 and xbp1 are master regulators of a general secretion program. creb3l1/creb3l2 additionally activate an extracellular matrix secretion program while xbp1 partners with bhlha15 to activate a gland specific secretion program. Our study offers an integrated approach for functional gene module identification and illustrates how transcription factors confer general and specialized cellular functions. Overall design: scRNA seq experiments were conducted to study the regulatory roles of the unfolded protein response UPR pathway transcription factors TFs during zebrafish embryogenesis. We focused on the four UPR TFs xbp1 atf6 creb3l1 and creb3l2 that are expressed during the early differentiation of the notochord and/or the hatch gland. We hypothesized that the UPR TFs regulate the secretory machinery genes in these two cell types. To identify the endogenous target genes of the UPR TFs we performed scRNA seq of UPR TF loss of function embryos at 12 hpf when UPR TFs and secretory pathway genes are normally highly expressed in the notochord and hatch gland. Loss of function embryos were generated by CRISPR mediated mutagenesis. Crispants were created by injecting Cas9 protein and guide …		pubmed:38234833;pubmed:39591963	xbp1 s me batch C 70pg	GSM7992598	source name:Whole embryo\|tissue:Whole embryo\|strain:TL/AB\|developmental stage:8 hpf\|genotype:xbp1 s mis expression in xbp1+atf6 double crispant\|geo loc name:missing\|collection date:missing	xbp1 s me batch C 70pg	The cellranger command line tool was used to map reads in the fastq files to reference transcriptomes with the "cellranger count" command For libraries that include xbp1 s misexpression ME E 5 to ME E 8 the reference transcriptome was modified: the mis expressed codon optimized xbp1 s sequence was appended to the reference transcriptome. Assembly: dr99 Supplementary files format and content: All processed data are output from the "cellranger count" command. barcodes.tsv.gz features.tsv.gz and matrix.mtx.gz can be collectively input into third party packages to allow users to wrangle the barcode feature matrix. The matrix contains only detected cell associated barcodes. Each element of the matrix is the number of UMIs associated with a feature row and a barcode column. The filtered feature bc matrix.h5 files contain the same detected cell associated feature and barcode information in HDF5 format.	Whole embryo	1 cell stage embryos were either injected with Cas9 and gRNA injected with mRNA or uninjected according to experimental conditions.	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer’s solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	Zebrafish embryos were collected at 1 cell stage and cultured in standard E3 medium in a 27°C incubator until desired stages.	tissue:Whole embryo\|strain:TL/AB\|developmental stage:8 hpf\|genotype:xbp1 s mis expression in xbp1+atf6 double crispant	GSM7992598	GSM7992598: xbp1 s me batch C 70pg; Danio rerio; RNA Seq	GSM7992598 r1	GSM7992598	1	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer's solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP480147	loader:fastq load.py	ME_E_6_S7_L001_I1_001.fastq.gz ME_E_6_S7_L001_I2_001.fastq.gz ME_E_6_S7_L001_R1_001.fastq.gz ME_E_6_S7_L001_R2_001.fastq.gz	fastq fastq fastq fastq	5772411522.0	41829069.0	GSM7992598 r1	0:10 1:10 2:28 3:90	A:1071977325;C:808460271;G:918967243;T:965119818;N:91553	10	10	28	90	1071977325	808460271	918967243	965119818	91553	SRX23028821	SRS19990704	SRA1775820	Schier Lab, Harvard University	Schier Lab, Harvard University	1	0.92142		0.18137		0.80886		0.56195		90		B		usable mapping rate	illumina	novaseq_era	full_length	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-12-26	Gastrula	Embryo	Whole Organism	All anatomical structures
29450	29450	SRR27352067	SRX23028821	SRS19990704	SRP480147	PRJNA1057153	Gene module reconstruction elucidates cellular differentiation processes and the regulatory logic of specialized secretion	GSE252032	Transcriptome Analysis	During differentiation cells become structurally and functionally specialized but comprehensive views of the underlying remodeling processes are elusive. Here we leverage scRNA seq developmental trajectories to reconstruct differentiation using two secretory tissues as a model system – the zebrafish notochord and hatch gland. First we present an approach MIMIR to integrate expression and functional similarities for gene module identification revealing dozens of gene modules representing known and newly associated differentiation processes and their temporal ordering. Second we focused on the unfolded protein response UPR transducer module to study how general versus cell type specific secretory functions are regulated. By profiling loss and gain of function embryos we found that the UPR transcription factors creb3l1 creb3l2 and xbp1 are master regulators of a general secretion program. creb3l1/creb3l2 additionally activate an extracellular matrix secretion program while xbp1 partners with bhlha15 to activate a gland specific secretion program. Our study offers an integrated approach for functional gene module identification and illustrates how transcription factors confer general and specialized cellular functions. Overall design: scRNA seq experiments were conducted to study the regulatory roles of the unfolded protein response UPR pathway transcription factors TFs during zebrafish embryogenesis. We focused on the four UPR TFs xbp1 atf6 creb3l1 and creb3l2 that are expressed during the early differentiation of the notochord and/or the hatch gland. We hypothesized that the UPR TFs regulate the secretory machinery genes in these two cell types. To identify the endogenous target genes of the UPR TFs we performed scRNA seq of UPR TF loss of function embryos at 12 hpf when UPR TFs and secretory pathway genes are normally highly expressed in the notochord and hatch gland. Loss of function embryos were generated by CRISPR mediated mutagenesis. Crispants were created by injecting Cas9 protein and guide …		pubmed:38234833;pubmed:39591963	xbp1 s me batch C 70pg	GSM7992598	source name:Whole embryo\|tissue:Whole embryo\|strain:TL/AB\|developmental stage:8 hpf\|genotype:xbp1 s mis expression in xbp1+atf6 double crispant\|geo loc name:missing\|collection date:missing	xbp1 s me batch C 70pg	The cellranger command line tool was used to map reads in the fastq files to reference transcriptomes with the "cellranger count" command For libraries that include xbp1 s misexpression ME E 5 to ME E 8 the reference transcriptome was modified: the mis expressed codon optimized xbp1 s sequence was appended to the reference transcriptome. Assembly: dr99 Supplementary files format and content: All processed data are output from the "cellranger count" command. barcodes.tsv.gz features.tsv.gz and matrix.mtx.gz can be collectively input into third party packages to allow users to wrangle the barcode feature matrix. The matrix contains only detected cell associated barcodes. Each element of the matrix is the number of UMIs associated with a feature row and a barcode column. The filtered feature bc matrix.h5 files contain the same detected cell associated feature and barcode information in HDF5 format.	Whole embryo	1 cell stage embryos were either injected with Cas9 and gRNA injected with mRNA or uninjected according to experimental conditions.	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer’s solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	Zebrafish embryos were collected at 1 cell stage and cultured in standard E3 medium in a 27°C incubator until desired stages.	tissue:Whole embryo\|strain:TL/AB\|developmental stage:8 hpf\|genotype:xbp1 s mis expression in xbp1+atf6 double crispant	GSM7992598	GSM7992598: xbp1 s me batch C 70pg; Danio rerio; RNA Seq	GSM7992598 r1	GSM7992598	1	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer's solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP480147	loader:fastq load.py	ME_E_6_S7_L002_I1_001.fastq.gz ME_E_6_S7_L002_I2_001.fastq.gz ME_E_6_S7_L002_R1_001.fastq.gz ME_E_6_S7_L002_R2_001.fastq.gz	fastq fastq fastq fastq	5866797312.0	42513024.0	GSM7992598 r2	0:10 1:10 2:28 3:90	A:1090114611;C:821302663;G:933644617;T:981060240;N:50029	10	10	28	90	1090114611	821302663	933644617	981060240	50029	SRX23028821	SRS19990704	SRA1775820	Schier Lab, Harvard University	Schier Lab, Harvard University	1	0.91937		0.18015		0.81201		0.56252		90		B		usable mapping rate	illumina	novaseq_era	full_length	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-12-26	Gastrula	Embryo	Whole Organism	All anatomical structures
29451	29451	SRR27352068	SRX23028820	SRS19990703	SRP480147	PRJNA1057153	Gene module reconstruction elucidates cellular differentiation processes and the regulatory logic of specialized secretion	GSE252032	Transcriptome Analysis	During differentiation cells become structurally and functionally specialized but comprehensive views of the underlying remodeling processes are elusive. Here we leverage scRNA seq developmental trajectories to reconstruct differentiation using two secretory tissues as a model system – the zebrafish notochord and hatch gland. First we present an approach MIMIR to integrate expression and functional similarities for gene module identification revealing dozens of gene modules representing known and newly associated differentiation processes and their temporal ordering. Second we focused on the unfolded protein response UPR transducer module to study how general versus cell type specific secretory functions are regulated. By profiling loss and gain of function embryos we found that the UPR transcription factors creb3l1 creb3l2 and xbp1 are master regulators of a general secretion program. creb3l1/creb3l2 additionally activate an extracellular matrix secretion program while xbp1 partners with bhlha15 to activate a gland specific secretion program. Our study offers an integrated approach for functional gene module identification and illustrates how transcription factors confer general and specialized cellular functions. Overall design: scRNA seq experiments were conducted to study the regulatory roles of the unfolded protein response UPR pathway transcription factors TFs during zebrafish embryogenesis. We focused on the four UPR TFs xbp1 atf6 creb3l1 and creb3l2 that are expressed during the early differentiation of the notochord and/or the hatch gland. We hypothesized that the UPR TFs regulate the secretory machinery genes in these two cell types. To identify the endogenous target genes of the UPR TFs we performed scRNA seq of UPR TF loss of function embryos at 12 hpf when UPR TFs and secretory pathway genes are normally highly expressed in the notochord and hatch gland. Loss of function embryos were generated by CRISPR mediated mutagenesis. Crispants were created by injecting Cas9 protein and guide …		pubmed:38234833;pubmed:39591963	mCherry me batch C 120pg	GSM7992597	source name:Whole embryo\|tissue:Whole embryo\|strain:TL/AB\|developmental stage:8 hpf\|genotype:nls mCherry mis expression in xbp1+atf6 double crispant\|geo loc name:missing\|collection date:missing	mCherry me batch C 120pg	The cellranger command line tool was used to map reads in the fastq files to reference transcriptomes with the "cellranger count" command For libraries that include xbp1 s misexpression ME E 5 to ME E 8 the reference transcriptome was modified: the mis expressed codon optimized xbp1 s sequence was appended to the reference transcriptome. Assembly: dr99 Supplementary files format and content: All processed data are output from the "cellranger count" command. barcodes.tsv.gz features.tsv.gz and matrix.mtx.gz can be collectively input into third party packages to allow users to wrangle the barcode feature matrix. The matrix contains only detected cell associated barcodes. Each element of the matrix is the number of UMIs associated with a feature row and a barcode column. The filtered feature bc matrix.h5 files contain the same detected cell associated feature and barcode information in HDF5 format.	Whole embryo	1 cell stage embryos were either injected with Cas9 and gRNA injected with mRNA or uninjected according to experimental conditions.	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer’s solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	Zebrafish embryos were collected at 1 cell stage and cultured in standard E3 medium in a 27°C incubator until desired stages.	tissue:Whole embryo\|strain:TL/AB\|developmental stage:8 hpf\|genotype:nls mCherry mis expression in xbp1+atf6 double crispant	GSM7992597	GSM7992597: mCherry me batch C 120pg; Danio rerio; RNA Seq	GSM7992597 r1	GSM7992597	1	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer's solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP480147	loader:fastq load.py	ME_E_5_S8_L001_I1_001.fastq.gz ME_E_5_S8_L001_I2_001.fastq.gz ME_E_5_S8_L001_R1_001.fastq.gz ME_E_5_S8_L001_R2_001.fastq.gz	fastq fastq fastq fastq	8749401480.0	63401460.0	GSM7992597 r1	0:10 1:10 2:28 3:90	A:1660203125;C:1179357258;G:1367846490;T:1498581063;N:143464	10	10	28	90	1660203125	1179357258	1367846490	1498581063	143464	SRX23028820	SRS19990703	SRA1775820	Schier Lab, Harvard University	Schier Lab, Harvard University	1	0.89798		0.13736		0.8128		0.52474		90		B		usable mapping rate	illumina	novaseq_era	full_length	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-12-26	Gastrula	Embryo	Whole Organism	All anatomical structures
29452	29452	SRR27352069	SRX23028820	SRS19990703	SRP480147	PRJNA1057153	Gene module reconstruction elucidates cellular differentiation processes and the regulatory logic of specialized secretion	GSE252032	Transcriptome Analysis	During differentiation cells become structurally and functionally specialized but comprehensive views of the underlying remodeling processes are elusive. Here we leverage scRNA seq developmental trajectories to reconstruct differentiation using two secretory tissues as a model system – the zebrafish notochord and hatch gland. First we present an approach MIMIR to integrate expression and functional similarities for gene module identification revealing dozens of gene modules representing known and newly associated differentiation processes and their temporal ordering. Second we focused on the unfolded protein response UPR transducer module to study how general versus cell type specific secretory functions are regulated. By profiling loss and gain of function embryos we found that the UPR transcription factors creb3l1 creb3l2 and xbp1 are master regulators of a general secretion program. creb3l1/creb3l2 additionally activate an extracellular matrix secretion program while xbp1 partners with bhlha15 to activate a gland specific secretion program. Our study offers an integrated approach for functional gene module identification and illustrates how transcription factors confer general and specialized cellular functions. Overall design: scRNA seq experiments were conducted to study the regulatory roles of the unfolded protein response UPR pathway transcription factors TFs during zebrafish embryogenesis. We focused on the four UPR TFs xbp1 atf6 creb3l1 and creb3l2 that are expressed during the early differentiation of the notochord and/or the hatch gland. We hypothesized that the UPR TFs regulate the secretory machinery genes in these two cell types. To identify the endogenous target genes of the UPR TFs we performed scRNA seq of UPR TF loss of function embryos at 12 hpf when UPR TFs and secretory pathway genes are normally highly expressed in the notochord and hatch gland. Loss of function embryos were generated by CRISPR mediated mutagenesis. Crispants were created by injecting Cas9 protein and guide …		pubmed:38234833;pubmed:39591963	mCherry me batch C 120pg	GSM7992597	source name:Whole embryo\|tissue:Whole embryo\|strain:TL/AB\|developmental stage:8 hpf\|genotype:nls mCherry mis expression in xbp1+atf6 double crispant\|geo loc name:missing\|collection date:missing	mCherry me batch C 120pg	The cellranger command line tool was used to map reads in the fastq files to reference transcriptomes with the "cellranger count" command For libraries that include xbp1 s misexpression ME E 5 to ME E 8 the reference transcriptome was modified: the mis expressed codon optimized xbp1 s sequence was appended to the reference transcriptome. Assembly: dr99 Supplementary files format and content: All processed data are output from the "cellranger count" command. barcodes.tsv.gz features.tsv.gz and matrix.mtx.gz can be collectively input into third party packages to allow users to wrangle the barcode feature matrix. The matrix contains only detected cell associated barcodes. Each element of the matrix is the number of UMIs associated with a feature row and a barcode column. The filtered feature bc matrix.h5 files contain the same detected cell associated feature and barcode information in HDF5 format.	Whole embryo	1 cell stage embryos were either injected with Cas9 and gRNA injected with mRNA or uninjected according to experimental conditions.	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer’s solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	Zebrafish embryos were collected at 1 cell stage and cultured in standard E3 medium in a 27°C incubator until desired stages.	tissue:Whole embryo\|strain:TL/AB\|developmental stage:8 hpf\|genotype:nls mCherry mis expression in xbp1+atf6 double crispant	GSM7992597	GSM7992597: mCherry me batch C 120pg; Danio rerio; RNA Seq	GSM7992597 r1	GSM7992597	1	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer's solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP480147	loader:fastq load.py	ME_E_5_S8_L002_I1_001.fastq.gz ME_E_5_S8_L002_I2_001.fastq.gz ME_E_5_S8_L002_R1_001.fastq.gz ME_E_5_S8_L002_R2_001.fastq.gz	fastq fastq fastq fastq	8882619504.0	64366808.0	GSM7992597 r2	0:10 1:10 2:28 3:90	A:1686216142;C:1196995709;G:1388087801;T:1521636659;N:76409	10	10	28	90	1686216142	1196995709	1388087801	1521636659	76409	SRX23028820	SRS19990703	SRA1775820	Schier Lab, Harvard University	Schier Lab, Harvard University	1	0.89805		0.13979		0.81314		0.52494		90		B		usable mapping rate	illumina	novaseq_era	full_length	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-12-26	Gastrula	Embryo	Whole Organism	All anatomical structures
29453	29453	SRR27352070	SRX23028819	SRS19990702	SRP480147	PRJNA1057153	Gene module reconstruction elucidates cellular differentiation processes and the regulatory logic of specialized secretion	GSE252032	Transcriptome Analysis	During differentiation cells become structurally and functionally specialized but comprehensive views of the underlying remodeling processes are elusive. Here we leverage scRNA seq developmental trajectories to reconstruct differentiation using two secretory tissues as a model system – the zebrafish notochord and hatch gland. First we present an approach MIMIR to integrate expression and functional similarities for gene module identification revealing dozens of gene modules representing known and newly associated differentiation processes and their temporal ordering. Second we focused on the unfolded protein response UPR transducer module to study how general versus cell type specific secretory functions are regulated. By profiling loss and gain of function embryos we found that the UPR transcription factors creb3l1 creb3l2 and xbp1 are master regulators of a general secretion program. creb3l1/creb3l2 additionally activate an extracellular matrix secretion program while xbp1 partners with bhlha15 to activate a gland specific secretion program. Our study offers an integrated approach for functional gene module identification and illustrates how transcription factors confer general and specialized cellular functions. Overall design: scRNA seq experiments were conducted to study the regulatory roles of the unfolded protein response UPR pathway transcription factors TFs during zebrafish embryogenesis. We focused on the four UPR TFs xbp1 atf6 creb3l1 and creb3l2 that are expressed during the early differentiation of the notochord and/or the hatch gland. We hypothesized that the UPR TFs regulate the secretory machinery genes in these two cell types. To identify the endogenous target genes of the UPR TFs we performed scRNA seq of UPR TF loss of function embryos at 12 hpf when UPR TFs and secretory pathway genes are normally highly expressed in the notochord and hatch gland. Loss of function embryos were generated by CRISPR mediated mutagenesis. Crispants were created by injecting Cas9 protein and guide …		pubmed:38234833;pubmed:39591963	creb3l2 N me 40pg	GSM7992596	source name:Whole embryo\|tissue:Whole embryo\|strain:TL/AB\|developmental stage:8 hpf\|genotype:creb3l2 N mis expression in xbp1 crispant\|geo loc name:missing\|collection date:missing	creb3l2 N me 40pg	The cellranger command line tool was used to map reads in the fastq files to reference transcriptomes with the "cellranger count" command For libraries that include xbp1 s misexpression ME E 5 to ME E 8 the reference transcriptome was modified: the mis expressed codon optimized xbp1 s sequence was appended to the reference transcriptome. Assembly: dr99 Supplementary files format and content: All processed data are output from the "cellranger count" command. barcodes.tsv.gz features.tsv.gz and matrix.mtx.gz can be collectively input into third party packages to allow users to wrangle the barcode feature matrix. The matrix contains only detected cell associated barcodes. Each element of the matrix is the number of UMIs associated with a feature row and a barcode column. The filtered feature bc matrix.h5 files contain the same detected cell associated feature and barcode information in HDF5 format.	Whole embryo	1 cell stage embryos were either injected with Cas9 and gRNA injected with mRNA or uninjected according to experimental conditions.	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer’s solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	Zebrafish embryos were collected at 1 cell stage and cultured in standard E3 medium in a 27°C incubator until desired stages.	tissue:Whole embryo\|strain:TL/AB\|developmental stage:8 hpf\|genotype:creb3l2 N mis expression in xbp1 crispant	GSM7992596	GSM7992596: creb3l2 N me 40pg; Danio rerio; RNA Seq	GSM7992596 r1	GSM7992596	1	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer's solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP480147	loader:fastq load.py	ME_D_6_S6_L001_R2_001.fastq.gz ME_D_6_S6_L001_R1_001.fastq.gz ME_D_6_S6_L001_I1_001.fastq.gz	fastq fastq fastq	53307532026.0	423075651.0	GSM7992596 r1	0:8 1:28 2:90	A:10926383189;C:7941787834;G:8886027055;T:10318943731;N:3666781	8	28	90		10926383189	7941787834	8886027055	10318943731	3666781	SRX23028819	SRS19990702	SRA1775820	Schier Lab, Harvard University	Schier Lab, Harvard University	1	0.91179		0.15023		0.80359		0.54471		90		B		usable mapping rate	illumina	novaseq_era	full_length	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-12-26	Gastrula	Embryo	Whole Organism	All anatomical structures
29454	29454	SRR27352071	SRX23028819	SRS19990702	SRP480147	PRJNA1057153	Gene module reconstruction elucidates cellular differentiation processes and the regulatory logic of specialized secretion	GSE252032	Transcriptome Analysis	During differentiation cells become structurally and functionally specialized but comprehensive views of the underlying remodeling processes are elusive. Here we leverage scRNA seq developmental trajectories to reconstruct differentiation using two secretory tissues as a model system – the zebrafish notochord and hatch gland. First we present an approach MIMIR to integrate expression and functional similarities for gene module identification revealing dozens of gene modules representing known and newly associated differentiation processes and their temporal ordering. Second we focused on the unfolded protein response UPR transducer module to study how general versus cell type specific secretory functions are regulated. By profiling loss and gain of function embryos we found that the UPR transcription factors creb3l1 creb3l2 and xbp1 are master regulators of a general secretion program. creb3l1/creb3l2 additionally activate an extracellular matrix secretion program while xbp1 partners with bhlha15 to activate a gland specific secretion program. Our study offers an integrated approach for functional gene module identification and illustrates how transcription factors confer general and specialized cellular functions. Overall design: scRNA seq experiments were conducted to study the regulatory roles of the unfolded protein response UPR pathway transcription factors TFs during zebrafish embryogenesis. We focused on the four UPR TFs xbp1 atf6 creb3l1 and creb3l2 that are expressed during the early differentiation of the notochord and/or the hatch gland. We hypothesized that the UPR TFs regulate the secretory machinery genes in these two cell types. To identify the endogenous target genes of the UPR TFs we performed scRNA seq of UPR TF loss of function embryos at 12 hpf when UPR TFs and secretory pathway genes are normally highly expressed in the notochord and hatch gland. Loss of function embryos were generated by CRISPR mediated mutagenesis. Crispants were created by injecting Cas9 protein and guide …		pubmed:38234833;pubmed:39591963	creb3l2 N me 40pg	GSM7992596	source name:Whole embryo\|tissue:Whole embryo\|strain:TL/AB\|developmental stage:8 hpf\|genotype:creb3l2 N mis expression in xbp1 crispant\|geo loc name:missing\|collection date:missing	creb3l2 N me 40pg	The cellranger command line tool was used to map reads in the fastq files to reference transcriptomes with the "cellranger count" command For libraries that include xbp1 s misexpression ME E 5 to ME E 8 the reference transcriptome was modified: the mis expressed codon optimized xbp1 s sequence was appended to the reference transcriptome. Assembly: dr99 Supplementary files format and content: All processed data are output from the "cellranger count" command. barcodes.tsv.gz features.tsv.gz and matrix.mtx.gz can be collectively input into third party packages to allow users to wrangle the barcode feature matrix. The matrix contains only detected cell associated barcodes. Each element of the matrix is the number of UMIs associated with a feature row and a barcode column. The filtered feature bc matrix.h5 files contain the same detected cell associated feature and barcode information in HDF5 format.	Whole embryo	1 cell stage embryos were either injected with Cas9 and gRNA injected with mRNA or uninjected according to experimental conditions.	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer’s solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	Zebrafish embryos were collected at 1 cell stage and cultured in standard E3 medium in a 27°C incubator until desired stages.	tissue:Whole embryo\|strain:TL/AB\|developmental stage:8 hpf\|genotype:creb3l2 N mis expression in xbp1 crispant	GSM7992596	GSM7992596: creb3l2 N me 40pg; Danio rerio; RNA Seq	GSM7992596 r1	GSM7992596	1	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer's solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP480147	loader:fastq load.py	ME_D_6_S7_L004_R2_001.fastq.gz ME_D_6_S7_L004_R1_001.fastq.gz ME_D_6_S7_L004_I1_001.fastq.gz	fastq fastq fastq	21499800210.0	102380001.0	GSM7992596 r2	0:8 1:101 2:101	A:5731045724;C:3931487777;G:4014771792;T:7002424207;N:1030702	8	101	101		5731045724	3931487777	4014771792	7002424207	1030702	SRX23028819	SRS19990702	SRA1775820	Schier Lab, Harvard University	Schier Lab, Harvard University	2	0.0	0.91139	0.0	0.15189	1.0	0.80702		0.54085	101	101	T	B	mate1 technical by mapping diff	illumina	novaseq_era	full_length	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-12-26	Gastrula	Embryo	Whole Organism	All anatomical structures
29455	29455	SRR27352072	SRX23028818	SRS19990701	SRP480147	PRJNA1057153	Gene module reconstruction elucidates cellular differentiation processes and the regulatory logic of specialized secretion	GSE252032	Transcriptome Analysis	During differentiation cells become structurally and functionally specialized but comprehensive views of the underlying remodeling processes are elusive. Here we leverage scRNA seq developmental trajectories to reconstruct differentiation using two secretory tissues as a model system – the zebrafish notochord and hatch gland. First we present an approach MIMIR to integrate expression and functional similarities for gene module identification revealing dozens of gene modules representing known and newly associated differentiation processes and their temporal ordering. Second we focused on the unfolded protein response UPR transducer module to study how general versus cell type specific secretory functions are regulated. By profiling loss and gain of function embryos we found that the UPR transcription factors creb3l1 creb3l2 and xbp1 are master regulators of a general secretion program. creb3l1/creb3l2 additionally activate an extracellular matrix secretion program while xbp1 partners with bhlha15 to activate a gland specific secretion program. Our study offers an integrated approach for functional gene module identification and illustrates how transcription factors confer general and specialized cellular functions. Overall design: scRNA seq experiments were conducted to study the regulatory roles of the unfolded protein response UPR pathway transcription factors TFs during zebrafish embryogenesis. We focused on the four UPR TFs xbp1 atf6 creb3l1 and creb3l2 that are expressed during the early differentiation of the notochord and/or the hatch gland. We hypothesized that the UPR TFs regulate the secretory machinery genes in these two cell types. To identify the endogenous target genes of the UPR TFs we performed scRNA seq of UPR TF loss of function embryos at 12 hpf when UPR TFs and secretory pathway genes are normally highly expressed in the notochord and hatch gland. Loss of function embryos were generated by CRISPR mediated mutagenesis. Crispants were created by injecting Cas9 protein and guide …		pubmed:38234833;pubmed:39591963	creb3l1 N me 40pg	GSM7992595	source name:Whole embryo\|tissue:Whole embryo\|strain:TL/AB\|developmental stage:8 hpf\|genotype:creb3l1 N mis expression in xbp1 crispant\|geo loc name:missing\|collection date:missing	creb3l1 N me 40pg	The cellranger command line tool was used to map reads in the fastq files to reference transcriptomes with the "cellranger count" command For libraries that include xbp1 s misexpression ME E 5 to ME E 8 the reference transcriptome was modified: the mis expressed codon optimized xbp1 s sequence was appended to the reference transcriptome. Assembly: dr99 Supplementary files format and content: All processed data are output from the "cellranger count" command. barcodes.tsv.gz features.tsv.gz and matrix.mtx.gz can be collectively input into third party packages to allow users to wrangle the barcode feature matrix. The matrix contains only detected cell associated barcodes. Each element of the matrix is the number of UMIs associated with a feature row and a barcode column. The filtered feature bc matrix.h5 files contain the same detected cell associated feature and barcode information in HDF5 format.	Whole embryo	1 cell stage embryos were either injected with Cas9 and gRNA injected with mRNA or uninjected according to experimental conditions.	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer’s solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	Zebrafish embryos were collected at 1 cell stage and cultured in standard E3 medium in a 27°C incubator until desired stages.	tissue:Whole embryo\|strain:TL/AB\|developmental stage:8 hpf\|genotype:creb3l1 N mis expression in xbp1 crispant	GSM7992595	GSM7992595: creb3l1 N me 40pg; Danio rerio; RNA Seq	GSM7992595 r1	GSM7992595	1	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer's solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP480147	loader:fastq load.py	ME_D_5_S5_L001_I1_001.fastq.gz ME_D_5_S5_L001_R1_001.fastq.gz ME_D_5_S5_L001_R2_001.fastq.gz	fastq fastq fastq	39710838132.0	315165382.0	GSM7992595 r1	0:8 1:28 2:90	A:8134239938;C:5939509853;G:6667896902;T:7620537309;N:2700378	8	28	90		8134239938	5939509853	6667896902	7620537309	2700378	SRX23028818	SRS19990701	SRA1775820	Schier Lab, Harvard University	Schier Lab, Harvard University	1	0.91062		0.15355		0.80432		0.56447		90		B		usable mapping rate	illumina	novaseq_era	full_length	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-12-26	Gastrula	Embryo	Whole Organism	All anatomical structures
29456	29456	SRR27352073	SRX23028818	SRS19990701	SRP480147	PRJNA1057153	Gene module reconstruction elucidates cellular differentiation processes and the regulatory logic of specialized secretion	GSE252032	Transcriptome Analysis	During differentiation cells become structurally and functionally specialized but comprehensive views of the underlying remodeling processes are elusive. Here we leverage scRNA seq developmental trajectories to reconstruct differentiation using two secretory tissues as a model system – the zebrafish notochord and hatch gland. First we present an approach MIMIR to integrate expression and functional similarities for gene module identification revealing dozens of gene modules representing known and newly associated differentiation processes and their temporal ordering. Second we focused on the unfolded protein response UPR transducer module to study how general versus cell type specific secretory functions are regulated. By profiling loss and gain of function embryos we found that the UPR transcription factors creb3l1 creb3l2 and xbp1 are master regulators of a general secretion program. creb3l1/creb3l2 additionally activate an extracellular matrix secretion program while xbp1 partners with bhlha15 to activate a gland specific secretion program. Our study offers an integrated approach for functional gene module identification and illustrates how transcription factors confer general and specialized cellular functions. Overall design: scRNA seq experiments were conducted to study the regulatory roles of the unfolded protein response UPR pathway transcription factors TFs during zebrafish embryogenesis. We focused on the four UPR TFs xbp1 atf6 creb3l1 and creb3l2 that are expressed during the early differentiation of the notochord and/or the hatch gland. We hypothesized that the UPR TFs regulate the secretory machinery genes in these two cell types. To identify the endogenous target genes of the UPR TFs we performed scRNA seq of UPR TF loss of function embryos at 12 hpf when UPR TFs and secretory pathway genes are normally highly expressed in the notochord and hatch gland. Loss of function embryos were generated by CRISPR mediated mutagenesis. Crispants were created by injecting Cas9 protein and guide …		pubmed:38234833;pubmed:39591963	creb3l1 N me 40pg	GSM7992595	source name:Whole embryo\|tissue:Whole embryo\|strain:TL/AB\|developmental stage:8 hpf\|genotype:creb3l1 N mis expression in xbp1 crispant\|geo loc name:missing\|collection date:missing	creb3l1 N me 40pg	The cellranger command line tool was used to map reads in the fastq files to reference transcriptomes with the "cellranger count" command For libraries that include xbp1 s misexpression ME E 5 to ME E 8 the reference transcriptome was modified: the mis expressed codon optimized xbp1 s sequence was appended to the reference transcriptome. Assembly: dr99 Supplementary files format and content: All processed data are output from the "cellranger count" command. barcodes.tsv.gz features.tsv.gz and matrix.mtx.gz can be collectively input into third party packages to allow users to wrangle the barcode feature matrix. The matrix contains only detected cell associated barcodes. Each element of the matrix is the number of UMIs associated with a feature row and a barcode column. The filtered feature bc matrix.h5 files contain the same detected cell associated feature and barcode information in HDF5 format.	Whole embryo	1 cell stage embryos were either injected with Cas9 and gRNA injected with mRNA or uninjected according to experimental conditions.	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer’s solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	Zebrafish embryos were collected at 1 cell stage and cultured in standard E3 medium in a 27°C incubator until desired stages.	tissue:Whole embryo\|strain:TL/AB\|developmental stage:8 hpf\|genotype:creb3l1 N mis expression in xbp1 crispant	GSM7992595	GSM7992595: creb3l1 N me 40pg; Danio rerio; RNA Seq	GSM7992595 r1	GSM7992595	1	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer's solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP480147	loader:fastq load.py	ME_D_5_S6_L004_I1_001.fastq.gz ME_D_5_S6_L004_R1_001.fastq.gz ME_D_5_S6_L004_R2_001.fastq.gz	fastq fastq fastq	24091335030.0	114720643.0	GSM7992595 r2	0:8 1:101 2:101	A:6381365861;C:4422323917;G:4533780207;T:7834947754;N:1152147	8	101	101		6381365861	4422323917	4533780207	7834947754	1152147	SRX23028818	SRS19990701	SRA1775820	Schier Lab, Harvard University	Schier Lab, Harvard University	2	0.0	0.90836	0.0	0.1531	1.0	0.80718		0.56329	101	101	T	B	mate1 technical by mapping diff	illumina	novaseq_era	full_length	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-12-26	Gastrula	Embryo	Whole Organism	All anatomical structures
29473	29473	SRR27352090	SRX23028809	SRS19990692	SRP480147	PRJNA1057153	Gene module reconstruction elucidates cellular differentiation processes and the regulatory logic of specialized secretion	GSE252032	Transcriptome Analysis	During differentiation cells become structurally and functionally specialized but comprehensive views of the underlying remodeling processes are elusive. Here we leverage scRNA seq developmental trajectories to reconstruct differentiation using two secretory tissues as a model system – the zebrafish notochord and hatch gland. First we present an approach MIMIR to integrate expression and functional similarities for gene module identification revealing dozens of gene modules representing known and newly associated differentiation processes and their temporal ordering. Second we focused on the unfolded protein response UPR transducer module to study how general versus cell type specific secretory functions are regulated. By profiling loss and gain of function embryos we found that the UPR transcription factors creb3l1 creb3l2 and xbp1 are master regulators of a general secretion program. creb3l1/creb3l2 additionally activate an extracellular matrix secretion program while xbp1 partners with bhlha15 to activate a gland specific secretion program. Our study offers an integrated approach for functional gene module identification and illustrates how transcription factors confer general and specialized cellular functions. Overall design: scRNA seq experiments were conducted to study the regulatory roles of the unfolded protein response UPR pathway transcription factors TFs during zebrafish embryogenesis. We focused on the four UPR TFs xbp1 atf6 creb3l1 and creb3l2 that are expressed during the early differentiation of the notochord and/or the hatch gland. We hypothesized that the UPR TFs regulate the secretory machinery genes in these two cell types. To identify the endogenous target genes of the UPR TFs we performed scRNA seq of UPR TF loss of function embryos at 12 hpf when UPR TFs and secretory pathway genes are normally highly expressed in the notochord and hatch gland. Loss of function embryos were generated by CRISPR mediated mutagenesis. Crispants were created by injecting Cas9 protein and guide …		pubmed:38234833;pubmed:39591963	atf6 N me 40pg	GSM7992594	source name:Whole embryo\|tissue:Whole embryo\|strain:TL/AB\|developmental stage:8 hpf\|genotype:atf6 N mis expression in xbp1 crispant\|geo loc name:missing\|collection date:missing	atf6 N me 40pg	The cellranger command line tool was used to map reads in the fastq files to reference transcriptomes with the "cellranger count" command For libraries that include xbp1 s misexpression ME E 5 to ME E 8 the reference transcriptome was modified: the mis expressed codon optimized xbp1 s sequence was appended to the reference transcriptome. Assembly: dr99 Supplementary files format and content: All processed data are output from the "cellranger count" command. barcodes.tsv.gz features.tsv.gz and matrix.mtx.gz can be collectively input into third party packages to allow users to wrangle the barcode feature matrix. The matrix contains only detected cell associated barcodes. Each element of the matrix is the number of UMIs associated with a feature row and a barcode column. The filtered feature bc matrix.h5 files contain the same detected cell associated feature and barcode information in HDF5 format.	Whole embryo	1 cell stage embryos were either injected with Cas9 and gRNA injected with mRNA or uninjected according to experimental conditions.	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer’s solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	Zebrafish embryos were collected at 1 cell stage and cultured in standard E3 medium in a 27°C incubator until desired stages.	tissue:Whole embryo\|strain:TL/AB\|developmental stage:8 hpf\|genotype:atf6 N mis expression in xbp1 crispant	GSM7992594	GSM7992594: atf6 N me 40pg; Danio rerio; RNA Seq	GSM7992594 r1	GSM7992594	1	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer's solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP480147	loader:fastq load.py	ME_D_4_S7_L001_R2_001.fastq.gz ME_D_4_S7_L001_R1_001.fastq.gz ME_D_4_S7_L001_I1_001.fastq.gz	fastq fastq fastq	34201406232.0	271439732.0	GSM7992594 r1	0:8 1:28 2:90	A:6970137729;C:5129294511;G:5749174804;T:6578660562;N:2308274	8	28	90		6970137729	5129294511	5749174804	6578660562	2308274	SRX23028809	SRS19990692	SRA1775820	Schier Lab, Harvard University	Schier Lab, Harvard University	1	0.91553		0.16107		0.79835		0.5523		90		B		usable mapping rate	illumina	novaseq_era	full_length	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-12-26	Gastrula	Embryo	Whole Organism	All anatomical structures
29474	29474	SRR27352091	SRX23028809	SRS19990692	SRP480147	PRJNA1057153	Gene module reconstruction elucidates cellular differentiation processes and the regulatory logic of specialized secretion	GSE252032	Transcriptome Analysis	During differentiation cells become structurally and functionally specialized but comprehensive views of the underlying remodeling processes are elusive. Here we leverage scRNA seq developmental trajectories to reconstruct differentiation using two secretory tissues as a model system – the zebrafish notochord and hatch gland. First we present an approach MIMIR to integrate expression and functional similarities for gene module identification revealing dozens of gene modules representing known and newly associated differentiation processes and their temporal ordering. Second we focused on the unfolded protein response UPR transducer module to study how general versus cell type specific secretory functions are regulated. By profiling loss and gain of function embryos we found that the UPR transcription factors creb3l1 creb3l2 and xbp1 are master regulators of a general secretion program. creb3l1/creb3l2 additionally activate an extracellular matrix secretion program while xbp1 partners with bhlha15 to activate a gland specific secretion program. Our study offers an integrated approach for functional gene module identification and illustrates how transcription factors confer general and specialized cellular functions. Overall design: scRNA seq experiments were conducted to study the regulatory roles of the unfolded protein response UPR pathway transcription factors TFs during zebrafish embryogenesis. We focused on the four UPR TFs xbp1 atf6 creb3l1 and creb3l2 that are expressed during the early differentiation of the notochord and/or the hatch gland. We hypothesized that the UPR TFs regulate the secretory machinery genes in these two cell types. To identify the endogenous target genes of the UPR TFs we performed scRNA seq of UPR TF loss of function embryos at 12 hpf when UPR TFs and secretory pathway genes are normally highly expressed in the notochord and hatch gland. Loss of function embryos were generated by CRISPR mediated mutagenesis. Crispants were created by injecting Cas9 protein and guide …		pubmed:38234833;pubmed:39591963	atf6 N me 40pg	GSM7992594	source name:Whole embryo\|tissue:Whole embryo\|strain:TL/AB\|developmental stage:8 hpf\|genotype:atf6 N mis expression in xbp1 crispant\|geo loc name:missing\|collection date:missing	atf6 N me 40pg	The cellranger command line tool was used to map reads in the fastq files to reference transcriptomes with the "cellranger count" command For libraries that include xbp1 s misexpression ME E 5 to ME E 8 the reference transcriptome was modified: the mis expressed codon optimized xbp1 s sequence was appended to the reference transcriptome. Assembly: dr99 Supplementary files format and content: All processed data are output from the "cellranger count" command. barcodes.tsv.gz features.tsv.gz and matrix.mtx.gz can be collectively input into third party packages to allow users to wrangle the barcode feature matrix. The matrix contains only detected cell associated barcodes. Each element of the matrix is the number of UMIs associated with a feature row and a barcode column. The filtered feature bc matrix.h5 files contain the same detected cell associated feature and barcode information in HDF5 format.	Whole embryo	1 cell stage embryos were either injected with Cas9 and gRNA injected with mRNA or uninjected according to experimental conditions.	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer’s solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	Zebrafish embryos were collected at 1 cell stage and cultured in standard E3 medium in a 27°C incubator until desired stages.	tissue:Whole embryo\|strain:TL/AB\|developmental stage:8 hpf\|genotype:atf6 N mis expression in xbp1 crispant	GSM7992594	GSM7992594: atf6 N me 40pg; Danio rerio; RNA Seq	GSM7992594 r1	GSM7992594	1	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer's solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP480147	loader:fastq load.py	ME_D_4_S8_L004_R2_001.fastq.gz ME_D_4_S8_L004_R1_001.fastq.gz ME_D_4_S8_L004_I1_001.fastq.gz	fastq fastq fastq	22385290830.0	106596623.0	GSM7992594 r2	0:8 1:101 2:101	A:5920329288;C:4138677002;G:4227668821;T:7244770032;N:1072703	8	101	101		5920329288	4138677002	4227668821	7244770032	1072703	SRX23028809	SRS19990692	SRA1775820	Schier Lab, Harvard University	Schier Lab, Harvard University	2	0.0	0.91524	0.0	0.16081	1.0	0.80113		0.55582	101	101	T	B	mate1 technical by mapping diff	illumina	novaseq_era	full_length	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-12-26	Gastrula	Embryo	Whole Organism	All anatomical structures
29475	29475	SRR27352092	SRX23028808	SRS19990691	SRP480147	PRJNA1057153	Gene module reconstruction elucidates cellular differentiation processes and the regulatory logic of specialized secretion	GSE252032	Transcriptome Analysis	During differentiation cells become structurally and functionally specialized but comprehensive views of the underlying remodeling processes are elusive. Here we leverage scRNA seq developmental trajectories to reconstruct differentiation using two secretory tissues as a model system – the zebrafish notochord and hatch gland. First we present an approach MIMIR to integrate expression and functional similarities for gene module identification revealing dozens of gene modules representing known and newly associated differentiation processes and their temporal ordering. Second we focused on the unfolded protein response UPR transducer module to study how general versus cell type specific secretory functions are regulated. By profiling loss and gain of function embryos we found that the UPR transcription factors creb3l1 creb3l2 and xbp1 are master regulators of a general secretion program. creb3l1/creb3l2 additionally activate an extracellular matrix secretion program while xbp1 partners with bhlha15 to activate a gland specific secretion program. Our study offers an integrated approach for functional gene module identification and illustrates how transcription factors confer general and specialized cellular functions. Overall design: scRNA seq experiments were conducted to study the regulatory roles of the unfolded protein response UPR pathway transcription factors TFs during zebrafish embryogenesis. We focused on the four UPR TFs xbp1 atf6 creb3l1 and creb3l2 that are expressed during the early differentiation of the notochord and/or the hatch gland. We hypothesized that the UPR TFs regulate the secretory machinery genes in these two cell types. To identify the endogenous target genes of the UPR TFs we performed scRNA seq of UPR TF loss of function embryos at 12 hpf when UPR TFs and secretory pathway genes are normally highly expressed in the notochord and hatch gland. Loss of function embryos were generated by CRISPR mediated mutagenesis. Crispants were created by injecting Cas9 protein and guide …		pubmed:38234833;pubmed:39591963	mCherry me 40pg	GSM7992593	source name:Whole embryo\|tissue:Whole embryo\|strain:TL/AB\|developmental stage:8 hpf\|genotype:NLS mCherry mis expression in xbp1 crispant\|geo loc name:missing\|collection date:missing	mCherry me 40pg	The cellranger command line tool was used to map reads in the fastq files to reference transcriptomes with the "cellranger count" command For libraries that include xbp1 s misexpression ME E 5 to ME E 8 the reference transcriptome was modified: the mis expressed codon optimized xbp1 s sequence was appended to the reference transcriptome. Assembly: dr99 Supplementary files format and content: All processed data are output from the "cellranger count" command. barcodes.tsv.gz features.tsv.gz and matrix.mtx.gz can be collectively input into third party packages to allow users to wrangle the barcode feature matrix. The matrix contains only detected cell associated barcodes. Each element of the matrix is the number of UMIs associated with a feature row and a barcode column. The filtered feature bc matrix.h5 files contain the same detected cell associated feature and barcode information in HDF5 format.	Whole embryo	1 cell stage embryos were either injected with Cas9 and gRNA injected with mRNA or uninjected according to experimental conditions.	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer’s solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	Zebrafish embryos were collected at 1 cell stage and cultured in standard E3 medium in a 27°C incubator until desired stages.	tissue:Whole embryo\|strain:TL/AB\|developmental stage:8 hpf\|genotype:NLS mCherry mis expression in xbp1 crispant	GSM7992593	GSM7992593: mCherry me 40pg; Danio rerio; RNA Seq	GSM7992593 r1	GSM7992593	1	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer's solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP480147	loader:fastq load.py	ME_D_3_S4_L001_R2_001.fastq.gz ME_D_3_S4_L001_R1_001.fastq.gz ME_D_3_S4_L001_I1_001.fastq.gz	fastq fastq fastq	31946333832.0	253542332.0	GSM7992593 r1	0:8 1:28 2:90	A:6560614856;C:4781373893;G:5380587448;T:6094065607;N:2168076	8	28	90		6560614856	4781373893	5380587448	6094065607	2168076	SRX23028808	SRS19990691	SRA1775820	Schier Lab, Harvard University	Schier Lab, Harvard University	1	0.90476		0.15614		0.81391		0.56731		90		B		usable mapping rate	illumina	novaseq_era	full_length	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-12-26	Gastrula	Embryo	Whole Organism	All anatomical structures
29476	29476	SRR27352093	SRX23028808	SRS19990691	SRP480147	PRJNA1057153	Gene module reconstruction elucidates cellular differentiation processes and the regulatory logic of specialized secretion	GSE252032	Transcriptome Analysis	During differentiation cells become structurally and functionally specialized but comprehensive views of the underlying remodeling processes are elusive. Here we leverage scRNA seq developmental trajectories to reconstruct differentiation using two secretory tissues as a model system – the zebrafish notochord and hatch gland. First we present an approach MIMIR to integrate expression and functional similarities for gene module identification revealing dozens of gene modules representing known and newly associated differentiation processes and their temporal ordering. Second we focused on the unfolded protein response UPR transducer module to study how general versus cell type specific secretory functions are regulated. By profiling loss and gain of function embryos we found that the UPR transcription factors creb3l1 creb3l2 and xbp1 are master regulators of a general secretion program. creb3l1/creb3l2 additionally activate an extracellular matrix secretion program while xbp1 partners with bhlha15 to activate a gland specific secretion program. Our study offers an integrated approach for functional gene module identification and illustrates how transcription factors confer general and specialized cellular functions. Overall design: scRNA seq experiments were conducted to study the regulatory roles of the unfolded protein response UPR pathway transcription factors TFs during zebrafish embryogenesis. We focused on the four UPR TFs xbp1 atf6 creb3l1 and creb3l2 that are expressed during the early differentiation of the notochord and/or the hatch gland. We hypothesized that the UPR TFs regulate the secretory machinery genes in these two cell types. To identify the endogenous target genes of the UPR TFs we performed scRNA seq of UPR TF loss of function embryos at 12 hpf when UPR TFs and secretory pathway genes are normally highly expressed in the notochord and hatch gland. Loss of function embryos were generated by CRISPR mediated mutagenesis. Crispants were created by injecting Cas9 protein and guide …		pubmed:38234833;pubmed:39591963	mCherry me 40pg	GSM7992593	source name:Whole embryo\|tissue:Whole embryo\|strain:TL/AB\|developmental stage:8 hpf\|genotype:NLS mCherry mis expression in xbp1 crispant\|geo loc name:missing\|collection date:missing	mCherry me 40pg	The cellranger command line tool was used to map reads in the fastq files to reference transcriptomes with the "cellranger count" command For libraries that include xbp1 s misexpression ME E 5 to ME E 8 the reference transcriptome was modified: the mis expressed codon optimized xbp1 s sequence was appended to the reference transcriptome. Assembly: dr99 Supplementary files format and content: All processed data are output from the "cellranger count" command. barcodes.tsv.gz features.tsv.gz and matrix.mtx.gz can be collectively input into third party packages to allow users to wrangle the barcode feature matrix. The matrix contains only detected cell associated barcodes. Each element of the matrix is the number of UMIs associated with a feature row and a barcode column. The filtered feature bc matrix.h5 files contain the same detected cell associated feature and barcode information in HDF5 format.	Whole embryo	1 cell stage embryos were either injected with Cas9 and gRNA injected with mRNA or uninjected according to experimental conditions.	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer’s solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	Zebrafish embryos were collected at 1 cell stage and cultured in standard E3 medium in a 27°C incubator until desired stages.	tissue:Whole embryo\|strain:TL/AB\|developmental stage:8 hpf\|genotype:NLS mCherry mis expression in xbp1 crispant	GSM7992593	GSM7992593: mCherry me 40pg; Danio rerio; RNA Seq	GSM7992593 r1	GSM7992593	1	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer's solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP480147	loader:fastq load.py	ME_D_3_S5_L004_I1_001.fastq.gz ME_D_3_S5_L004_R1_001.fastq.gz ME_D_3_S5_L004_R2_001.fastq.gz	fastq fastq fastq	23152132290.0	110248249.0	GSM7992593 r2	0:8 1:101 2:101	A:6128844846;C:4261101648;G:4373973829;T:7505119299;N:1106676	8	101	101		6128844846	4261101648	4373973829	7505119299	1106676	SRX23028808	SRS19990691	SRA1775820	Schier Lab, Harvard University	Schier Lab, Harvard University	2	0.0	0.90407	0.0	0.15893	1.0	0.81734		0.56376	101	101	T	B	mate1 technical by mapping diff	illumina	novaseq_era	full_length	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-12-26	Gastrula	Embryo	Whole Organism	All anatomical structures
29477	29477	SRR27352094	SRX23028807	SRS19990690	SRP480147	PRJNA1057153	Gene module reconstruction elucidates cellular differentiation processes and the regulatory logic of specialized secretion	GSE252032	Transcriptome Analysis	During differentiation cells become structurally and functionally specialized but comprehensive views of the underlying remodeling processes are elusive. Here we leverage scRNA seq developmental trajectories to reconstruct differentiation using two secretory tissues as a model system – the zebrafish notochord and hatch gland. First we present an approach MIMIR to integrate expression and functional similarities for gene module identification revealing dozens of gene modules representing known and newly associated differentiation processes and their temporal ordering. Second we focused on the unfolded protein response UPR transducer module to study how general versus cell type specific secretory functions are regulated. By profiling loss and gain of function embryos we found that the UPR transcription factors creb3l1 creb3l2 and xbp1 are master regulators of a general secretion program. creb3l1/creb3l2 additionally activate an extracellular matrix secretion program while xbp1 partners with bhlha15 to activate a gland specific secretion program. Our study offers an integrated approach for functional gene module identification and illustrates how transcription factors confer general and specialized cellular functions. Overall design: scRNA seq experiments were conducted to study the regulatory roles of the unfolded protein response UPR pathway transcription factors TFs during zebrafish embryogenesis. We focused on the four UPR TFs xbp1 atf6 creb3l1 and creb3l2 that are expressed during the early differentiation of the notochord and/or the hatch gland. We hypothesized that the UPR TFs regulate the secretory machinery genes in these two cell types. To identify the endogenous target genes of the UPR TFs we performed scRNA seq of UPR TF loss of function embryos at 12 hpf when UPR TFs and secretory pathway genes are normally highly expressed in the notochord and hatch gland. Loss of function embryos were generated by CRISPR mediated mutagenesis. Crispants were created by injecting Cas9 protein and guide …		pubmed:38234833;pubmed:39591963	creb3l2 full me 40pg	GSM7992592	source name:Whole embryo\|tissue:Whole embryo\|strain:TL/AB\|developmental stage:8 hpf\|genotype:creb3l2 full length mis exprerssion\|geo loc name:missing\|collection date:missing	creb3l2 full me 40pg	The cellranger command line tool was used to map reads in the fastq files to reference transcriptomes with the "cellranger count" command For libraries that include xbp1 s misexpression ME E 5 to ME E 8 the reference transcriptome was modified: the mis expressed codon optimized xbp1 s sequence was appended to the reference transcriptome. Assembly: dr99 Supplementary files format and content: All processed data are output from the "cellranger count" command. barcodes.tsv.gz features.tsv.gz and matrix.mtx.gz can be collectively input into third party packages to allow users to wrangle the barcode feature matrix. The matrix contains only detected cell associated barcodes. Each element of the matrix is the number of UMIs associated with a feature row and a barcode column. The filtered feature bc matrix.h5 files contain the same detected cell associated feature and barcode information in HDF5 format.	Whole embryo	1 cell stage embryos were either injected with Cas9 and gRNA injected with mRNA or uninjected according to experimental conditions.	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer’s solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	Zebrafish embryos were collected at 1 cell stage and cultured in standard E3 medium in a 27°C incubator until desired stages.	tissue:Whole embryo\|strain:TL/AB\|developmental stage:8 hpf\|genotype:creb3l2 full length mis exprerssion	GSM7992592	GSM7992592: creb3l2 full me 40pg; Danio rerio; RNA Seq	GSM7992592 r1	GSM7992592	1	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer's solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP480147	loader:fastq load.py	ME_D_2_S13_L001_I1_001.fastq.gz ME_D_2_S13_L001_R1_001.fastq.gz ME_D_2_S13_L001_R2_001.fastq.gz	fastq fastq fastq	15222166848.0	120810848.0	GSM7992592 r1	0:8 1:28 2:90	A:3076061131;C:2328534823;G:2595273328;T:2872069911;N:1037127	8	28	90		3076061131	2328534823	2595273328	2872069911	1037127	SRX23028807	SRS19990690	SRA1775820	Schier Lab, Harvard University	Schier Lab, Harvard University	1	0.91719		0.16191		0.80837		0.55344		90		B		usable mapping rate	illumina	novaseq_era	full_length	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-12-26	Gastrula	Embryo	Whole Organism	All anatomical structures
29478	29478	SRR27352095	SRX23028807	SRS19990690	SRP480147	PRJNA1057153	Gene module reconstruction elucidates cellular differentiation processes and the regulatory logic of specialized secretion	GSE252032	Transcriptome Analysis	During differentiation cells become structurally and functionally specialized but comprehensive views of the underlying remodeling processes are elusive. Here we leverage scRNA seq developmental trajectories to reconstruct differentiation using two secretory tissues as a model system – the zebrafish notochord and hatch gland. First we present an approach MIMIR to integrate expression and functional similarities for gene module identification revealing dozens of gene modules representing known and newly associated differentiation processes and their temporal ordering. Second we focused on the unfolded protein response UPR transducer module to study how general versus cell type specific secretory functions are regulated. By profiling loss and gain of function embryos we found that the UPR transcription factors creb3l1 creb3l2 and xbp1 are master regulators of a general secretion program. creb3l1/creb3l2 additionally activate an extracellular matrix secretion program while xbp1 partners with bhlha15 to activate a gland specific secretion program. Our study offers an integrated approach for functional gene module identification and illustrates how transcription factors confer general and specialized cellular functions. Overall design: scRNA seq experiments were conducted to study the regulatory roles of the unfolded protein response UPR pathway transcription factors TFs during zebrafish embryogenesis. We focused on the four UPR TFs xbp1 atf6 creb3l1 and creb3l2 that are expressed during the early differentiation of the notochord and/or the hatch gland. We hypothesized that the UPR TFs regulate the secretory machinery genes in these two cell types. To identify the endogenous target genes of the UPR TFs we performed scRNA seq of UPR TF loss of function embryos at 12 hpf when UPR TFs and secretory pathway genes are normally highly expressed in the notochord and hatch gland. Loss of function embryos were generated by CRISPR mediated mutagenesis. Crispants were created by injecting Cas9 protein and guide …		pubmed:38234833;pubmed:39591963	creb3l2 full me 40pg	GSM7992592	source name:Whole embryo\|tissue:Whole embryo\|strain:TL/AB\|developmental stage:8 hpf\|genotype:creb3l2 full length mis exprerssion\|geo loc name:missing\|collection date:missing	creb3l2 full me 40pg	The cellranger command line tool was used to map reads in the fastq files to reference transcriptomes with the "cellranger count" command For libraries that include xbp1 s misexpression ME E 5 to ME E 8 the reference transcriptome was modified: the mis expressed codon optimized xbp1 s sequence was appended to the reference transcriptome. Assembly: dr99 Supplementary files format and content: All processed data are output from the "cellranger count" command. barcodes.tsv.gz features.tsv.gz and matrix.mtx.gz can be collectively input into third party packages to allow users to wrangle the barcode feature matrix. The matrix contains only detected cell associated barcodes. Each element of the matrix is the number of UMIs associated with a feature row and a barcode column. The filtered feature bc matrix.h5 files contain the same detected cell associated feature and barcode information in HDF5 format.	Whole embryo	1 cell stage embryos were either injected with Cas9 and gRNA injected with mRNA or uninjected according to experimental conditions.	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer’s solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	Zebrafish embryos were collected at 1 cell stage and cultured in standard E3 medium in a 27°C incubator until desired stages.	tissue:Whole embryo\|strain:TL/AB\|developmental stage:8 hpf\|genotype:creb3l2 full length mis exprerssion	GSM7992592	GSM7992592: creb3l2 full me 40pg; Danio rerio; RNA Seq	GSM7992592 r1	GSM7992592	1	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer's solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP480147	loader:fastq load.py	ME_D_2_S14_L004_I1_001.fastq.gz ME_D_2_S14_L004_R1_001.fastq.gz ME_D_2_S14_L004_R2_001.fastq.gz	fastq fastq fastq	20633376540.0	98254174.0	GSM7992592 r2	0:8 1:101 2:101	A:5431963590;C:3898811025;G:3951937782;T:6563643256;N:987495	8	101	101		5431963590	3898811025	3951937782	6563643256	987495	SRX23028807	SRS19990690	SRA1775820	Schier Lab, Harvard University	Schier Lab, Harvard University	2	0.0	0.91717	0.0	0.16142	1.0	0.81063		0.52718	101	101	T	B	mate1 technical by mapping diff	illumina	novaseq_era	full_length	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-12-26	Gastrula	Embryo	Whole Organism	All anatomical structures
29479	29479	SRR27352096	SRX23028806	SRS19990689	SRP480147	PRJNA1057153	Gene module reconstruction elucidates cellular differentiation processes and the regulatory logic of specialized secretion	GSE252032	Transcriptome Analysis	During differentiation cells become structurally and functionally specialized but comprehensive views of the underlying remodeling processes are elusive. Here we leverage scRNA seq developmental trajectories to reconstruct differentiation using two secretory tissues as a model system – the zebrafish notochord and hatch gland. First we present an approach MIMIR to integrate expression and functional similarities for gene module identification revealing dozens of gene modules representing known and newly associated differentiation processes and their temporal ordering. Second we focused on the unfolded protein response UPR transducer module to study how general versus cell type specific secretory functions are regulated. By profiling loss and gain of function embryos we found that the UPR transcription factors creb3l1 creb3l2 and xbp1 are master regulators of a general secretion program. creb3l1/creb3l2 additionally activate an extracellular matrix secretion program while xbp1 partners with bhlha15 to activate a gland specific secretion program. Our study offers an integrated approach for functional gene module identification and illustrates how transcription factors confer general and specialized cellular functions. Overall design: scRNA seq experiments were conducted to study the regulatory roles of the unfolded protein response UPR pathway transcription factors TFs during zebrafish embryogenesis. We focused on the four UPR TFs xbp1 atf6 creb3l1 and creb3l2 that are expressed during the early differentiation of the notochord and/or the hatch gland. We hypothesized that the UPR TFs regulate the secretory machinery genes in these two cell types. To identify the endogenous target genes of the UPR TFs we performed scRNA seq of UPR TF loss of function embryos at 12 hpf when UPR TFs and secretory pathway genes are normally highly expressed in the notochord and hatch gland. Loss of function embryos were generated by CRISPR mediated mutagenesis. Crispants were created by injecting Cas9 protein and guide …		pubmed:38234833;pubmed:39591963	mCherry me 125pg	GSM7992591	source name:Whole embryo\|tissue:Whole embryo\|strain:TL/AB\|developmental stage:8 hpf\|genotype:nls mCherry mis expression\|geo loc name:missing\|collection date:missing	mCherry me 125pg	The cellranger command line tool was used to map reads in the fastq files to reference transcriptomes with the "cellranger count" command For libraries that include xbp1 s misexpression ME E 5 to ME E 8 the reference transcriptome was modified: the mis expressed codon optimized xbp1 s sequence was appended to the reference transcriptome. Assembly: dr99 Supplementary files format and content: All processed data are output from the "cellranger count" command. barcodes.tsv.gz features.tsv.gz and matrix.mtx.gz can be collectively input into third party packages to allow users to wrangle the barcode feature matrix. The matrix contains only detected cell associated barcodes. Each element of the matrix is the number of UMIs associated with a feature row and a barcode column. The filtered feature bc matrix.h5 files contain the same detected cell associated feature and barcode information in HDF5 format.	Whole embryo	1 cell stage embryos were either injected with Cas9 and gRNA injected with mRNA or uninjected according to experimental conditions.	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer’s solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	Zebrafish embryos were collected at 1 cell stage and cultured in standard E3 medium in a 27°C incubator until desired stages.	tissue:Whole embryo\|strain:TL/AB\|developmental stage:8 hpf\|genotype:nls mCherry mis expression	GSM7992591	GSM7992591: mCherry me 125pg; Danio rerio; RNA Seq	GSM7992591 r1	GSM7992591	1	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer's solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP480147	loader:fastq load.py	ME_D_1_S11_L001_R2_001.fastq.gz ME_D_1_S11_L001_R1_001.fastq.gz ME_D_1_S11_L001_I1_001.fastq.gz	fastq fastq fastq	7592631102.0	60258977.0	GSM7992591 r1	0:8 1:28 2:90	A:1549191430;C:1138023380;G:1260358863;T:1475225062;N:509195	8	28	90		1549191430	1138023380	1260358863	1475225062	509195	SRX23028806	SRS19990689	SRA1775820	Schier Lab, Harvard University	Schier Lab, Harvard University	1	0.91893		0.15048		0.80517		0.54261		90		B		usable mapping rate	illumina	novaseq_era	full_length	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-12-26	Gastrula	Embryo	Whole Organism	All anatomical structures
29480	29480	SRR27352097	SRX23028806	SRS19990689	SRP480147	PRJNA1057153	Gene module reconstruction elucidates cellular differentiation processes and the regulatory logic of specialized secretion	GSE252032	Transcriptome Analysis	During differentiation cells become structurally and functionally specialized but comprehensive views of the underlying remodeling processes are elusive. Here we leverage scRNA seq developmental trajectories to reconstruct differentiation using two secretory tissues as a model system – the zebrafish notochord and hatch gland. First we present an approach MIMIR to integrate expression and functional similarities for gene module identification revealing dozens of gene modules representing known and newly associated differentiation processes and their temporal ordering. Second we focused on the unfolded protein response UPR transducer module to study how general versus cell type specific secretory functions are regulated. By profiling loss and gain of function embryos we found that the UPR transcription factors creb3l1 creb3l2 and xbp1 are master regulators of a general secretion program. creb3l1/creb3l2 additionally activate an extracellular matrix secretion program while xbp1 partners with bhlha15 to activate a gland specific secretion program. Our study offers an integrated approach for functional gene module identification and illustrates how transcription factors confer general and specialized cellular functions. Overall design: scRNA seq experiments were conducted to study the regulatory roles of the unfolded protein response UPR pathway transcription factors TFs during zebrafish embryogenesis. We focused on the four UPR TFs xbp1 atf6 creb3l1 and creb3l2 that are expressed during the early differentiation of the notochord and/or the hatch gland. We hypothesized that the UPR TFs regulate the secretory machinery genes in these two cell types. To identify the endogenous target genes of the UPR TFs we performed scRNA seq of UPR TF loss of function embryos at 12 hpf when UPR TFs and secretory pathway genes are normally highly expressed in the notochord and hatch gland. Loss of function embryos were generated by CRISPR mediated mutagenesis. Crispants were created by injecting Cas9 protein and guide …		pubmed:38234833;pubmed:39591963	mCherry me 125pg	GSM7992591	source name:Whole embryo\|tissue:Whole embryo\|strain:TL/AB\|developmental stage:8 hpf\|genotype:nls mCherry mis expression\|geo loc name:missing\|collection date:missing	mCherry me 125pg	The cellranger command line tool was used to map reads in the fastq files to reference transcriptomes with the "cellranger count" command For libraries that include xbp1 s misexpression ME E 5 to ME E 8 the reference transcriptome was modified: the mis expressed codon optimized xbp1 s sequence was appended to the reference transcriptome. Assembly: dr99 Supplementary files format and content: All processed data are output from the "cellranger count" command. barcodes.tsv.gz features.tsv.gz and matrix.mtx.gz can be collectively input into third party packages to allow users to wrangle the barcode feature matrix. The matrix contains only detected cell associated barcodes. Each element of the matrix is the number of UMIs associated with a feature row and a barcode column. The filtered feature bc matrix.h5 files contain the same detected cell associated feature and barcode information in HDF5 format.	Whole embryo	1 cell stage embryos were either injected with Cas9 and gRNA injected with mRNA or uninjected according to experimental conditions.	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer’s solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1	Zebrafish embryos were collected at 1 cell stage and cultured in standard E3 medium in a 27°C incubator until desired stages.	tissue:Whole embryo\|strain:TL/AB\|developmental stage:8 hpf\|genotype:nls mCherry mis expression	GSM7992591	GSM7992591: mCherry me 125pg; Danio rerio; RNA Seq	GSM7992591 r1	GSM7992591	1	At desired developmental stages 8hpf or 12hpf approximately 30 embryos per sample were de chonrionated with pronase. For libraries prepared with 10x chromium Single Cell three prime V3 chemistry embryos for each condition were transferred into a 2ml eppendorf tube containing ice cold deyolking buffer buffer 55 mM NaCl 1.8 mM KCl 1.25 mM NaHCO3. Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer 10 mM Tris pH 8.5 110 mM NaCl 3.5 mM KCl 2.7 mM CaCl2 was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM gibco 11594426 with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell three prime V3.1 chemistry several modifications were made to the dissociation protocol described above. Briefly post being transferred to 2ml Eppendorf tubes embryos were first incubated in a protease solution 10 mg/ml BI protease [Sigma P5380] 125 U/ml DNaseI 2.5 mM EDTA in DPBS on ice for 4min. Embryos were then washed with a stop solution 30% FBS 0.875 mM CaCl2 in DPBS and gently triturated by pipetting in Ringer's solution. Centrifuging resuspending and filtering steps were then performed as in the previous protocol but with the Ringer's solution used as the wash buffer. Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell three prime Reagent Kits V3 and V3.1		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP480147	loader:fastq load.py	ME_D_1_S12_L004_I1_001.fastq.gz ME_D_1_S12_L004_R1_001.fastq.gz ME_D_1_S12_L004_R2_001.fastq.gz	fastq fastq fastq	22469033160.0	106995396.0	GSM7992591 r2	0:8 1:101 2:101	A:5978154538;C:4132913966;G:4202172487;T:7298755208;N:1073793	8	101	101		5978154538	4132913966	4202172487	7298755208	1073793	SRX23028806	SRS19990689	SRA1775820	Schier Lab, Harvard University	Schier Lab, Harvard University	2	0.0	0.91624	0.0	0.15006	1.0	0.80643		0.54121	101	101	T	B	mate1 technical by mapping diff	illumina	novaseq_era	full_length	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-12-26	Gastrula	Embryo	Whole Organism	All anatomical structures
32134	32134	SRR29020075	SRX24545646	SRS21290023	SRP507567	PRJNA1111448	rbm24a is an organizer component of germ plasm to determine germ cell fate	GSE267406	Transcriptome Analysis	The formation of germ cells is a critical issue for the continuation of species. A large group of animals follow a preformation strategy to generate their primordial germ cells PGCs. They produce a set of localized maternal mRNAs and proteins to form phase separated germ plasm that functions as the PGC determinants but the mechanisms underlying the assembly of germ plasm is poorly understood. This study identifies Rbm24a as an enssential localized germ plasm protein component that controls the formation of large and functional germ plasm granules. Rbm24a is complexed with Buc and interacts with germ plasm mRNAs which determines the specific grasp of germ plasm mRNAs into the phase separated aggregates. Rbm24a absent granules fail to undergo kinesin dependent transport towards the cleavage furrows where small particles fuse into large ones. The loss of maternal rbm24a causes the complete degradation of germ plasm components and the disappearance of PGCs resulting in totally sterile animals. Our work establishes that Rbm24 is a critical nucleating organizer component of germ plasm highlighting an emerging common mechanism to read and recruit RNA component into phase separated condensates. Overall design: We performed single cell RNA seq scRNA seq for shield stage embryos to compare gene expression between Mrbm24a and sibling embryos. Another purpose of this omic analysis is to examine possible cell populations that can be affected by the loss of maternal Rbm24a.			Zebrafish scRNAseq shield sibling 2	GSM8265296	source name:whole embryo\|tissue:whole embryo\|cell line:shield stage\|cell type:embryonic cell\|genotype:wild type\|geo loc name:missing\|collection date:missing	Zebrafish scRNAseq shield sibling 2	To remove any remaining biochemical reagents and primers from the post GEM reaction mixture silane magnetic beads were employed. The full length barcoded cDNAs were subsequently amplified by PCR to generate sufficient mass for library construction. During GEM incubation the molecules had R1 Read 1 primer sequence added to them. P5 P7 a sample index and R2 Read 2 primer sequence were added during library construction through processes such as End Repair A tailing Adaptor Ligation and PCR. The final libraries contained the P5 and P7 primers required for Illumina bridge amplification. The Single Cell three prime Protocol generated Illumina ready sequencing libraries. Each Single Cell three prime Library consisted of standard Illumina paired end constructs that began and ended with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI were encoded in Read 1 while Read 2 was utilized to sequence the cDNA fragment. Sample index sequences were incorporated as the i7 index read. Read 1 and Read 2 corresponded to the standard Illumina® sequencing primer sites used in paired end sequencing. Assembly: GRCz10 Supplementary files format and content: Tab separated values files and matrix files	whole embryo		For the preparation of single cell suspensions a total of thirty three mutant embryos of Mrbm24a or wild type embryos at the shield stage were collected. These cellular suspensions were then loaded onto a 10X Genomics GemCode Single cell instrument which generates single cell Gel Bead In EMulsion GEMs. Libraries were generated and sequenced from the cDNAs using Chromium Next GEM Single Cell three prime Reagent Kits v3.1. Upon dissolution of the Gel Bead within a GEM primers containing an Illumina® R1 sequence Read 1 sequencing primer a 16 nt 10x Barcode a 10 nt Unique Molecular Identifier UMI and a poly dT primer sequence were released. These primers were mixed with the cell lysate and Master Mix. Full length barcoded cDNAs were then reverse transcribed from poly adenylated mRNA	Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C	tissue:whole embryo\|cell line:shield stage\|cell type:embryonic cell\|genotype:wild type	GSM8265296	GSM8265296: Zebrafish scRNAseq shield sibling 2; Danio rerio; RNA Seq	GSM8265296 r1	GSM8265296	1	For the preparation of single cell suspensions a total of thirty three mutant embryos of Mrbm24a or wild type embryos at the shield stage were collected. These cellular suspensions were then loaded onto a 10X Genomics GemCode Single cell instrument which generates single cell Gel Bead In EMulsion GEMs. Libraries were generated and sequenced from the cDNAs using Chromium Next GEM Single Cell three prime Reagent Kits v3.1. Upon dissolution of the Gel Bead within a GEM primers containing an Illumina® R1 sequence Read 1 sequencing primer a 16 nt 10x Barcode a 10 nt Unique Molecular Identifier UMI and a poly dT primer sequence were released. These primers were mixed with the cell lysate and Master Mix. Full length barcoded cDNAs were then reverse transcribed from poly adenylated mRNA		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP507567		J23090498_R2_001.fastq.gz J23090498_R1_001.fastq.gz	fastq fastq	106757315400.0	355857718.0	GSM8265296 r1	0:150 1:150	A:33082219289;C:20599674613;G:20857073591;T:32217553311;N:794596	150	150			33082219289	20599674613	20857073591	32217553311	794596	SRX24545646	SRS21290023	SRA1866413	shao ming lab, school of life sciences, shandong university	shao ming lab, school of life sciences, shandong university	2	0.2631	0.91686	0.0934	0.16341	0.98742	0.78798	0.70164	0.53109	150	150	T	B	mate1 technical by mapping diff	illumina	nextseq	3prime	random_priming	unknown	sc	single_cell_droplet	10x	China	2024-05-14	Gastrula	Embryo	Whole Organism	All anatomical structures
32135	32135	SRR29020076	SRX24545645	SRS21290022	SRP507567	PRJNA1111448	rbm24a is an organizer component of germ plasm to determine germ cell fate	GSE267406	Transcriptome Analysis	The formation of germ cells is a critical issue for the continuation of species. A large group of animals follow a preformation strategy to generate their primordial germ cells PGCs. They produce a set of localized maternal mRNAs and proteins to form phase separated germ plasm that functions as the PGC determinants but the mechanisms underlying the assembly of germ plasm is poorly understood. This study identifies Rbm24a as an enssential localized germ plasm protein component that controls the formation of large and functional germ plasm granules. Rbm24a is complexed with Buc and interacts with germ plasm mRNAs which determines the specific grasp of germ plasm mRNAs into the phase separated aggregates. Rbm24a absent granules fail to undergo kinesin dependent transport towards the cleavage furrows where small particles fuse into large ones. The loss of maternal rbm24a causes the complete degradation of germ plasm components and the disappearance of PGCs resulting in totally sterile animals. Our work establishes that Rbm24 is a critical nucleating organizer component of germ plasm highlighting an emerging common mechanism to read and recruit RNA component into phase separated condensates. Overall design: We performed single cell RNA seq scRNA seq for shield stage embryos to compare gene expression between Mrbm24a and sibling embryos. Another purpose of this omic analysis is to examine possible cell populations that can be affected by the loss of maternal Rbm24a.			Zebrafish scRNAseq shield sibling 1	GSM8265295	source name:whole embryo\|tissue:whole embryo\|cell line:shield stage\|cell type:embryonic cell\|genotype:wild type\|geo loc name:missing\|collection date:missing	Zebrafish scRNAseq shield sibling 1	To remove any remaining biochemical reagents and primers from the post GEM reaction mixture silane magnetic beads were employed. The full length barcoded cDNAs were subsequently amplified by PCR to generate sufficient mass for library construction. During GEM incubation the molecules had R1 Read 1 primer sequence added to them. P5 P7 a sample index and R2 Read 2 primer sequence were added during library construction through processes such as End Repair A tailing Adaptor Ligation and PCR. The final libraries contained the P5 and P7 primers required for Illumina bridge amplification. The Single Cell three prime Protocol generated Illumina ready sequencing libraries. Each Single Cell three prime Library consisted of standard Illumina paired end constructs that began and ended with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI were encoded in Read 1 while Read 2 was utilized to sequence the cDNA fragment. Sample index sequences were incorporated as the i7 index read. Read 1 and Read 2 corresponded to the standard Illumina® sequencing primer sites used in paired end sequencing. Assembly: GRCz10 Supplementary files format and content: Tab separated values files and matrix files	whole embryo		For the preparation of single cell suspensions a total of thirty three mutant embryos of Mrbm24a or wild type embryos at the shield stage were collected. These cellular suspensions were then loaded onto a 10X Genomics GemCode Single cell instrument which generates single cell Gel Bead In EMulsion GEMs. Libraries were generated and sequenced from the cDNAs using Chromium Next GEM Single Cell three prime Reagent Kits v3.1. Upon dissolution of the Gel Bead within a GEM primers containing an Illumina® R1 sequence Read 1 sequencing primer a 16 nt 10x Barcode a 10 nt Unique Molecular Identifier UMI and a poly dT primer sequence were released. These primers were mixed with the cell lysate and Master Mix. Full length barcoded cDNAs were then reverse transcribed from poly adenylated mRNA	Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C	tissue:whole embryo\|cell line:shield stage\|cell type:embryonic cell\|genotype:wild type	GSM8265295	GSM8265295: Zebrafish scRNAseq shield sibling 1; Danio rerio; RNA Seq	GSM8265295 r1	GSM8265295	1	For the preparation of single cell suspensions a total of thirty three mutant embryos of Mrbm24a or wild type embryos at the shield stage were collected. These cellular suspensions were then loaded onto a 10X Genomics GemCode Single cell instrument which generates single cell Gel Bead In EMulsion GEMs. Libraries were generated and sequenced from the cDNAs using Chromium Next GEM Single Cell three prime Reagent Kits v3.1. Upon dissolution of the Gel Bead within a GEM primers containing an Illumina® R1 sequence Read 1 sequencing primer a 16 nt 10x Barcode a 10 nt Unique Molecular Identifier UMI and a poly dT primer sequence were released. These primers were mixed with the cell lysate and Master Mix. Full length barcoded cDNAs were then reverse transcribed from poly adenylated mRNA		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP507567		J23090497_R1_001.fastq.gz J23090497_R2_001.fastq.gz	fastq fastq	106697824200.0	355659414.0	GSM8265295 r1	0:150 1:150	A:33526661561;C:19978357135;G:20431377225;T:32760687892;N:740387	150	150			33526661561	19978357135	20431377225	32760687892	740387	SRX24545645	SRS21290022	SRA1866413	shao ming lab, school of life sciences, shandong university	shao ming lab, school of life sciences, shandong university	2	0.16292	0.91415	0.04208	0.15118	0.98859	0.78914	0.58909	0.51597	150	150	T	B	mate1 technical by mapping diff	illumina	nextseq	3prime	random_priming	unknown	sc	single_cell_droplet	10x	China	2024-05-14	Gastrula	Embryo	Whole Organism	All anatomical structures
32136	32136	SRR29020077	SRX24545644	SRS21290021	SRP507567	PRJNA1111448	rbm24a is an organizer component of germ plasm to determine germ cell fate	GSE267406	Transcriptome Analysis	The formation of germ cells is a critical issue for the continuation of species. A large group of animals follow a preformation strategy to generate their primordial germ cells PGCs. They produce a set of localized maternal mRNAs and proteins to form phase separated germ plasm that functions as the PGC determinants but the mechanisms underlying the assembly of germ plasm is poorly understood. This study identifies Rbm24a as an enssential localized germ plasm protein component that controls the formation of large and functional germ plasm granules. Rbm24a is complexed with Buc and interacts with germ plasm mRNAs which determines the specific grasp of germ plasm mRNAs into the phase separated aggregates. Rbm24a absent granules fail to undergo kinesin dependent transport towards the cleavage furrows where small particles fuse into large ones. The loss of maternal rbm24a causes the complete degradation of germ plasm components and the disappearance of PGCs resulting in totally sterile animals. Our work establishes that Rbm24 is a critical nucleating organizer component of germ plasm highlighting an emerging common mechanism to read and recruit RNA component into phase separated condensates. Overall design: We performed single cell RNA seq scRNA seq for shield stage embryos to compare gene expression between Mrbm24a and sibling embryos. Another purpose of this omic analysis is to examine possible cell populations that can be affected by the loss of maternal Rbm24a.			Zebrafish scRNAseq shield Mrbm24a 2	GSM8265294	source name:whole embryo\|tissue:whole embryo\|cell line:shield stage\|cell type:embryonic cell\|genotype:Mrbm24a\|geo loc name:missing\|collection date:missing	Zebrafish scRNAseq shield Mrbm24a 2	To remove any remaining biochemical reagents and primers from the post GEM reaction mixture silane magnetic beads were employed. The full length barcoded cDNAs were subsequently amplified by PCR to generate sufficient mass for library construction. During GEM incubation the molecules had R1 Read 1 primer sequence added to them. P5 P7 a sample index and R2 Read 2 primer sequence were added during library construction through processes such as End Repair A tailing Adaptor Ligation and PCR. The final libraries contained the P5 and P7 primers required for Illumina bridge amplification. The Single Cell three prime Protocol generated Illumina ready sequencing libraries. Each Single Cell three prime Library consisted of standard Illumina paired end constructs that began and ended with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI were encoded in Read 1 while Read 2 was utilized to sequence the cDNA fragment. Sample index sequences were incorporated as the i7 index read. Read 1 and Read 2 corresponded to the standard Illumina® sequencing primer sites used in paired end sequencing. Assembly: GRCz10 Supplementary files format and content: Tab separated values files and matrix files	whole embryo		For the preparation of single cell suspensions a total of thirty three mutant embryos of Mrbm24a or wild type embryos at the shield stage were collected. These cellular suspensions were then loaded onto a 10X Genomics GemCode Single cell instrument which generates single cell Gel Bead In EMulsion GEMs. Libraries were generated and sequenced from the cDNAs using Chromium Next GEM Single Cell three prime Reagent Kits v3.1. Upon dissolution of the Gel Bead within a GEM primers containing an Illumina® R1 sequence Read 1 sequencing primer a 16 nt 10x Barcode a 10 nt Unique Molecular Identifier UMI and a poly dT primer sequence were released. These primers were mixed with the cell lysate and Master Mix. Full length barcoded cDNAs were then reverse transcribed from poly adenylated mRNA	Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C	tissue:whole embryo\|cell line:shield stage\|cell type:embryonic cell\|genotype:Mrbm24a	GSM8265294	GSM8265294: Zebrafish scRNAseq shield Mrbm24a 2; Danio rerio; RNA Seq	GSM8265294 r1	GSM8265294	1	For the preparation of single cell suspensions a total of thirty three mutant embryos of Mrbm24a or wild type embryos at the shield stage were collected. These cellular suspensions were then loaded onto a 10X Genomics GemCode Single cell instrument which generates single cell Gel Bead In EMulsion GEMs. Libraries were generated and sequenced from the cDNAs using Chromium Next GEM Single Cell three prime Reagent Kits v3.1. Upon dissolution of the Gel Bead within a GEM primers containing an Illumina® R1 sequence Read 1 sequencing primer a 16 nt 10x Barcode a 10 nt Unique Molecular Identifier UMI and a poly dT primer sequence were released. These primers were mixed with the cell lysate and Master Mix. Full length barcoded cDNAs were then reverse transcribed from poly adenylated mRNA		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP507567		J23090496_R2_001.fastq.gz J23090496_R1_001.fastq.gz	fastq fastq	107289285600.0	357630952.0	GSM8265294 r1	0:150 1:150	A:33671128260;C:20203779331;G:20583824987;T:32829771822;N:781200	150	150			33671128260	20203779331	20583824987	32829771822	781200	SRX24545644	SRS21290021	SRA1866413	shao ming lab, school of life sciences, shandong university	shao ming lab, school of life sciences, shandong university	2	0.17098	0.91193	0.0312	0.14762	0.98772	0.789	0.58127	0.51217	150	150	T	B	mate1 technical by mapping diff	illumina	nextseq	3prime	random_priming	unknown	sc	single_cell_droplet	10x	China	2024-05-14	Gastrula	Embryo	Whole Organism	All anatomical structures
32137	32137	SRR29020078	SRX24545643	SRS21290020	SRP507567	PRJNA1111448	rbm24a is an organizer component of germ plasm to determine germ cell fate	GSE267406	Transcriptome Analysis	The formation of germ cells is a critical issue for the continuation of species. A large group of animals follow a preformation strategy to generate their primordial germ cells PGCs. They produce a set of localized maternal mRNAs and proteins to form phase separated germ plasm that functions as the PGC determinants but the mechanisms underlying the assembly of germ plasm is poorly understood. This study identifies Rbm24a as an enssential localized germ plasm protein component that controls the formation of large and functional germ plasm granules. Rbm24a is complexed with Buc and interacts with germ plasm mRNAs which determines the specific grasp of germ plasm mRNAs into the phase separated aggregates. Rbm24a absent granules fail to undergo kinesin dependent transport towards the cleavage furrows where small particles fuse into large ones. The loss of maternal rbm24a causes the complete degradation of germ plasm components and the disappearance of PGCs resulting in totally sterile animals. Our work establishes that Rbm24 is a critical nucleating organizer component of germ plasm highlighting an emerging common mechanism to read and recruit RNA component into phase separated condensates. Overall design: We performed single cell RNA seq scRNA seq for shield stage embryos to compare gene expression between Mrbm24a and sibling embryos. Another purpose of this omic analysis is to examine possible cell populations that can be affected by the loss of maternal Rbm24a.			Zebrafish scRNAseq shield Mrbm24a 1	GSM8265293	source name:whole embryo\|tissue:whole embryo\|cell line:shield stage\|cell type:embryonic cell\|genotype:Mrbm24a\|geo loc name:missing\|collection date:missing	Zebrafish scRNAseq shield Mrbm24a 1	To remove any remaining biochemical reagents and primers from the post GEM reaction mixture silane magnetic beads were employed. The full length barcoded cDNAs were subsequently amplified by PCR to generate sufficient mass for library construction. During GEM incubation the molecules had R1 Read 1 primer sequence added to them. P5 P7 a sample index and R2 Read 2 primer sequence were added during library construction through processes such as End Repair A tailing Adaptor Ligation and PCR. The final libraries contained the P5 and P7 primers required for Illumina bridge amplification. The Single Cell three prime Protocol generated Illumina ready sequencing libraries. Each Single Cell three prime Library consisted of standard Illumina paired end constructs that began and ended with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI were encoded in Read 1 while Read 2 was utilized to sequence the cDNA fragment. Sample index sequences were incorporated as the i7 index read. Read 1 and Read 2 corresponded to the standard Illumina® sequencing primer sites used in paired end sequencing. Assembly: GRCz10 Supplementary files format and content: Tab separated values files and matrix files	whole embryo		For the preparation of single cell suspensions a total of thirty three mutant embryos of Mrbm24a or wild type embryos at the shield stage were collected. These cellular suspensions were then loaded onto a 10X Genomics GemCode Single cell instrument which generates single cell Gel Bead In EMulsion GEMs. Libraries were generated and sequenced from the cDNAs using Chromium Next GEM Single Cell three prime Reagent Kits v3.1. Upon dissolution of the Gel Bead within a GEM primers containing an Illumina® R1 sequence Read 1 sequencing primer a 16 nt 10x Barcode a 10 nt Unique Molecular Identifier UMI and a poly dT primer sequence were released. These primers were mixed with the cell lysate and Master Mix. Full length barcoded cDNAs were then reverse transcribed from poly adenylated mRNA	Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C	tissue:whole embryo\|cell line:shield stage\|cell type:embryonic cell\|genotype:Mrbm24a	GSM8265293	GSM8265293: Zebrafish scRNAseq shield Mrbm24a 1; Danio rerio; RNA Seq	GSM8265293 r1	GSM8265293	1	For the preparation of single cell suspensions a total of thirty three mutant embryos of Mrbm24a or wild type embryos at the shield stage were collected. These cellular suspensions were then loaded onto a 10X Genomics GemCode Single cell instrument which generates single cell Gel Bead In EMulsion GEMs. Libraries were generated and sequenced from the cDNAs using Chromium Next GEM Single Cell three prime Reagent Kits v3.1. Upon dissolution of the Gel Bead within a GEM primers containing an Illumina® R1 sequence Read 1 sequencing primer a 16 nt 10x Barcode a 10 nt Unique Molecular Identifier UMI and a poly dT primer sequence were released. These primers were mixed with the cell lysate and Master Mix. Full length barcoded cDNAs were then reverse transcribed from poly adenylated mRNA		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP507567		J23090495_R1_001.fastq.gz J23090495_R2_001.fastq.gz	fastq fastq	98193373500.0	327311245.0	GSM8265293 r1	0:150 1:150	A:27502195548;C:18458481431;G:18979601074;T:33252654514;N:440933	150	150			27502195548	18458481431	18979601074	33252654514	440933	SRX24545643	SRS21290020	SRA1866413	shao ming lab, school of life sciences, shandong university	shao ming lab, school of life sciences, shandong university	2	0.00149	0.9183	0.00037	0.14737	0.99947	0.79125	0.51851	0.50318	150	150	T	B	mate1 technical by mapping diff	illumina	nextseq	3prime	random_priming	unknown	sc	single_cell_droplet	10x	China	2024-05-14	Gastrula	Embryo	Whole Organism	All anatomical structures
33864	33864	SRR30779425	SRX26181412	SRS22725400	SRP534298	PRJNA1164307	Time resolved single cell Multiomic zebrafish atlas	PRJNA1164307	Other	During development dynamic interplay between transcription factors chromatin and genes termed gene regulatory network GRN shapes the cell fate determination along the developmental trajectory. Recent advances in joint measurement of chromatin accessibility and gene expression enabled the genome wide identification of regulatory relationships. Here we assess the dynamics of the gene regulatory network in zebrafish development using joint single cell ATAC and single cell RNA sequencing. We discovered some key regulatory modules that exhibit cell type and time dependent activity suggesting that the role of transcription factors vary over cell type and timepoints. With time resolved GRNs combined with linear modeling framework we performed a systematic in silico knock out simulation using CellOracle. This in silico knock out simulation revealed that the role of transcription factors is shared between mesodermal and neuro ectodermal lineages in the early timepoints but later commit significantly to either lineages. Together we provide a dataset and a framework to systematically dissect the role of transcription factors during the zebrafish embryonic development.			TDR126	TDR126 10hpf EKW NA none 10xmultiome	strain:EKW\|dev stage:Bud stage 10 hpf\|collection date:2023 11 22\|geo loc name:USA: San Francisco\|sex:N/A\|tissue:organism\|BioSampleModel:Model organism or animal									TDR126 10hpf RNA	TDR126 10hpf RNA EKW NA none 10xmultiome	TDR126 10hpf RNA EKW NA none 10xmultiome	10x multiome nuc seq			RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP534298		TDR126_10hpf_RNA_EKW_NA_none_10xmultiome_S4_L001_I1_001.fastq.gz TDR126_10hpf_RNA_EKW_NA_none_10xmultiome_S4_L001_I2_001.fastq.gz TDR126_10hpf_RNA_EKW_NA_none_10xmultiome_S4_L001_R1_001.fastq.gz TDR126_10hpf_RNA_EKW_NA_none_10xmultiome_S4_L001_R2_001.fastq.gz TDR126_10hpf_RNA_EKW_NA_none_10xmultiome_S4_L002_I1_001.fastq.gz TDR126_10hpf_RNA_EKW_NA_none_10xmultiome_S4_L002_I2_001.fastq.gz TDR126_10hpf_RNA_EKW_NA_none_10xmultiome_S4_L002_R1_001.fastq.gz TDR126_10hpf_RNA_EKW_NA_none_10xmultiome_S4_L002_R2_001.fastq.gz TDR126_10hpf_RNA_EKW_NA_none_10xmultiome_S4_L003_I1_001.fastq.gz TDR126_10hpf_RNA_EKW_NA_none_10xmultiome_S4_L003_I2_001.fastq.gz TDR126_10hpf_RNA_EKW_NA_none_10xmultiome_S4_L003_R1_001.fastq.gz TDR126_10hpf_RNA_EKW_NA_none_10xmultiome_S4_L003_R2_001.fastq.gz TDR126_10hpf_RNA_EKW_NA_none_10xmultiome_S4_L004_I1_001.fastq.gz TDR126_10hpf_RNA_EKW_NA_none_10xmultiome_S4_L004_I2_001.fastq.gz TDR126_10hpf_RNA_EKW_NA_none_10xmultiome_S4_L004_R1_001.fastq.gz TDR126_10hpf_RNA_EKW_NA_none_10xmultiome_S4_L004_R2_001.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq			TDR126 10hpf RNA EKW NA none 10xmultiome S4 L001 I1 001.fastq.gz												SRX26181412		SRA1977819	Chan Zuckerberg Biohub San Francisco\|Computational Biology	Chan Zuckerberg Biohub San Francisco															illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-09-23	Gastrula	Embryo	Undetermined	Embryo Imprecise
55651	55651	SRR10611684	SRX7290956	SRS5784117	SRP235262	PRJNA594336	Single cell sequencing reveals heterogeneity effects of bisphenol A on zebrafish embryonic development	GSE141664	Transcriptome Analysis	Embryonic period is sensitive window of bisphenol A BPA exposure. However embryonic development is a highly dynamic process with changing cell populations and gene expression profiles. Heterogeneity effects of BPA on fish embryonic development remain not clear. This study applied single cell RNA sequencing to analyze the impact of BPA exposure on transcriptome heterogeneity of 64683 cells from zebrafish embryos at 8 12 hpf and 30 hpf. A total of 38 cell populations were identified and gene expression profiles of 16 cell populations were significantly altered by BPA exposure. The strongest toxic effects of BPA were found at 12 hpf of segmentation stage which is an active stage of cell differentiation. At 8 hpf BPA mainly influenced the outer layer cell populations of embryos such as neural plate border and enveloping layer cells. At 12 hpf and 30 hpf nervous system formation and heart morphogenesis were disturbed. Differential process of neural plate border neural crest and neuron cells was altered leading to increased neurogenesis. For the forebrain midbrain neurons and optic cells the altered cell division and DNA replication and repair were identified. Our study for the first time provides the comprehensive understanding of BPA toxicity on fish embryo development at single cell levels. Overall design: Single cell RNA sequencing were adopted to learn the transcriptional variation in zebrafish embryonic development following exposure to bisphenol A at different stage gastrulation segmentation and pharyngula.			BP 8h	GSM4210783	source name:zebrafish embryo\|tissue:embryonic single cell suspension\|age:8hpf\|exposed pollutants:100ppb BPA	BP 8h	We use FastQC to perform basic statistics on the quality of the raw reads. Then those read sequences produced by the Illumina pipeline in FASTQ format were pre processed through Trimmomatic software which can be summarized as below:1 Remove low quality reads: scan the read with a 4 base wide sliding window cutting when the average quality per base drops below 10 SLIDINGWINDOW: 4:10 2 Remove trailing low quality or N bases below quality 3 TRAILING:3 3 Remove adapters : there are two modes to remove the adapter sequence: a. alignment with the adapter sequence the number of matching bases were greater than 7 and mismatch=2; b.when read1 and read2 overlapping base scoring greater than 30 removed non overlapping portions ILLUMINACLIP: adapter.fa: 2: 30: 7 4 Drop reads below the 26 bases long 5 Discard those reads that can not form paired The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last we use FastQC to perform basic statistics on the quality of the clean reads. Cell Ranger uses an aligner called STAR which peforms splicing aware alignment of reads to the genome. Cell Ranger then uses the transcript annotation GTF to bucket the reads into exonic intronic and intergenic and by whether the reads align confidently to the genome. A read is exonic if at least 50% of it intersects an exon intronic if it is non exonic and intersects an intron and intergenic otherwise. For reads that align to a single exonic locus but also align to 1 or more non exonic loci the exonic locus is prioritized and the read is considered to be confidently mapped to the exonic locus with MAPQ 255. Cell Ranger further aligns exonic reads to annotated transcripts looking for compatibility. A read that is compatible with the exons of an annotated transcript and aligned to the same strand is considered mapped to the transcriptome. If the read is compatible with a single gene annotation it is considered uniquely confidently mapped to the transcrip…	zebrafish embryo	Exposure solutions were prepared by adding 100 μg/L BPA to culture medium. The exposure solution were was replaced every 12 hours.At three different stages gasturla segmentation and pharyngula zebrafish embryo were collected.	The zebrafish embryo was digested into cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell 3’ Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer’s protocol. Libraries were sequenced on an illumina Xten.		tissue:embryonic single cell suspension\|age:8hpf\|exposed pollutants:100ppb BPA	GSM4210783	GSM4210783: BP 8h; Danio rerio; RNA Seq	GSM4210783		1	The zebrafish embryo was digested into cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell three prime Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer's protocol. Libraries were sequenced on an illumina Xten.	GEO Accession:GSM4210783	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	HiSeq X Ten	SRP235262		BP-8h_S2_L002_R1_001.fastq.gz BP-8h_S2_L002_R2_001.fastq.gz	fastq fastq	112920017284.0	373907342.0	GSM4210783 r1	0:151 1:151	A:29091217868;C:18813523727;G:19294526701;T:45706210539;N:14538449	151	151			29091217868	18813523727	19294526701	45706210539	14538449	SRX7290956	SRS5784117	SRA1008496	GEO	Nanjing University	2	0.13456	0.90846	0.01758	0.09803	0.98293	0.81826	0.55099	0.50254	151	151	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2019-12-09	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
55654	55654	SRR10611681	SRX7290953	SRS5784118	SRP235262	PRJNA594336	Single cell sequencing reveals heterogeneity effects of bisphenol A on zebrafish embryonic development	GSE141664	Transcriptome Analysis	Embryonic period is sensitive window of bisphenol A BPA exposure. However embryonic development is a highly dynamic process with changing cell populations and gene expression profiles. Heterogeneity effects of BPA on fish embryonic development remain not clear. This study applied single cell RNA sequencing to analyze the impact of BPA exposure on transcriptome heterogeneity of 64683 cells from zebrafish embryos at 8 12 hpf and 30 hpf. A total of 38 cell populations were identified and gene expression profiles of 16 cell populations were significantly altered by BPA exposure. The strongest toxic effects of BPA were found at 12 hpf of segmentation stage which is an active stage of cell differentiation. At 8 hpf BPA mainly influenced the outer layer cell populations of embryos such as neural plate border and enveloping layer cells. At 12 hpf and 30 hpf nervous system formation and heart morphogenesis were disturbed. Differential process of neural plate border neural crest and neuron cells was altered leading to increased neurogenesis. For the forebrain midbrain neurons and optic cells the altered cell division and DNA replication and repair were identified. Our study for the first time provides the comprehensive understanding of BPA toxicity on fish embryo development at single cell levels. Overall design: Single cell RNA sequencing were adopted to learn the transcriptional variation in zebrafish embryonic development following exposure to bisphenol A at different stage gastrulation segmentation and pharyngula.			CK 8h	GSM4210780	source name:zebrafish embryo\|tissue:embryonic single cell suspension\|age:8hpf\|exposed pollutants:n1	CK 8h	We use FastQC to perform basic statistics on the quality of the raw reads. Then those read sequences produced by the Illumina pipeline in FASTQ format were pre processed through Trimmomatic software which can be summarized as below:1 Remove low quality reads: scan the read with a 4 base wide sliding window cutting when the average quality per base drops below 10 SLIDINGWINDOW: 4:10 2 Remove trailing low quality or N bases below quality 3 TRAILING:3 3 Remove adapters : there are two modes to remove the adapter sequence: a. alignment with the adapter sequence the number of matching bases were greater than 7 and mismatch=2; b.when read1 and read2 overlapping base scoring greater than 30 removed non overlapping portions ILLUMINACLIP: adapter.fa: 2: 30: 7 4 Drop reads below the 26 bases long 5 Discard those reads that can not form paired The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last we use FastQC to perform basic statistics on the quality of the clean reads. Cell Ranger uses an aligner called STAR which peforms splicing aware alignment of reads to the genome. Cell Ranger then uses the transcript annotation GTF to bucket the reads into exonic intronic and intergenic and by whether the reads align confidently to the genome. A read is exonic if at least 50% of it intersects an exon intronic if it is non exonic and intersects an intron and intergenic otherwise. For reads that align to a single exonic locus but also align to 1 or more non exonic loci the exonic locus is prioritized and the read is considered to be confidently mapped to the exonic locus with MAPQ 255. Cell Ranger further aligns exonic reads to annotated transcripts looking for compatibility. A read that is compatible with the exons of an annotated transcript and aligned to the same strand is considered mapped to the transcriptome. If the read is compatible with a single gene annotation it is considered uniquely confidently mapped to the transcrip…	zebrafish embryo	Exposure solutions were prepared by adding 100 μg/L BPA to culture medium. The exposure solution were was replaced every 12 hours.At three different stages gasturla segmentation and pharyngula zebrafish embryo were collected.	The zebrafish embryo was digested into cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell 3’ Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer’s protocol. Libraries were sequenced on an illumina Xten.		tissue:embryonic single cell suspension\|age:8hpf\|exposed pollutants:n1	GSM4210780	GSM4210780: CK 8h; Danio rerio; RNA Seq	GSM4210780		1	The zebrafish embryo was digested into cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell three prime Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer's protocol. Libraries were sequenced on an illumina Xten.	GEO Accession:GSM4210780	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	HiSeq X Ten	SRP235262		CK-8h_S1_L001_R1_001.fastq.gz CK-8h_S1_L001_R2_001.fastq.gz	fastq fastq	117112087438.0	387788369.0	GSM4210780 r1	0:151 1:151	A:30237691607;C:19643608086;G:20051803632;T:47157015762;N:21968351	151	151			30237691607	19643608086	20051803632	47157015762	21968351	SRX7290953	SRS5784118	SRA1008496	GEO	Nanjing University	2	0.12513	0.90183	0.01627	0.09322	0.98255	0.81937	0.56652	0.49202	151	151	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2019-12-09	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
56746	56746	SRR15813443	SRX12105547	SRS10085839	SRP249509	PRJNA606682	CellOracle: Dissecting cell identity via network inference and in silico gene perturbation	GSE145298	Other	Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.		pubmed:36755098	wt s6	GSM5567817	tissue:wt reference hpf 10\|strain:WT\|Stage:10 hpf\|experiment:WT embryo	wt s6	Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz	wt reference hpf 10		10x Genomcis Chromium single cell preparation		strain:WT\|Stage:10 hpf\|experiment:WT embryo	GSM5567817	GSM5567817: wt s6; Danio rerio; RNA Seq	GSM5567817		1	10x Genomcis Chromium single cell preparation	GEO Accession:GSM5567817	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP249509	assembly:GRCz11\|intentional duplicate	wt_s6_possorted_genome_bam.bam	10X Genomics bam file	10559763630.0	117330707.0	GSM5567817 r1	0:90	A:3140440043;C:2269672250;G:2444938588;T:2701186457;N:3526292	90				3140440043	2269672250	2444938588	2701186457	3526292	SRX12105547	SRS10085839	SRA1042742	GEO	Washington University in St Louis	1	0.91901		0.24752		0.80736		0.6329		90		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-09-08	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
56747	56747	SRR15813442	SRX12105546	SRS10085840	SRP249509	PRJNA606682	CellOracle: Dissecting cell identity via network inference and in silico gene perturbation	GSE145298	Other	Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.		pubmed:36755098	wt s5	GSM5567816	tissue:wt reference hpf 10\|strain:WT\|Stage:10 hpf\|experiment:WT embryo	wt s5	Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz	wt reference hpf 10		10x Genomcis Chromium single cell preparation		strain:WT\|Stage:10 hpf\|experiment:WT embryo	GSM5567816	GSM5567816: wt s5; Danio rerio; RNA Seq	GSM5567816		1	10x Genomcis Chromium single cell preparation	GEO Accession:GSM5567816	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP249509	assembly:GRCz11\|intentional duplicate	wt_s5_possorted_genome_bam.bam	10X Genomics bam file	7404734700.0	82274830.0	GSM5567816 r1	0:90	A:2195721377;C:1607643736;G:1735950843;T:1863072717;N:2346027	90				2195721377	1607643736	1735950843	1863072717	2346027	SRX12105546	SRS10085840	SRA1042742	GEO	Washington University in St Louis	1	0.91448		0.23763		0.80933		0.63338		90		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-09-08	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
56748	56748	SRR15813441	SRX12105545	SRS10085841	SRP249509	PRJNA606682	CellOracle: Dissecting cell identity via network inference and in silico gene perturbation	GSE145298	Other	Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.		pubmed:36755098	wt s4	GSM5567815	tissue:wt reference hpf 8\|strain:WT\|Stage:8 hpf\|experiment:WT embryo	wt s4	Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz	wt reference hpf 8		10x Genomcis Chromium single cell preparation		strain:WT\|Stage:8 hpf\|experiment:WT embryo	GSM5567815	GSM5567815: wt s4; Danio rerio; RNA Seq	GSM5567815		1	10x Genomcis Chromium single cell preparation	GEO Accession:GSM5567815	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP249509	assembly:GRCz11\|intentional duplicate	wt_s4_possorted_genome_bam.bam	10X Genomics bam file	16164581310.0	179606459.0	GSM5567815 r1	0:90	A:4832582846;C:3490996022;G:3746675672;T:4088577265;N:5749505	90				4832582846	3490996022	3746675672	4088577265	5749505	SRX12105545	SRS10085841	SRA1042742	GEO	Washington University in St Louis	1	0.90609		0.22195		0.82085		0.64383		90		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-09-08	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
56749	56749	SRR15813440	SRX12105544	SRS10085838	SRP249509	PRJNA606682	CellOracle: Dissecting cell identity via network inference and in silico gene perturbation	GSE145298	Other	Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.		pubmed:36755098	wt s3	GSM5567814	tissue:wt reference hpf 8\|strain:WT\|Stage:8 hpf\|experiment:WT embryo	wt s3	Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz	wt reference hpf 8		10x Genomcis Chromium single cell preparation		strain:WT\|Stage:8 hpf\|experiment:WT embryo	GSM5567814	GSM5567814: wt s3; Danio rerio; RNA Seq	GSM5567814		1	10x Genomcis Chromium single cell preparation	GEO Accession:GSM5567814	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP249509	assembly:GRCz11\|intentional duplicate	wt_s3_possorted_genome_bam.bam	10X Genomics bam file	13357030950.0	148411455.0	GSM5567814 r1	0:90	A:3992336370;C:2912423812;G:3128958676;T:3318661163;N:4650929	90				3992336370	2912423812	3128958676	3318661163	4650929	SRX12105544	SRS10085838	SRA1042742	GEO	Washington University in St Louis	1	0.9059		0.21809		0.82578		0.64796		90		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-09-08	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
56750	56750	SRR15813439	SRX12105543	SRS10085837	SRP249509	PRJNA606682	CellOracle: Dissecting cell identity via network inference and in silico gene perturbation	GSE145298	Other	Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.		pubmed:36755098	wt s2	GSM5567813	tissue:wt reference hpf 6\|strain:WT\|Stage:6 hpf\|experiment:WT embryo	wt s2	Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz	wt reference hpf 6		10x Genomcis Chromium single cell preparation		strain:WT\|Stage:6 hpf\|experiment:WT embryo	GSM5567813	GSM5567813: wt s2; Danio rerio; RNA Seq	GSM5567813		1	10x Genomcis Chromium single cell preparation	GEO Accession:GSM5567813	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP249509	assembly:GRCz11\|intentional duplicate	wt_s2_possorted_genome_bam.bam	10X Genomics bam file	16886072430.0	187623027.0	GSM5567813 r1	0:90	A:4987160925;C:3716401392;G:4001055160;T:4174238739;N:7216214	90				4987160925	3716401392	4001055160	4174238739	7216214	SRX12105543	SRS10085837	SRA1042742	GEO	Washington University in St Louis	1	0.9034		0.19315		0.81038		0.65382		90		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-09-08	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
56751	56751	SRR15813438	SRX12105542	SRS10085835	SRP249509	PRJNA606682	CellOracle: Dissecting cell identity via network inference and in silico gene perturbation	GSE145298	Other	Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.		pubmed:36755098	wt s1	GSM5567812	tissue:wt reference hpf 6\|strain:WT\|Stage:6 hpf\|experiment:WT embryo	wt s1	Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz	wt reference hpf 6		10x Genomcis Chromium single cell preparation		strain:WT\|Stage:6 hpf\|experiment:WT embryo	GSM5567812	GSM5567812: wt s1; Danio rerio; RNA Seq	GSM5567812		1	10x Genomcis Chromium single cell preparation	GEO Accession:GSM5567812	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP249509	assembly:GRCz11\|intentional duplicate	wt_s1_possorted_genome_bam.bam	10X Genomics bam file	19790815230.0	219897947.0	GSM5567812 r1	0:90	A:5848816040;C:4330412374;G:4675552886;T:4927327121;N:8706809	90				5848816040	4330412374	4675552886	4927327121	8706809	SRX12105542	SRS10085835	SRA1042742	GEO	Washington University in St Louis	1	0.90894		0.18849		0.80771		0.64881		90		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-09-08	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
56752	56752	SRR15813437	SRX12105541	SRS10085836	SRP249509	PRJNA606682	CellOracle: Dissecting cell identity via network inference and in silico gene perturbation	GSE145298	Other	Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.		pubmed:36755098	tyr 7	GSM5567811	tissue:tyr crispant\|strain:tyr crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	tyr 7	Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz	tyr crispant		10x Genomcis Chromium single cell preparation		strain:tyr crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	GSM5567811	GSM5567811: tyr 7; Danio rerio; RNA Seq	GSM5567811		1	10x Genomcis Chromium single cell preparation	GEO Accession:GSM5567811	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP249509	assembly:GRCz11\|intentional duplicate	tyr_7_possorted_genome_bam.bam	10X Genomics bam file	17956913490.0	199521261.0	GSM5567811 r1	0:90	A:5196658241;C:3876984519;G:4299586871;T:4578633727;N:5050132	90				5196658241	3876984519	4299586871	4578633727	5050132	SRX12105541	SRS10085836	SRA1042742	GEO	Washington University in St Louis	1	0.91768		0.22887		0.82108		0.56033		90		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-09-08	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
56753	56753	SRR15813436	SRX12105540	SRS10085834	SRP249509	PRJNA606682	CellOracle: Dissecting cell identity via network inference and in silico gene perturbation	GSE145298	Other	Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.		pubmed:36755098	tyr 6	GSM5567810	tissue:tyr crispant\|strain:tyr crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	tyr 6	Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz	tyr crispant		10x Genomcis Chromium single cell preparation		strain:tyr crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	GSM5567810	GSM5567810: tyr 6; Danio rerio; RNA Seq	GSM5567810		1	10x Genomcis Chromium single cell preparation	GEO Accession:GSM5567810	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP249509	assembly:GRCz11\|intentional duplicate	tyr_6_possorted_genome_bam.bam	10X Genomics bam file	20779298370.0	230881093.0	GSM5567810 r1	0:90	A:5921943503;C:4559349693;G:5076139988;T:5215980107;N:5885079	90				5921943503	4559349693	5076139988	5215980107	5885079	SRX12105540	SRS10085834	SRA1042742	GEO	Washington University in St Louis	1	0.92027		0.21718		0.82558		0.55659		90		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-09-08	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
56754	56754	SRR15813435	SRX12105539	SRS10085833	SRP249509	PRJNA606682	CellOracle: Dissecting cell identity via network inference and in silico gene perturbation	GSE145298	Other	Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.		pubmed:36755098	tyr 5	GSM5567809	tissue:tyr crispant\|strain:tyr crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	tyr 5	Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz	tyr crispant		10x Genomcis Chromium single cell preparation		strain:tyr crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	GSM5567809	GSM5567809: tyr 5; Danio rerio; RNA Seq	GSM5567809		1	10x Genomcis Chromium single cell preparation	GEO Accession:GSM5567809	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP249509	assembly:GRCz11\|intentional duplicate	tyr_5_possorted_genome_bam.bam	10X Genomics bam file	11100581280.0	123339792.0	GSM5567809 r1	0:90	A:3139119132;C:2435865589;G:2721973969;T:2802951898;N:670692	90				3139119132	2435865589	2721973969	2802951898	670692	SRX12105539	SRS10085833	SRA1042742	GEO	Washington University in St Louis	1	0.93417		0.15847		0.83347		0.5442		90		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-09-08	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
56755	56755	SRR15813434	SRX12105538	SRS10085832	SRP249509	PRJNA606682	CellOracle: Dissecting cell identity via network inference and in silico gene perturbation	GSE145298	Other	Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.		pubmed:36755098	tyr 4	GSM5567808	tissue:tyr crispant\|strain:tyr crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	tyr 4	Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz	tyr crispant		10x Genomcis Chromium single cell preparation		strain:tyr crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	GSM5567808	GSM5567808: tyr 4; Danio rerio; RNA Seq	GSM5567808		1	10x Genomcis Chromium single cell preparation	GEO Accession:GSM5567808	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP249509	assembly:GRCz11\|intentional duplicate	tyr_4_possorted_genome_bam.bam	10X Genomics bam file	12537663570.0	139307373.0	GSM5567808 r1	0:90	A:3622205893;C:2682389272;G:2969276928;T:3261280923;N:2510554	90				3622205893	2682389272	2969276928	3261280923	2510554	SRX12105538	SRS10085832	SRA1042742	GEO	Washington University in St Louis	1	0.93183		0.17593		0.82674		0.54339		90		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-09-08	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
56756	56756	SRR15813433	SRX12105537	SRS10085831	SRP249509	PRJNA606682	CellOracle: Dissecting cell identity via network inference and in silico gene perturbation	GSE145298	Other	Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.		pubmed:36755098	tyr 3	GSM5567807	tissue:tyr crispant\|strain:tyr crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	tyr 3	Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz	tyr crispant		10x Genomcis Chromium single cell preparation		strain:tyr crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	GSM5567807	GSM5567807: tyr 3; Danio rerio; RNA Seq	GSM5567807		1	10x Genomcis Chromium single cell preparation	GEO Accession:GSM5567807	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP249509	assembly:GRCz11\|intentional duplicate	tyr_3_possorted_genome_bam.bam	10X Genomics bam file	14347674270.0	159418603.0	GSM5567807 r1	0:90	A:4145829296;C:3058277848;G:3413742462;T:3725775591;N:4049073	90				4145829296	3058277848	3413742462	3725775591	4049073	SRX12105537	SRS10085831	SRA1042742	GEO	Washington University in St Louis	1	0.92892		0.16288		0.82724		0.52654		90		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-09-08	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
56757	56757	SRR15813432	SRX12105536	SRS10085830	SRP249509	PRJNA606682	CellOracle: Dissecting cell identity via network inference and in silico gene perturbation	GSE145298	Other	Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.		pubmed:36755098	tyr 2	GSM5567806	tissue:tyr crispant\|strain:tyr crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	tyr 2	Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz	tyr crispant		10x Genomcis Chromium single cell preparation		strain:tyr crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	GSM5567806	GSM5567806: tyr 2; Danio rerio; RNA Seq	GSM5567806		1	10x Genomcis Chromium single cell preparation	GEO Accession:GSM5567806	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP249509	assembly:GRCz11\|intentional duplicate	tyr_2_possorted_genome_bam.bam	10X Genomics bam file	10069177770.0	111879753.0	GSM5567806 r1	0:90	A:2905395164;C:2177772281;G:2406688540;T:2577323490;N:1998295	90				2905395164	2177772281	2406688540	2577323490	1998295	SRX12105536	SRS10085830	SRA1042742	GEO	Washington University in St Louis	1	0.92725		0.19411		0.831		0.57759		90		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-09-08	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
56758	56758	SRR15813431	SRX12105535	SRS10085829	SRP249509	PRJNA606682	CellOracle: Dissecting cell identity via network inference and in silico gene perturbation	GSE145298	Other	Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.		pubmed:36755098	tyr 1	GSM5567805	tissue:tyr crispant\|strain:tyr crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	tyr 1	Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz	tyr crispant		10x Genomcis Chromium single cell preparation		strain:tyr crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	GSM5567805	GSM5567805: tyr 1; Danio rerio; RNA Seq	GSM5567805		1	10x Genomcis Chromium single cell preparation	GEO Accession:GSM5567805	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP249509	assembly:GRCz11\|intentional duplicate	tyr_1_possorted_genome_bam.bam	10X Genomics bam file	13916932740.0	154632586.0	GSM5567805 r1	0:90	A:4011009499;C:3001925064;G:3335796140;T:3563954880;N:4247157	90				4011009499	3001925064	3335796140	3563954880	4247157	SRX12105535	SRS10085829	SRA1042742	GEO	Washington University in St Louis	1	0.92833		0.18624		0.82584		0.55384		90		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-09-08	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
56759	56759	SRR15813430	SRX12105534	SRS10085828	SRP249509	PRJNA606682	CellOracle: Dissecting cell identity via network inference and in silico gene perturbation	GSE145298	Other	Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.		pubmed:36755098	sebox 3	GSM5567804	tissue:sebox crispant\|strain:sebox crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	sebox 3	Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz	sebox crispant		10x Genomcis Chromium single cell preparation		strain:sebox crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	GSM5567804	GSM5567804: sebox 3; Danio rerio; RNA Seq	GSM5567804		1	10x Genomcis Chromium single cell preparation	GEO Accession:GSM5567804	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP249509	assembly:GRCz11\|intentional duplicate	sebox_3_possorted_genome_bam.bam	10X Genomics bam file	15063590430.0	167373227.0	GSM5567804 r1	0:90	A:4342780592;C:3200398068;G:3565351581;T:3953977957;N:1082232	90				4342780592	3200398068	3565351581	3953977957	1082232	SRX12105534	SRS10085828	SRA1042742	GEO	Washington University in St Louis	1	0.92955		0.17763		0.82382		0.5348		90		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-09-08	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
56760	56760	SRR15813429	SRX12105533	SRS10085827	SRP249509	PRJNA606682	CellOracle: Dissecting cell identity via network inference and in silico gene perturbation	GSE145298	Other	Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.		pubmed:36755098	sebox 2	GSM5567803	tissue:sebox crispant\|strain:sebox crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	sebox 2	Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz	sebox crispant		10x Genomcis Chromium single cell preparation		strain:sebox crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	GSM5567803	GSM5567803: sebox 2; Danio rerio; RNA Seq	GSM5567803		1	10x Genomcis Chromium single cell preparation	GEO Accession:GSM5567803	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP249509	assembly:GRCz11\|intentional duplicate	sebox_2_possorted_genome_bam.bam	10X Genomics bam file	10155028230.0	112833647.0	GSM5567803 r1	0:90	A:2847715131;C:2249340222;G:2497174890;T:2560077085;N:720902	90				2847715131	2249340222	2497174890	2560077085	720902	SRX12105533	SRS10085827	SRA1042742	GEO	Washington University in St Louis	1	0.9413		0.17155		0.83236		0.5478		90		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-09-08	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
56761	56761	SRR15813428	SRX12105532	SRS10085826	SRP249509	PRJNA606682	CellOracle: Dissecting cell identity via network inference and in silico gene perturbation	GSE145298	Other	Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.		pubmed:36755098	sebox 1	GSM5567802	tissue:sebox crispant\|strain:sebox crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	sebox 1	Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz	sebox crispant		10x Genomcis Chromium single cell preparation		strain:sebox crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	GSM5567802	GSM5567802: sebox 1; Danio rerio; RNA Seq	GSM5567802		1	10x Genomcis Chromium single cell preparation	GEO Accession:GSM5567802	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP249509	assembly:GRCz11\|intentional duplicate	sebox_1_possorted_genome_bam.bam	10X Genomics bam file	15631632990.0	173684811.0	GSM5567802 r1	0:90	A:4504570341;C:3335848026;G:3720024502;T:4070070942;N:1119179	90				4504570341	3335848026	3720024502	4070070942	1119179	SRX12105532	SRS10085826	SRA1042742	GEO	Washington University in St Louis	1	0.91841		0.19		0.82367		0.54474		90		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-09-08	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
56762	56762	SRR15813427	SRX12105531	SRS10085825	SRP249509	PRJNA606682	CellOracle: Dissecting cell identity via network inference and in silico gene perturbation	GSE145298	Other	Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.		pubmed:36755098	noto 3	GSM5567801	tissue:noto crispant\|strain:noto crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	noto 3	Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz	noto crispant		10x Genomcis Chromium single cell preparation		strain:noto crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	GSM5567801	GSM5567801: noto 3; Danio rerio; RNA Seq	GSM5567801		1	10x Genomcis Chromium single cell preparation	GEO Accession:GSM5567801	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP249509	assembly:GRCz11\|intentional duplicate	noto_3_possorted_genome_bam.bam	10X Genomics bam file	9696476250.0	107738625.0	GSM5567801 r1	0:90	A:2759552091;C:2046867650;G:2381514508;T:2503080064;N:5461937	90				2759552091	2046867650	2381514508	2503080064	5461937	SRX12105531	SRS10085825	SRA1042742	GEO	Washington University in St Louis	1	0.88572		0.24263		0.83228		0.5118		90		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-09-08	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
56763	56763	SRR15813426	SRX12105530	SRS10085824	SRP249509	PRJNA606682	CellOracle: Dissecting cell identity via network inference and in silico gene perturbation	GSE145298	Other	Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.		pubmed:36755098	noto 2	GSM5567800	tissue:noto crispant\|strain:noto crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	noto 2	Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz	noto crispant		10x Genomcis Chromium single cell preparation		strain:noto crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	GSM5567800	GSM5567800: noto 2; Danio rerio; RNA Seq	GSM5567800		1	10x Genomcis Chromium single cell preparation	GEO Accession:GSM5567800	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP249509	assembly:GRCz11\|intentional duplicate	noto_2_possorted_genome_bam.bam	10X Genomics bam file	6805896120.0	75621068.0	GSM5567800 r1	0:90	A:1937849673;C:1444333862;G:1669710397;T:1750230467;N:3771721	90				1937849673	1444333862	1669710397	1750230467	3771721	SRX12105530	SRS10085824	SRA1042742	GEO	Washington University in St Louis	1	0.88304		0.22942		0.82958		0.50945		90		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-09-08	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
56764	56764	SRR15813425	SRX12105529	SRS10085822	SRP249509	PRJNA606682	CellOracle: Dissecting cell identity via network inference and in silico gene perturbation	GSE145298	Other	Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.		pubmed:36755098	noto 1	GSM5567799	tissue:noto crispant\|strain:noto crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	noto 1	Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz	noto crispant		10x Genomcis Chromium single cell preparation		strain:noto crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	GSM5567799	GSM5567799: noto 1; Danio rerio; RNA Seq	GSM5567799		1	10x Genomcis Chromium single cell preparation	GEO Accession:GSM5567799	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP249509	assembly:GRCz11\|intentional duplicate	noto_1_possorted_genome_bam.bam	10X Genomics bam file	7424025120.0	82489168.0	GSM5567799 r1	0:90	A:2111968765;C:1577509540;G:1827370183;T:1903046323;N:4130309	90				2111968765	1577509540	1827370183	1903046323	4130309	SRX12105529	SRS10085822	SRA1042742	GEO	Washington University in St Louis	1	0.86603		0.22594		0.83073		0.51508		90		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-09-08	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
56765	56765	SRR15813424	SRX12105528	SRS10085823	SRP249509	PRJNA606682	CellOracle: Dissecting cell identity via network inference and in silico gene perturbation	GSE145298	Other	Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.		pubmed:36755098	lhx1a 4	GSM5567798	tissue:lhx1a crispant\|strain:lhx1a crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	lhx1a 4	Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz	lhx1a crispant		10x Genomcis Chromium single cell preparation		strain:lhx1a crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	GSM5567798	GSM5567798: lhx1a 4; Danio rerio; RNA Seq	GSM5567798		1	10x Genomcis Chromium single cell preparation	GEO Accession:GSM5567798	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP249509	assembly:GRCz11\|intentional duplicate	lhx1a_4_possorted_genome_bam.bam	10X Genomics bam file	22087787670.0	245419863.0	GSM5567798 r1	0:90	A:6475797345;C:4735192179;G:5275258568;T:5599207862;N:2331716	90				6475797345	4735192179	5275258568	5599207862	2331716	SRX12105528	SRS10085823	SRA1042742	GEO	Washington University in St Louis	1	0.91015		0.22744		0.83278		0.55743		90		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-09-08	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
56766	56766	SRR15813423	SRX12105527	SRS10085820	SRP249509	PRJNA606682	CellOracle: Dissecting cell identity via network inference and in silico gene perturbation	GSE145298	Other	Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.		pubmed:36755098	lhx1a 3	GSM5567797	tissue:lhx1a crispant\|strain:lhx1a crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	lhx1a 3	Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz	lhx1a crispant		10x Genomcis Chromium single cell preparation		strain:lhx1a crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	GSM5567797	GSM5567797: lhx1a 3; Danio rerio; RNA Seq	GSM5567797		1	10x Genomcis Chromium single cell preparation	GEO Accession:GSM5567797	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP249509	assembly:GRCz11\|intentional duplicate	lhx1a_3_possorted_genome_bam.bam	10X Genomics bam file	20620567800.0	229117420.0	GSM5567797 r1	0:90	A:5887591442;C:4508984476;G:5046355704;T:5175484329;N:2151849	90				5887591442	4508984476	5046355704	5175484329	2151849	SRX12105527	SRS10085820	SRA1042742	GEO	Washington University in St Louis	1	0.92195		0.22061		0.83224		0.56225		90		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-09-08	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
56767	56767	SRR15813422	SRX12105526	SRS10085821	SRP249509	PRJNA606682	CellOracle: Dissecting cell identity via network inference and in silico gene perturbation	GSE145298	Other	Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.		pubmed:36755098	lhx1a 2	GSM5567796	tissue:lhx1a crispant\|strain:lhx1a crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	lhx1a 2	Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz	lhx1a crispant		10x Genomcis Chromium single cell preparation		strain:lhx1a crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	GSM5567796	GSM5567796: lhx1a 2; Danio rerio; RNA Seq	GSM5567796		1	10x Genomcis Chromium single cell preparation	GEO Accession:GSM5567796	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP249509	assembly:GRCz11\|intentional duplicate	lhx1a_2_possorted_genome_bam.bam	10X Genomics bam file	9946966230.0	110521847.0	GSM5567796 r1	0:90	A:2788146910;C:2206643231;G:2469755316;T:2481819884;N:600889	90				2788146910	2206643231	2469755316	2481819884	600889	SRX12105526	SRS10085821	SRA1042742	GEO	Washington University in St Louis	1	0.91371		0.24403		0.82629		0.58866		90		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-09-08	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
56768	56768	SRR15813421	SRX12105525	SRS10085819	SRP249509	PRJNA606682	CellOracle: Dissecting cell identity via network inference and in silico gene perturbation	GSE145298	Other	Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.		pubmed:36755098	lhx1a 1	GSM5567795	tissue:lhx1a crispant\|strain:lhx1a crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	lhx1a 1	Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz	lhx1a crispant		10x Genomcis Chromium single cell preparation		strain:lhx1a crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	GSM5567795	GSM5567795: lhx1a 1; Danio rerio; RNA Seq	GSM5567795		1	10x Genomcis Chromium single cell preparation	GEO Accession:GSM5567795	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP249509	assembly:GRCz11\|intentional duplicate	lhx1a_1_possorted_genome_bam.bam	10X Genomics bam file	19493469630.0	216594107.0	GSM5567795 r1	0:90	A:5626093917;C:4175669632;G:4665965196;T:5024562911;N:1177974	90				5626093917	4175669632	4665965196	5024562911	1177974	SRX12105525	SRS10085819	SRA1042742	GEO	Washington University in St Louis	1	0.90552		0.2132		0.81921		0.56307		90		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-09-08	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
56769	56769	SRR15813420	SRX12105524	SRS10085818	SRP249509	PRJNA606682	CellOracle: Dissecting cell identity via network inference and in silico gene perturbation	GSE145298	Other	Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.		pubmed:36755098	irx3a 3	GSM5567794	tissue:irx3a crispant\|strain:irx3a crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	irx3a 3	Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz	irx3a crispant		10x Genomcis Chromium single cell preparation		strain:irx3a crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	GSM5567794	GSM5567794: irx3a 3; Danio rerio; RNA Seq	GSM5567794		1	10x Genomcis Chromium single cell preparation	GEO Accession:GSM5567794	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP249509	assembly:GRCz11\|intentional duplicate	irx3a_3_possorted_genome_bam.bam	10X Genomics bam file	8702629560.0	96695884.0	GSM5567794 r1	0:90	A:2502778147;C:1869454970;G:2100874536;T:2226298889;N:3223018	90				2502778147	1869454970	2100874536	2226298889	3223018	SRX12105524	SRS10085818	SRA1042742	GEO	Washington University in St Louis	1	0.93135		0.17699		0.83031		0.56065		90		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-09-08	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
56770	56770	SRR15813419	SRX12105523	SRS10085814	SRP249509	PRJNA606682	CellOracle: Dissecting cell identity via network inference and in silico gene perturbation	GSE145298	Other	Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.		pubmed:36755098	irx3a 2	GSM5567793	tissue:irx3a crispant\|strain:irx3a crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	irx3a 2	Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz	irx3a crispant		10x Genomcis Chromium single cell preparation		strain:irx3a crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	GSM5567793	GSM5567793: irx3a 2; Danio rerio; RNA Seq	GSM5567793		1	10x Genomcis Chromium single cell preparation	GEO Accession:GSM5567793	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP249509	assembly:GRCz11\|intentional duplicate	irx3a_2_possorted_genome_bam.bam	10X Genomics bam file	13516567200.0	150184080.0	GSM5567793 r1	0:90	A:3934125495;C:2881926208;G:3210954290;T:3485647605;N:3913602	90				3934125495	2881926208	3210954290	3485647605	3913602	SRX12105523	SRS10085814	SRA1042742	GEO	Washington University in St Louis	1	0.92263		0.18193		0.8267		0.55492		90		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-09-08	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
56771	56771	SRR15813418	SRX12105522	SRS10085815	SRP249509	PRJNA606682	CellOracle: Dissecting cell identity via network inference and in silico gene perturbation	GSE145298	Other	Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.		pubmed:36755098	irx3a 1	GSM5567792	tissue:irx3a crispant\|strain:irx3a crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	irx3a 1	Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz	irx3a crispant		10x Genomcis Chromium single cell preparation		strain:irx3a crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	GSM5567792	GSM5567792: irx3a 1; Danio rerio; RNA Seq	GSM5567792		1	10x Genomcis Chromium single cell preparation	GEO Accession:GSM5567792	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP249509	assembly:GRCz11\|intentional duplicate	irx3a_1_possorted_genome_bam.bam	10X Genomics bam file	14095641960.0	156618244.0	GSM5567792 r1	0:90	A:4094793830;C:2977588403;G:3309296706;T:3709972016;N:3991005	90				4094793830	2977588403	3309296706	3709972016	3991005	SRX12105522	SRS10085815	SRA1042742	GEO	Washington University in St Louis	1	0.93495		0.16833		0.82505		0.54259		90		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-09-08	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
56772	56772	SRR15813417	SRX12105521	SRS10085817	SRP249509	PRJNA606682	CellOracle: Dissecting cell identity via network inference and in silico gene perturbation	GSE145298	Other	Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.		pubmed:36755098	flh mut 2	GSM5567791	tissue:flh mutant\|strain:floating head mutant n1/n1\|Stage:10 hpf\|experiment:Mutant embryos were generated by crossing heterozygous and selecting mutants based on their morphology at 10 hpf.	flh mut 2	Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz	flh mutant		10x Genomcis Chromium single cell preparation		strain:floating head mutant n1/n1\|Stage:10 hpf\|experiment:Mutant embryos were generated by crossing heterozygous and selecting mutants based on their morphology at 10 hpf.	GSM5567791	GSM5567791: flh mut 2; Danio rerio; RNA Seq	GSM5567791		1	10x Genomcis Chromium single cell preparation	GEO Accession:GSM5567791	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP249509	assembly:GRCz11\|intentional duplicate	flh_mut_2_possorted_genome_bam.bam	10X Genomics bam file	16092806220.0	178808958.0	GSM5567791 r1	0:90	A:4808364717;C:3262784563;G:3632229222;T:4384293862;N:5133856	90				4808364717	3262784563	3632229222	4384293862	5133856	SRX12105521	SRS10085817	SRA1042742	GEO	Washington University in St Louis	1	0.91587		0.25603		0.8199		0.54642		90		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-09-08	Gastrula	Embryo	Head	Nervous System
56773	56773	SRR15813416	SRX12105520	SRS10085816	SRP249509	PRJNA606682	CellOracle: Dissecting cell identity via network inference and in silico gene perturbation	GSE145298	Other	Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.		pubmed:36755098	flh mut 1	GSM5567790	tissue:flh mutant\|strain:floating head mutant n1/n1\|Stage:10 hpf\|experiment:Mutant embryos were generated by crossing heterozygous and selecting mutants based on their morphology at 10 hpf.	flh mut 1	Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz	flh mutant		10x Genomcis Chromium single cell preparation		strain:floating head mutant n1/n1\|Stage:10 hpf\|experiment:Mutant embryos were generated by crossing heterozygous and selecting mutants based on their morphology at 10 hpf.	GSM5567790	GSM5567790: flh mut 1; Danio rerio; RNA Seq	GSM5567790		1	10x Genomcis Chromium single cell preparation	GEO Accession:GSM5567790	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP249509	assembly:GRCz11\|intentional duplicate	flh_mut_1_possorted_genome_bam.bam	10X Genomics bam file	20399851800.0	226665020.0	GSM5567790 r1	0:90	A:6026150068;C:4212547690;G:4691267625;T:5463467796;N:6418621	90				6026150068	4212547690	4691267625	5463467796	6418621	SRX12105520	SRS10085816	SRA1042742	GEO	Washington University in St Louis	1	0.91268		0.26785		0.81288		0.49462		90		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-09-08	Gastrula	Embryo	Head	Nervous System
56774	56774	SRR15813415	SRX12105519	SRS10085813	SRP249509	PRJNA606682	CellOracle: Dissecting cell identity via network inference and in silico gene perturbation	GSE145298	Other	Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.		pubmed:36755098	flh control 2	GSM5567789	tissue:control of flh mutant\|strain:floating head mutant +/+ and +/n1\|Stage:10 hpf\|experiment:Control embryos were generated by crossing heterozygous and selecting mutants based on their morphology at 10 hpf.	flh control 2	Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz	control of flh mutant		10x Genomcis Chromium single cell preparation		strain:floating head mutant +/+ and +/n1\|Stage:10 hpf\|experiment:Control embryos were generated by crossing heterozygous and selecting mutants based on their morphology at 10 hpf.	GSM5567789	GSM5567789: flh control 2; Danio rerio; RNA Seq	GSM5567789		1	10x Genomcis Chromium single cell preparation	GEO Accession:GSM5567789	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP249509	assembly:GRCz11\|intentional duplicate	flh_control_2_possorted_genome_bam.bam	10X Genomics bam file	24602487300.0	273360970.0	GSM5567789 r1	0:90	A:7284609077;C:5102535766;G:5760617216;T:6447307892;N:7417349	90				7284609077	5102535766	5760617216	6447307892	7417349	SRX12105519	SRS10085813	SRA1042742	GEO	Washington University in St Louis	1	0.91331		0.19905		0.82925		0.53189		90		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-09-08	Gastrula	Embryo	Head	Nervous System
56775	56775	SRR15813414	SRX12105518	SRS10085811	SRP249509	PRJNA606682	CellOracle: Dissecting cell identity via network inference and in silico gene perturbation	GSE145298	Other	Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.		pubmed:36755098	flh control 1	GSM5567788	tissue:control of flh mutant\|strain:floating head mutant +/+ and +/n1\|Stage:10 hpf\|experiment:Control embryos were generated by crossing heterozygous and selecting mutants based on their morphology at 10 hpf.	flh control 1	Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz	control of flh mutant		10x Genomcis Chromium single cell preparation		strain:floating head mutant +/+ and +/n1\|Stage:10 hpf\|experiment:Control embryos were generated by crossing heterozygous and selecting mutants based on their morphology at 10 hpf.	GSM5567788	GSM5567788: flh control 1; Danio rerio; RNA Seq	GSM5567788		1	10x Genomcis Chromium single cell preparation	GEO Accession:GSM5567788	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP249509	assembly:GRCz11\|intentional duplicate	flh_control_1_possorted_genome_bam.bam	10X Genomics bam file	15510481200.0	172338680.0	GSM5567788 r1	0:90	A:4537923297;C:3229068006;G:3600057890;T:4138746065;N:4685942	90				4537923297	3229068006	3600057890	4138746065	4685942	SRX12105518	SRS10085811	SRA1042742	GEO	Washington University in St Louis	1	0.92203		0.24638		0.81274		0.51857		90		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-09-08	Gastrula	Embryo	Head	Nervous System
61425	61425	SRR12749598	SRX9221555	SRS7455256	SRP285948	PRJNA666689	Spatio temporal mRNA tracking in the early zebrafish embryo	GSE158849	Other	We performed spatially resolved transcriptomics with sub single cell resolution in zebrafish embryos at the one cell stage which allowed us to identify a class of mRNAs that is specifically localized at an extraembryonic position in the yolk sac the vegetal pole. The three prime UTRs of these localized genes are enriched in specific sequence motifs. Comparison to two frog species revealed relatively low conservation of localized genes but high conservation of sequence motifs. In vivo RNA labeling followed by scRNA seq revealed that a large number of the localized transcripts are specifically transported to the primordial germ cells. Overall design: Spatial transcriptomic data tomo seq from zebrafish one cell stage embroys mature X. laevis and X. tropicalis oocytes. Single cell metabolic labeling scSLAM seq of zebrafish embryos at 6 hpf.		pubmed:34099733	scSLAM seq replicate 1	GSM4812182	tissue:shield stage embryos 6 hpf\|strain:AB wildtype\|treatment:4sUTP injected\|extraction protocol:Methanol fixed single cell suspension 10x Genomics transcriptome.	scSLAM seq replicate 1	zebrafish tomo seq demultiplexing with bcl2fastq v2.18.0.12 mapping with STAR v2.5.3a split counts by section barcode Genome build: GRCz10 release 90 Supplementary files format and content: csv file containing gene counts per section xenopus tomo seq demultiplexing with bcl2fastq v2.18.0.12 mapping with STAR v2.5.3a split counts by section barcode and translate gene identifier to gene names Genome build: X. tropicalis v9.1 genome assembly X.laevis v9.2 genome assembly Supplementary files format and content: csv file containing gene counts per section scSLAM seq zebrafish demultiplexing using cellranger mkfastq v3.0.2 mapping and whitelisting of cells with cellranger v3.0.2 splitting labeled reads >1 T C mutation from unlabeled into separate fastq files submitted to this GEO entry mapping with STARsolo v2.7.0f 0328 single cell analysis in seurat v3.1.2 Genome build: GRCz11 Supplementary files format and content: barcodes.tsv list of barcodes genes.tsv list of genes and matrix.tsv count matrix	shield stage embryos 6 hpf		none provided by the submitter		strain:AB wildtype\|treatment:4sUTP injected\|extraction protocol:Methanol fixed single cell suspension 10x Genomics transcriptome.	GSM4812182	GSM4812182: scSLAM seq replicate 1; Danio rerio; RNA Seq	GSM4812182		1	none provided by the submitter	GEO Accession:GSM4812182	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP285948		scSLAMseq.zebrafish.6hpf.R1.fastq.gz scSLAMseq.zebrafish.6hpf.R2.fastq.gz	fastq fastq	18763873688.0	151321562.0	GSM4812182 r1	0:26 1:98	A:5330726187;C:3994611684;G:4055930332;T:5373535151;N:9070334	26	98			5330726187	3994611684	4055930332	5373535151	9070334	SRX9221555	SRS7455256	SRA1136461	GEO	Junker, BIMSB, MDC	2	0.00126	0.81459	0.0004	0.05503	0.99717	0.82674	0.52121	0.58038	26	98	T	B	sc-like readlen	illumina	hiseq_era	3prime	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Germany	2020-09-30	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
63039	63039	SRR13565187	SRX9963431	SRS8137097	SRP303506	PRJNA695274	Single cell response landscape of graded Nodal signaling in zebrafish explants [single cell RNA seq]	GSE165653	Transcriptome Analysis	Purpose: To construct cell landscape of graded Nodal signaling in zebrafish explants. Methods: Nodal injected explants injected with 10pg ndr2 mRNA were harvested at xxxhpf 5hpf 6hpf 8hpf 10hpf 24hpf. Libraries were prepared using Chromium Controller and Chromium Single Cell three primeLibrary & Gel Bead Kit v2 10x Genomics PN 120237 according to the manufacturer's protocol for 10000 cells recovery. Results: A total of 42 317 single cell transcriptomes were collected post stringent quality control measures. Conclusions: 19 Cell types from 6 developmental stages were identified Nodal explant mainly contains the axial mesoderm prechordal plate and notochord and anterior posterior patterned head structures. Overall design: zebrafish explants injected with 10pg ndr2 mRNA were harvested at xxxhpf 5hpf 6hpf 8hpf 10hpf 24hpf for scRNA seq.	parent bioproject:PRJNA695267	pubmed:37729057	zebrafish Nodal explants 10hpf	GSM5047615	source name:zebrafish cells\|strain:AB\|tissue:embryonic cells\|age:10hpf\|treatment:injected with 10pg ndr2 mRNA	zebrafish Nodal explants 10hpf	Illumina sequencing reads were aligned to the zebrafish mRNA reference genome GRCz11 or GRCz10 using the 10x Genomics CellRanger pipeline version 2.1.1 with default parameters. Genome build: GRCz11/GRCz10 Supplementary files format and content: tar compressed files included filtered gene bc matrices post running CellRanger pipeline	zebrafish cells	10pg of ndr2 mRNA was injected to one cell of embryonic animal pole at xxx cell stage. All embryos were incubated in 0.3x Danieau buffer until 1k stage then were transferred to Dulbecco's Modified Eagle Medium. Animal pole explants corresponding roughly to half of the blastula were incubated to 4hpf 5hpf 6hpf 8hpf 10hpf and 24hpf corresponding to embryonic developmental stage separately.	Libraries were prepared using Chromium Controller and Chromium Single Cell 3’Library & Gel Bead Kit v2 10x Genomics PN 120237 according to the manufacturer’s protocol for 10000 cells recovery.	explants were cultured in a Petri dish coated with 1.5% agarose filled with Dulbecco's Modified Eagle Medium	strain:AB\|tissue:embryonic cells\|age:10hpf\|treatment:injected with 10pg ndr2 mRNA	GSM5047615	GSM5047615: zebrafish Nodal explants 10hpf; Danio rerio; RNA Seq	GSM5047615		1	Libraries were prepared using Chromium Controller and Chromium Single Cell three primeLibrary & Gel Bead Kit v2 10x Genomics PN 120237 according to the manufacturer's protocol for 10000 cells recovery.	GEO Accession:GSM5047615	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP303506		wt_cyc_10hpf_S4_L002_R1_001.fastq.gz wt_cyc_10hpf_S4_L002_R2_001.fastq.gz	fastq fastq	91961453064.0	519556232.0	GSM5047615 r1	0:26 1:151	A:27264345194;C:18865491810;G:20605255683;T:25224284164;N:2076213	26	151			27264345194	18865491810	20605255683	25224284164	2076213	SRX9963431	SRS8137097	SRA1188621	GEO	Institute of genetics, Zhejiang University	2	0.00462	0.90539	0.00122	0.10015	0.99022	0.81513	0.43095	0.51015	26	151	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2021-01-27	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
63040	63040	SRR13565186	SRX9963430	SRS8137096	SRP303506	PRJNA695274	Single cell response landscape of graded Nodal signaling in zebrafish explants [single cell RNA seq]	GSE165653	Transcriptome Analysis	Purpose: To construct cell landscape of graded Nodal signaling in zebrafish explants. Methods: Nodal injected explants injected with 10pg ndr2 mRNA were harvested at xxxhpf 5hpf 6hpf 8hpf 10hpf 24hpf. Libraries were prepared using Chromium Controller and Chromium Single Cell three primeLibrary & Gel Bead Kit v2 10x Genomics PN 120237 according to the manufacturer's protocol for 10000 cells recovery. Results: A total of 42 317 single cell transcriptomes were collected post stringent quality control measures. Conclusions: 19 Cell types from 6 developmental stages were identified Nodal explant mainly contains the axial mesoderm prechordal plate and notochord and anterior posterior patterned head structures. Overall design: zebrafish explants injected with 10pg ndr2 mRNA were harvested at xxxhpf 5hpf 6hpf 8hpf 10hpf 24hpf for scRNA seq.	parent bioproject:PRJNA695267	pubmed:37729057	zebrafish Nodal explants 8hpf	GSM5047614	source name:zebrafish cells\|strain:AB\|tissue:embryonic cells\|age:8hpf\|treatment:injected with 10pg ndr2 mRNA	zebrafish Nodal explants 8hpf	Illumina sequencing reads were aligned to the zebrafish mRNA reference genome GRCz11 or GRCz10 using the 10x Genomics CellRanger pipeline version 2.1.1 with default parameters. Genome build: GRCz11/GRCz10 Supplementary files format and content: tar compressed files included filtered gene bc matrices post running CellRanger pipeline	zebrafish cells	10pg of ndr2 mRNA was injected to one cell of embryonic animal pole at xxx cell stage. All embryos were incubated in 0.3x Danieau buffer until 1k stage then were transferred to Dulbecco's Modified Eagle Medium. Animal pole explants corresponding roughly to half of the blastula were incubated to 4hpf 5hpf 6hpf 8hpf 10hpf and 24hpf corresponding to embryonic developmental stage separately.	Libraries were prepared using Chromium Controller and Chromium Single Cell 3’Library & Gel Bead Kit v2 10x Genomics PN 120237 according to the manufacturer’s protocol for 10000 cells recovery.	explants were cultured in a Petri dish coated with 1.5% agarose filled with Dulbecco's Modified Eagle Medium	strain:AB\|tissue:embryonic cells\|age:8hpf\|treatment:injected with 10pg ndr2 mRNA	GSM5047614	GSM5047614: zebrafish Nodal explants 8hpf; Danio rerio; RNA Seq	GSM5047614		1	Libraries were prepared using Chromium Controller and Chromium Single Cell three primeLibrary & Gel Bead Kit v2 10x Genomics PN 120237 according to the manufacturer's protocol for 10000 cells recovery.	GEO Accession:GSM5047614	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP303506		wt_cyc_8hpf_S3_L002_R1_001.fastq.gz wt_cyc_8hpf_S3_L002_R2_001.fastq.gz	fastq fastq	85243156635.0	481599755.0	GSM5047614 r1	0:26 1:151	A:25256590409;C:17389002254;G:18983505108;T:23612132946;N:1925918	26	151			25256590409	17389002254	18983505108	23612132946	1925918	SRX9963430	SRS8137096	SRA1188621	GEO	Institute of genetics, Zhejiang University	2	0.00722	0.90801	0.0016	0.10314	0.98545	0.80931	0.45087	0.53205	26	151	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2021-01-27	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
63041	63041	SRR13565185	SRX9963429	SRS8137099	SRP303506	PRJNA695274	Single cell response landscape of graded Nodal signaling in zebrafish explants [single cell RNA seq]	GSE165653	Transcriptome Analysis	Purpose: To construct cell landscape of graded Nodal signaling in zebrafish explants. Methods: Nodal injected explants injected with 10pg ndr2 mRNA were harvested at xxxhpf 5hpf 6hpf 8hpf 10hpf 24hpf. Libraries were prepared using Chromium Controller and Chromium Single Cell three primeLibrary & Gel Bead Kit v2 10x Genomics PN 120237 according to the manufacturer's protocol for 10000 cells recovery. Results: A total of 42 317 single cell transcriptomes were collected post stringent quality control measures. Conclusions: 19 Cell types from 6 developmental stages were identified Nodal explant mainly contains the axial mesoderm prechordal plate and notochord and anterior posterior patterned head structures. Overall design: zebrafish explants injected with 10pg ndr2 mRNA were harvested at xxxhpf 5hpf 6hpf 8hpf 10hpf 24hpf for scRNA seq.	parent bioproject:PRJNA695267	pubmed:37729057	zebrafish Nodal explants 6hpf	GSM5047613	source name:zebrafish cells\|strain:AB\|tissue:embryonic cells\|age:6hpf\|treatment:injected with 10pg ndr2 mRNA	zebrafish Nodal explants 6hpf	Illumina sequencing reads were aligned to the zebrafish mRNA reference genome GRCz11 or GRCz10 using the 10x Genomics CellRanger pipeline version 2.1.1 with default parameters. Genome build: GRCz11/GRCz10 Supplementary files format and content: tar compressed files included filtered gene bc matrices post running CellRanger pipeline	zebrafish cells	10pg of ndr2 mRNA was injected to one cell of embryonic animal pole at xxx cell stage. All embryos were incubated in 0.3x Danieau buffer until 1k stage then were transferred to Dulbecco's Modified Eagle Medium. Animal pole explants corresponding roughly to half of the blastula were incubated to 4hpf 5hpf 6hpf 8hpf 10hpf and 24hpf corresponding to embryonic developmental stage separately.	Libraries were prepared using Chromium Controller and Chromium Single Cell 3’Library & Gel Bead Kit v2 10x Genomics PN 120237 according to the manufacturer’s protocol for 10000 cells recovery.	explants were cultured in a Petri dish coated with 1.5% agarose filled with Dulbecco's Modified Eagle Medium	strain:AB\|tissue:embryonic cells\|age:6hpf\|treatment:injected with 10pg ndr2 mRNA	GSM5047613	GSM5047613: zebrafish Nodal explants 6hpf; Danio rerio; RNA Seq	GSM5047613		1	Libraries were prepared using Chromium Controller and Chromium Single Cell three primeLibrary & Gel Bead Kit v2 10x Genomics PN 120237 according to the manufacturer's protocol for 10000 cells recovery.	GEO Accession:GSM5047613	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP303506		wt_cyc_6hpf_S1_L004_R1_001.fastq.gz wt_cyc_6hpf_S1_L004_R2_001.fastq.gz	fastq fastq	120375311594.0	398593747.0	GSM5047613 r1	0:151 1:151	A:31070717775;C:21268441476;G:21658594109;T:46362015215;N:15543019	151	151			31070717775	21268441476	21658594109	46362015215	15543019	SRX9963429	SRS8137099	SRA1188621	GEO	Institute of genetics, Zhejiang University	2	0.11581	0.88209	0.0154	0.11076	0.97153	0.79813	0.51657	0.53551	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2021-01-27	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
64415	64415	SRR14703474	SRX11041474	SRS9110402	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 scRNA seq rep2	GSM5351829	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 scRNA 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.	Cell dissociation protocol was based on a previously described method Farrell et al. 2018 with modifications to adapt it for 10x Genomics platform. Briefly dnmt1 mKD and control embryos were collected 20 min post fertilization and cultured as mentioned before. Then 15 embryos at dome or shield stages for each sample were transferred into plastic Petri dishes that had previously been coated with 2% agarose and soaked with DMEM/F12 media Gibco/Life Technologies Cat 11330032 at least 2hrs. Next embryos at desired stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 µl DMEM/F12 media. Dissections were performed for up 15 min. The volume of DMEM/F12 meida containing embryos was adjusted to 200 µl then cells were mechanically dissociated by flicking the tube 30 times and pipetting mixture 10 times through a 200 µl tip. The volume was adjusted to 1 ml with PBS containing 1.0% BSA and spun to pellet cells at 300 g for 30s. The supernatant was removed and cells were resuspended in 80 µl of PBS containing 0.1% BSA and 20% Optiprep StemCell Cat 07820 aiming for a concentration above 100 cells/µl. Cells were then passed through a cell sieve 100 µm for dome stage and 70 µm for shield stage. Single cell RNA seq library was performed with Chromium Next GEM Single Cell kit 10x Genomics Cat PN 1000121 based on standard protocol. 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	GSM5351829	GSM5351829: Shield dnmt1 mKD scRNA seq rep2; Danio rerio; RNA Seq	GSM5351829		1	Cell dissociation protocol was based on a previously described method Farrell et al. 2018 with modifications to adapt it for 10x Genomics platform. Briefly dnmt1 mKD and control embryos were collected 20 min post fertilization and cultured as mentioned before. Then 15 embryos at dome or shield stages for each sample were transferred into plastic Petri dishes that had previously been coated with 2% agarose and soaked with DMEM/F12 media Gibco/Life Technologies Cat 11330032 at least 2hrs. Next embryos at desired stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 µl DMEM/F12 media. Dissections were performed for up 15 min. The volume of DMEM/F12 meida containing embryos was adjusted to 200 µl then cells were mechanically dissociated by flicking the tube 30 times and pipetting mixture 10 times through a 200 µl tip. The volume was adjusted to 1 ml with PBS containing 1.0% BSA and spun to pellet cells at 300 g for 30s. The supernatant was removed and cells were resuspended in 80 µl of PBS containing 0.1% BSA and 20% Optiprep StemCell Cat 07820 aiming for a concentration above 100 cells/µl. Cells were then passed through a cell sieve 100 µm for dome stage and 70 µm for shield stage. Single cell RNA seq library was performed with Chromium Next GEM Single Cell kit 10x Genomics Cat PN 1000121 based on standard protocol. All libraries were sequenced by Illumina Hi Seq 1500 or 2500 or XTen platform according to manufacturer's instruction.	GEO Accession:GSM5351829	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 1500	SRP322195	loader:fastq load.py	Shield_dnmt1_mKD_scRNA_seq_rep2_1_r1.fq.gz Shield_dnmt1_mKD_scRNA_seq_rep2_1_r2.fq.gz	fastq fastq	8320528500.0	27735095.0	GSM5351829 r1	0:150 1:150	A:2105597099;C:1420133786;G:1547205190;T:3246212304;N:1380121	150	150			2105597099	1420133786	1547205190	3246212304	1380121	SRX11041474	SRS9110402	SRA1239365	GEO	THU-PKU Center for Life Sciences, Tsinghua University	2	0.30443	0.87115	0.06891	0.14527	0.95538	0.79011	0.57012	0.52481	150	150	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2021-06-01	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
64416	64416	SRR14703475	SRX11041474	SRS9110402	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 scRNA seq rep2	GSM5351829	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 scRNA 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.	Cell dissociation protocol was based on a previously described method Farrell et al. 2018 with modifications to adapt it for 10x Genomics platform. Briefly dnmt1 mKD and control embryos were collected 20 min post fertilization and cultured as mentioned before. Then 15 embryos at dome or shield stages for each sample were transferred into plastic Petri dishes that had previously been coated with 2% agarose and soaked with DMEM/F12 media Gibco/Life Technologies Cat 11330032 at least 2hrs. Next embryos at desired stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 µl DMEM/F12 media. Dissections were performed for up 15 min. The volume of DMEM/F12 meida containing embryos was adjusted to 200 µl then cells were mechanically dissociated by flicking the tube 30 times and pipetting mixture 10 times through a 200 µl tip. The volume was adjusted to 1 ml with PBS containing 1.0% BSA and spun to pellet cells at 300 g for 30s. The supernatant was removed and cells were resuspended in 80 µl of PBS containing 0.1% BSA and 20% Optiprep StemCell Cat 07820 aiming for a concentration above 100 cells/µl. Cells were then passed through a cell sieve 100 µm for dome stage and 70 µm for shield stage. Single cell RNA seq library was performed with Chromium Next GEM Single Cell kit 10x Genomics Cat PN 1000121 based on standard protocol. 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	GSM5351829	GSM5351829: Shield dnmt1 mKD scRNA seq rep2; Danio rerio; RNA Seq	GSM5351829		1	Cell dissociation protocol was based on a previously described method Farrell et al. 2018 with modifications to adapt it for 10x Genomics platform. Briefly dnmt1 mKD and control embryos were collected 20 min post fertilization and cultured as mentioned before. Then 15 embryos at dome or shield stages for each sample were transferred into plastic Petri dishes that had previously been coated with 2% agarose and soaked with DMEM/F12 media Gibco/Life Technologies Cat 11330032 at least 2hrs. Next embryos at desired stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 µl DMEM/F12 media. Dissections were performed for up 15 min. The volume of DMEM/F12 meida containing embryos was adjusted to 200 µl then cells were mechanically dissociated by flicking the tube 30 times and pipetting mixture 10 times through a 200 µl tip. The volume was adjusted to 1 ml with PBS containing 1.0% BSA and spun to pellet cells at 300 g for 30s. The supernatant was removed and cells were resuspended in 80 µl of PBS containing 0.1% BSA and 20% Optiprep StemCell Cat 07820 aiming for a concentration above 100 cells/µl. Cells were then passed through a cell sieve 100 µm for dome stage and 70 µm for shield stage. Single cell RNA seq library was performed with Chromium Next GEM Single Cell kit 10x Genomics Cat PN 1000121 based on standard protocol. All libraries were sequenced by Illumina Hi Seq 1500 or 2500 or XTen platform according to manufacturer's instruction.	GEO Accession:GSM5351829	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 1500	SRP322195	loader:fastq load.py	Shield_dnmt1_mKD_scRNA_seq_rep2_2_r1.fq.gz Shield_dnmt1_mKD_scRNA_seq_rep2_2_r2.fq.gz	fastq fastq	6318978300.0	21063261.0	GSM5351829 r2	0:150 1:150	A:1598979634;C:1081496399;G:1178603557;T:2458910615;N:988095	150	150			1598979634	1081496399	1178603557	2458910615	988095	SRX11041474	SRS9110402	SRA1239365	GEO	THU-PKU Center for Life Sciences, Tsinghua University	2	0.31116	0.86738	0.07245	0.14419	0.95461	0.79178	0.57077	0.52679	150	150	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2021-06-01	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
64417	64417	SRR14703476	SRX11041474	SRS9110402	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 scRNA seq rep2	GSM5351829	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 scRNA 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.	Cell dissociation protocol was based on a previously described method Farrell et al. 2018 with modifications to adapt it for 10x Genomics platform. Briefly dnmt1 mKD and control embryos were collected 20 min post fertilization and cultured as mentioned before. Then 15 embryos at dome or shield stages for each sample were transferred into plastic Petri dishes that had previously been coated with 2% agarose and soaked with DMEM/F12 media Gibco/Life Technologies Cat 11330032 at least 2hrs. Next embryos at desired stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 µl DMEM/F12 media. Dissections were performed for up 15 min. The volume of DMEM/F12 meida containing embryos was adjusted to 200 µl then cells were mechanically dissociated by flicking the tube 30 times and pipetting mixture 10 times through a 200 µl tip. The volume was adjusted to 1 ml with PBS containing 1.0% BSA and spun to pellet cells at 300 g for 30s. The supernatant was removed and cells were resuspended in 80 µl of PBS containing 0.1% BSA and 20% Optiprep StemCell Cat 07820 aiming for a concentration above 100 cells/µl. Cells were then passed through a cell sieve 100 µm for dome stage and 70 µm for shield stage. Single cell RNA seq library was performed with Chromium Next GEM Single Cell kit 10x Genomics Cat PN 1000121 based on standard protocol. 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	GSM5351829	GSM5351829: Shield dnmt1 mKD scRNA seq rep2; Danio rerio; RNA Seq	GSM5351829		1	Cell dissociation protocol was based on a previously described method Farrell et al. 2018 with modifications to adapt it for 10x Genomics platform. Briefly dnmt1 mKD and control embryos were collected 20 min post fertilization and cultured as mentioned before. Then 15 embryos at dome or shield stages for each sample were transferred into plastic Petri dishes that had previously been coated with 2% agarose and soaked with DMEM/F12 media Gibco/Life Technologies Cat 11330032 at least 2hrs. Next embryos at desired stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 µl DMEM/F12 media. Dissections were performed for up 15 min. The volume of DMEM/F12 meida containing embryos was adjusted to 200 µl then cells were mechanically dissociated by flicking the tube 30 times and pipetting mixture 10 times through a 200 µl tip. The volume was adjusted to 1 ml with PBS containing 1.0% BSA and spun to pellet cells at 300 g for 30s. The supernatant was removed and cells were resuspended in 80 µl of PBS containing 0.1% BSA and 20% Optiprep StemCell Cat 07820 aiming for a concentration above 100 cells/µl. Cells were then passed through a cell sieve 100 µm for dome stage and 70 µm for shield stage. Single cell RNA seq library was performed with Chromium Next GEM Single Cell kit 10x Genomics Cat PN 1000121 based on standard protocol. All libraries were sequenced by Illumina Hi Seq 1500 or 2500 or XTen platform according to manufacturer's instruction.	GEO Accession:GSM5351829	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 1500	SRP322195	loader:fastq load.py	Shield_dnmt1_mKD_scRNA_seq_rep2_3_r1.fq.gz Shield_dnmt1_mKD_scRNA_seq_rep2_3_r2.fq.gz	fastq fastq	9050701800.0	30169006.0	GSM5351829 r3	0:150 1:150	A:2288002561;C:1548337479;G:1689150326;T:3523745942;N:1465492	150	150			2288002561	1548337479	1689150326	3523745942	1465492	SRX11041474	SRS9110402	SRA1239365	GEO	THU-PKU Center for Life Sciences, Tsinghua University	2	0.31352	0.86933	0.07266	0.14625	0.95424	0.7903	0.57067	0.53204	150	150	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2021-06-01	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
64418	64418	SRR14703477	SRX11041474	SRS9110402	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 scRNA seq rep2	GSM5351829	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 scRNA 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.	Cell dissociation protocol was based on a previously described method Farrell et al. 2018 with modifications to adapt it for 10x Genomics platform. Briefly dnmt1 mKD and control embryos were collected 20 min post fertilization and cultured as mentioned before. Then 15 embryos at dome or shield stages for each sample were transferred into plastic Petri dishes that had previously been coated with 2% agarose and soaked with DMEM/F12 media Gibco/Life Technologies Cat 11330032 at least 2hrs. Next embryos at desired stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 µl DMEM/F12 media. Dissections were performed for up 15 min. The volume of DMEM/F12 meida containing embryos was adjusted to 200 µl then cells were mechanically dissociated by flicking the tube 30 times and pipetting mixture 10 times through a 200 µl tip. The volume was adjusted to 1 ml with PBS containing 1.0% BSA and spun to pellet cells at 300 g for 30s. The supernatant was removed and cells were resuspended in 80 µl of PBS containing 0.1% BSA and 20% Optiprep StemCell Cat 07820 aiming for a concentration above 100 cells/µl. Cells were then passed through a cell sieve 100 µm for dome stage and 70 µm for shield stage. Single cell RNA seq library was performed with Chromium Next GEM Single Cell kit 10x Genomics Cat PN 1000121 based on standard protocol. 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	GSM5351829	GSM5351829: Shield dnmt1 mKD scRNA seq rep2; Danio rerio; RNA Seq	GSM5351829		1	Cell dissociation protocol was based on a previously described method Farrell et al. 2018 with modifications to adapt it for 10x Genomics platform. Briefly dnmt1 mKD and control embryos were collected 20 min post fertilization and cultured as mentioned before. Then 15 embryos at dome or shield stages for each sample were transferred into plastic Petri dishes that had previously been coated with 2% agarose and soaked with DMEM/F12 media Gibco/Life Technologies Cat 11330032 at least 2hrs. Next embryos at desired stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 µl DMEM/F12 media. Dissections were performed for up 15 min. The volume of DMEM/F12 meida containing embryos was adjusted to 200 µl then cells were mechanically dissociated by flicking the tube 30 times and pipetting mixture 10 times through a 200 µl tip. The volume was adjusted to 1 ml with PBS containing 1.0% BSA and spun to pellet cells at 300 g for 30s. The supernatant was removed and cells were resuspended in 80 µl of PBS containing 0.1% BSA and 20% Optiprep StemCell Cat 07820 aiming for a concentration above 100 cells/µl. Cells were then passed through a cell sieve 100 µm for dome stage and 70 µm for shield stage. Single cell RNA seq library was performed with Chromium Next GEM Single Cell kit 10x Genomics Cat PN 1000121 based on standard protocol. All libraries were sequenced by Illumina Hi Seq 1500 or 2500 or XTen platform according to manufacturer's instruction.	GEO Accession:GSM5351829	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 1500	SRP322195	loader:fastq load.py	Shield_dnmt1_mKD_scRNA_seq_rep2_4_r1.fq.gz Shield_dnmt1_mKD_scRNA_seq_rep2_4_r2.fq.gz	fastq fastq	8862319500.0	29541065.0	GSM5351829 r4	0:150 1:150	A:2244457768;C:1514505215;G:1651568806;T:3450328965;N:1458746	150	150			2244457768	1514505215	1651568806	3450328965	1458746	SRX11041474	SRS9110402	SRA1239365	GEO	THU-PKU Center for Life Sciences, Tsinghua University	2	0.30948	0.86911	0.07131	0.14341	0.95469	0.78873	0.57167	0.52854	150	150	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2021-06-01	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
64419	64419	SRR14703470	SRX11041473	SRS9110400	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 scRNA seq rep1	GSM5351828	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 scRNA 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.	Cell dissociation protocol was based on a previously described method Farrell et al. 2018 with modifications to adapt it for 10x Genomics platform. Briefly dnmt1 mKD and control embryos were collected 20 min post fertilization and cultured as mentioned before. Then 15 embryos at dome or shield stages for each sample were transferred into plastic Petri dishes that had previously been coated with 2% agarose and soaked with DMEM/F12 media Gibco/Life Technologies Cat 11330032 at least 2hrs. Next embryos at desired stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 µl DMEM/F12 media. Dissections were performed for up 15 min. The volume of DMEM/F12 meida containing embryos was adjusted to 200 µl then cells were mechanically dissociated by flicking the tube 30 times and pipetting mixture 10 times through a 200 µl tip. The volume was adjusted to 1 ml with PBS containing 1.0% BSA and spun to pellet cells at 300 g for 30s. The supernatant was removed and cells were resuspended in 80 µl of PBS containing 0.1% BSA and 20% Optiprep StemCell Cat 07820 aiming for a concentration above 100 cells/µl. Cells were then passed through a cell sieve 100 µm for dome stage and 70 µm for shield stage. Single cell RNA seq library was performed with Chromium Next GEM Single Cell kit 10x Genomics Cat PN 1000121 based on standard protocol. 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	GSM5351828	GSM5351828: Shield dnmt1 mKD scRNA seq rep1; Danio rerio; RNA Seq	GSM5351828		1	Cell dissociation protocol was based on a previously described method Farrell et al. 2018 with modifications to adapt it for 10x Genomics platform. Briefly dnmt1 mKD and control embryos were collected 20 min post fertilization and cultured as mentioned before. Then 15 embryos at dome or shield stages for each sample were transferred into plastic Petri dishes that had previously been coated with 2% agarose and soaked with DMEM/F12 media Gibco/Life Technologies Cat 11330032 at least 2hrs. Next embryos at desired stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 µl DMEM/F12 media. Dissections were performed for up 15 min. The volume of DMEM/F12 meida containing embryos was adjusted to 200 µl then cells were mechanically dissociated by flicking the tube 30 times and pipetting mixture 10 times through a 200 µl tip. The volume was adjusted to 1 ml with PBS containing 1.0% BSA and spun to pellet cells at 300 g for 30s. The supernatant was removed and cells were resuspended in 80 µl of PBS containing 0.1% BSA and 20% Optiprep StemCell Cat 07820 aiming for a concentration above 100 cells/µl. Cells were then passed through a cell sieve 100 µm for dome stage and 70 µm for shield stage. Single cell RNA seq library was performed with Chromium Next GEM Single Cell kit 10x Genomics Cat PN 1000121 based on standard protocol. All libraries were sequenced by Illumina Hi Seq 1500 or 2500 or XTen platform according to manufacturer's instruction.	GEO Accession:GSM5351828	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 1500	SRP322195	loader:fastq load.py	Shield_dnmt1_mKD_scRNA_seq_rep1_1_r1.fq.gz Shield_dnmt1_mKD_scRNA_seq_rep1_1_r2.fq.gz	fastq fastq	14255591400.0	47518638.0	GSM5351828 r1	0:150 1:150	A:3482332941;C:2727265509;G:2901494394;T:5143512105;N:986451	150	150			3482332941	2727265509	2901494394	5143512105	986451	SRX11041473	SRS9110400	SRA1239365	GEO	THU-PKU Center for Life Sciences, Tsinghua University	2	0.59011	0.90923	0.1963	0.20724	0.95974	0.77678	0.61246	0.4963	150	150	B	B	mate1-mate2 similar by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2021-06-01	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
64420	64420	SRR14703471	SRX11041473	SRS9110400	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 scRNA seq rep1	GSM5351828	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 scRNA 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.	Cell dissociation protocol was based on a previously described method Farrell et al. 2018 with modifications to adapt it for 10x Genomics platform. Briefly dnmt1 mKD and control embryos were collected 20 min post fertilization and cultured as mentioned before. Then 15 embryos at dome or shield stages for each sample were transferred into plastic Petri dishes that had previously been coated with 2% agarose and soaked with DMEM/F12 media Gibco/Life Technologies Cat 11330032 at least 2hrs. Next embryos at desired stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 µl DMEM/F12 media. Dissections were performed for up 15 min. The volume of DMEM/F12 meida containing embryos was adjusted to 200 µl then cells were mechanically dissociated by flicking the tube 30 times and pipetting mixture 10 times through a 200 µl tip. The volume was adjusted to 1 ml with PBS containing 1.0% BSA and spun to pellet cells at 300 g for 30s. The supernatant was removed and cells were resuspended in 80 µl of PBS containing 0.1% BSA and 20% Optiprep StemCell Cat 07820 aiming for a concentration above 100 cells/µl. Cells were then passed through a cell sieve 100 µm for dome stage and 70 µm for shield stage. Single cell RNA seq library was performed with Chromium Next GEM Single Cell kit 10x Genomics Cat PN 1000121 based on standard protocol. 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	GSM5351828	GSM5351828: Shield dnmt1 mKD scRNA seq rep1; Danio rerio; RNA Seq	GSM5351828		1	Cell dissociation protocol was based on a previously described method Farrell et al. 2018 with modifications to adapt it for 10x Genomics platform. Briefly dnmt1 mKD and control embryos were collected 20 min post fertilization and cultured as mentioned before. Then 15 embryos at dome or shield stages for each sample were transferred into plastic Petri dishes that had previously been coated with 2% agarose and soaked with DMEM/F12 media Gibco/Life Technologies Cat 11330032 at least 2hrs. Next embryos at desired stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 µl DMEM/F12 media. Dissections were performed for up 15 min. The volume of DMEM/F12 meida containing embryos was adjusted to 200 µl then cells were mechanically dissociated by flicking the tube 30 times and pipetting mixture 10 times through a 200 µl tip. The volume was adjusted to 1 ml with PBS containing 1.0% BSA and spun to pellet cells at 300 g for 30s. The supernatant was removed and cells were resuspended in 80 µl of PBS containing 0.1% BSA and 20% Optiprep StemCell Cat 07820 aiming for a concentration above 100 cells/µl. Cells were then passed through a cell sieve 100 µm for dome stage and 70 µm for shield stage. Single cell RNA seq library was performed with Chromium Next GEM Single Cell kit 10x Genomics Cat PN 1000121 based on standard protocol. All libraries were sequenced by Illumina Hi Seq 1500 or 2500 or XTen platform according to manufacturer's instruction.	GEO Accession:GSM5351828	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 1500	SRP322195	loader:fastq load.py	Shield_dnmt1_mKD_scRNA_seq_rep1_2_r1.fq.gz Shield_dnmt1_mKD_scRNA_seq_rep1_2_r2.fq.gz	fastq fastq	14937687600.0	49792292.0	GSM5351828 r2	0:150 1:150	A:3647549567;C:2855150136;G:3024269993;T:5409675339;N:1042565	150	150			3647549567	2855150136	3024269993	5409675339	1042565	SRX11041473	SRS9110400	SRA1239365	GEO	THU-PKU Center for Life Sciences, Tsinghua University	2	0.58483	0.91017	0.19691	0.20681	0.96067	0.77542	0.59579	0.49927	150	150	B	B	mate1-mate2 similar by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2021-06-01	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
64421	64421	SRR14703472	SRX11041473	SRS9110400	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 scRNA seq rep1	GSM5351828	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 scRNA 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.	Cell dissociation protocol was based on a previously described method Farrell et al. 2018 with modifications to adapt it for 10x Genomics platform. Briefly dnmt1 mKD and control embryos were collected 20 min post fertilization and cultured as mentioned before. Then 15 embryos at dome or shield stages for each sample were transferred into plastic Petri dishes that had previously been coated with 2% agarose and soaked with DMEM/F12 media Gibco/Life Technologies Cat 11330032 at least 2hrs. Next embryos at desired stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 µl DMEM/F12 media. Dissections were performed for up 15 min. The volume of DMEM/F12 meida containing embryos was adjusted to 200 µl then cells were mechanically dissociated by flicking the tube 30 times and pipetting mixture 10 times through a 200 µl tip. The volume was adjusted to 1 ml with PBS containing 1.0% BSA and spun to pellet cells at 300 g for 30s. The supernatant was removed and cells were resuspended in 80 µl of PBS containing 0.1% BSA and 20% Optiprep StemCell Cat 07820 aiming for a concentration above 100 cells/µl. Cells were then passed through a cell sieve 100 µm for dome stage and 70 µm for shield stage. Single cell RNA seq library was performed with Chromium Next GEM Single Cell kit 10x Genomics Cat PN 1000121 based on standard protocol. 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	GSM5351828	GSM5351828: Shield dnmt1 mKD scRNA seq rep1; Danio rerio; RNA Seq	GSM5351828		1	Cell dissociation protocol was based on a previously described method Farrell et al. 2018 with modifications to adapt it for 10x Genomics platform. Briefly dnmt1 mKD and control embryos were collected 20 min post fertilization and cultured as mentioned before. Then 15 embryos at dome or shield stages for each sample were transferred into plastic Petri dishes that had previously been coated with 2% agarose and soaked with DMEM/F12 media Gibco/Life Technologies Cat 11330032 at least 2hrs. Next embryos at desired stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 µl DMEM/F12 media. Dissections were performed for up 15 min. The volume of DMEM/F12 meida containing embryos was adjusted to 200 µl then cells were mechanically dissociated by flicking the tube 30 times and pipetting mixture 10 times through a 200 µl tip. The volume was adjusted to 1 ml with PBS containing 1.0% BSA and spun to pellet cells at 300 g for 30s. The supernatant was removed and cells were resuspended in 80 µl of PBS containing 0.1% BSA and 20% Optiprep StemCell Cat 07820 aiming for a concentration above 100 cells/µl. Cells were then passed through a cell sieve 100 µm for dome stage and 70 µm for shield stage. Single cell RNA seq library was performed with Chromium Next GEM Single Cell kit 10x Genomics Cat PN 1000121 based on standard protocol. All libraries were sequenced by Illumina Hi Seq 1500 or 2500 or XTen platform according to manufacturer's instruction.	GEO Accession:GSM5351828	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 1500	SRP322195	loader:fastq load.py	Shield_dnmt1_mKD_scRNA_seq_rep1_3_r1.fq.gz Shield_dnmt1_mKD_scRNA_seq_rep1_3_r2.fq.gz	fastq fastq	13794848400.0	45982828.0	GSM5351828 r3	0:150 1:150	A:3369892321;C:2623491729;G:2799241270;T:5001255880;N:967200	150	150			3369892321	2623491729	2799241270	5001255880	967200	SRX11041473	SRS9110400	SRA1239365	GEO	THU-PKU Center for Life Sciences, Tsinghua University	2	0.57873	0.90804	0.18871	0.2078	0.95954	0.77684	0.6229	0.49565	150	150	B	B	mate1-mate2 similar by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2021-06-01	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
64422	64422	SRR14703473	SRX11041473	SRS9110400	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 scRNA seq rep1	GSM5351828	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 scRNA 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.	Cell dissociation protocol was based on a previously described method Farrell et al. 2018 with modifications to adapt it for 10x Genomics platform. Briefly dnmt1 mKD and control embryos were collected 20 min post fertilization and cultured as mentioned before. Then 15 embryos at dome or shield stages for each sample were transferred into plastic Petri dishes that had previously been coated with 2% agarose and soaked with DMEM/F12 media Gibco/Life Technologies Cat 11330032 at least 2hrs. Next embryos at desired stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 µl DMEM/F12 media. Dissections were performed for up 15 min. The volume of DMEM/F12 meida containing embryos was adjusted to 200 µl then cells were mechanically dissociated by flicking the tube 30 times and pipetting mixture 10 times through a 200 µl tip. The volume was adjusted to 1 ml with PBS containing 1.0% BSA and spun to pellet cells at 300 g for 30s. The supernatant was removed and cells were resuspended in 80 µl of PBS containing 0.1% BSA and 20% Optiprep StemCell Cat 07820 aiming for a concentration above 100 cells/µl. Cells were then passed through a cell sieve 100 µm for dome stage and 70 µm for shield stage. Single cell RNA seq library was performed with Chromium Next GEM Single Cell kit 10x Genomics Cat PN 1000121 based on standard protocol. 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	GSM5351828	GSM5351828: Shield dnmt1 mKD scRNA seq rep1; Danio rerio; RNA Seq	GSM5351828		1	Cell dissociation protocol was based on a previously described method Farrell et al. 2018 with modifications to adapt it for 10x Genomics platform. Briefly dnmt1 mKD and control embryos were collected 20 min post fertilization and cultured as mentioned before. Then 15 embryos at dome or shield stages for each sample were transferred into plastic Petri dishes that had previously been coated with 2% agarose and soaked with DMEM/F12 media Gibco/Life Technologies Cat 11330032 at least 2hrs. Next embryos at desired stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 µl DMEM/F12 media. Dissections were performed for up 15 min. The volume of DMEM/F12 meida containing embryos was adjusted to 200 µl then cells were mechanically dissociated by flicking the tube 30 times and pipetting mixture 10 times through a 200 µl tip. The volume was adjusted to 1 ml with PBS containing 1.0% BSA and spun to pellet cells at 300 g for 30s. The supernatant was removed and cells were resuspended in 80 µl of PBS containing 0.1% BSA and 20% Optiprep StemCell Cat 07820 aiming for a concentration above 100 cells/µl. Cells were then passed through a cell sieve 100 µm for dome stage and 70 µm for shield stage. Single cell RNA seq library was performed with Chromium Next GEM Single Cell kit 10x Genomics Cat PN 1000121 based on standard protocol. All libraries were sequenced by Illumina Hi Seq 1500 or 2500 or XTen platform according to manufacturer's instruction.	GEO Accession:GSM5351828	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 1500	SRP322195	loader:fastq load.py	Shield_dnmt1_mKD_scRNA_seq_rep1_4_r1.fq.gz Shield_dnmt1_mKD_scRNA_seq_rep1_4_r2.fq.gz	fastq fastq	13130310600.0	43767702.0	GSM5351828 r4	0:150 1:150	A:3205653594;C:2513183584;G:2667999711;T:4742558968;N:914743	150	150			3205653594	2513183584	2667999711	4742558968	914743	SRX11041473	SRS9110400	SRA1239365	GEO	THU-PKU Center for Life Sciences, Tsinghua University	2	0.58341	0.90813	0.18926	0.2066	0.95988	0.77733	0.60889	0.49833	150	150	B	B	mate1-mate2 similar by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2021-06-01	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
64423	64423	SRR14703466	SRX11041472	SRS9110401	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 scRNA seq rep2	GSM5351827	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 scRNA 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.	Cell dissociation protocol was based on a previously described method Farrell et al. 2018 with modifications to adapt it for 10x Genomics platform. Briefly dnmt1 mKD and control embryos were collected 20 min post fertilization and cultured as mentioned before. Then 15 embryos at dome or shield stages for each sample were transferred into plastic Petri dishes that had previously been coated with 2% agarose and soaked with DMEM/F12 media Gibco/Life Technologies Cat 11330032 at least 2hrs. Next embryos at desired stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 µl DMEM/F12 media. Dissections were performed for up 15 min. The volume of DMEM/F12 meida containing embryos was adjusted to 200 µl then cells were mechanically dissociated by flicking the tube 30 times and pipetting mixture 10 times through a 200 µl tip. The volume was adjusted to 1 ml with PBS containing 1.0% BSA and spun to pellet cells at 300 g for 30s. The supernatant was removed and cells were resuspended in 80 µl of PBS containing 0.1% BSA and 20% Optiprep StemCell Cat 07820 aiming for a concentration above 100 cells/µl. Cells were then passed through a cell sieve 100 µm for dome stage and 70 µm for shield stage. Single cell RNA seq library was performed with Chromium Next GEM Single Cell kit 10x Genomics Cat PN 1000121 based on standard protocol. 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	GSM5351827	GSM5351827: Shield ctrl scRNA seq rep2; Danio rerio; RNA Seq	GSM5351827		1	Cell dissociation protocol was based on a previously described method Farrell et al. 2018 with modifications to adapt it for 10x Genomics platform. Briefly dnmt1 mKD and control embryos were collected 20 min post fertilization and cultured as mentioned before. Then 15 embryos at dome or shield stages for each sample were transferred into plastic Petri dishes that had previously been coated with 2% agarose and soaked with DMEM/F12 media Gibco/Life Technologies Cat 11330032 at least 2hrs. Next embryos at desired stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 µl DMEM/F12 media. Dissections were performed for up 15 min. The volume of DMEM/F12 meida containing embryos was adjusted to 200 µl then cells were mechanically dissociated by flicking the tube 30 times and pipetting mixture 10 times through a 200 µl tip. The volume was adjusted to 1 ml with PBS containing 1.0% BSA and spun to pellet cells at 300 g for 30s. The supernatant was removed and cells were resuspended in 80 µl of PBS containing 0.1% BSA and 20% Optiprep StemCell Cat 07820 aiming for a concentration above 100 cells/µl. Cells were then passed through a cell sieve 100 µm for dome stage and 70 µm for shield stage. Single cell RNA seq library was performed with Chromium Next GEM Single Cell kit 10x Genomics Cat PN 1000121 based on standard protocol. All libraries were sequenced by Illumina Hi Seq 1500 or 2500 or XTen platform according to manufacturer's instruction.	GEO Accession:GSM5351827	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 1500	SRP322195	loader:fastq load.py	Shield_ctrl_scRNA_seq_rep2_1_r1.fq.gz Shield_ctrl_scRNA_seq_rep2_1_r2.fq.gz	fastq fastq	6266320500.0	20887735.0	GSM5351827 r1	0:150 1:150	A:1568783611;C:1080550241;G:1179916201;T:2436028815;N:1041632	150	150			1568783611	1080550241	1179916201	2436028815	1041632	SRX11041472	SRS9110401	SRA1239365	GEO	THU-PKU Center for Life Sciences, Tsinghua University	2	0.29393	0.87861	0.07912	0.14498	0.96114	0.80779	0.59136	0.54496	150	150	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2021-06-01	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
64424	64424	SRR14703467	SRX11041472	SRS9110401	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 scRNA seq rep2	GSM5351827	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 scRNA 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.	Cell dissociation protocol was based on a previously described method Farrell et al. 2018 with modifications to adapt it for 10x Genomics platform. Briefly dnmt1 mKD and control embryos were collected 20 min post fertilization and cultured as mentioned before. Then 15 embryos at dome or shield stages for each sample were transferred into plastic Petri dishes that had previously been coated with 2% agarose and soaked with DMEM/F12 media Gibco/Life Technologies Cat 11330032 at least 2hrs. Next embryos at desired stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 µl DMEM/F12 media. Dissections were performed for up 15 min. The volume of DMEM/F12 meida containing embryos was adjusted to 200 µl then cells were mechanically dissociated by flicking the tube 30 times and pipetting mixture 10 times through a 200 µl tip. The volume was adjusted to 1 ml with PBS containing 1.0% BSA and spun to pellet cells at 300 g for 30s. The supernatant was removed and cells were resuspended in 80 µl of PBS containing 0.1% BSA and 20% Optiprep StemCell Cat 07820 aiming for a concentration above 100 cells/µl. Cells were then passed through a cell sieve 100 µm for dome stage and 70 µm for shield stage. Single cell RNA seq library was performed with Chromium Next GEM Single Cell kit 10x Genomics Cat PN 1000121 based on standard protocol. 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	GSM5351827	GSM5351827: Shield ctrl scRNA seq rep2; Danio rerio; RNA Seq	GSM5351827		1	Cell dissociation protocol was based on a previously described method Farrell et al. 2018 with modifications to adapt it for 10x Genomics platform. Briefly dnmt1 mKD and control embryos were collected 20 min post fertilization and cultured as mentioned before. Then 15 embryos at dome or shield stages for each sample were transferred into plastic Petri dishes that had previously been coated with 2% agarose and soaked with DMEM/F12 media Gibco/Life Technologies Cat 11330032 at least 2hrs. Next embryos at desired stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 µl DMEM/F12 media. Dissections were performed for up 15 min. The volume of DMEM/F12 meida containing embryos was adjusted to 200 µl then cells were mechanically dissociated by flicking the tube 30 times and pipetting mixture 10 times through a 200 µl tip. The volume was adjusted to 1 ml with PBS containing 1.0% BSA and spun to pellet cells at 300 g for 30s. The supernatant was removed and cells were resuspended in 80 µl of PBS containing 0.1% BSA and 20% Optiprep StemCell Cat 07820 aiming for a concentration above 100 cells/µl. Cells were then passed through a cell sieve 100 µm for dome stage and 70 µm for shield stage. Single cell RNA seq library was performed with Chromium Next GEM Single Cell kit 10x Genomics Cat PN 1000121 based on standard protocol. All libraries were sequenced by Illumina Hi Seq 1500 or 2500 or XTen platform according to manufacturer's instruction.	GEO Accession:GSM5351827	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 1500	SRP322195	loader:fastq load.py	Shield_ctrl_scRNA_seq_rep2_2_r1.fq.gz Shield_ctrl_scRNA_seq_rep2_2_r2.fq.gz	fastq fastq	8009683500.0	26698945.0	GSM5351827 r2	0:150 1:150	A:2004444677;C:1384605958;G:1511333804;T:3107983581;N:1315480	150	150			2004444677	1384605958	1511333804	3107983581	1315480	SRX11041472	SRS9110401	SRA1239365	GEO	THU-PKU Center for Life Sciences, Tsinghua University	2	0.29521	0.87887	0.08139	0.14526	0.96256	0.80744	0.59585	0.53734	150	150	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2021-06-01	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
64425	64425	SRR14703468	SRX11041472	SRS9110401	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 scRNA seq rep2	GSM5351827	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 scRNA 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.	Cell dissociation protocol was based on a previously described method Farrell et al. 2018 with modifications to adapt it for 10x Genomics platform. Briefly dnmt1 mKD and control embryos were collected 20 min post fertilization and cultured as mentioned before. Then 15 embryos at dome or shield stages for each sample were transferred into plastic Petri dishes that had previously been coated with 2% agarose and soaked with DMEM/F12 media Gibco/Life Technologies Cat 11330032 at least 2hrs. Next embryos at desired stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 µl DMEM/F12 media. Dissections were performed for up 15 min. The volume of DMEM/F12 meida containing embryos was adjusted to 200 µl then cells were mechanically dissociated by flicking the tube 30 times and pipetting mixture 10 times through a 200 µl tip. The volume was adjusted to 1 ml with PBS containing 1.0% BSA and spun to pellet cells at 300 g for 30s. The supernatant was removed and cells were resuspended in 80 µl of PBS containing 0.1% BSA and 20% Optiprep StemCell Cat 07820 aiming for a concentration above 100 cells/µl. Cells were then passed through a cell sieve 100 µm for dome stage and 70 µm for shield stage. Single cell RNA seq library was performed with Chromium Next GEM Single Cell kit 10x Genomics Cat PN 1000121 based on standard protocol. 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	GSM5351827	GSM5351827: Shield ctrl scRNA seq rep2; Danio rerio; RNA Seq	GSM5351827		1	Cell dissociation protocol was based on a previously described method Farrell et al. 2018 with modifications to adapt it for 10x Genomics platform. Briefly dnmt1 mKD and control embryos were collected 20 min post fertilization and cultured as mentioned before. Then 15 embryos at dome or shield stages for each sample were transferred into plastic Petri dishes that had previously been coated with 2% agarose and soaked with DMEM/F12 media Gibco/Life Technologies Cat 11330032 at least 2hrs. Next embryos at desired stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 µl DMEM/F12 media. Dissections were performed for up 15 min. The volume of DMEM/F12 meida containing embryos was adjusted to 200 µl then cells were mechanically dissociated by flicking the tube 30 times and pipetting mixture 10 times through a 200 µl tip. The volume was adjusted to 1 ml with PBS containing 1.0% BSA and spun to pellet cells at 300 g for 30s. The supernatant was removed and cells were resuspended in 80 µl of PBS containing 0.1% BSA and 20% Optiprep StemCell Cat 07820 aiming for a concentration above 100 cells/µl. Cells were then passed through a cell sieve 100 µm for dome stage and 70 µm for shield stage. Single cell RNA seq library was performed with Chromium Next GEM Single Cell kit 10x Genomics Cat PN 1000121 based on standard protocol. All libraries were sequenced by Illumina Hi Seq 1500 or 2500 or XTen platform according to manufacturer's instruction.	GEO Accession:GSM5351827	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 1500	SRP322195	loader:fastq load.py	Shield_ctrl_scRNA_seq_rep2_3_r1.fq.gz Shield_ctrl_scRNA_seq_rep2_3_r2.fq.gz	fastq fastq	9895554900.0	32985183.0	GSM5351827 r3	0:150 1:150	A:2473046635;C:1714495451;G:1872696492;T:3833724038;N:1592284	150	150			2473046635	1714495451	1872696492	3833724038	1592284	SRX11041472	SRS9110401	SRA1239365	GEO	THU-PKU Center for Life Sciences, Tsinghua University	2	0.30329	0.88102	0.08119	0.14636	0.96193	0.80775	0.60553	0.53579	150	150	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2021-06-01	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
64426	64426	SRR14703469	SRX11041472	SRS9110401	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 scRNA seq rep2	GSM5351827	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 scRNA 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.	Cell dissociation protocol was based on a previously described method Farrell et al. 2018 with modifications to adapt it for 10x Genomics platform. Briefly dnmt1 mKD and control embryos were collected 20 min post fertilization and cultured as mentioned before. Then 15 embryos at dome or shield stages for each sample were transferred into plastic Petri dishes that had previously been coated with 2% agarose and soaked with DMEM/F12 media Gibco/Life Technologies Cat 11330032 at least 2hrs. Next embryos at desired stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 µl DMEM/F12 media. Dissections were performed for up 15 min. The volume of DMEM/F12 meida containing embryos was adjusted to 200 µl then cells were mechanically dissociated by flicking the tube 30 times and pipetting mixture 10 times through a 200 µl tip. The volume was adjusted to 1 ml with PBS containing 1.0% BSA and spun to pellet cells at 300 g for 30s. The supernatant was removed and cells were resuspended in 80 µl of PBS containing 0.1% BSA and 20% Optiprep StemCell Cat 07820 aiming for a concentration above 100 cells/µl. Cells were then passed through a cell sieve 100 µm for dome stage and 70 µm for shield stage. Single cell RNA seq library was performed with Chromium Next GEM Single Cell kit 10x Genomics Cat PN 1000121 based on standard protocol. 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	GSM5351827	GSM5351827: Shield ctrl scRNA seq rep2; Danio rerio; RNA Seq	GSM5351827		1	Cell dissociation protocol was based on a previously described method Farrell et al. 2018 with modifications to adapt it for 10x Genomics platform. Briefly dnmt1 mKD and control embryos were collected 20 min post fertilization and cultured as mentioned before. Then 15 embryos at dome or shield stages for each sample were transferred into plastic Petri dishes that had previously been coated with 2% agarose and soaked with DMEM/F12 media Gibco/Life Technologies Cat 11330032 at least 2hrs. Next embryos at desired stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 µl DMEM/F12 media. Dissections were performed for up 15 min. The volume of DMEM/F12 meida containing embryos was adjusted to 200 µl then cells were mechanically dissociated by flicking the tube 30 times and pipetting mixture 10 times through a 200 µl tip. The volume was adjusted to 1 ml with PBS containing 1.0% BSA and spun to pellet cells at 300 g for 30s. The supernatant was removed and cells were resuspended in 80 µl of PBS containing 0.1% BSA and 20% Optiprep StemCell Cat 07820 aiming for a concentration above 100 cells/µl. Cells were then passed through a cell sieve 100 µm for dome stage and 70 µm for shield stage. Single cell RNA seq library was performed with Chromium Next GEM Single Cell kit 10x Genomics Cat PN 1000121 based on standard protocol. All libraries were sequenced by Illumina Hi Seq 1500 or 2500 or XTen platform according to manufacturer's instruction.	GEO Accession:GSM5351827	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 1500	SRP322195	loader:fastq load.py	Shield_ctrl_scRNA_seq_rep2_4_r1.fq.gz Shield_ctrl_scRNA_seq_rep2_4_r2.fq.gz	fastq fastq	8068755900.0	26895853.0	GSM5351827 r4	0:150 1:150	A:2020847923;C:1393779914;G:1520845525;T:3131970174;N:1312364	150	150			2020847923	1393779914	1520845525	3131970174	1312364	SRX11041472	SRS9110401	SRA1239365	GEO	THU-PKU Center for Life Sciences, Tsinghua University	2	0.29331	0.87943	0.07824	0.14389	0.96088	0.80783	0.59529	0.53996	150	150	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2021-06-01	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
64427	64427	SRR14703462	SRX11041471	SRS9110399	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 scRNA seq rep1	GSM5351826	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 scRNA 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.	Cell dissociation protocol was based on a previously described method Farrell et al. 2018 with modifications to adapt it for 10x Genomics platform. Briefly dnmt1 mKD and control embryos were collected 20 min post fertilization and cultured as mentioned before. Then 15 embryos at dome or shield stages for each sample were transferred into plastic Petri dishes that had previously been coated with 2% agarose and soaked with DMEM/F12 media Gibco/Life Technologies Cat 11330032 at least 2hrs. Next embryos at desired stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 µl DMEM/F12 media. Dissections were performed for up 15 min. The volume of DMEM/F12 meida containing embryos was adjusted to 200 µl then cells were mechanically dissociated by flicking the tube 30 times and pipetting mixture 10 times through a 200 µl tip. The volume was adjusted to 1 ml with PBS containing 1.0% BSA and spun to pellet cells at 300 g for 30s. The supernatant was removed and cells were resuspended in 80 µl of PBS containing 0.1% BSA and 20% Optiprep StemCell Cat 07820 aiming for a concentration above 100 cells/µl. Cells were then passed through a cell sieve 100 µm for dome stage and 70 µm for shield stage. Single cell RNA seq library was performed with Chromium Next GEM Single Cell kit 10x Genomics Cat PN 1000121 based on standard protocol. 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	GSM5351826	GSM5351826: Shield ctrl scRNA seq rep1; Danio rerio; RNA Seq	GSM5351826		1	Cell dissociation protocol was based on a previously described method Farrell et al. 2018 with modifications to adapt it for 10x Genomics platform. Briefly dnmt1 mKD and control embryos were collected 20 min post fertilization and cultured as mentioned before. Then 15 embryos at dome or shield stages for each sample were transferred into plastic Petri dishes that had previously been coated with 2% agarose and soaked with DMEM/F12 media Gibco/Life Technologies Cat 11330032 at least 2hrs. Next embryos at desired stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 µl DMEM/F12 media. Dissections were performed for up 15 min. The volume of DMEM/F12 meida containing embryos was adjusted to 200 µl then cells were mechanically dissociated by flicking the tube 30 times and pipetting mixture 10 times through a 200 µl tip. The volume was adjusted to 1 ml with PBS containing 1.0% BSA and spun to pellet cells at 300 g for 30s. The supernatant was removed and cells were resuspended in 80 µl of PBS containing 0.1% BSA and 20% Optiprep StemCell Cat 07820 aiming for a concentration above 100 cells/µl. Cells were then passed through a cell sieve 100 µm for dome stage and 70 µm for shield stage. Single cell RNA seq library was performed with Chromium Next GEM Single Cell kit 10x Genomics Cat PN 1000121 based on standard protocol. All libraries were sequenced by Illumina Hi Seq 1500 or 2500 or XTen platform according to manufacturer's instruction.	GEO Accession:GSM5351826	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 1500	SRP322195	loader:fastq load.py	Shield_ctrl_scRNA_seq_rep1_1_r1.fq.gz Shield_ctrl_scRNA_seq_rep1_1_r2.fq.gz	fastq fastq	12388530000.0	41295100.0	GSM5351826 r1	0:150 1:150	A:3168179903;C:2205795330;G:2362700115;T:4650988236;N:866416	150	150			3168179903	2205795330	2362700115	4650988236	866416	SRX11041471	SRS9110399	SRA1239365	GEO	THU-PKU Center for Life Sciences, Tsinghua University	2	0.42133	0.9087	0.09976	0.13648	0.96924	0.79935	0.56786	0.53021	150	150	B	B	mate1-mate2 similar by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2021-06-01	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
64428	64428	SRR14703463	SRX11041471	SRS9110399	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 scRNA seq rep1	GSM5351826	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 scRNA 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.	Cell dissociation protocol was based on a previously described method Farrell et al. 2018 with modifications to adapt it for 10x Genomics platform. Briefly dnmt1 mKD and control embryos were collected 20 min post fertilization and cultured as mentioned before. Then 15 embryos at dome or shield stages for each sample were transferred into plastic Petri dishes that had previously been coated with 2% agarose and soaked with DMEM/F12 media Gibco/Life Technologies Cat 11330032 at least 2hrs. Next embryos at desired stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 µl DMEM/F12 media. Dissections were performed for up 15 min. The volume of DMEM/F12 meida containing embryos was adjusted to 200 µl then cells were mechanically dissociated by flicking the tube 30 times and pipetting mixture 10 times through a 200 µl tip. The volume was adjusted to 1 ml with PBS containing 1.0% BSA and spun to pellet cells at 300 g for 30s. The supernatant was removed and cells were resuspended in 80 µl of PBS containing 0.1% BSA and 20% Optiprep StemCell Cat 07820 aiming for a concentration above 100 cells/µl. Cells were then passed through a cell sieve 100 µm for dome stage and 70 µm for shield stage. Single cell RNA seq library was performed with Chromium Next GEM Single Cell kit 10x Genomics Cat PN 1000121 based on standard protocol. 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	GSM5351826	GSM5351826: Shield ctrl scRNA seq rep1; Danio rerio; RNA Seq	GSM5351826		1	Cell dissociation protocol was based on a previously described method Farrell et al. 2018 with modifications to adapt it for 10x Genomics platform. Briefly dnmt1 mKD and control embryos were collected 20 min post fertilization and cultured as mentioned before. Then 15 embryos at dome or shield stages for each sample were transferred into plastic Petri dishes that had previously been coated with 2% agarose and soaked with DMEM/F12 media Gibco/Life Technologies Cat 11330032 at least 2hrs. Next embryos at desired stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 µl DMEM/F12 media. Dissections were performed for up 15 min. The volume of DMEM/F12 meida containing embryos was adjusted to 200 µl then cells were mechanically dissociated by flicking the tube 30 times and pipetting mixture 10 times through a 200 µl tip. The volume was adjusted to 1 ml with PBS containing 1.0% BSA and spun to pellet cells at 300 g for 30s. The supernatant was removed and cells were resuspended in 80 µl of PBS containing 0.1% BSA and 20% Optiprep StemCell Cat 07820 aiming for a concentration above 100 cells/µl. Cells were then passed through a cell sieve 100 µm for dome stage and 70 µm for shield stage. Single cell RNA seq library was performed with Chromium Next GEM Single Cell kit 10x Genomics Cat PN 1000121 based on standard protocol. All libraries were sequenced by Illumina Hi Seq 1500 or 2500 or XTen platform according to manufacturer's instruction.	GEO Accession:GSM5351826	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 1500	SRP322195	loader:fastq load.py	Shield_ctrl_scRNA_seq_rep1_2_r1.fq.gz Shield_ctrl_scRNA_seq_rep1_2_r2.fq.gz	fastq fastq	13605566400.0	45351888.0	GSM5351826 r2	0:150 1:150	A:3475099366;C:2428280614;G:2593872760;T:5107362000;N:951660	150	150			3475099366	2428280614	2593872760	5107362000	951660	SRX11041471	SRS9110399	SRA1239365	GEO	THU-PKU Center for Life Sciences, Tsinghua University	2	0.43281	0.9068	0.106	0.13613	0.96924	0.79904	0.5668	0.53489	150	150	B	B	mate1-mate2 similar by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2021-06-01	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
64429	64429	SRR14703464	SRX11041471	SRS9110399	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 scRNA seq rep1	GSM5351826	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 scRNA 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.	Cell dissociation protocol was based on a previously described method Farrell et al. 2018 with modifications to adapt it for 10x Genomics platform. Briefly dnmt1 mKD and control embryos were collected 20 min post fertilization and cultured as mentioned before. Then 15 embryos at dome or shield stages for each sample were transferred into plastic Petri dishes that had previously been coated with 2% agarose and soaked with DMEM/F12 media Gibco/Life Technologies Cat 11330032 at least 2hrs. Next embryos at desired stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 µl DMEM/F12 media. Dissections were performed for up 15 min. The volume of DMEM/F12 meida containing embryos was adjusted to 200 µl then cells were mechanically dissociated by flicking the tube 30 times and pipetting mixture 10 times through a 200 µl tip. The volume was adjusted to 1 ml with PBS containing 1.0% BSA and spun to pellet cells at 300 g for 30s. The supernatant was removed and cells were resuspended in 80 µl of PBS containing 0.1% BSA and 20% Optiprep StemCell Cat 07820 aiming for a concentration above 100 cells/µl. Cells were then passed through a cell sieve 100 µm for dome stage and 70 µm for shield stage. Single cell RNA seq library was performed with Chromium Next GEM Single Cell kit 10x Genomics Cat PN 1000121 based on standard protocol. 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	GSM5351826	GSM5351826: Shield ctrl scRNA seq rep1; Danio rerio; RNA Seq	GSM5351826		1	Cell dissociation protocol was based on a previously described method Farrell et al. 2018 with modifications to adapt it for 10x Genomics platform. Briefly dnmt1 mKD and control embryos were collected 20 min post fertilization and cultured as mentioned before. Then 15 embryos at dome or shield stages for each sample were transferred into plastic Petri dishes that had previously been coated with 2% agarose and soaked with DMEM/F12 media Gibco/Life Technologies Cat 11330032 at least 2hrs. Next embryos at desired stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 µl DMEM/F12 media. Dissections were performed for up 15 min. The volume of DMEM/F12 meida containing embryos was adjusted to 200 µl then cells were mechanically dissociated by flicking the tube 30 times and pipetting mixture 10 times through a 200 µl tip. The volume was adjusted to 1 ml with PBS containing 1.0% BSA and spun to pellet cells at 300 g for 30s. The supernatant was removed and cells were resuspended in 80 µl of PBS containing 0.1% BSA and 20% Optiprep StemCell Cat 07820 aiming for a concentration above 100 cells/µl. Cells were then passed through a cell sieve 100 µm for dome stage and 70 µm for shield stage. Single cell RNA seq library was performed with Chromium Next GEM Single Cell kit 10x Genomics Cat PN 1000121 based on standard protocol. All libraries were sequenced by Illumina Hi Seq 1500 or 2500 or XTen platform according to manufacturer's instruction.	GEO Accession:GSM5351826	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 1500	SRP322195	loader:fastq load.py	Shield_ctrl_scRNA_seq_rep1_3_r1.fq.gz Shield_ctrl_scRNA_seq_rep1_3_r2.fq.gz	fastq fastq	13548465000.0	45161550.0	GSM5351826 r3	0:150 1:150	A:3460710142;C:2418737322;G:2568875695;T:5099180449;N:961392	150	150			3460710142	2418737322	2568875695	5099180449	961392	SRX11041471	SRS9110399	SRA1239365	GEO	THU-PKU Center for Life Sciences, Tsinghua University	2	0.43175	0.9084	0.10409	0.13724	0.96895	0.80056	0.56745	0.529	150	150	B	B	mate1-mate2 similar by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2021-06-01	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
64430	64430	SRR14703465	SRX11041471	SRS9110399	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 scRNA seq rep1	GSM5351826	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 scRNA 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.	Cell dissociation protocol was based on a previously described method Farrell et al. 2018 with modifications to adapt it for 10x Genomics platform. Briefly dnmt1 mKD and control embryos were collected 20 min post fertilization and cultured as mentioned before. Then 15 embryos at dome or shield stages for each sample were transferred into plastic Petri dishes that had previously been coated with 2% agarose and soaked with DMEM/F12 media Gibco/Life Technologies Cat 11330032 at least 2hrs. Next embryos at desired stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 µl DMEM/F12 media. Dissections were performed for up 15 min. The volume of DMEM/F12 meida containing embryos was adjusted to 200 µl then cells were mechanically dissociated by flicking the tube 30 times and pipetting mixture 10 times through a 200 µl tip. The volume was adjusted to 1 ml with PBS containing 1.0% BSA and spun to pellet cells at 300 g for 30s. The supernatant was removed and cells were resuspended in 80 µl of PBS containing 0.1% BSA and 20% Optiprep StemCell Cat 07820 aiming for a concentration above 100 cells/µl. Cells were then passed through a cell sieve 100 µm for dome stage and 70 µm for shield stage. Single cell RNA seq library was performed with Chromium Next GEM Single Cell kit 10x Genomics Cat PN 1000121 based on standard protocol. 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	GSM5351826	GSM5351826: Shield ctrl scRNA seq rep1; Danio rerio; RNA Seq	GSM5351826		1	Cell dissociation protocol was based on a previously described method Farrell et al. 2018 with modifications to adapt it for 10x Genomics platform. Briefly dnmt1 mKD and control embryos were collected 20 min post fertilization and cultured as mentioned before. Then 15 embryos at dome or shield stages for each sample were transferred into plastic Petri dishes that had previously been coated with 2% agarose and soaked with DMEM/F12 media Gibco/Life Technologies Cat 11330032 at least 2hrs. Next embryos at desired stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 µl DMEM/F12 media. Dissections were performed for up 15 min. The volume of DMEM/F12 meida containing embryos was adjusted to 200 µl then cells were mechanically dissociated by flicking the tube 30 times and pipetting mixture 10 times through a 200 µl tip. The volume was adjusted to 1 ml with PBS containing 1.0% BSA and spun to pellet cells at 300 g for 30s. The supernatant was removed and cells were resuspended in 80 µl of PBS containing 0.1% BSA and 20% Optiprep StemCell Cat 07820 aiming for a concentration above 100 cells/µl. Cells were then passed through a cell sieve 100 µm for dome stage and 70 µm for shield stage. Single cell RNA seq library was performed with Chromium Next GEM Single Cell kit 10x Genomics Cat PN 1000121 based on standard protocol. All libraries were sequenced by Illumina Hi Seq 1500 or 2500 or XTen platform according to manufacturer's instruction.	GEO Accession:GSM5351826	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 1500	SRP322195	loader:fastq load.py	Shield_ctrl_scRNA_seq_rep1_4_r1.fq.gz Shield_ctrl_scRNA_seq_rep1_4_r2.fq.gz	fastq fastq	15810558600.0	52701862.0	GSM5351826 r4	0:150 1:150	A:4031453189;C:2842600265;G:3013905880;T:5921496537;N:1102729	150	150			4031453189	2842600265	3013905880	5921496537	1102729	SRX11041471	SRS9110399	SRA1239365	GEO	THU-PKU Center for Life Sciences, Tsinghua University	2	0.43764	0.9082	0.10636	0.13709	0.9685	0.79707	0.57315	0.53965	150	150	B	B	mate1-mate2 similar by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2021-06-01	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
72588	72588	SRR22797023	SRX18756814	SRS16192272	SRP413556	PRJNA913420	Nodal coordinates the anterior posterior patterning of germ layers and induces head formation in zebrafish explants.	GSE221220	Other	Purpose: To investingate cell types in wild type zebrafish explants. Methods: Wild type explants injected with phenol red were harvested at xxxhpf. Libraries were prepared using Chromium Controller and Chromium Single Cell three primeLibrary & Gel Bead Kit v3 10x Genomics PN 1000075 according to the manufacturer's protocol for 10000 cells recovery. Results: A total of 9 968 single cell transcriptomes were collected post stringent quality control measures. Conclusions: 6 Cell types were identified wild type explants mainly contains the anterior neural ectoderm and epidermis at 10 hpf. Overall design: Wild type zebrafish explants were harvested at 10hpf for scRNA seq.		pubmed:37729057	zebrafish wild type explant 10hpf	GSM6856370	source name:zebrafish cells\|strain:AB\|tissue:embryonic cells\|age:10hpf\|genotype:wild type	zebrafish wild type explant 10hpf	Illumina sequencing reads were aligned to the zebrafish mRNA reference genome GRCz11 using the 10x Genomics CellRanger pipeline version 3.0.2 with default parameters. Assembly: GRCz11 Supplementary files format and content: tar compressed files included filtered gene bc matrices post running CellRanger pipeline	zebrafish cells	phenol red was injected to one cell of embryonic animal pole at xxx cell stage. All embryos were incubated in 0.3x Danieau buffer until 1k stage then were transferred to Dulbecco's Modified Eagle Medium. Animal pole explants corresponding roughly to half of the blastula were incubated to 10hpfcorresponding to embryonic developmental stage separately.	Libraries were prepared using Chromium Controller and Chromium Single Cell 3’Library & Gel Bead Kit v3 10x Genomics PN 1000075 according to the manufacturer’s protocol for 10000 cells recovery.	explants were cultured in a Petri dish coated with 1.5% agarose filled with Dulbecco's Modified Eagle Medium	strain:AB\|tissue:embryonic cells\|age:10hpf\|genotype:wild type	GSM6856370	GSM6856370: zebrafish wild type explant 10hpf; Danio rerio; RNA Seq	GSM6856370 r1	GSM6856370	1	Libraries were prepared using Chromium Controller and Chromium Single Cell three primeLibrary & Gel Bead Kit v3 10x Genomics PN 1000075 according to the manufacturer's protocol for 10000 cells recovery.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP413556	loader:fastq load.py	WT_10hpf_S1_L001_R1_001.fastq.gz WT_10hpf_S1_L001_R2_001.fastq.gz	fastq fastq	144284560800.0	480948536.0	GSM6856370 r1	0:150 1:150	A:61459567540;C:25433070866;G:24459703281;T:32928214337;N:4004776	150	150			61459567540	25433070866	24459703281	32928214337	4004776	SRX18756814	SRS16192272	SRA1561216	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University	2	0.0	0.92423	0.0	0.16334	1.0	0.78228		0.51889	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2022-12-17	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
72833	72833	SRR23210472	SRX19158411	SRS16570832	SRP418915	PRJNA927004	Differential Nodal level promotes mesendoderm cell fate segregation mediated by chromatin organization	GSE223636	Other	Purpose: To investigate the mechanism of prechordal plate and anterior endoderm separation . Methods: Nodal injected explants injected with 10pg ndr2 mRNA constructed from lft1 mutants and ndr1 morphants were harvested at xxxhpf. Libraries were prepared using Chromium Controller and Chromium Single Cell three primeLibrary & Gel Bead Kit v3 10x Genomics PN 1000075 according to the manufacturer's protocol for 10000 cells recovery. For single cell multiomics zebrafish embryos at 6 hpf were harvested. Libraries were prepared using Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle 10x Genomics 4 rxns PN 1000285 according to the manufacturer's protocol for 10000 cells recovery. Results: A total of 10 614 single cell transcriptomes and 4 335 multiomics were collected post stringent quality control measures. Conclusions: A slight bias in Nodal signaling promotes a differential chromatin structure between prechordal plate and endoderm which drives a differential expression of those key regulators such as gsc and ripply1 in these two cell lineages and further regulates mesendoderm cell fate separation. Overall design: zebrafish Nodal explants constructed from lft1 mutants and ndr1 morphants were harvested at 6hpf for scRNA seq. Zebrafish embryos were harvested at 6hpf for single cell multiomics.			zebrafish embryo multiomics expression	GSM6969677	source name:zebrafish cells\|strain:AB\|tissue:embryonic cells\|age:6hpf	zebrafish embryo multiomics expression	Illumina sequencing reads were aligned to the zebrafish mRNA reference genome GRCz11 using the 10x Genomics CellRanger pipeline version 6.1.2 and cellranger arc version 2.0.0 with default parameters. Assembly: GRCz11 Supplementary files format and content: tar archivr or gzip compressed files included filtered gene bc matrices and ATAC fragments post running CellRanger or cellranger arc pipeline. Library strategy: scMultiome GEX	zebrafish cells	10pg of ndr2 mRNA was injected to one cell of embryonic animal pole at xxx cell stage. All embryos were incubated in 0.3x Danieau buffer until 1k stage then were transferred to Dulbecco's Modified Eagle Medium. Animal pole explants corresponding roughly to half of the blastula were incubated to 6hpf corresponding to embryonic developmental stage.	Libraries were prepared using Chromium Controller and Chromium Single Cell 3’Library & Gel Bead Kit v3 10x Genomics PN 1000075 and Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle 10x Genomics 4 rxns PN 1000285 according to the manufacturer’s protocol for 10000 cells recovery.	Explants were cultured in a Petri dish coated with 1.5% agarose filled with Dulbecco's Modified Eagle Medium	strain:AB\|tissue:embryonic cells\|age:6hpf	GSM6969677	GSM6969677: zebrafish embryo multiomics expression; Danio rerio; OTHER	GSM6969677 r1	GSM6969677	1	Libraries were prepared using Chromium Controller and Chromium Single Cell three primeLibrary & Gel Bead Kit v3 10x Genomics PN 1000075 and Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle 10x Genomics 4 rxns PN 1000285 according to the manufacturer's protocol for 10000 cells recovery.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP418915	loader:fastq load.py	6-M-GEX-merge_S1_L001_R1_001.fastq.gz 6-M-GEX-merge_S1_L001_R2_001.fastq.gz	fastq fastq	67059456600.0	223531522.0	GSM6969677 r1	0:150 1:150	A:20681044309;C:12370348813;G:11664316954;T:22341885756;N:1860768	150	150			20681044309	12370348813	11664316954	22341885756	1860768	SRX19158411	SRS16570832	SRA1581154	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University	2	0.45314	0.8745	0.16489	0.2261	0.99072	0.82641	0.79221	0.75799	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	other	unknown	sc	single_cell_droplet	10x	China	2023-01-24	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
72834	72834	SRR23210473	SRX19158410	SRS16570831	SRP418915	PRJNA927004	Differential Nodal level promotes mesendoderm cell fate segregation mediated by chromatin organization	GSE223636	Other	Purpose: To investigate the mechanism of prechordal plate and anterior endoderm separation . Methods: Nodal injected explants injected with 10pg ndr2 mRNA constructed from lft1 mutants and ndr1 morphants were harvested at xxxhpf. Libraries were prepared using Chromium Controller and Chromium Single Cell three primeLibrary & Gel Bead Kit v3 10x Genomics PN 1000075 according to the manufacturer's protocol for 10000 cells recovery. For single cell multiomics zebrafish embryos at 6 hpf were harvested. Libraries were prepared using Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle 10x Genomics 4 rxns PN 1000285 according to the manufacturer's protocol for 10000 cells recovery. Results: A total of 10 614 single cell transcriptomes and 4 335 multiomics were collected post stringent quality control measures. Conclusions: A slight bias in Nodal signaling promotes a differential chromatin structure between prechordal plate and endoderm which drives a differential expression of those key regulators such as gsc and ripply1 in these two cell lineages and further regulates mesendoderm cell fate separation. Overall design: zebrafish Nodal explants constructed from lft1 mutants and ndr1 morphants were harvested at 6hpf for scRNA seq. Zebrafish embryos were harvested at 6hpf for single cell multiomics.			zebrafish Nodal explants constructed from ndr1 morphants	GSM6969676	source name:zebrafish cells\|strain:AB\|tissue:embryonic cells\|age:6hpf	zebrafish Nodal explants constructed from ndr1 morphants	Illumina sequencing reads were aligned to the zebrafish mRNA reference genome GRCz11 using the 10x Genomics CellRanger pipeline version 6.1.2 and cellranger arc version 2.0.0 with default parameters. Assembly: GRCz11 Supplementary files format and content: tar archivr or gzip compressed files included filtered gene bc matrices and ATAC fragments post running CellRanger or cellranger arc pipeline.	zebrafish cells	10pg of ndr2 mRNA was injected to one cell of embryonic animal pole at xxx cell stage. All embryos were incubated in 0.3x Danieau buffer until 1k stage then were transferred to Dulbecco's Modified Eagle Medium. Animal pole explants corresponding roughly to half of the blastula were incubated to 6hpf corresponding to embryonic developmental stage.	Libraries were prepared using Chromium Controller and Chromium Single Cell 3’Library & Gel Bead Kit v3 10x Genomics PN 1000075 and Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle 10x Genomics 4 rxns PN 1000285 according to the manufacturer’s protocol for 10000 cells recovery.	Explants were cultured in a Petri dish coated with 1.5% agarose filled with Dulbecco's Modified Eagle Medium	strain:AB\|tissue:embryonic cells\|age:6hpf	GSM6969676	GSM6969676: zebrafish Nodal explants constructed from ndr1 morphants; Danio rerio; RNA Seq	GSM6969676 r1	GSM6969676	1	Libraries were prepared using Chromium Controller and Chromium Single Cell three primeLibrary & Gel Bead Kit v3 10x Genomics PN 1000075 and Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle 10x Genomics 4 rxns PN 1000285 according to the manufacturer's protocol for 10000 cells recovery.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP418915		ndr1Mo_cyc_6hpf_S5_L002_R1_001.fastq.gz ndr1Mo_cyc_6hpf_S5_L002_R2_001.fastq.gz	fastq fastq	82246861872.0	464671536.0	GSM6969676 r1	0:26 1:151	A:23306781803;C:17200141798;G:18609129782;T:23129217367;N:1591122	26	151			23306781803	17200141798	18609129782	23129217367	1591122	SRX19158410	SRS16570831	SRA1581154	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University	2	0.00753	0.93187	0.00244	0.09764	0.9867	0.79813	0.42974	0.53736	26	151	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2023-01-24	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
72835	72835	SRR23210474	SRX19158409	SRS16570830	SRP418915	PRJNA927004	Differential Nodal level promotes mesendoderm cell fate segregation mediated by chromatin organization	GSE223636	Other	Purpose: To investigate the mechanism of prechordal plate and anterior endoderm separation . Methods: Nodal injected explants injected with 10pg ndr2 mRNA constructed from lft1 mutants and ndr1 morphants were harvested at xxxhpf. Libraries were prepared using Chromium Controller and Chromium Single Cell three primeLibrary & Gel Bead Kit v3 10x Genomics PN 1000075 according to the manufacturer's protocol for 10000 cells recovery. For single cell multiomics zebrafish embryos at 6 hpf were harvested. Libraries were prepared using Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle 10x Genomics 4 rxns PN 1000285 according to the manufacturer's protocol for 10000 cells recovery. Results: A total of 10 614 single cell transcriptomes and 4 335 multiomics were collected post stringent quality control measures. Conclusions: A slight bias in Nodal signaling promotes a differential chromatin structure between prechordal plate and endoderm which drives a differential expression of those key regulators such as gsc and ripply1 in these two cell lineages and further regulates mesendoderm cell fate separation. Overall design: zebrafish Nodal explants constructed from lft1 mutants and ndr1 morphants were harvested at 6hpf for scRNA seq. Zebrafish embryos were harvested at 6hpf for single cell multiomics.			zebrafish Nodal explants constructed from lft1 mutants	GSM6969675	source name:zebrafish cells\|strain:lft1 mutant\|tissue:embryonic cells\|age:6hpf	zebrafish Nodal explants constructed from lft1 mutants	Illumina sequencing reads were aligned to the zebrafish mRNA reference genome GRCz11 using the 10x Genomics CellRanger pipeline version 6.1.2 and cellranger arc version 2.0.0 with default parameters. Assembly: GRCz11 Supplementary files format and content: tar archivr or gzip compressed files included filtered gene bc matrices and ATAC fragments post running CellRanger or cellranger arc pipeline.	zebrafish cells	10pg of ndr2 mRNA was injected to one cell of embryonic animal pole at xxx cell stage. All embryos were incubated in 0.3x Danieau buffer until 1k stage then were transferred to Dulbecco's Modified Eagle Medium. Animal pole explants corresponding roughly to half of the blastula were incubated to 6hpf corresponding to embryonic developmental stage.	Libraries were prepared using Chromium Controller and Chromium Single Cell 3’Library & Gel Bead Kit v3 10x Genomics PN 1000075 and Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle 10x Genomics 4 rxns PN 1000285 according to the manufacturer’s protocol for 10000 cells recovery.	Explants were cultured in a Petri dish coated with 1.5% agarose filled with Dulbecco's Modified Eagle Medium	strain:lft1 mutant\|tissue:embryonic cells\|age:6hpf	GSM6969675	GSM6969675: zebrafish Nodal explants constructed from lft1 mutants; Danio rerio; RNA Seq	GSM6969675 r1	GSM6969675	1	Libraries were prepared using Chromium Controller and Chromium Single Cell three primeLibrary & Gel Bead Kit v3 10x Genomics PN 1000075 and Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle 10x Genomics 4 rxns PN 1000285 according to the manufacturer's protocol for 10000 cells recovery.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP418915		lft1Mu_cyc_6hpf_S1_L001_R1_001.fastq.gz lft1Mu_cyc_6hpf_S1_L001_R2_001.fastq.gz	fastq fastq	89053334922.0	503126186.0	GSM6969675 r1	0:26 1:151	A:26667371583;C:17898813431;G:19518773309;T:24966420492;N:1956107	26	151			26667371583	17898813431	19518773309	24966420492	1956107	SRX19158409	SRS16570830	SRA1581154	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University	2	0.01205	0.89743	0.00297	0.09338	0.98082	0.80961	0.48847	0.58599	26	151	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2023-01-24	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");;