metadata: run_metadata: 1,838 rows where devstage_curation = "Multi-stage" and tissue

1,838 rows where devstage_curation = "Multi-stage" and tissue_curation = "Embryo Imprecise"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.description	sample.title	sample.alias	sample.centername	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.title	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.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
9892	9892	ERR4172795	ERX4136409	ERS4580819	ERP121885	PRJEB38455	RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf	E-MTAB-9113	Transcriptome Analysis	RNA was extracted from whole zebrafish embryos at 24 hpf to examine changes in gene expression and splicing in sfpq null mutants	ENA FIRST PUBLIC:2021 01 27\|ENA LAST UPDATE:2020 05 22		Protocols: Embryos were collected from in crosses of sfpq+/ adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library constructed with ribodepletion	sibling 3	SAMEA6853229	Centre for Developmental Neurobiology King's College London	ENA FIRST PUBLIC:2020 12 01T04:08:08Z\|ENA LAST UPDATE:2020 05 22T17:13:15Z\|External Id:SAMEA6853229\|INSDC center name:Centre for Developmental Neurobiology King's College London\|INSDC first public:2020 12 01T04:08:08Z\|INSDC last update:2020 05 22T17:13:15Z\|INSDC status:public\|Submitter Id:E MTAB 9113:sibling 3\|age:24\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo\|genotype:wild type genotype\|sample name:E MTAB 9113:sibling 3\|scientific name:Danio rerio									Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf	E MTAB 9113:sibling 3 p	sibling 3 p	RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf	Embryos were collected from in crosses of sfpq+/ adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library constructed with ribodepletion	Experimental Factor: genotype:wild type genotype	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP121885	Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf	ENA FIRST PUBLIC:2021 01 27\|ENA LAST UPDATE:2020 06 19	UCLGNS1141-gfp-sibs-3_S6_R1.fastq.gz UCLGNS1141-gfp-sibs-3_S6_R2.fastq.gz	fastq fastq			E MTAB 9113:UCLGNS1141 gfp sibs 3 S6 R	0:81 1:81	A:1144578958;C:1113109875;G:1138809559;T:1117038434;N:213932	81	81	1144578958	1113109875	1138809559	1117038434	213932	ERX4136409	ERS4580819	ERA2625401	Centre for Developmental Neurobiology King	Centre for Developmental Neurobiology King	2	0.96684	0.96492	0.03244	0.0317	0.71236	0.71514	0.45871	0.46189	81	81	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2020-05-22	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
9893	9893	ERR4172794	ERX4136408	ERS4580818	ERP121885	PRJEB38455	RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf	E-MTAB-9113	Transcriptome Analysis	RNA was extracted from whole zebrafish embryos at 24 hpf to examine changes in gene expression and splicing in sfpq null mutants	ENA FIRST PUBLIC:2021 01 27\|ENA LAST UPDATE:2020 05 22		Protocols: Embryos were collected from in crosses of sfpq+/ adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library constructed with ribodepletion	sibling 2	SAMEA6853228	Centre for Developmental Neurobiology King's College London	ENA FIRST PUBLIC:2020 12 01T04:08:08Z\|ENA LAST UPDATE:2020 05 22T17:13:15Z\|External Id:SAMEA6853228\|INSDC center name:Centre for Developmental Neurobiology King's College London\|INSDC first public:2020 12 01T04:08:08Z\|INSDC last update:2020 05 22T17:13:15Z\|INSDC status:public\|Submitter Id:E MTAB 9113:sibling 2\|age:24\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo\|genotype:wild type genotype\|sample name:E MTAB 9113:sibling 2\|scientific name:Danio rerio									Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf	E MTAB 9113:sibling 2 p	sibling 2 p	RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf	Embryos were collected from in crosses of sfpq+/ adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library constructed with ribodepletion	Experimental Factor: genotype:wild type genotype	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP121885	Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf	ENA FIRST PUBLIC:2021 01 27\|ENA LAST UPDATE:2020 06 19	UCLGNS1141-gfp-sibs-2_S4_R1.fastq.gz UCLGNS1141-gfp-sibs-2_S4_R2.fastq.gz	fastq fastq			E MTAB 9113:UCLGNS1141 gfp sibs 2 S4 R	0:81 1:81	A:1056280368;C:1036355469;G:1045429486;T:1035773622;N:189389	81	81	1056280368	1036355469	1045429486	1035773622	189389	ERX4136408	ERS4580818	ERA2625401	Centre for Developmental Neurobiology King	Centre for Developmental Neurobiology King	2	0.95511	0.95696	0.02941	0.02903	0.71492	0.71628	0.45765	0.46537	81	81	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2020-05-22	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
9894	9894	ERR4172793	ERX4136407	ERS4580817	ERP121885	PRJEB38455	RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf	E-MTAB-9113	Transcriptome Analysis	RNA was extracted from whole zebrafish embryos at 24 hpf to examine changes in gene expression and splicing in sfpq null mutants	ENA FIRST PUBLIC:2021 01 27\|ENA LAST UPDATE:2020 05 22		Protocols: Embryos were collected from in crosses of sfpq+/ adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library constructed with ribodepletion	sibling 1	SAMEA6853227	Centre for Developmental Neurobiology King's College London	ENA FIRST PUBLIC:2020 12 01T04:08:08Z\|ENA LAST UPDATE:2020 05 22T17:13:15Z\|External Id:SAMEA6853227\|INSDC center name:Centre for Developmental Neurobiology King's College London\|INSDC first public:2020 12 01T04:08:08Z\|INSDC last update:2020 05 22T17:13:15Z\|INSDC status:public\|Submitter Id:E MTAB 9113:sibling 1\|age:24\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo\|genotype:wild type genotype\|sample name:E MTAB 9113:sibling 1\|scientific name:Danio rerio									Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf	E MTAB 9113:sibling 1 p	sibling 1 p	RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf	Embryos were collected from in crosses of sfpq+/ adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library constructed with ribodepletion	Experimental Factor: genotype:wild type genotype	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP121885	Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf	ENA FIRST PUBLIC:2021 01 27\|ENA LAST UPDATE:2020 06 19	UCLGNS1141-gfp-sibs-1_S2_R1.fastq.gz UCLGNS1141-gfp-sibs-1_S2_R2.fastq.gz	fastq fastq			E MTAB 9113:UCLGNS1141 gfp sibs 1 S2 R	0:81 1:81	A:1121176859;C:1093927654;G:1108608188;T:1101082277;N:209264	81	81	1121176859	1093927654	1108608188	1101082277	209264	ERX4136407	ERS4580817	ERA2625401	Centre for Developmental Neurobiology King	Centre for Developmental Neurobiology King	2	0.95795	0.96004	0.02885	0.02854	0.71648	0.71756	0.44348	0.43956	81	81	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2020-05-22	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
9895	9895	ERR4172792	ERX4136406	ERS4580816	ERP121885	PRJEB38455	RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf	E-MTAB-9113	Transcriptome Analysis	RNA was extracted from whole zebrafish embryos at 24 hpf to examine changes in gene expression and splicing in sfpq null mutants	ENA FIRST PUBLIC:2021 01 27\|ENA LAST UPDATE:2020 05 22		Protocols: Embryos were collected from in crosses of sfpq+/ adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library constructed with ribodepletion	sfpq 3	SAMEA6853226	Centre for Developmental Neurobiology King's College London	ENA FIRST PUBLIC:2020 12 01T04:08:08Z\|ENA LAST UPDATE:2020 05 22T17:13:15Z\|External Id:SAMEA6853226\|INSDC center name:Centre for Developmental Neurobiology King's College London\|INSDC first public:2020 12 01T04:08:08Z\|INSDC last update:2020 05 22T17:13:15Z\|INSDC status:public\|Submitter Id:E MTAB 9113:sfpq 3\|age:24\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo\|genotype:sfpq / \|sample name:E MTAB 9113:sfpq 3\|scientific name:Danio rerio									Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf	E MTAB 9113:sfpq 3 p	sfpq 3 p	RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf	Embryos were collected from in crosses of sfpq+/ adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library constructed with ribodepletion	Experimental Factor: genotype:sfpq /	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP121885	Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf	ENA FIRST PUBLIC:2021 01 27\|ENA LAST UPDATE:2020 06 19	UCLGNS1141-gfp-neg_3_S5_R1.fastq.gz UCLGNS1141-gfp-neg_3_S5_R2.fastq.gz	fastq fastq			E MTAB 9113:UCLGNS1141 gfp neg 3 S5 R	0:81 1:81	A:845849249;C:772302798;G:911660213;T:787409272;N:154042	81	81	845849249	772302798	911660213	787409272	154042	ERX4136406	ERS4580816	ERA2625401	Centre for Developmental Neurobiology King	Centre for Developmental Neurobiology King	2	0.96298	0.95486	0.03415	0.03476	0.7167	0.73503	0.4665	0.45947	81	81	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2020-05-22	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
9896	9896	ERR4172791	ERX4136405	ERS4580815	ERP121885	PRJEB38455	RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf	E-MTAB-9113	Transcriptome Analysis	RNA was extracted from whole zebrafish embryos at 24 hpf to examine changes in gene expression and splicing in sfpq null mutants	ENA FIRST PUBLIC:2021 01 27\|ENA LAST UPDATE:2020 05 22		Protocols: Embryos were collected from in crosses of sfpq+/ adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library constructed with ribodepletion	sfpq 2	SAMEA6853225	Centre for Developmental Neurobiology King's College London	ENA FIRST PUBLIC:2020 12 01T04:08:08Z\|ENA LAST UPDATE:2020 05 22T17:13:15Z\|External Id:SAMEA6853225\|INSDC center name:Centre for Developmental Neurobiology King's College London\|INSDC first public:2020 12 01T04:08:08Z\|INSDC last update:2020 05 22T17:13:15Z\|INSDC status:public\|Submitter Id:E MTAB 9113:sfpq 2\|age:24\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo\|genotype:sfpq / \|sample name:E MTAB 9113:sfpq 2\|scientific name:Danio rerio									Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf	E MTAB 9113:sfpq 2 p	sfpq 2 p	RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf	Embryos were collected from in crosses of sfpq+/ adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library constructed with ribodepletion	Experimental Factor: genotype:sfpq /	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP121885	Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf	ENA FIRST PUBLIC:2021 01 27\|ENA LAST UPDATE:2020 06 19	UCLGNS1141-gfp-neg-2_S3_R1.fastq.gz UCLGNS1141-gfp-neg-2_S3_R2.fastq.gz	fastq fastq			E MTAB 9113:UCLGNS1141 gfp neg 2 S3 R	0:81 1:81	A:961156886;C:917011292;G:942713581;T:936109877;N:157724	81	81	961156886	917011292	942713581	936109877	157724	ERX4136405	ERS4580815	ERA2625401	Centre for Developmental Neurobiology King	Centre for Developmental Neurobiology King	2	0.96276	0.96147	0.03436	0.03382	0.71892	0.72021	0.4581	0.46402	81	81	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2020-05-22	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
9897	9897	ERR4172790	ERX4136404	ERS4580814	ERP121885	PRJEB38455	RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf	E-MTAB-9113	Transcriptome Analysis	RNA was extracted from whole zebrafish embryos at 24 hpf to examine changes in gene expression and splicing in sfpq null mutants	ENA FIRST PUBLIC:2021 01 27\|ENA LAST UPDATE:2020 05 22		Protocols: Embryos were collected from in crosses of sfpq+/ adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library constructed with ribodepletion	sfpq 1	SAMEA6853224	Centre for Developmental Neurobiology King's College London	ENA FIRST PUBLIC:2020 12 01T04:08:08Z\|ENA LAST UPDATE:2020 05 22T17:13:15Z\|External Id:SAMEA6853224\|INSDC center name:Centre for Developmental Neurobiology King's College London\|INSDC first public:2020 12 01T04:08:08Z\|INSDC last update:2020 05 22T17:13:15Z\|INSDC status:public\|Submitter Id:E MTAB 9113:sfpq 1\|age:24\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo\|genotype:sfpq / \|sample name:E MTAB 9113:sfpq 1\|scientific name:Danio rerio									Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf	E MTAB 9113:sfpq 1 p	sfpq 1 p	RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf	Embryos were collected from in crosses of sfpq+/ adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library constructed with ribodepletion	Experimental Factor: genotype:sfpq /	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP121885	Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf	ENA FIRST PUBLIC:2021 01 27\|ENA LAST UPDATE:2020 06 19	UCLGNS1141-gfp-neg-1_S1_R1.fastq.gz UCLGNS1141-gfp-neg-1_S1_R2.fastq.gz	fastq fastq			E MTAB 9113:UCLGNS1141 gfp neg 1 S1 R	0:81 1:81	A:1046317524;C:1014946275;G:1036910299;T:1023619857;N:185237	81	81	1046317524	1014946275	1036910299	1023619857	185237	ERX4136404	ERS4580814	ERA2625401	Centre for Developmental Neurobiology King	Centre for Developmental Neurobiology King	2	0.96015	0.96173	0.03114	0.03098	0.7175	0.71865	0.46666	0.46399	81	81	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2020-05-22	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
9898	9898	ERR4194114	ERX4155254	ERS4601292	ERP122151	PRJEB38705	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E-MTAB-9193	Transcriptome Analysis	TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01		Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Sample 2	SAMEA6873729	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada	ENA FIRST PUBLIC:2020 12 31T11:11:47Z\|ENA LAST UPDATE:2020 06 04T16:16:46Z\|External Id:SAMEA6873729\|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada\|INSDC first public:2020 12 31T11:11:47Z\|INSDC last update:2020 06 04T16:16:46Z\|INSDC status:public\|Submitter Id:E MTAB 9193:Sample 2\|age:8\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo stage\|genotype:TgBACgata5: EGFPpd25\|immunophenotype:GFP+\|individual:embryo pool 100 200\|organism part:mesendoderm\|sample name:E MTAB 9193:Sample 2\|scientific name:Danio rerio\|sex:mixed									Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E MTAB 9193:Sample 2 s	Sample 2 s	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Experimental Factor: age:8\|Experimental Factor: RNA interference:n1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP122151	Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01	cDNA8h_1_S2_L001.bam	bam	10087287534.0	99874134.0	E MTAB 9193:cDNA8h 1 S2 L001	0:101	A:2892833391;C:2022466595;G:2198646699;T:2962268446;N:11072403	101		2892833391	2022466595	2198646699	2962268446	11072403	ERX4155254	ERS4601292	ERA2667966	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	1	0.93609		0.12902		0.82158		0.5062		101		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Canada	2020-06-04	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
9899	9899	ERR4194115	ERX4155254	ERS4601292	ERP122151	PRJEB38705	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E-MTAB-9193	Transcriptome Analysis	TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01		Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Sample 2	SAMEA6873729	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada	ENA FIRST PUBLIC:2020 12 31T11:11:47Z\|ENA LAST UPDATE:2020 06 04T16:16:46Z\|External Id:SAMEA6873729\|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada\|INSDC first public:2020 12 31T11:11:47Z\|INSDC last update:2020 06 04T16:16:46Z\|INSDC status:public\|Submitter Id:E MTAB 9193:Sample 2\|age:8\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo stage\|genotype:TgBACgata5: EGFPpd25\|immunophenotype:GFP+\|individual:embryo pool 100 200\|organism part:mesendoderm\|sample name:E MTAB 9193:Sample 2\|scientific name:Danio rerio\|sex:mixed									Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E MTAB 9193:Sample 2 s	Sample 2 s	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Experimental Factor: age:8\|Experimental Factor: RNA interference:n1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP122151	Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01	cDNA8h_1_S2_L002.bam	bam	10191911414.0	100910014.0	E MTAB 9193:cDNA8h 1 S2 L002	0:101	A:2923216190;C:2043975715;G:2221734566;T:2992798366;N:10186577	101		2923216190	2043975715	2221734566	2992798366	10186577	ERX4155254	ERS4601292	ERA2667966	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	1	0.93445		0.13038		0.824		0.49774		101		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Canada	2020-06-04	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
9900	9900	ERR4194112	ERX4155253	ERS4601291	ERP122151	PRJEB38705	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E-MTAB-9193	Transcriptome Analysis	TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01		Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Sample 1	SAMEA6873728	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada	ENA FIRST PUBLIC:2020 12 31T11:11:47Z\|ENA LAST UPDATE:2020 06 04T16:16:46Z\|External Id:SAMEA6873728\|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada\|INSDC first public:2020 12 31T11:11:47Z\|INSDC last update:2020 06 04T16:16:46Z\|INSDC status:public\|Submitter Id:E MTAB 9193:Sample 1\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo stage\|genotype:TgBACgata5: EGFPpd25\|immunophenotype:GFP+\|individual:embryo pool 100 200\|organism part:mesendoderm\|sample name:E MTAB 9193:Sample 1\|scientific name:Danio rerio\|sex:mixed									Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E MTAB 9193:Sample 1 s	Sample 1 s	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Experimental Factor: age:6\|Experimental Factor: RNA interference:n1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP122151	Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01	cDNA6h_1_S1_L001.bam	bam	7181772357.0	71106657.0	E MTAB 9193:cDNA6h 1 S1 L001	0:101	A:2074032710;C:1415439071;G:1544274166;T:2140112533;N:7913877	101		2074032710	1415439071	1544274166	2140112533	7913877	ERX4155253	ERS4601291	ERA2667966	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	1	0.9297		0.12156		0.8117		0.51457		101		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Canada	2020-06-04	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
9901	9901	ERR4194113	ERX4155253	ERS4601291	ERP122151	PRJEB38705	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E-MTAB-9193	Transcriptome Analysis	TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01		Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Sample 1	SAMEA6873728	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada	ENA FIRST PUBLIC:2020 12 31T11:11:47Z\|ENA LAST UPDATE:2020 06 04T16:16:46Z\|External Id:SAMEA6873728\|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada\|INSDC first public:2020 12 31T11:11:47Z\|INSDC last update:2020 06 04T16:16:46Z\|INSDC status:public\|Submitter Id:E MTAB 9193:Sample 1\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo stage\|genotype:TgBACgata5: EGFPpd25\|immunophenotype:GFP+\|individual:embryo pool 100 200\|organism part:mesendoderm\|sample name:E MTAB 9193:Sample 1\|scientific name:Danio rerio\|sex:mixed									Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E MTAB 9193:Sample 1 s	Sample 1 s	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Experimental Factor: age:6\|Experimental Factor: RNA interference:n1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP122151	Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01	cDNA6h_1_S1_L002.bam	bam	7256542253.0	71846953.0	E MTAB 9193:cDNA6h 1 S1 L002	0:101	A:2096163385;C:1430325700;G:1560530043;T:2162265616;N:7257509	101		2096163385	1430325700	1560530043	2162265616	7257509	ERX4155253	ERS4601291	ERA2667966	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	1	0.92882		0.12127		0.81162		0.51457		101		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Canada	2020-06-04	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
9902	9902	ERR4194128	ERX4155256	ERS4601294	ERP122151	PRJEB38705	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E-MTAB-9193	Transcriptome Analysis	TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01		Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Sample 4	SAMEA6873731	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada	ENA FIRST PUBLIC:2020 12 31T11:11:47Z\|ENA LAST UPDATE:2020 06 04T16:16:46Z\|External Id:SAMEA6873731\|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada\|INSDC first public:2020 12 31T11:11:47Z\|INSDC last update:2020 06 04T16:16:46Z\|INSDC status:public\|Submitter Id:E MTAB 9193:Sample 4\|age:13\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo stage\|genotype:TgBACgata5: EGFPpd25\|immunophenotype:GFP+\|individual:embryo pool 100 200\|organism part:mesendoderm\|sample name:E MTAB 9193:Sample 4\|scientific name:Danio rerio\|sex:mixed									Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E MTAB 9193:Sample 4 s	Sample 4 s	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Experimental Factor: age:13\|Experimental Factor: RNA interference:n1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP122151	Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01	cDNA13h_1_control_S1_L001.bam	bam	10785974123.0	106791823.0	E MTAB 9193:cDNA13h 1 control S1 L001	0:101	A:3007305661;C:2241057062;G:2505494392;T:2986021199;N:46095809	101		3007305661	2241057062	2505494392	2986021199	46095809	ERX4155256	ERS4601294	ERA2667966	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	1	0.67094		0.07571		0.92951		0.5272		101		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Canada	2020-06-04	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
9903	9903	ERR4194129	ERX4155256	ERS4601294	ERP122151	PRJEB38705	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E-MTAB-9193	Transcriptome Analysis	TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01		Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Sample 4	SAMEA6873731	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada	ENA FIRST PUBLIC:2020 12 31T11:11:47Z\|ENA LAST UPDATE:2020 06 04T16:16:46Z\|External Id:SAMEA6873731\|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada\|INSDC first public:2020 12 31T11:11:47Z\|INSDC last update:2020 06 04T16:16:46Z\|INSDC status:public\|Submitter Id:E MTAB 9193:Sample 4\|age:13\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo stage\|genotype:TgBACgata5: EGFPpd25\|immunophenotype:GFP+\|individual:embryo pool 100 200\|organism part:mesendoderm\|sample name:E MTAB 9193:Sample 4\|scientific name:Danio rerio\|sex:mixed									Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E MTAB 9193:Sample 4 s	Sample 4 s	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Experimental Factor: age:13\|Experimental Factor: RNA interference:n1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP122151	Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01	cDNA13h_1_control_S1_L002.bam	bam	10595192294.0	104902894.0	E MTAB 9193:cDNA13h 1 control S1 L002	0:101	A:2971916419;C:2204229263;G:2390854035;T:2949877754;N:78314823	101		2971916419	2204229263	2390854035	2949877754	78314823	ERX4155256	ERS4601294	ERA2667966	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	1	0.67255		0.08054		0.91583		0.52661		101		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Canada	2020-06-04	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
9904	9904	ERR4194116	ERX4155255	ERS4601293	ERP122151	PRJEB38705	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E-MTAB-9193	Transcriptome Analysis	TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01		Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Sample 3	SAMEA6873730	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada	ENA FIRST PUBLIC:2020 12 31T11:11:47Z\|ENA LAST UPDATE:2020 06 04T16:16:46Z\|External Id:SAMEA6873730\|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada\|INSDC first public:2020 12 31T11:11:47Z\|INSDC last update:2020 06 04T16:16:46Z\|INSDC status:public\|Submitter Id:E MTAB 9193:Sample 3\|age:10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo stage\|genotype:TgBACgata5: EGFPpd25\|immunophenotype:GFP+\|individual:embryo pool 100 200\|organism part:mesendoderm\|sample name:E MTAB 9193:Sample 3\|scientific name:Danio rerio\|sex:mixed									Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E MTAB 9193:Sample 3 s	Sample 3 s	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Experimental Factor: age:10\|Experimental Factor: RNA interference:n1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP122151	Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01	cDNA10h_1_S3_L001.bam	bam	1622536412.0	16556494.0	E MTAB 9193:cDNA10h 1 S3 L001	0:98	A:491141175;C:317161060;G:354179755;T:459976409;N:78013	98		491141175	317161060	354179755	459976409	78013	ERX4155255	ERS4601293	ERA2667966	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	1	0.93238		0.13033		0.89132		0.47076		98		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Canada	2020-06-04	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
9905	9905	ERR4194117	ERX4155255	ERS4601293	ERP122151	PRJEB38705	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E-MTAB-9193	Transcriptome Analysis	TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01		Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Sample 3	SAMEA6873730	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada	ENA FIRST PUBLIC:2020 12 31T11:11:47Z\|ENA LAST UPDATE:2020 06 04T16:16:46Z\|External Id:SAMEA6873730\|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada\|INSDC first public:2020 12 31T11:11:47Z\|INSDC last update:2020 06 04T16:16:46Z\|INSDC status:public\|Submitter Id:E MTAB 9193:Sample 3\|age:10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo stage\|genotype:TgBACgata5: EGFPpd25\|immunophenotype:GFP+\|individual:embryo pool 100 200\|organism part:mesendoderm\|sample name:E MTAB 9193:Sample 3\|scientific name:Danio rerio\|sex:mixed									Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E MTAB 9193:Sample 3 s	Sample 3 s	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Experimental Factor: age:10\|Experimental Factor: RNA interference:n1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP122151	Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01	cDNA10h_1_S3_L002.bam	bam	1484328776.0	15146212.0	E MTAB 9193:cDNA10h 1 S3 L002	0:98	A:450782055;C:290088574;G:322801188;T:420570801;N:86158	98		450782055	290088574	322801188	420570801	86158	ERX4155255	ERS4601293	ERA2667966	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	1	0.92846		0.13128		0.89923		0.46879		98		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Canada	2020-06-04	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
9906	9906	ERR4194118	ERX4155255	ERS4601293	ERP122151	PRJEB38705	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E-MTAB-9193	Transcriptome Analysis	TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01		Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Sample 3	SAMEA6873730	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada	ENA FIRST PUBLIC:2020 12 31T11:11:47Z\|ENA LAST UPDATE:2020 06 04T16:16:46Z\|External Id:SAMEA6873730\|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada\|INSDC first public:2020 12 31T11:11:47Z\|INSDC last update:2020 06 04T16:16:46Z\|INSDC status:public\|Submitter Id:E MTAB 9193:Sample 3\|age:10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo stage\|genotype:TgBACgata5: EGFPpd25\|immunophenotype:GFP+\|individual:embryo pool 100 200\|organism part:mesendoderm\|sample name:E MTAB 9193:Sample 3\|scientific name:Danio rerio\|sex:mixed									Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E MTAB 9193:Sample 3 s	Sample 3 s	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Experimental Factor: age:10\|Experimental Factor: RNA interference:n1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP122151	Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01	cDNA10h_1_S3_L003.bam	bam	1578833116.0	16110542.0	E MTAB 9193:cDNA10h 1 S3 L003	0:98	A:477600666;C:308260969;G:347303289;T:445467384;N:200808	98		477600666	308260969	347303289	445467384	200808	ERX4155255	ERS4601293	ERA2667966	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	1	0.93107		0.12965		0.91265		0.47375		98		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Canada	2020-06-04	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
9907	9907	ERR4194119	ERX4155255	ERS4601293	ERP122151	PRJEB38705	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E-MTAB-9193	Transcriptome Analysis	TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01		Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Sample 3	SAMEA6873730	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada	ENA FIRST PUBLIC:2020 12 31T11:11:47Z\|ENA LAST UPDATE:2020 06 04T16:16:46Z\|External Id:SAMEA6873730\|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada\|INSDC first public:2020 12 31T11:11:47Z\|INSDC last update:2020 06 04T16:16:46Z\|INSDC status:public\|Submitter Id:E MTAB 9193:Sample 3\|age:10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo stage\|genotype:TgBACgata5: EGFPpd25\|immunophenotype:GFP+\|individual:embryo pool 100 200\|organism part:mesendoderm\|sample name:E MTAB 9193:Sample 3\|scientific name:Danio rerio\|sex:mixed									Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E MTAB 9193:Sample 3 s	Sample 3 s	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Experimental Factor: age:10\|Experimental Factor: RNA interference:n1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP122151	Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01	cDNA10h_1_S3_L004.bam	bam	1859564994.0	18975153.0	E MTAB 9193:cDNA10h 1 S3 L004	0:98	A:562936790;C:364057256;G:406607636;T:525811595;N:151717	98		562936790	364057256	406607636	525811595	151717	ERX4155255	ERS4601293	ERA2667966	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	1	0.93453		0.1266		0.87714		0.46957		98		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Canada	2020-06-04	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
9908	9908	ERR4194120	ERX4155255	ERS4601293	ERP122151	PRJEB38705	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E-MTAB-9193	Transcriptome Analysis	TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01		Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Sample 3	SAMEA6873730	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada	ENA FIRST PUBLIC:2020 12 31T11:11:47Z\|ENA LAST UPDATE:2020 06 04T16:16:46Z\|External Id:SAMEA6873730\|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada\|INSDC first public:2020 12 31T11:11:47Z\|INSDC last update:2020 06 04T16:16:46Z\|INSDC status:public\|Submitter Id:E MTAB 9193:Sample 3\|age:10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo stage\|genotype:TgBACgata5: EGFPpd25\|immunophenotype:GFP+\|individual:embryo pool 100 200\|organism part:mesendoderm\|sample name:E MTAB 9193:Sample 3\|scientific name:Danio rerio\|sex:mixed									Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E MTAB 9193:Sample 3 s	Sample 3 s	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Experimental Factor: age:10\|Experimental Factor: RNA interference:n1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP122151	Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01	cDNA10h_2_S3_L001.bam	bam	1156341102.0	11799399.0	E MTAB 9193:cDNA10h 2 S3 L001	0:98	A:345857612;C:224453195;G:257551986;T:327969064;N:509245	98		345857612	224453195	257551986	327969064	509245	ERX4155255	ERS4601293	ERA2667966	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	1	0.93863		0.10744		0.81984		0.501		98		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Canada	2020-06-04	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
9909	9909	ERR4194121	ERX4155255	ERS4601293	ERP122151	PRJEB38705	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E-MTAB-9193	Transcriptome Analysis	TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01		Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Sample 3	SAMEA6873730	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada	ENA FIRST PUBLIC:2020 12 31T11:11:47Z\|ENA LAST UPDATE:2020 06 04T16:16:46Z\|External Id:SAMEA6873730\|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada\|INSDC first public:2020 12 31T11:11:47Z\|INSDC last update:2020 06 04T16:16:46Z\|INSDC status:public\|Submitter Id:E MTAB 9193:Sample 3\|age:10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo stage\|genotype:TgBACgata5: EGFPpd25\|immunophenotype:GFP+\|individual:embryo pool 100 200\|organism part:mesendoderm\|sample name:E MTAB 9193:Sample 3\|scientific name:Danio rerio\|sex:mixed									Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E MTAB 9193:Sample 3 s	Sample 3 s	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Experimental Factor: age:10\|Experimental Factor: RNA interference:n1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP122151	Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01	cDNA10h_2_S3_L002.bam	bam	1105219696.0	11277752.0	E MTAB 9193:cDNA10h 2 S3 L002	0:98	A:331051973;C:214369903;G:246546338;T:312897773;N:353709	98		331051973	214369903	246546338	312897773	353709	ERX4155255	ERS4601293	ERA2667966	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	1	0.93941		0.10818		0.82211		0.50079		98		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Canada	2020-06-04	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
9910	9910	ERR4194122	ERX4155255	ERS4601293	ERP122151	PRJEB38705	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E-MTAB-9193	Transcriptome Analysis	TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01		Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Sample 3	SAMEA6873730	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada	ENA FIRST PUBLIC:2020 12 31T11:11:47Z\|ENA LAST UPDATE:2020 06 04T16:16:46Z\|External Id:SAMEA6873730\|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada\|INSDC first public:2020 12 31T11:11:47Z\|INSDC last update:2020 06 04T16:16:46Z\|INSDC status:public\|Submitter Id:E MTAB 9193:Sample 3\|age:10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo stage\|genotype:TgBACgata5: EGFPpd25\|immunophenotype:GFP+\|individual:embryo pool 100 200\|organism part:mesendoderm\|sample name:E MTAB 9193:Sample 3\|scientific name:Danio rerio\|sex:mixed									Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E MTAB 9193:Sample 3 s	Sample 3 s	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Experimental Factor: age:10\|Experimental Factor: RNA interference:n1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP122151	Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01	cDNA10h_2_S3_L003.bam	bam	1105199606.0	11277547.0	E MTAB 9193:cDNA10h 2 S3 L003	0:98	A:331158619;C:214305131;G:246465559;T:312930408;N:339889	98		331158619	214305131	246465559	312930408	339889	ERX4155255	ERS4601293	ERA2667966	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	1	0.93767		0.10645		0.82329		0.50057		98		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Canada	2020-06-04	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
9911	9911	ERR4194123	ERX4155255	ERS4601293	ERP122151	PRJEB38705	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E-MTAB-9193	Transcriptome Analysis	TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01		Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Sample 3	SAMEA6873730	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada	ENA FIRST PUBLIC:2020 12 31T11:11:47Z\|ENA LAST UPDATE:2020 06 04T16:16:46Z\|External Id:SAMEA6873730\|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada\|INSDC first public:2020 12 31T11:11:47Z\|INSDC last update:2020 06 04T16:16:46Z\|INSDC status:public\|Submitter Id:E MTAB 9193:Sample 3\|age:10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo stage\|genotype:TgBACgata5: EGFPpd25\|immunophenotype:GFP+\|individual:embryo pool 100 200\|organism part:mesendoderm\|sample name:E MTAB 9193:Sample 3\|scientific name:Danio rerio\|sex:mixed									Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E MTAB 9193:Sample 3 s	Sample 3 s	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Experimental Factor: age:10\|Experimental Factor: RNA interference:n1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP122151	Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01	cDNA10h_2_S3_L004.bam	bam	1108707712.0	11313344.0	E MTAB 9193:cDNA10h 2 S3 L004	0:98	A:331374433;C:215925150;G:247131942;T:313865174;N:411013	98		331374433	215925150	247131942	313865174	411013	ERX4155255	ERS4601293	ERA2667966	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	1	0.93827		0.10842		0.82031		0.49241		98		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Canada	2020-06-04	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
9912	9912	ERR4194124	ERX4155255	ERS4601293	ERP122151	PRJEB38705	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E-MTAB-9193	Transcriptome Analysis	TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01		Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Sample 3	SAMEA6873730	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada	ENA FIRST PUBLIC:2020 12 31T11:11:47Z\|ENA LAST UPDATE:2020 06 04T16:16:46Z\|External Id:SAMEA6873730\|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada\|INSDC first public:2020 12 31T11:11:47Z\|INSDC last update:2020 06 04T16:16:46Z\|INSDC status:public\|Submitter Id:E MTAB 9193:Sample 3\|age:10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo stage\|genotype:TgBACgata5: EGFPpd25\|immunophenotype:GFP+\|individual:embryo pool 100 200\|organism part:mesendoderm\|sample name:E MTAB 9193:Sample 3\|scientific name:Danio rerio\|sex:mixed									Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E MTAB 9193:Sample 3 s	Sample 3 s	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Experimental Factor: age:10\|Experimental Factor: RNA interference:n1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP122151	Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01	cDNA10h_2_S3_L005.bam	bam	1110084612.0	11327394.0	E MTAB 9193:cDNA10h 2 S3 L005	0:98	A:332881960;C:215360330;G:247563319;T:313842331;N:436672	98		332881960	215360330	247563319	313842331	436672	ERX4155255	ERS4601293	ERA2667966	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	1	0.93827		0.10719		0.8238		0.50406		98		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Canada	2020-06-04	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
9913	9913	ERR4194125	ERX4155255	ERS4601293	ERP122151	PRJEB38705	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E-MTAB-9193	Transcriptome Analysis	TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01		Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Sample 3	SAMEA6873730	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada	ENA FIRST PUBLIC:2020 12 31T11:11:47Z\|ENA LAST UPDATE:2020 06 04T16:16:46Z\|External Id:SAMEA6873730\|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada\|INSDC first public:2020 12 31T11:11:47Z\|INSDC last update:2020 06 04T16:16:46Z\|INSDC status:public\|Submitter Id:E MTAB 9193:Sample 3\|age:10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo stage\|genotype:TgBACgata5: EGFPpd25\|immunophenotype:GFP+\|individual:embryo pool 100 200\|organism part:mesendoderm\|sample name:E MTAB 9193:Sample 3\|scientific name:Danio rerio\|sex:mixed									Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E MTAB 9193:Sample 3 s	Sample 3 s	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Experimental Factor: age:10\|Experimental Factor: RNA interference:n1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP122151	Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01	cDNA10h_2_S3_L006.bam	bam	1113812728.0	11365436.0	E MTAB 9193:cDNA10h 2 S3 L006	0:98	A:333112288;C:216649152;G:248341020;T:315338848;N:371420	98		333112288	216649152	248341020	315338848	371420	ERX4155255	ERS4601293	ERA2667966	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	1	0.93843		0.10675		0.82079		0.49284		98		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Canada	2020-06-04	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
9914	9914	ERR4194126	ERX4155255	ERS4601293	ERP122151	PRJEB38705	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E-MTAB-9193	Transcriptome Analysis	TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01		Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Sample 3	SAMEA6873730	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada	ENA FIRST PUBLIC:2020 12 31T11:11:47Z\|ENA LAST UPDATE:2020 06 04T16:16:46Z\|External Id:SAMEA6873730\|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada\|INSDC first public:2020 12 31T11:11:47Z\|INSDC last update:2020 06 04T16:16:46Z\|INSDC status:public\|Submitter Id:E MTAB 9193:Sample 3\|age:10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo stage\|genotype:TgBACgata5: EGFPpd25\|immunophenotype:GFP+\|individual:embryo pool 100 200\|organism part:mesendoderm\|sample name:E MTAB 9193:Sample 3\|scientific name:Danio rerio\|sex:mixed									Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E MTAB 9193:Sample 3 s	Sample 3 s	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Experimental Factor: age:10\|Experimental Factor: RNA interference:n1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP122151	Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01	cDNA10h_2_S3_L007.bam	bam	1119495748.0	11423426.0	E MTAB 9193:cDNA10h 2 S3 L007	0:98	A:335288339;C:217283719;G:249624836;T:316900388;N:398466	98		335288339	217283719	249624836	316900388	398466	ERX4155255	ERS4601293	ERA2667966	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	1	0.93711		0.10749		0.82266		0.49382		98		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Canada	2020-06-04	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
9915	9915	ERR4194127	ERX4155255	ERS4601293	ERP122151	PRJEB38705	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E-MTAB-9193	Transcriptome Analysis	TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01		Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Sample 3	SAMEA6873730	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada	ENA FIRST PUBLIC:2020 12 31T11:11:47Z\|ENA LAST UPDATE:2020 06 04T16:16:46Z\|External Id:SAMEA6873730\|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada\|INSDC first public:2020 12 31T11:11:47Z\|INSDC last update:2020 06 04T16:16:46Z\|INSDC status:public\|Submitter Id:E MTAB 9193:Sample 3\|age:10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo stage\|genotype:TgBACgata5: EGFPpd25\|immunophenotype:GFP+\|individual:embryo pool 100 200\|organism part:mesendoderm\|sample name:E MTAB 9193:Sample 3\|scientific name:Danio rerio\|sex:mixed									Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E MTAB 9193:Sample 3 s	Sample 3 s	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Experimental Factor: age:10\|Experimental Factor: RNA interference:n1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP122151	Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01	cDNA10h_2_S3_L008.bam	bam	1175946688.0	11999456.0	E MTAB 9193:cDNA10h 2 S3 L008	0:98	A:351364169;C:228318193;G:261971072;T:333863943;N:429311	98		351364169	228318193	261971072	333863943	429311	ERX4155255	ERS4601293	ERA2667966	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	1	0.93851		0.10755		0.82158		0.49895		98		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Canada	2020-06-04	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
9916	9916	ERR4194130	ERX4155257	ERS4601295	ERP122151	PRJEB38705	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E-MTAB-9193	Transcriptome Analysis	TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01		Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Sample 5	SAMEA6873732	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada	ENA FIRST PUBLIC:2020 12 31T11:11:47Z\|ENA LAST UPDATE:2020 06 04T16:16:46Z\|External Id:SAMEA6873732\|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada\|INSDC first public:2020 12 31T11:11:47Z\|INSDC last update:2020 06 04T16:16:46Z\|INSDC status:public\|Submitter Id:E MTAB 9193:Sample 5\|age:13\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo stage\|genotype:TgBACgata5: EGFPpd25\|immunophenotype:GFP+\|individual:embryo pool 100 200\|organism part:mesendoderm\|sample name:E MTAB 9193:Sample 5\|scientific name:Danio rerio\|sex:mixed									Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E MTAB 9193:Sample 5 s	Sample 5 s	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Experimental Factor: age:13\|Experimental Factor: RNA interference:morpholino mediated Gata5/6 knockdown	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP122151	Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01	cDNA13h_2_gata56KD_S2_L001.bam	bam	7791309377.0	77141677.0	E MTAB 9193:cDNA13h 2 gata56KD S2 L001	0:101	A:2198242220;C:1593746618;G:1784167452;T:2181979820;N:33173267	101		2198242220	1593746618	1784167452	2181979820	33173267	ERX4155257	ERS4601295	ERA2667966	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	1	0.66736		0.08039		0.93026		0.50796		101		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Canada	2020-06-04	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
9917	9917	ERR4194131	ERX4155257	ERS4601295	ERP122151	PRJEB38705	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E-MTAB-9193	Transcriptome Analysis	TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01		Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Sample 5	SAMEA6873732	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada	ENA FIRST PUBLIC:2020 12 31T11:11:47Z\|ENA LAST UPDATE:2020 06 04T16:16:46Z\|External Id:SAMEA6873732\|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada\|INSDC first public:2020 12 31T11:11:47Z\|INSDC last update:2020 06 04T16:16:46Z\|INSDC status:public\|Submitter Id:E MTAB 9193:Sample 5\|age:13\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo stage\|genotype:TgBACgata5: EGFPpd25\|immunophenotype:GFP+\|individual:embryo pool 100 200\|organism part:mesendoderm\|sample name:E MTAB 9193:Sample 5\|scientific name:Danio rerio\|sex:mixed									Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	E MTAB 9193:Sample 5 s	Sample 5 s	Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.	Experimental Factor: age:13\|Experimental Factor: RNA interference:morpholino mediated Gata5/6 knockdown	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 2500	ERP122151	Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish	ENA FIRST PUBLIC:2021 06 02\|ENA LAST UPDATE:2021 12 01	cDNA13h_2_gata56KD_S2_L002.bam	bam	7658149967.0	75823267.0	E MTAB 9193:cDNA13h 2 gata56KD S2 L002	0:101	A:2172230233;C:1568805100;G:1703587704;T:2157181071;N:56345859	101		2172230233	1568805100	1703587704	2157181071	56345859	ERX4155257	ERS4601295	ERA2667966	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada\|European Nucleotide Archive	1	0.66565		0.08597		0.91804		0.51772		101		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Canada	2020-06-04	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
25182	25182	SRR25670729	SRX21396042	SRS18636200	SRP455680	PRJNA1006406	Control of polyA tail length and translation in vertebrate oocytes and early embryos	GSE241107	Other	During oocyte maturation and early embryonic development polyA tail lengths strongly influence mRNA translation. However how tail lengths are controlled at different developmental stages has been unclear. Here we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs mice and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time polyA tail lengths of endogenous mRNAs from frog oocytes and embryos fish embryos and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6 2024.				Fish embryo mRNA germ ring PAL seq v4	GSM7716871		source name:embryo\|tissue:embryo\|treatment:N1\|geo loc name:missing\|collection date:missing	Fish embryo mRNA germ ring PAL seq v4	For gene specific tail seq of mRNA reporters data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4 reads were trimmed with cutadapt v3.7 with the parameters “ m 15 quality base=64 q 20 20 match read wildcards e 0.05 a NNNNATCTCGTATGCCGTCTTCTGCTTG O 7”. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained the genomic sequences of humans or fish depending on which spike in RNAs were used and the sequences of the polyA standards generated previously with the parameters “ runThreadN 16 runMode alignReads outFilterMultimapNmax 1 outReadsUnmapped Fastx outFilterType BySJout outSAMattributes All outSAMtype BAM Unsorted SortedByCoordinate”. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4 primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4–7 tail lengths at quantile 10 25 75 and 90. Supplementary files format and content: For PAL seq v3 or v4 tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4	embryo		Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna…		tissue:embryo\|treatment:N1	GSM7716871	GSM7716871: Fish embryo mRNA germ ring PAL seq v4; Danio rerio; OTHER	GSM7716871 r1	GSM7716871	1	Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna…		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP455680			Fish_embryo_mRNA_germ_ring_PAL_seq_v4_rep1_raw_read2.fastq.gz Fish_embryo_mRNA_germ_ring_PAL_seq_v4_rep1_raw_read1.fastq.gz	fastq fastq	2834842912.0	9234016.0	GSM7716871 r1	0:52 1:255	A:725811118;C:702410592;G:747583409;T:651018348;N:8019445	52	255	725811118	702410592	747583409	651018348	8019445	SRX21396042	SRS18636200	SRA1694849	Whitehead Institute	Whitehead Institute	2	0.00023	0.30494	8e-05	0.01793	0.99967	0.99971	0.5	1.0	52	255	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2023-08-17	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
25183	25183	SRR25670730	SRX21396042	SRS18636200	SRP455680	PRJNA1006406	Control of polyA tail length and translation in vertebrate oocytes and early embryos	GSE241107	Other	During oocyte maturation and early embryonic development polyA tail lengths strongly influence mRNA translation. However how tail lengths are controlled at different developmental stages has been unclear. Here we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs mice and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time polyA tail lengths of endogenous mRNAs from frog oocytes and embryos fish embryos and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6 2024.				Fish embryo mRNA germ ring PAL seq v4	GSM7716871		source name:embryo\|tissue:embryo\|treatment:N1\|geo loc name:missing\|collection date:missing	Fish embryo mRNA germ ring PAL seq v4	For gene specific tail seq of mRNA reporters data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4 reads were trimmed with cutadapt v3.7 with the parameters “ m 15 quality base=64 q 20 20 match read wildcards e 0.05 a NNNNATCTCGTATGCCGTCTTCTGCTTG O 7”. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained the genomic sequences of humans or fish depending on which spike in RNAs were used and the sequences of the polyA standards generated previously with the parameters “ runThreadN 16 runMode alignReads outFilterMultimapNmax 1 outReadsUnmapped Fastx outFilterType BySJout outSAMattributes All outSAMtype BAM Unsorted SortedByCoordinate”. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4 primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4–7 tail lengths at quantile 10 25 75 and 90. Supplementary files format and content: For PAL seq v3 or v4 tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4	embryo		Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna…		tissue:embryo\|treatment:N1	GSM7716871	GSM7716871: Fish embryo mRNA germ ring PAL seq v4; Danio rerio; OTHER	GSM7716871 r1	GSM7716871	1	Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna…		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP455680			Fish_embryo_mRNA_germ_ring_PAL_seq_v4_rep2_raw_read1.fastq.gz Fish_embryo_mRNA_germ_ring_PAL_seq_v4_rep2_raw_read2.fastq.gz	fastq fastq	3473033898.0	11312814.0	GSM7716871 r2	0:52 1:255	A:853178471;C:899976159;G:962100712;T:750811461;N:6967095	52	255	853178471	899976159	962100712	750811461	6967095	SRX21396042	SRS18636200	SRA1694849	Whitehead Institute	Whitehead Institute	2	0.00049	0.0	0.00012	0.0	0.99941	1.0	0.64864		52	255	T	T	mates < 9% mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2023-08-17	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
25184	25184	SRR25670731	SRX21396041	SRS18636199	SRP455680	PRJNA1006406	Control of polyA tail length and translation in vertebrate oocytes and early embryos	GSE241107	Other	During oocyte maturation and early embryonic development polyA tail lengths strongly influence mRNA translation. However how tail lengths are controlled at different developmental stages has been unclear. Here we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs mice and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time polyA tail lengths of endogenous mRNAs from frog oocytes and embryos fish embryos and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6 2024.				Fish embryo mRNA zfs:0000015 PAL seq v4	GSM7716870		source name:embryo\|tissue:embryo\|treatment:N1\|geo loc name:missing\|collection date:missing	Fish embryo mRNA zfs:0000015 PAL seq v4	For gene specific tail seq of mRNA reporters data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4 reads were trimmed with cutadapt v3.7 with the parameters “ m 15 quality base=64 q 20 20 match read wildcards e 0.05 a NNNNATCTCGTATGCCGTCTTCTGCTTG O 7”. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained the genomic sequences of humans or fish depending on which spike in RNAs were used and the sequences of the polyA standards generated previously with the parameters “ runThreadN 16 runMode alignReads outFilterMultimapNmax 1 outReadsUnmapped Fastx outFilterType BySJout outSAMattributes All outSAMtype BAM Unsorted SortedByCoordinate”. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4 primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4–7 tail lengths at quantile 10 25 75 and 90. Supplementary files format and content: For PAL seq v3 or v4 tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4	embryo		Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna…		tissue:embryo\|treatment:N1	GSM7716870	GSM7716870: Fish embryo mRNA zfs:0000015 PAL seq v4; Danio rerio; OTHER	GSM7716870 r1	GSM7716870	1	Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna…		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP455680			Fish_embryo_mRNA_30percent_epiboly_PAL_seq_v4_rep1_raw_read1.fastq.gz Fish_embryo_mRNA_30percent_epiboly_PAL_seq_v4_rep1_raw_read2.fastq.gz	fastq fastq	2695203962.0	8779166.0	GSM7716870 r1	0:52 1:255	A:684535386;C:669852151;G:719008886;T:614209811;N:7597728	52	255	684535386	669852151	719008886	614209811	7597728	SRX21396041	SRS18636199	SRA1694849	Whitehead Institute	Whitehead Institute	2	0.00117	0.35837	0.00017	0.00682	0.99859	0.99963	0.69473	1.0	52	255	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2023-08-17	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
25185	25185	SRR25670732	SRX21396041	SRS18636199	SRP455680	PRJNA1006406	Control of polyA tail length and translation in vertebrate oocytes and early embryos	GSE241107	Other	During oocyte maturation and early embryonic development polyA tail lengths strongly influence mRNA translation. However how tail lengths are controlled at different developmental stages has been unclear. Here we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs mice and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time polyA tail lengths of endogenous mRNAs from frog oocytes and embryos fish embryos and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6 2024.				Fish embryo mRNA zfs:0000015 PAL seq v4	GSM7716870		source name:embryo\|tissue:embryo\|treatment:N1\|geo loc name:missing\|collection date:missing	Fish embryo mRNA zfs:0000015 PAL seq v4	For gene specific tail seq of mRNA reporters data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4 reads were trimmed with cutadapt v3.7 with the parameters “ m 15 quality base=64 q 20 20 match read wildcards e 0.05 a NNNNATCTCGTATGCCGTCTTCTGCTTG O 7”. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained the genomic sequences of humans or fish depending on which spike in RNAs were used and the sequences of the polyA standards generated previously with the parameters “ runThreadN 16 runMode alignReads outFilterMultimapNmax 1 outReadsUnmapped Fastx outFilterType BySJout outSAMattributes All outSAMtype BAM Unsorted SortedByCoordinate”. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4 primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4–7 tail lengths at quantile 10 25 75 and 90. Supplementary files format and content: For PAL seq v3 or v4 tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4	embryo		Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna…		tissue:embryo\|treatment:N1	GSM7716870	GSM7716870: Fish embryo mRNA zfs:0000015 PAL seq v4; Danio rerio; OTHER	GSM7716870 r1	GSM7716870	1	Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna…		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP455680			Fish_embryo_mRNA_30percent_epiboly_PAL_seq_v4_rep2_raw_read2.fastq.gz Fish_embryo_mRNA_30percent_epiboly_PAL_seq_v4_rep2_raw_read1.fastq.gz	fastq fastq	3476338446.0	11323578.0	GSM7716870 r2	0:52 1:255	A:841832234;C:898325199;G:968774318;T:760398070;N:7008625	52	255	841832234	898325199	968774318	760398070	7008625	SRX21396041	SRS18636199	SRA1694849	Whitehead Institute	Whitehead Institute	2	0.00245	0.0	0.00047	0.0	0.99803	1.0	0.58536		52	255	T	T	mates < 9% mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2023-08-17	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
25186	25186	SRR25670733	SRX21396040	SRS18636198	SRP455680	PRJNA1006406	Control of polyA tail length and translation in vertebrate oocytes and early embryos	GSE241107	Other	During oocyte maturation and early embryonic development polyA tail lengths strongly influence mRNA translation. However how tail lengths are controlled at different developmental stages has been unclear. Here we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs mice and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time polyA tail lengths of endogenous mRNAs from frog oocytes and embryos fish embryos and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6 2024.				Fish embryo mRNA sphere PAL seq v4	GSM7716869		source name:embryo\|tissue:embryo\|treatment:N1\|geo loc name:missing\|collection date:missing	Fish embryo mRNA sphere PAL seq v4	For gene specific tail seq of mRNA reporters data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4 reads were trimmed with cutadapt v3.7 with the parameters “ m 15 quality base=64 q 20 20 match read wildcards e 0.05 a NNNNATCTCGTATGCCGTCTTCTGCTTG O 7”. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained the genomic sequences of humans or fish depending on which spike in RNAs were used and the sequences of the polyA standards generated previously with the parameters “ runThreadN 16 runMode alignReads outFilterMultimapNmax 1 outReadsUnmapped Fastx outFilterType BySJout outSAMattributes All outSAMtype BAM Unsorted SortedByCoordinate”. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4 primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4–7 tail lengths at quantile 10 25 75 and 90. Supplementary files format and content: For PAL seq v3 or v4 tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4	embryo		Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna…		tissue:embryo\|treatment:N1	GSM7716869	GSM7716869: Fish embryo mRNA sphere PAL seq v4; Danio rerio; OTHER	GSM7716869 r1	GSM7716869	1	Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna…		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP455680			Fish_embryo_mRNA_sphere_PAL_seq_v4_rep1_raw_read1.fastq.gz Fish_embryo_mRNA_sphere_PAL_seq_v4_rep1_raw_read2.fastq.gz	fastq fastq	3211687254.0	10461522.0	GSM7716869 r1	0:52 1:255	A:813560400;C:775326762;G:854563477;T:759161458;N:9075157	52	255	813560400	775326762	854563477	759161458	9075157	SRX21396040	SRS18636198	SRA1694849	Whitehead Institute	Whitehead Institute	2	0.00088	0.43191	0.0004	0.01556	0.99916	0.99961	0.55769	1.0	52	255	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2023-08-17	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
25187	25187	SRR25670734	SRX21396040	SRS18636198	SRP455680	PRJNA1006406	Control of polyA tail length and translation in vertebrate oocytes and early embryos	GSE241107	Other	During oocyte maturation and early embryonic development polyA tail lengths strongly influence mRNA translation. However how tail lengths are controlled at different developmental stages has been unclear. Here we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs mice and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time polyA tail lengths of endogenous mRNAs from frog oocytes and embryos fish embryos and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6 2024.				Fish embryo mRNA sphere PAL seq v4	GSM7716869		source name:embryo\|tissue:embryo\|treatment:N1\|geo loc name:missing\|collection date:missing	Fish embryo mRNA sphere PAL seq v4	For gene specific tail seq of mRNA reporters data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4 reads were trimmed with cutadapt v3.7 with the parameters “ m 15 quality base=64 q 20 20 match read wildcards e 0.05 a NNNNATCTCGTATGCCGTCTTCTGCTTG O 7”. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained the genomic sequences of humans or fish depending on which spike in RNAs were used and the sequences of the polyA standards generated previously with the parameters “ runThreadN 16 runMode alignReads outFilterMultimapNmax 1 outReadsUnmapped Fastx outFilterType BySJout outSAMattributes All outSAMtype BAM Unsorted SortedByCoordinate”. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4 primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4–7 tail lengths at quantile 10 25 75 and 90. Supplementary files format and content: For PAL seq v3 or v4 tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4	embryo		Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna…		tissue:embryo\|treatment:N1	GSM7716869	GSM7716869: Fish embryo mRNA sphere PAL seq v4; Danio rerio; OTHER	GSM7716869 r1	GSM7716869	1	Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna…		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP455680			Fish_embryo_mRNA_sphere_PAL_seq_v4_rep2_raw_read1.fastq.gz Fish_embryo_mRNA_sphere_PAL_seq_v4_rep2_raw_read2.fastq.gz	fastq fastq	3179916131.0	10358033.0	GSM7716869 r2	0:52 1:255	A:771755667;C:804256300;G:883166175;T:714242073;N:6495916	52	255	771755667	804256300	883166175	714242073	6495916	SRX21396040	SRS18636198	SRA1694849	Whitehead Institute	Whitehead Institute	2	0.00186	0.0	0.00088	0.0	0.99862	1.0	0.64705		52	255	T	T	mates < 9% mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2023-08-17	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
25190	25190	SRR25670737	SRX21396038	SRS18636196	SRP455680	PRJNA1006406	Control of polyA tail length and translation in vertebrate oocytes and early embryos	GSE241107	Other	During oocyte maturation and early embryonic development polyA tail lengths strongly influence mRNA translation. However how tail lengths are controlled at different developmental stages has been unclear. Here we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs mice and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time polyA tail lengths of endogenous mRNAs from frog oocytes and embryos fish embryos and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6 2024.				Fish embryo mRNA 128cell PAL seq v4	GSM7716867		source name:embryo\|tissue:embryo\|treatment:N1\|geo loc name:missing\|collection date:missing	Fish embryo mRNA 128cell PAL seq v4	For gene specific tail seq of mRNA reporters data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4 reads were trimmed with cutadapt v3.7 with the parameters “ m 15 quality base=64 q 20 20 match read wildcards e 0.05 a NNNNATCTCGTATGCCGTCTTCTGCTTG O 7”. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained the genomic sequences of humans or fish depending on which spike in RNAs were used and the sequences of the polyA standards generated previously with the parameters “ runThreadN 16 runMode alignReads outFilterMultimapNmax 1 outReadsUnmapped Fastx outFilterType BySJout outSAMattributes All outSAMtype BAM Unsorted SortedByCoordinate”. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4 primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4–7 tail lengths at quantile 10 25 75 and 90. Supplementary files format and content: For PAL seq v3 or v4 tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4	embryo		Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna…		tissue:embryo\|treatment:N1	GSM7716867	GSM7716867: Fish embryo mRNA 128cell PAL seq v4; Danio rerio; OTHER	GSM7716867 r1	GSM7716867	1	Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna…		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP455680			Fish_embryo_mRNA_128cell_PAL_seq_v4_rep1_raw_read1.fastq.gz Fish_embryo_mRNA_128cell_PAL_seq_v4_rep1_raw_read2.fastq.gz	fastq fastq	2104868443.0	6856249.0	GSM7716867 r1	0:52 1:255	A:539122676;C:505234642;G:558793048;T:495876292;N:5841785	52	255	539122676	505234642	558793048	495876292	5841785	SRX21396038	SRS18636196	SRA1694849	Whitehead Institute	Whitehead Institute	2	0.00035	0.29379	7e-05	0.01129	0.99949	0.99971	0.55882	0.79591	52	255	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2023-08-17	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
25191	25191	SRR25670738	SRX21396038	SRS18636196	SRP455680	PRJNA1006406	Control of polyA tail length and translation in vertebrate oocytes and early embryos	GSE241107	Other	During oocyte maturation and early embryonic development polyA tail lengths strongly influence mRNA translation. However how tail lengths are controlled at different developmental stages has been unclear. Here we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs mice and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time polyA tail lengths of endogenous mRNAs from frog oocytes and embryos fish embryos and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6 2024.				Fish embryo mRNA 128cell PAL seq v4	GSM7716867		source name:embryo\|tissue:embryo\|treatment:N1\|geo loc name:missing\|collection date:missing	Fish embryo mRNA 128cell PAL seq v4	For gene specific tail seq of mRNA reporters data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4 reads were trimmed with cutadapt v3.7 with the parameters “ m 15 quality base=64 q 20 20 match read wildcards e 0.05 a NNNNATCTCGTATGCCGTCTTCTGCTTG O 7”. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained the genomic sequences of humans or fish depending on which spike in RNAs were used and the sequences of the polyA standards generated previously with the parameters “ runThreadN 16 runMode alignReads outFilterMultimapNmax 1 outReadsUnmapped Fastx outFilterType BySJout outSAMattributes All outSAMtype BAM Unsorted SortedByCoordinate”. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4 primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4–7 tail lengths at quantile 10 25 75 and 90. Supplementary files format and content: For PAL seq v3 or v4 tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4	embryo		Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna…		tissue:embryo\|treatment:N1	GSM7716867	GSM7716867: Fish embryo mRNA 128cell PAL seq v4; Danio rerio; OTHER	GSM7716867 r1	GSM7716867	1	Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna…		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP455680			Fish_embryo_mRNA_128cell_PAL_seq_v4_rep2_raw_read1.fastq.gz Fish_embryo_mRNA_128cell_PAL_seq_v4_rep2_raw_read2.fastq.gz	fastq fastq	3135806371.0	10214353.0	GSM7716867 r2	0:52 1:255	A:776612486;C:774126305;G:853951502;T:724788612;N:6327466	52	255	776612486	774126305	853951502	724788612	6327466	SRX21396038	SRS18636196	SRA1694849	Whitehead Institute	Whitehead Institute	2	0.00066	0.0	0.00011	0.0	0.99939	1.0	0.55737		52	255	T	T	mates < 9% mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2023-08-17	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
25192	25192	SRR25670739	SRX21396037	SRS18636195	SRP455680	PRJNA1006406	Control of polyA tail length and translation in vertebrate oocytes and early embryos	GSE241107	Other	During oocyte maturation and early embryonic development polyA tail lengths strongly influence mRNA translation. However how tail lengths are controlled at different developmental stages has been unclear. Here we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs mice and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time polyA tail lengths of endogenous mRNAs from frog oocytes and embryos fish embryos and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6 2024.				Fish embryo mRNA 8cell PAL seq v4	GSM7716866		source name:embryo\|tissue:embryo\|treatment:N1\|geo loc name:missing\|collection date:missing	Fish embryo mRNA 8cell PAL seq v4	For gene specific tail seq of mRNA reporters data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4 reads were trimmed with cutadapt v3.7 with the parameters “ m 15 quality base=64 q 20 20 match read wildcards e 0.05 a NNNNATCTCGTATGCCGTCTTCTGCTTG O 7”. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained the genomic sequences of humans or fish depending on which spike in RNAs were used and the sequences of the polyA standards generated previously with the parameters “ runThreadN 16 runMode alignReads outFilterMultimapNmax 1 outReadsUnmapped Fastx outFilterType BySJout outSAMattributes All outSAMtype BAM Unsorted SortedByCoordinate”. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4 primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4–7 tail lengths at quantile 10 25 75 and 90. Supplementary files format and content: For PAL seq v3 or v4 tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4	embryo		Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna…		tissue:embryo\|treatment:N1	GSM7716866	GSM7716866: Fish embryo mRNA 8cell PAL seq v4; Danio rerio; OTHER	GSM7716866 r1	GSM7716866	1	Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna…		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP455680			Fish_embryo_mRNA_8cell_PAL_seq_v4_rep1_raw_read1.fastq.gz Fish_embryo_mRNA_8cell_PAL_seq_v4_rep1_raw_read2.fastq.gz	fastq fastq	2618998887.0	8530941.0	GSM7716866 r1	0:52 1:255	A:673066508;C:641446717;G:706546263;T:590452494;N:7486905	52	255	673066508	641446717	706546263	590452494	7486905	SRX21396037	SRS18636195	SRA1694849	Whitehead Institute	Whitehead Institute	2	0.0009	0.43244	0.00014	0.0054	0.99902	0.99967	0.54901	1.0	52	255	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2023-08-17	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
25193	25193	SRR25670740	SRX21396037	SRS18636195	SRP455680	PRJNA1006406	Control of polyA tail length and translation in vertebrate oocytes and early embryos	GSE241107	Other	During oocyte maturation and early embryonic development polyA tail lengths strongly influence mRNA translation. However how tail lengths are controlled at different developmental stages has been unclear. Here we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs mice and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time polyA tail lengths of endogenous mRNAs from frog oocytes and embryos fish embryos and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6 2024.				Fish embryo mRNA 8cell PAL seq v4	GSM7716866		source name:embryo\|tissue:embryo\|treatment:N1\|geo loc name:missing\|collection date:missing	Fish embryo mRNA 8cell PAL seq v4	For gene specific tail seq of mRNA reporters data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4 reads were trimmed with cutadapt v3.7 with the parameters “ m 15 quality base=64 q 20 20 match read wildcards e 0.05 a NNNNATCTCGTATGCCGTCTTCTGCTTG O 7”. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained the genomic sequences of humans or fish depending on which spike in RNAs were used and the sequences of the polyA standards generated previously with the parameters “ runThreadN 16 runMode alignReads outFilterMultimapNmax 1 outReadsUnmapped Fastx outFilterType BySJout outSAMattributes All outSAMtype BAM Unsorted SortedByCoordinate”. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4 primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4–7 tail lengths at quantile 10 25 75 and 90. Supplementary files format and content: For PAL seq v3 or v4 tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4	embryo		Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna…		tissue:embryo\|treatment:N1	GSM7716866	GSM7716866: Fish embryo mRNA 8cell PAL seq v4; Danio rerio; OTHER	GSM7716866 r1	GSM7716866	1	Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5 100 mM KCl 5 mM MgCl2 1% [v/v] Triton X 100 100 µg/ml cycloheximide cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer] and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr denuded with 3 mg/ml hyaluronidase for 2 min washed and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases but for the N60 library injected into fish embryos and frog oocytes the N37 PAS N17 library injected into fish embryos and frog oocytes and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009 8 pmol KXSH010 and 2x SSC 0.3 M NaCl 30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher 65002 and incubated for 20 min at 23°C on a thermal mixer shaking with 15 sec on and 1 min 45 sec off. The superna…		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP455680			Fish_embryo_mRNA_8cell_PAL_seq_v4_rep2_raw_read1.fastq.gz Fish_embryo_mRNA_8cell_PAL_seq_v4_rep2_raw_read2.fastq.gz	fastq fastq	3028839589.0	9865927.0	GSM7716866 r2	0:52 1:255	A:756368817;C:758868409;G:836949742;T:670545278;N:6107343	52	255	756368817	758868409	836949742	670545278	6107343	SRX21396037	SRS18636195	SRA1694849	Whitehead Institute	Whitehead Institute	2	0.00156	0.0	0.00026	0.0	0.99835	1.0	0.44791		52	255	T	T	mates < 9% mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2023-08-17	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
25277	25277	SRR30160454	SRX25627658	SRS22272474	SRP457111	PRJNA1009808	Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq]	GSE241754	Transcriptome Analysis	Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points namelyat the 256 cell 2.5 hpf 1000 cell 3 hpf sphere 4 hpf shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis polysome profiling ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis.	parent bioproject:PRJNA1009800	pubmed:39402326		WT bud 10 hpf charged tRNA seqrep 3	GSM8441306		tissue:10 hpf embryos\|cell type:10 hpf embryos\|geo loc name:missing\|collection date:missing	WT bud 10 hpf charged tRNA seqrep 3	Read demultiplexing and adapter trimming performed with cutadapt v3.5 where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’ RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.3.8 using the parameters: species Drer cluster id 0.93 threads 40 min cov 0.001 deconv cov ratio 0.4 max mismatches 0.075 remap remap mismatches 0.075 max multi 10 max multi 6 remap remap mismatches 0.075 crosstalks. Assembly: GRCz11 Supplementary files format and content: csv; mim tRNAseq generated CCA proportions	10 hpf embryos		Total RNA from D.rerio embryos collected at the sphere 4 hpf or bud 10 hpf stage was extracted with TRIZOL under mild acidic conditions to preserve tRNA charging and subjected to oxidation and beta elimination Behrens and Nedialkova 2022. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens and Nedialkova 2022 and sequenced on an Illumina NovaSeq 6000 platform.		cell type:10 hpf embryos	GSM8441306	GSM8441306: WT bud 10 hpf charged tRNA seqrep 3; Danio rerio; ncRNA Seq	GSM8441306 r1	GSM8441306	1	Total RNA from D.rerio embryos collected at the sphere 4 hpf or bud 10 hpf stage was extracted with TRIZOL under mild acidic conditions to preserve tRNA charging and subjected to oxidation and beta elimination Behrens and Nedialkova 2022. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens and Nedialkova 2022 and sequenced on an Illumina NovaSeq 6000 platform.		ncRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP457111			10hpf_aa_rep3.fastq.gz	fastq	193965330.0	3367323.0	GSM8441306 r1	0:57.60	A:36799299;C:55100074;G:53758955;T:48306966;N:36	57		36799299	55100074	53758955	48306966	36	SRX25627658	SRS22272474	SRA1941998	Max Planck Institute of Biochemistry	Max Planck Institute of Biochemistry	1	0.34405		0.05049		0.89471		0.46469		88		B		usable mapping rate	illumina	novaseq_era	5prime	size_fractionation	unknown	bulk	unknown	unknown	Germany	2024-08-05	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
25278	25278	SRR30160455	SRX25627657	SRS22272473	SRP457111	PRJNA1009808	Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq]	GSE241754	Transcriptome Analysis	Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points namelyat the 256 cell 2.5 hpf 1000 cell 3 hpf sphere 4 hpf shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis polysome profiling ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis.	parent bioproject:PRJNA1009800	pubmed:39402326		WT bud 10 hpf charged tRNA seqrep 2	GSM8441305		tissue:10 hpf embryos\|cell type:10 hpf embryos\|geo loc name:missing\|collection date:missing	WT bud 10 hpf charged tRNA seqrep 2	Read demultiplexing and adapter trimming performed with cutadapt v3.5 where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’ RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.3.8 using the parameters: species Drer cluster id 0.93 threads 40 min cov 0.001 deconv cov ratio 0.4 max mismatches 0.075 remap remap mismatches 0.075 max multi 10 max multi 6 remap remap mismatches 0.075 crosstalks. Assembly: GRCz11 Supplementary files format and content: csv; mim tRNAseq generated CCA proportions	10 hpf embryos		Total RNA from D.rerio embryos collected at the sphere 4 hpf or bud 10 hpf stage was extracted with TRIZOL under mild acidic conditions to preserve tRNA charging and subjected to oxidation and beta elimination Behrens and Nedialkova 2022. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens and Nedialkova 2022 and sequenced on an Illumina NovaSeq 6000 platform.		cell type:10 hpf embryos	GSM8441305	GSM8441305: WT bud 10 hpf charged tRNA seqrep 2; Danio rerio; ncRNA Seq	GSM8441305 r1	GSM8441305	1	Total RNA from D.rerio embryos collected at the sphere 4 hpf or bud 10 hpf stage was extracted with TRIZOL under mild acidic conditions to preserve tRNA charging and subjected to oxidation and beta elimination Behrens and Nedialkova 2022. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens and Nedialkova 2022 and sequenced on an Illumina NovaSeq 6000 platform.		ncRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP457111			10hpf_aa_rep2.fastq.gz	fastq	138524715.0	2369009.0	GSM8441305 r1	0:58.47	A:26396279;C:39139297;G:38459048;T:34530060;N:31	58		26396279	39139297	38459048	34530060	31	SRX25627657	SRS22272473	SRA1941998	Max Planck Institute of Biochemistry	Max Planck Institute of Biochemistry	1	0.35458		0.05179		0.89424		0.46401		74		B		usable mapping rate	illumina	novaseq_era	5prime	size_fractionation	unknown	bulk	unknown	unknown	Germany	2024-08-05	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
25279	25279	SRR30160456	SRX25627656	SRS22272472	SRP457111	PRJNA1009808	Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq]	GSE241754	Transcriptome Analysis	Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points namelyat the 256 cell 2.5 hpf 1000 cell 3 hpf sphere 4 hpf shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis polysome profiling ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis.	parent bioproject:PRJNA1009800	pubmed:39402326		WT bud 10 hpf charged tRNA seqrep 1	GSM8441304		tissue:10 hpf embryos\|cell type:10 hpf embryos\|geo loc name:missing\|collection date:missing	WT bud 10 hpf charged tRNA seqrep 1	Read demultiplexing and adapter trimming performed with cutadapt v3.5 where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’ RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.3.8 using the parameters: species Drer cluster id 0.93 threads 40 min cov 0.001 deconv cov ratio 0.4 max mismatches 0.075 remap remap mismatches 0.075 max multi 10 max multi 6 remap remap mismatches 0.075 crosstalks. Assembly: GRCz11 Supplementary files format and content: csv; mim tRNAseq generated CCA proportions	10 hpf embryos		Total RNA from D.rerio embryos collected at the sphere 4 hpf or bud 10 hpf stage was extracted with TRIZOL under mild acidic conditions to preserve tRNA charging and subjected to oxidation and beta elimination Behrens and Nedialkova 2022. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens and Nedialkova 2022 and sequenced on an Illumina NovaSeq 6000 platform.		cell type:10 hpf embryos	GSM8441304	GSM8441304: WT bud 10 hpf charged tRNA seqrep 1; Danio rerio; ncRNA Seq	GSM8441304 r1	GSM8441304	1	Total RNA from D.rerio embryos collected at the sphere 4 hpf or bud 10 hpf stage was extracted with TRIZOL under mild acidic conditions to preserve tRNA charging and subjected to oxidation and beta elimination Behrens and Nedialkova 2022. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens and Nedialkova 2022 and sequenced on an Illumina NovaSeq 6000 platform.		ncRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP457111			10hpf_aa_rep1.fastq.gz	fastq	54473618.0	946419.0	GSM8441304 r1	0:57.56	A:10345022;C:15413782;G:15135500;T:13579304;N:10	57		10345022	15413782	15135500	13579304	10	SRX25627656	SRS22272472	SRA1941998	Max Planck Institute of Biochemistry	Max Planck Institute of Biochemistry	1	0.36103		0.0515		0.89227		0.4748		81		B		usable mapping rate	illumina	novaseq_era	5prime	size_fractionation	unknown	bulk	unknown	unknown	Germany	2024-08-05	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
25280	25280	SRR30160457	SRX25627655	SRS22272471	SRP457111	PRJNA1009808	Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq]	GSE241754	Transcriptome Analysis	Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points namelyat the 256 cell 2.5 hpf 1000 cell 3 hpf sphere 4 hpf shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis polysome profiling ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis.	parent bioproject:PRJNA1009800	pubmed:39402326		WT sphere 4 hpf charged tRNA seqrep 3	GSM8441303		tissue:4 hpf embryos\|cell type:4 hpf embryos\|geo loc name:missing\|collection date:missing	WT sphere 4 hpf charged tRNA seqrep 3	Read demultiplexing and adapter trimming performed with cutadapt v3.5 where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’ RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.3.8 using the parameters: species Drer cluster id 0.93 threads 40 min cov 0.001 deconv cov ratio 0.4 max mismatches 0.075 remap remap mismatches 0.075 max multi 10 max multi 6 remap remap mismatches 0.075 crosstalks. Assembly: GRCz11 Supplementary files format and content: csv; mim tRNAseq generated CCA proportions	4 hpf embryos		Total RNA from D.rerio embryos collected at the sphere 4 hpf or bud 10 hpf stage was extracted with TRIZOL under mild acidic conditions to preserve tRNA charging and subjected to oxidation and beta elimination Behrens and Nedialkova 2022. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens and Nedialkova 2022 and sequenced on an Illumina NovaSeq 6000 platform.		cell type:4 hpf embryos	GSM8441303	GSM8441303: WT sphere 4 hpf charged tRNA seqrep 3; Danio rerio; ncRNA Seq	GSM8441303 r1	GSM8441303	1	Total RNA from D.rerio embryos collected at the sphere 4 hpf or bud 10 hpf stage was extracted with TRIZOL under mild acidic conditions to preserve tRNA charging and subjected to oxidation and beta elimination Behrens and Nedialkova 2022. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens and Nedialkova 2022 and sequenced on an Illumina NovaSeq 6000 platform.		ncRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP457111			4hpf_aa_rep3.fastq.gz	fastq	100810543.0	1747597.0	GSM8441303 r1	0:57.69	A:20466558;C:28054923;G:26849246;T:25439798;N:18	57		20466558	28054923	26849246	25439798	18	SRX25627655	SRS22272471	SRA1941998	Max Planck Institute of Biochemistry	Max Planck Institute of Biochemistry	1	0.36374		0.06294		0.87316		0.54642		39		B		usable mapping rate	illumina	novaseq_era	5prime	size_fractionation	unknown	bulk	unknown	unknown	Germany	2024-08-05	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
25281	25281	SRR30160458	SRX25627654	SRS22272470	SRP457111	PRJNA1009808	Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq]	GSE241754	Transcriptome Analysis	Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points namelyat the 256 cell 2.5 hpf 1000 cell 3 hpf sphere 4 hpf shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis polysome profiling ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis.	parent bioproject:PRJNA1009800	pubmed:39402326		WT sphere 4 hpf charged tRNA seqrep 2	GSM8441302		tissue:4 hpf embryos\|cell type:4 hpf embryos\|geo loc name:missing\|collection date:missing	WT sphere 4 hpf charged tRNA seqrep 2	Read demultiplexing and adapter trimming performed with cutadapt v3.5 where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’ RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.3.8 using the parameters: species Drer cluster id 0.93 threads 40 min cov 0.001 deconv cov ratio 0.4 max mismatches 0.075 remap remap mismatches 0.075 max multi 10 max multi 6 remap remap mismatches 0.075 crosstalks. Assembly: GRCz11 Supplementary files format and content: csv; mim tRNAseq generated CCA proportions	4 hpf embryos		Total RNA from D.rerio embryos collected at the sphere 4 hpf or bud 10 hpf stage was extracted with TRIZOL under mild acidic conditions to preserve tRNA charging and subjected to oxidation and beta elimination Behrens and Nedialkova 2022. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens and Nedialkova 2022 and sequenced on an Illumina NovaSeq 6000 platform.		cell type:4 hpf embryos	GSM8441302	GSM8441302: WT sphere 4 hpf charged tRNA seqrep 2; Danio rerio; ncRNA Seq	GSM8441302 r1	GSM8441302	1	Total RNA from D.rerio embryos collected at the sphere 4 hpf or bud 10 hpf stage was extracted with TRIZOL under mild acidic conditions to preserve tRNA charging and subjected to oxidation and beta elimination Behrens and Nedialkova 2022. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens and Nedialkova 2022 and sequenced on an Illumina NovaSeq 6000 platform.		ncRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP457111			4hpf_aa_rep2.fastq.gz	fastq	121662759.0	2046536.0	GSM8441302 r1	0:59.45	A:24519095;C:33689156;G:32726095;T:30728382;N:31	59		24519095	33689156	32726095	30728382	31	SRX25627654	SRS22272470	SRA1941998	Max Planck Institute of Biochemistry	Max Planck Institute of Biochemistry	1	0.3726		0.06263		0.87136		0.55584		31		B		usable mapping rate	illumina	novaseq_era	5prime	size_fractionation	unknown	bulk	unknown	unknown	Germany	2024-08-05	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
25282	25282	SRR30160459	SRX25627653	SRS22272469	SRP457111	PRJNA1009808	Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq]	GSE241754	Transcriptome Analysis	Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points namelyat the 256 cell 2.5 hpf 1000 cell 3 hpf sphere 4 hpf shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis polysome profiling ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis.	parent bioproject:PRJNA1009800	pubmed:39402326		WT sphere 4 hpf charged tRNA seqrep 1	GSM8441301		tissue:4 hpf embryos\|cell type:4 hpf embryos\|geo loc name:missing\|collection date:missing	WT sphere 4 hpf charged tRNA seqrep 1	Read demultiplexing and adapter trimming performed with cutadapt v3.5 where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’ RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.3.8 using the parameters: species Drer cluster id 0.93 threads 40 min cov 0.001 deconv cov ratio 0.4 max mismatches 0.075 remap remap mismatches 0.075 max multi 10 max multi 6 remap remap mismatches 0.075 crosstalks. Assembly: GRCz11 Supplementary files format and content: csv; mim tRNAseq generated CCA proportions	4 hpf embryos		Total RNA from D.rerio embryos collected at the sphere 4 hpf or bud 10 hpf stage was extracted with TRIZOL under mild acidic conditions to preserve tRNA charging and subjected to oxidation and beta elimination Behrens and Nedialkova 2022. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens and Nedialkova 2022 and sequenced on an Illumina NovaSeq 6000 platform.		cell type:4 hpf embryos	GSM8441301	GSM8441301: WT sphere 4 hpf charged tRNA seqrep 1; Danio rerio; ncRNA Seq	GSM8441301 r1	GSM8441301	1	Total RNA from D.rerio embryos collected at the sphere 4 hpf or bud 10 hpf stage was extracted with TRIZOL under mild acidic conditions to preserve tRNA charging and subjected to oxidation and beta elimination Behrens and Nedialkova 2022. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens and Nedialkova 2022 and sequenced on an Illumina NovaSeq 6000 platform.		ncRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP457111			4hpf_aa_rep1.fastq.gz	fastq	124990980.0	2116213.0	GSM8441301 r1	0:59.06	A:25487542;C:34621140;G:33284460;T:31597816;N:22	59		25487542	34621140	33284460	31597816	22	SRX25627653	SRS22272469	SRA1941998	Max Planck Institute of Biochemistry	Max Planck Institute of Biochemistry	1	0.36013		0.05967		0.87387		0.55002		44		B		usable mapping rate	illumina	novaseq_era	5prime	size_fractionation	unknown	bulk	unknown	unknown	Germany	2024-08-05	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
31773	31773	SRR28590145	SRX24189497	SRS20963520	SRP500320	PRJNA1097627	GPI transamidase complex is required for primordial germ cell migration and development in zebrafish	GSE263481	Transcriptome Analysis	Proteins without xxx domains could be anchored to the cell surface for regulating various biological processes when covalently linked to glycosylphosphatidylinositol GPI molecules by the GPI transamidase GPIT complex. However it remains poorly understood whether and how the GPIT complex affects primordial germ cell PGC development. In this study we report the important roles of GPI transamidase in PGC migration and development in zebrafish embryos. Mutation of pigu or pigk both encoding essential GPIT complex subunits resulted in defective PGC migration with ectopically located PGCs and reduction of PGC counts. Notably a detailed analysis of filopodia in PGCs reveals the attenuated polarity of filopodia distribution along the migration direction in mutant embryos. PGC transplantation and PGC specific rescue experiments demonstrate that both PGC and somatic cell expressed Pigu are required for PGC migration. Furthermore expression levels of PGC specific genes are decreased in pigu mutant PGCs with the derepression of somatic cell genes. Hence we propose that the GPIT complex plays a critical role during PGC migration and development. Overall design: To reveal molecular mechanisms underlying GPI transamidase mediated PGC migration regulation we performed RNA seq of PGCs in wild type and pigu / embryos at the shield and bud stages. We manually picked GFP positive PGCs post cell dissociation of embryos at the shield and bud stages. Then post genotyping of rest somatic cells PGCs with the same genotypes were pooled together and lysed for Smart seq of two biological replicates.		pubmed:39741393		WT shield PGCs RNA rep2	GSM8193374		source name:embryo\|tissue:embryo\|cell line:germ cell\|cell type:PGCs\|genotype:Wile type\|geo loc name:missing\|collection date:missing	WT shield PGCs RNA rep2	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 danRer11 by STAR version: STAR 2.5.3a modified. The gene expression level was normalized to fragments per kilobase of transcript per million mapped FPKM values using Cufflinks version 2.2.1. Assembly: danRer11 Supplementary files format and content: tab delimited ext file includes FPKM values for each samples	embryo	GFP nanos1 3’UTR mRNA was injected into WT and pigu / zygotes respectively to label PGCs. Then the embryos at shield or bud stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 µl PBS. Dissections were performed for up to 5 min. The volume of PBS containing embryos was adjusted to 200 µl and then cells were mechanically dissociated by flicking the tube 30 times and pipetting the mixture 10 times through a 214 µl tip. Cells were then transported into a clear Petri dish and GFP labeled PGCs were manually picked under fluorescence microscope with mouth pipette. GFP nanos1 3’UTR mRNA was injected into WT and pigu / zygotes respectively to label PGCs. Then the embryos at shield or bud stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 µl PBS. Dissections were performed for up to 5 min. The volume of PBS containing embryos was adjusted to 200 µl and then cells were mechanically dissociated by flicking the tube 30 times and pipetting the mixture 10 times through a 200 µl tip. Cells were then transported into a clear Petri dish and GFP labeled PGCs were manually picked under fluorescence microscope with mouth pipette.	Total RNA of oocytes were purified using RNeasy Mini kit QIAGEN 74104 as recommended protocols. Total RNA 5 μg was DNase I Fermentas EN0521 treated at 37°C for 1 h. Poly A tailed mRNA was collected using DynabeadsTM mRNA Purification Kit Invitrogen 61006. RNA seq was carried out with the SMART seq2 protocol as previously described and subjected to paired end sequencing on the Nextseq 500 Illumina platform according to the manufacturer’s instructions. Notably SMART seq2 of low input RNA seq relies on polyA based amplification.	The wild type Tuebingen Tu and India strains were used throughout the experiments. The transgenic line Tgkop:EGFP nanos 3’UTR citation was described before. Unless stated all embryos were raised in Holtfreter’s solution at 28.5°C and staged as described previously.	tissue:embryo\|cell line:germ cell\|cell type:PGCs\|genotype:Wile type	GSM8193374	GSM8193374: WT shield PGCs RNA rep2; Danio rerio; RNA Seq	GSM8193374 r1	GSM8193374	1	Total RNA of oocytes were purified using RNeasy Mini kit QIAGEN 74104 as recommended protocols. Total RNA 5 μg was DNase I Fermentas EN0521 treated at 37°C for 1 h. Poly A tailed mRNA was collected using DynabeadsTM mRNA Purification Kit Invitrogen 61006. RNA seq was carried out with the SMART seq2 protocol as previously described and subjected to paired end sequencing on the Nextseq 500 Illumina platform according to the manufacturer's instructions. Notably SMART seq2 of low input RNA seq relies on polyA based amplification.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP500320			WT_shield_PGCs_RNA_rep2_r1.fq.gz WT_shield_PGCs_RNA_rep2_r2.fq.gz	fastq fastq	1476298800.0	4920996.0	GSM8193374 r1	0:150 1:150	A:364072227;C:345274481;G:387289011;T:379660776;N:2305	150	150	364072227	345274481	387289011	379660776	2305	SRX24189497	SRS20963520	SRA1842063	Tsinghua University	Tsinghua University	2	0.9277	0.92845	0.26727	0.2672	0.86803	0.86969	0.75933	0.75985	150	150	B	B	biological fallback assumption	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_plate	smartseq	China	2024-04-08	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
31774	31774	SRR28590146	SRX24189496	SRS20963519	SRP500320	PRJNA1097627	GPI transamidase complex is required for primordial germ cell migration and development in zebrafish	GSE263481	Transcriptome Analysis	Proteins without xxx domains could be anchored to the cell surface for regulating various biological processes when covalently linked to glycosylphosphatidylinositol GPI molecules by the GPI transamidase GPIT complex. However it remains poorly understood whether and how the GPIT complex affects primordial germ cell PGC development. In this study we report the important roles of GPI transamidase in PGC migration and development in zebrafish embryos. Mutation of pigu or pigk both encoding essential GPIT complex subunits resulted in defective PGC migration with ectopically located PGCs and reduction of PGC counts. Notably a detailed analysis of filopodia in PGCs reveals the attenuated polarity of filopodia distribution along the migration direction in mutant embryos. PGC transplantation and PGC specific rescue experiments demonstrate that both PGC and somatic cell expressed Pigu are required for PGC migration. Furthermore expression levels of PGC specific genes are decreased in pigu mutant PGCs with the derepression of somatic cell genes. Hence we propose that the GPIT complex plays a critical role during PGC migration and development. Overall design: To reveal molecular mechanisms underlying GPI transamidase mediated PGC migration regulation we performed RNA seq of PGCs in wild type and pigu / embryos at the shield and bud stages. We manually picked GFP positive PGCs post cell dissociation of embryos at the shield and bud stages. Then post genotyping of rest somatic cells PGCs with the same genotypes were pooled together and lysed for Smart seq of two biological replicates.		pubmed:39741393		WT shield PGCs RNA rep1	GSM8193373		source name:embryo\|tissue:embryo\|cell line:germ cell\|cell type:PGCs\|genotype:Wile type\|geo loc name:missing\|collection date:missing	WT shield PGCs RNA rep1	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 danRer11 by STAR version: STAR 2.5.3a modified. The gene expression level was normalized to fragments per kilobase of transcript per million mapped FPKM values using Cufflinks version 2.2.1. Assembly: danRer11 Supplementary files format and content: tab delimited ext file includes FPKM values for each samples	embryo	GFP nanos1 3’UTR mRNA was injected into WT and pigu / zygotes respectively to label PGCs. Then the embryos at shield or bud stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 µl PBS. Dissections were performed for up to 5 min. The volume of PBS containing embryos was adjusted to 200 µl and then cells were mechanically dissociated by flicking the tube 30 times and pipetting the mixture 10 times through a 212 µl tip. Cells were then transported into a clear Petri dish and GFP labeled PGCs were manually picked under fluorescence microscope with mouth pipette. GFP nanos1 3’UTR mRNA was injected into WT and pigu / zygotes respectively to label PGCs. Then the embryos at shield or bud stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 µl PBS. Dissections were performed for up to 5 min. The volume of PBS containing embryos was adjusted to 200 µl and then cells were mechanically dissociated by flicking the tube 30 times and pipetting the mixture 10 times through a 200 µl tip. Cells were then transported into a clear Petri dish and GFP labeled PGCs were manually picked under fluorescence microscope with mouth pipette.	Total RNA of oocytes were purified using RNeasy Mini kit QIAGEN 74104 as recommended protocols. Total RNA 5 μg was DNase I Fermentas EN0521 treated at 37°C for 1 h. Poly A tailed mRNA was collected using DynabeadsTM mRNA Purification Kit Invitrogen 61006. RNA seq was carried out with the SMART seq2 protocol as previously described and subjected to paired end sequencing on the Nextseq 500 Illumina platform according to the manufacturer’s instructions. Notably SMART seq2 of low input RNA seq relies on polyA based amplification.	The wild type Tuebingen Tu and India strains were used throughout the experiments. The transgenic line Tgkop:EGFP nanos 3’UTR citation was described before. Unless stated all embryos were raised in Holtfreter’s solution at 28.5°C and staged as described previously.	tissue:embryo\|cell line:germ cell\|cell type:PGCs\|genotype:Wile type	GSM8193373	GSM8193373: WT shield PGCs RNA rep1; Danio rerio; RNA Seq	GSM8193373 r1	GSM8193373	1	Total RNA of oocytes were purified using RNeasy Mini kit QIAGEN 74104 as recommended protocols. Total RNA 5 μg was DNase I Fermentas EN0521 treated at 37°C for 1 h. Poly A tailed mRNA was collected using DynabeadsTM mRNA Purification Kit Invitrogen 61006. RNA seq was carried out with the SMART seq2 protocol as previously described and subjected to paired end sequencing on the Nextseq 500 Illumina platform according to the manufacturer's instructions. Notably SMART seq2 of low input RNA seq relies on polyA based amplification.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP500320			WT_shield_PGCs_RNA_rep1_r2.fq.gz WT_shield_PGCs_RNA_rep1_r1.fq.gz	fastq fastq	2758778100.0	9195927.0	GSM8193373 r1	0:150 1:150	A:769058521;C:582931819;G:614181069;T:792602904;N:3787	150	150	769058521	582931819	614181069	792602904	3787	SRX24189496	SRS20963519	SRA1842063	Tsinghua University	Tsinghua University	2	0.93691	0.91581	0.06844	0.06665	0.7683	0.76995	0.53645	0.52363	150	150	B	B	biological fallback assumption	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_plate	smartseq	China	2024-04-08	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
31775	31775	SRR28590147	SRX24189495	SRS20963518	SRP500320	PRJNA1097627	GPI transamidase complex is required for primordial germ cell migration and development in zebrafish	GSE263481	Transcriptome Analysis	Proteins without xxx domains could be anchored to the cell surface for regulating various biological processes when covalently linked to glycosylphosphatidylinositol GPI molecules by the GPI transamidase GPIT complex. However it remains poorly understood whether and how the GPIT complex affects primordial germ cell PGC development. In this study we report the important roles of GPI transamidase in PGC migration and development in zebrafish embryos. Mutation of pigu or pigk both encoding essential GPIT complex subunits resulted in defective PGC migration with ectopically located PGCs and reduction of PGC counts. Notably a detailed analysis of filopodia in PGCs reveals the attenuated polarity of filopodia distribution along the migration direction in mutant embryos. PGC transplantation and PGC specific rescue experiments demonstrate that both PGC and somatic cell expressed Pigu are required for PGC migration. Furthermore expression levels of PGC specific genes are decreased in pigu mutant PGCs with the derepression of somatic cell genes. Hence we propose that the GPIT complex plays a critical role during PGC migration and development. Overall design: To reveal molecular mechanisms underlying GPI transamidase mediated PGC migration regulation we performed RNA seq of PGCs in wild type and pigu / embryos at the shield and bud stages. We manually picked GFP positive PGCs post cell dissociation of embryos at the shield and bud stages. Then post genotyping of rest somatic cells PGCs with the same genotypes were pooled together and lysed for Smart seq of two biological replicates.		pubmed:39741393		WT bud PGCs RNA rep2	GSM8193372		source name:embryo\|tissue:embryo\|cell line:germ cell\|cell type:PGCs\|genotype:Wile type\|geo loc name:missing\|collection date:missing	WT bud PGCs RNA rep2	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 danRer11 by STAR version: STAR 2.5.3a modified. The gene expression level was normalized to fragments per kilobase of transcript per million mapped FPKM values using Cufflinks version 2.2.1. Assembly: danRer11 Supplementary files format and content: tab delimited ext file includes FPKM values for each samples	embryo	GFP nanos1 3’UTR mRNA was injected into WT and pigu / zygotes respectively to label PGCs. Then the embryos at shield or bud stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 µl PBS. Dissections were performed for up to 5 min. The volume of PBS containing embryos was adjusted to 200 µl and then cells were mechanically dissociated by flicking the tube 30 times and pipetting the mixture 10 times through a 210 µl tip. Cells were then transported into a clear Petri dish and GFP labeled PGCs were manually picked under fluorescence microscope with mouth pipette. GFP nanos1 3’UTR mRNA was injected into WT and pigu / zygotes respectively to label PGCs. Then the embryos at shield or bud stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 µl PBS. Dissections were performed for up to 5 min. The volume of PBS containing embryos was adjusted to 200 µl and then cells were mechanically dissociated by flicking the tube 30 times and pipetting the mixture 10 times through a 200 µl tip. Cells were then transported into a clear Petri dish and GFP labeled PGCs were manually picked under fluorescence microscope with mouth pipette.	Total RNA of oocytes were purified using RNeasy Mini kit QIAGEN 74104 as recommended protocols. Total RNA 5 μg was DNase I Fermentas EN0521 treated at 37°C for 1 h. Poly A tailed mRNA was collected using DynabeadsTM mRNA Purification Kit Invitrogen 61006. RNA seq was carried out with the SMART seq2 protocol as previously described and subjected to paired end sequencing on the Nextseq 500 Illumina platform according to the manufacturer’s instructions. Notably SMART seq2 of low input RNA seq relies on polyA based amplification.	The wild type Tuebingen Tu and India strains were used throughout the experiments. The transgenic line Tgkop:EGFP nanos 3’UTR citation was described before. Unless stated all embryos were raised in Holtfreter’s solution at 28.5°C and staged as described previously.	tissue:embryo\|cell line:germ cell\|cell type:PGCs\|genotype:Wile type	GSM8193372	GSM8193372: WT bud PGCs RNA rep2; Danio rerio; RNA Seq	GSM8193372 r1	GSM8193372	1	Total RNA of oocytes were purified using RNeasy Mini kit QIAGEN 74104 as recommended protocols. Total RNA 5 μg was DNase I Fermentas EN0521 treated at 37°C for 1 h. Poly A tailed mRNA was collected using DynabeadsTM mRNA Purification Kit Invitrogen 61006. RNA seq was carried out with the SMART seq2 protocol as previously described and subjected to paired end sequencing on the Nextseq 500 Illumina platform according to the manufacturer's instructions. Notably SMART seq2 of low input RNA seq relies on polyA based amplification.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP500320			WT_bud_PGCs_RNA_rep2_r1.fq.gz WT_bud_PGCs_RNA_rep2_r2.fq.gz	fastq fastq	3111261300.0	10370871.0	GSM8193372 r1	0:150 1:150	A:817262319;C:691724200;G:751270343;T:850999265;N:5173	150	150	817262319	691724200	751270343	850999265	5173	SRX24189495	SRS20963518	SRA1842063	Tsinghua University	Tsinghua University	2	0.90729	0.9053	0.11596	0.1166	0.79963	0.79981	0.60276	0.59912	150	150	B	B	biological fallback assumption	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_plate	smartseq	China	2024-04-08	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
31776	31776	SRR28590148	SRX24189494	SRS20963517	SRP500320	PRJNA1097627	GPI transamidase complex is required for primordial germ cell migration and development in zebrafish	GSE263481	Transcriptome Analysis	Proteins without xxx domains could be anchored to the cell surface for regulating various biological processes when covalently linked to glycosylphosphatidylinositol GPI molecules by the GPI transamidase GPIT complex. However it remains poorly understood whether and how the GPIT complex affects primordial germ cell PGC development. In this study we report the important roles of GPI transamidase in PGC migration and development in zebrafish embryos. Mutation of pigu or pigk both encoding essential GPIT complex subunits resulted in defective PGC migration with ectopically located PGCs and reduction of PGC counts. Notably a detailed analysis of filopodia in PGCs reveals the attenuated polarity of filopodia distribution along the migration direction in mutant embryos. PGC transplantation and PGC specific rescue experiments demonstrate that both PGC and somatic cell expressed Pigu are required for PGC migration. Furthermore expression levels of PGC specific genes are decreased in pigu mutant PGCs with the derepression of somatic cell genes. Hence we propose that the GPIT complex plays a critical role during PGC migration and development. Overall design: To reveal molecular mechanisms underlying GPI transamidase mediated PGC migration regulation we performed RNA seq of PGCs in wild type and pigu / embryos at the shield and bud stages. We manually picked GFP positive PGCs post cell dissociation of embryos at the shield and bud stages. Then post genotyping of rest somatic cells PGCs with the same genotypes were pooled together and lysed for Smart seq of two biological replicates.		pubmed:39741393		WT bud PGCs RNA rep1	GSM8193371		source name:embryo\|tissue:embryo\|cell line:germ cell\|cell type:PGCs\|genotype:Wile type\|geo loc name:missing\|collection date:missing	WT bud PGCs RNA rep1	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 danRer11 by STAR version: STAR 2.5.3a modified. The gene expression level was normalized to fragments per kilobase of transcript per million mapped FPKM values using Cufflinks version 2.2.1. Assembly: danRer11 Supplementary files format and content: tab delimited ext file includes FPKM values for each samples	embryo	GFP nanos1 3’UTR mRNA was injected into WT and pigu / zygotes respectively to label PGCs. Then the embryos at shield or bud stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 µl PBS. Dissections were performed for up to 5 min. The volume of PBS containing embryos was adjusted to 200 µl and then cells were mechanically dissociated by flicking the tube 30 times and pipetting the mixture 10 times through a 208 µl tip. Cells were then transported into a clear Petri dish and GFP labeled PGCs were manually picked under fluorescence microscope with mouth pipette. GFP nanos1 3’UTR mRNA was injected into WT and pigu / zygotes respectively to label PGCs. Then the embryos at shield or bud stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 µl PBS. Dissections were performed for up to 5 min. The volume of PBS containing embryos was adjusted to 200 µl and then cells were mechanically dissociated by flicking the tube 30 times and pipetting the mixture 10 times through a 200 µl tip. Cells were then transported into a clear Petri dish and GFP labeled PGCs were manually picked under fluorescence microscope with mouth pipette.	Total RNA of oocytes were purified using RNeasy Mini kit QIAGEN 74104 as recommended protocols. Total RNA 5 μg was DNase I Fermentas EN0521 treated at 37°C for 1 h. Poly A tailed mRNA was collected using DynabeadsTM mRNA Purification Kit Invitrogen 61006. RNA seq was carried out with the SMART seq2 protocol as previously described and subjected to paired end sequencing on the Nextseq 500 Illumina platform according to the manufacturer’s instructions. Notably SMART seq2 of low input RNA seq relies on polyA based amplification.	The wild type Tuebingen Tu and India strains were used throughout the experiments. The transgenic line Tgkop:EGFP nanos 3’UTR citation was described before. Unless stated all embryos were raised in Holtfreter’s solution at 28.5°C and staged as described previously.	tissue:embryo\|cell line:germ cell\|cell type:PGCs\|genotype:Wile type	GSM8193371	GSM8193371: WT bud PGCs RNA rep1; Danio rerio; RNA Seq	GSM8193371 r1	GSM8193371	1	Total RNA of oocytes were purified using RNeasy Mini kit QIAGEN 74104 as recommended protocols. Total RNA 5 μg was DNase I Fermentas EN0521 treated at 37°C for 1 h. Poly A tailed mRNA was collected using DynabeadsTM mRNA Purification Kit Invitrogen 61006. RNA seq was carried out with the SMART seq2 protocol as previously described and subjected to paired end sequencing on the Nextseq 500 Illumina platform according to the manufacturer's instructions. Notably SMART seq2 of low input RNA seq relies on polyA based amplification.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP500320			WT_bud_PGCs_RNA_rep1_r1.fq.gz WT_bud_PGCs_RNA_rep1_r2.fq.gz	fastq fastq	3758269200.0	12527564.0	GSM8193371 r1	0:150 1:150	A:1041649283;C:801966468;G:845188264;T:1069459832;N:5353	150	150	1041649283	801966468	845188264	1069459832	5353	SRX24189494	SRS20963517	SRA1842063	Tsinghua University	Tsinghua University	2	0.93714	0.91161	0.07974	0.07673	0.75785	0.76037	0.52906	0.52822	150	150	B	B	biological fallback assumption	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_plate	smartseq	China	2024-04-08	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
31777	31777	SRR28590149	SRX24189493	SRS20963516	SRP500320	PRJNA1097627	GPI transamidase complex is required for primordial germ cell migration and development in zebrafish	GSE263481	Transcriptome Analysis	Proteins without xxx domains could be anchored to the cell surface for regulating various biological processes when covalently linked to glycosylphosphatidylinositol GPI molecules by the GPI transamidase GPIT complex. However it remains poorly understood whether and how the GPIT complex affects primordial germ cell PGC development. In this study we report the important roles of GPI transamidase in PGC migration and development in zebrafish embryos. Mutation of pigu or pigk both encoding essential GPIT complex subunits resulted in defective PGC migration with ectopically located PGCs and reduction of PGC counts. Notably a detailed analysis of filopodia in PGCs reveals the attenuated polarity of filopodia distribution along the migration direction in mutant embryos. PGC transplantation and PGC specific rescue experiments demonstrate that both PGC and somatic cell expressed Pigu are required for PGC migration. Furthermore expression levels of PGC specific genes are decreased in pigu mutant PGCs with the derepression of somatic cell genes. Hence we propose that the GPIT complex plays a critical role during PGC migration and development. Overall design: To reveal molecular mechanisms underlying GPI transamidase mediated PGC migration regulation we performed RNA seq of PGCs in wild type and pigu / embryos at the shield and bud stages. We manually picked GFP positive PGCs post cell dissociation of embryos at the shield and bud stages. Then post genotyping of rest somatic cells PGCs with the same genotypes were pooled together and lysed for Smart seq of two biological replicates.		pubmed:39741393		pigu homo shield PGCs RNA rep2	GSM8193370		source name:embryo\|tissue:embryo\|cell line:germ cell\|cell type:PGCs\|genotype:pigu homo\|geo loc name:missing\|collection date:missing	pigu homo shield PGCs RNA rep2	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 danRer11 by STAR version: STAR 2.5.3a modified. The gene expression level was normalized to fragments per kilobase of transcript per million mapped FPKM values using Cufflinks version 2.2.1. Assembly: danRer11 Supplementary files format and content: tab delimited ext file includes FPKM values for each samples	embryo	GFP nanos1 3’UTR mRNA was injected into WT and pigu / zygotes respectively to label PGCs. Then the embryos at shield or bud stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 µl PBS. Dissections were performed for up to 5 min. The volume of PBS containing embryos was adjusted to 200 µl and then cells were mechanically dissociated by flicking the tube 30 times and pipetting the mixture 10 times through a 206 µl tip. Cells were then transported into a clear Petri dish and GFP labeled PGCs were manually picked under fluorescence microscope with mouth pipette. GFP nanos1 3’UTR mRNA was injected into WT and pigu / zygotes respectively to label PGCs. Then the embryos at shield or bud stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 µl PBS. Dissections were performed for up to 5 min. The volume of PBS containing embryos was adjusted to 200 µl and then cells were mechanically dissociated by flicking the tube 30 times and pipetting the mixture 10 times through a 200 µl tip. Cells were then transported into a clear Petri dish and GFP labeled PGCs were manually picked under fluorescence microscope with mouth pipette.	Total RNA of oocytes were purified using RNeasy Mini kit QIAGEN 74104 as recommended protocols. Total RNA 5 μg was DNase I Fermentas EN0521 treated at 37°C for 1 h. Poly A tailed mRNA was collected using DynabeadsTM mRNA Purification Kit Invitrogen 61006. RNA seq was carried out with the SMART seq2 protocol as previously described and subjected to paired end sequencing on the Nextseq 500 Illumina platform according to the manufacturer’s instructions. Notably SMART seq2 of low input RNA seq relies on polyA based amplification.	The wild type Tuebingen Tu and India strains were used throughout the experiments. The transgenic line Tgkop:EGFP nanos 3’UTR citation was described before. Unless stated all embryos were raised in Holtfreter’s solution at 28.5°C and staged as described previously.	tissue:embryo\|cell line:germ cell\|cell type:PGCs\|genotype:pigu homo	GSM8193370	GSM8193370: pigu homo shield PGCs RNA rep2; Danio rerio; RNA Seq	GSM8193370 r1	GSM8193370	1	Total RNA of oocytes were purified using RNeasy Mini kit QIAGEN 74104 as recommended protocols. Total RNA 5 μg was DNase I Fermentas EN0521 treated at 37°C for 1 h. Poly A tailed mRNA was collected using DynabeadsTM mRNA Purification Kit Invitrogen 61006. RNA seq was carried out with the SMART seq2 protocol as previously described and subjected to paired end sequencing on the Nextseq 500 Illumina platform according to the manufacturer's instructions. Notably SMART seq2 of low input RNA seq relies on polyA based amplification.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP500320			pigu_homo_shield_PGCs_RNA_rep2_r2.fq.gz pigu_homo_shield_PGCs_RNA_rep2_r1.fq.gz	fastq fastq	875630700.0	2918769.0	GSM8193370 r1	0:150 1:150	A:229625544;C:190227589;G:217096984;T:238679075;N:1508	150	150	229625544	190227589	217096984	238679075	1508	SRX24189493	SRS20963516	SRA1842063	Tsinghua University	Tsinghua University	2	0.81852	0.81643	0.19346	0.19329	0.89852	0.89897	0.83525	0.83082	150	150	B	B	biological fallback assumption	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_plate	smartseq	China	2024-04-08	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
31778	31778	SRR28590150	SRX24189492	SRS20963515	SRP500320	PRJNA1097627	GPI transamidase complex is required for primordial germ cell migration and development in zebrafish	GSE263481	Transcriptome Analysis	Proteins without xxx domains could be anchored to the cell surface for regulating various biological processes when covalently linked to glycosylphosphatidylinositol GPI molecules by the GPI transamidase GPIT complex. However it remains poorly understood whether and how the GPIT complex affects primordial germ cell PGC development. In this study we report the important roles of GPI transamidase in PGC migration and development in zebrafish embryos. Mutation of pigu or pigk both encoding essential GPIT complex subunits resulted in defective PGC migration with ectopically located PGCs and reduction of PGC counts. Notably a detailed analysis of filopodia in PGCs reveals the attenuated polarity of filopodia distribution along the migration direction in mutant embryos. PGC transplantation and PGC specific rescue experiments demonstrate that both PGC and somatic cell expressed Pigu are required for PGC migration. Furthermore expression levels of PGC specific genes are decreased in pigu mutant PGCs with the derepression of somatic cell genes. Hence we propose that the GPIT complex plays a critical role during PGC migration and development. Overall design: To reveal molecular mechanisms underlying GPI transamidase mediated PGC migration regulation we performed RNA seq of PGCs in wild type and pigu / embryos at the shield and bud stages. We manually picked GFP positive PGCs post cell dissociation of embryos at the shield and bud stages. Then post genotyping of rest somatic cells PGCs with the same genotypes were pooled together and lysed for Smart seq of two biological replicates.		pubmed:39741393		pigu homo shield PGCs RNA rep1	GSM8193369		source name:embryo\|tissue:embryo\|cell line:germ cell\|cell type:PGCs\|genotype:pigu homo\|geo loc name:missing\|collection date:missing	pigu homo shield PGCs RNA rep1	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 danRer11 by STAR version: STAR 2.5.3a modified. The gene expression level was normalized to fragments per kilobase of transcript per million mapped FPKM values using Cufflinks version 2.2.1. Assembly: danRer11 Supplementary files format and content: tab delimited ext file includes FPKM values for each samples	embryo	GFP nanos1 3’UTR mRNA was injected into WT and pigu / zygotes respectively to label PGCs. Then the embryos at shield or bud stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 µl PBS. Dissections were performed for up to 5 min. The volume of PBS containing embryos was adjusted to 200 µl and then cells were mechanically dissociated by flicking the tube 30 times and pipetting the mixture 10 times through a 204 µl tip. Cells were then transported into a clear Petri dish and GFP labeled PGCs were manually picked under fluorescence microscope with mouth pipette. GFP nanos1 3’UTR mRNA was injected into WT and pigu / zygotes respectively to label PGCs. Then the embryos at shield or bud stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 µl PBS. Dissections were performed for up to 5 min. The volume of PBS containing embryos was adjusted to 200 µl and then cells were mechanically dissociated by flicking the tube 30 times and pipetting the mixture 10 times through a 200 µl tip. Cells were then transported into a clear Petri dish and GFP labeled PGCs were manually picked under fluorescence microscope with mouth pipette.	Total RNA of oocytes were purified using RNeasy Mini kit QIAGEN 74104 as recommended protocols. Total RNA 5 μg was DNase I Fermentas EN0521 treated at 37°C for 1 h. Poly A tailed mRNA was collected using DynabeadsTM mRNA Purification Kit Invitrogen 61006. RNA seq was carried out with the SMART seq2 protocol as previously described and subjected to paired end sequencing on the Nextseq 500 Illumina platform according to the manufacturer’s instructions. Notably SMART seq2 of low input RNA seq relies on polyA based amplification.	The wild type Tuebingen Tu and India strains were used throughout the experiments. The transgenic line Tgkop:EGFP nanos 3’UTR citation was described before. Unless stated all embryos were raised in Holtfreter’s solution at 28.5°C and staged as described previously.	tissue:embryo\|cell line:germ cell\|cell type:PGCs\|genotype:pigu homo	GSM8193369	GSM8193369: pigu homo shield PGCs RNA rep1; Danio rerio; RNA Seq	GSM8193369 r1	GSM8193369	1	Total RNA of oocytes were purified using RNeasy Mini kit QIAGEN 74104 as recommended protocols. Total RNA 5 μg was DNase I Fermentas EN0521 treated at 37°C for 1 h. Poly A tailed mRNA was collected using DynabeadsTM mRNA Purification Kit Invitrogen 61006. RNA seq was carried out with the SMART seq2 protocol as previously described and subjected to paired end sequencing on the Nextseq 500 Illumina platform according to the manufacturer's instructions. Notably SMART seq2 of low input RNA seq relies on polyA based amplification.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP500320			pigu_homo_shield_PGCs_RNA_rep1_r2.fq.gz pigu_homo_shield_PGCs_RNA_rep1_r1.fq.gz	fastq fastq	2204383800.0	7347946.0	GSM8193369 r1	0:150 1:150	A:618947181;C:459789570;G:491705141;T:633938869;N:3039	150	150	618947181	459789570	491705141	633938869	3039	SRX24189492	SRS20963515	SRA1842063	Tsinghua University	Tsinghua University	2	0.91971	0.9203	0.0732	0.07256	0.77512	0.77516	0.53347	0.53419	150	150	B	B	biological fallback assumption	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_plate	smartseq	China	2024-04-08	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
31779	31779	SRR28590151	SRX24189491	SRS20963514	SRP500320	PRJNA1097627	GPI transamidase complex is required for primordial germ cell migration and development in zebrafish	GSE263481	Transcriptome Analysis	Proteins without xxx domains could be anchored to the cell surface for regulating various biological processes when covalently linked to glycosylphosphatidylinositol GPI molecules by the GPI transamidase GPIT complex. However it remains poorly understood whether and how the GPIT complex affects primordial germ cell PGC development. In this study we report the important roles of GPI transamidase in PGC migration and development in zebrafish embryos. Mutation of pigu or pigk both encoding essential GPIT complex subunits resulted in defective PGC migration with ectopically located PGCs and reduction of PGC counts. Notably a detailed analysis of filopodia in PGCs reveals the attenuated polarity of filopodia distribution along the migration direction in mutant embryos. PGC transplantation and PGC specific rescue experiments demonstrate that both PGC and somatic cell expressed Pigu are required for PGC migration. Furthermore expression levels of PGC specific genes are decreased in pigu mutant PGCs with the derepression of somatic cell genes. Hence we propose that the GPIT complex plays a critical role during PGC migration and development. Overall design: To reveal molecular mechanisms underlying GPI transamidase mediated PGC migration regulation we performed RNA seq of PGCs in wild type and pigu / embryos at the shield and bud stages. We manually picked GFP positive PGCs post cell dissociation of embryos at the shield and bud stages. Then post genotyping of rest somatic cells PGCs with the same genotypes were pooled together and lysed for Smart seq of two biological replicates.		pubmed:39741393		pigu homo bud PGCs RNA rep2	GSM8193368		source name:embryo\|tissue:embryo\|cell line:germ cell\|cell type:PGCs\|genotype:pigu homo\|geo loc name:missing\|collection date:missing	pigu homo bud PGCs RNA rep2	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 danRer11 by STAR version: STAR 2.5.3a modified. The gene expression level was normalized to fragments per kilobase of transcript per million mapped FPKM values using Cufflinks version 2.2.1. Assembly: danRer11 Supplementary files format and content: tab delimited ext file includes FPKM values for each samples	embryo	GFP nanos1 3’UTR mRNA was injected into WT and pigu / zygotes respectively to label PGCs. Then the embryos at shield or bud stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 µl PBS. Dissections were performed for up to 5 min. The volume of PBS containing embryos was adjusted to 200 µl and then cells were mechanically dissociated by flicking the tube 30 times and pipetting the mixture 10 times through a 202 µl tip. Cells were then transported into a clear Petri dish and GFP labeled PGCs were manually picked under fluorescence microscope with mouth pipette. GFP nanos1 3’UTR mRNA was injected into WT and pigu / zygotes respectively to label PGCs. Then the embryos at shield or bud stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 µl PBS. Dissections were performed for up to 5 min. The volume of PBS containing embryos was adjusted to 200 µl and then cells were mechanically dissociated by flicking the tube 30 times and pipetting the mixture 10 times through a 200 µl tip. Cells were then transported into a clear Petri dish and GFP labeled PGCs were manually picked under fluorescence microscope with mouth pipette.	Total RNA of oocytes were purified using RNeasy Mini kit QIAGEN 74104 as recommended protocols. Total RNA 5 μg was DNase I Fermentas EN0521 treated at 37°C for 1 h. Poly A tailed mRNA was collected using DynabeadsTM mRNA Purification Kit Invitrogen 61006. RNA seq was carried out with the SMART seq2 protocol as previously described and subjected to paired end sequencing on the Nextseq 500 Illumina platform according to the manufacturer’s instructions. Notably SMART seq2 of low input RNA seq relies on polyA based amplification.	The wild type Tuebingen Tu and India strains were used throughout the experiments. The transgenic line Tgkop:EGFP nanos 3’UTR citation was described before. Unless stated all embryos were raised in Holtfreter’s solution at 28.5°C and staged as described previously.	tissue:embryo\|cell line:germ cell\|cell type:PGCs\|genotype:pigu homo	GSM8193368	GSM8193368: pigu homo bud PGCs RNA rep2; Danio rerio; RNA Seq	GSM8193368 r1	GSM8193368	1	Total RNA of oocytes were purified using RNeasy Mini kit QIAGEN 74104 as recommended protocols. Total RNA 5 μg was DNase I Fermentas EN0521 treated at 37°C for 1 h. Poly A tailed mRNA was collected using DynabeadsTM mRNA Purification Kit Invitrogen 61006. RNA seq was carried out with the SMART seq2 protocol as previously described and subjected to paired end sequencing on the Nextseq 500 Illumina platform according to the manufacturer's instructions. Notably SMART seq2 of low input RNA seq relies on polyA based amplification.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP500320			pigu_homo_bud_PGCs_RNA_rep2_r1.fq.gz pigu_homo_bud_PGCs_RNA_rep2_r2.fq.gz	fastq fastq	2137638000.0	7125460.0	GSM8193368 r1	0:150 1:150	A:588045273;C:460739300;G:496293927;T:592556088;N:3412	150	150	588045273	460739300	496293927	592556088	3412	SRX24189491	SRS20963514	SRA1842063	Tsinghua University	Tsinghua University	2	0.36533	0.36278	0.05703	0.057	0.87754	0.87811	0.60206	0.59677	150	150	B	B	biological fallback assumption	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_plate	smartseq	China	2024-04-08	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
31780	31780	SRR28590152	SRX24189490	SRS20963513	SRP500320	PRJNA1097627	GPI transamidase complex is required for primordial germ cell migration and development in zebrafish	GSE263481	Transcriptome Analysis	Proteins without xxx domains could be anchored to the cell surface for regulating various biological processes when covalently linked to glycosylphosphatidylinositol GPI molecules by the GPI transamidase GPIT complex. However it remains poorly understood whether and how the GPIT complex affects primordial germ cell PGC development. In this study we report the important roles of GPI transamidase in PGC migration and development in zebrafish embryos. Mutation of pigu or pigk both encoding essential GPIT complex subunits resulted in defective PGC migration with ectopically located PGCs and reduction of PGC counts. Notably a detailed analysis of filopodia in PGCs reveals the attenuated polarity of filopodia distribution along the migration direction in mutant embryos. PGC transplantation and PGC specific rescue experiments demonstrate that both PGC and somatic cell expressed Pigu are required for PGC migration. Furthermore expression levels of PGC specific genes are decreased in pigu mutant PGCs with the derepression of somatic cell genes. Hence we propose that the GPIT complex plays a critical role during PGC migration and development. Overall design: To reveal molecular mechanisms underlying GPI transamidase mediated PGC migration regulation we performed RNA seq of PGCs in wild type and pigu / embryos at the shield and bud stages. We manually picked GFP positive PGCs post cell dissociation of embryos at the shield and bud stages. Then post genotyping of rest somatic cells PGCs with the same genotypes were pooled together and lysed for Smart seq of two biological replicates.		pubmed:39741393		pigu homo bud PGCs RNA rep1	GSM8193367		source name:embryo\|tissue:embryo\|cell line:germ cell\|cell type:PGCs\|genotype:pigu homo\|geo loc name:missing\|collection date:missing	pigu homo bud PGCs RNA rep1	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 danRer11 by STAR version: STAR 2.5.3a modified. The gene expression level was normalized to fragments per kilobase of transcript per million mapped FPKM values using Cufflinks version 2.2.1. Assembly: danRer11 Supplementary files format and content: tab delimited ext file includes FPKM values for each samples	embryo	GFP nanos1 3’UTR mRNA was injected into WT and pigu / zygotes respectively to label PGCs. Then the embryos at shield or bud stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 µl PBS. Dissections were performed for up to 5 min. The volume of PBS containing embryos was adjusted to 200 µl and then cells were mechanically dissociated by flicking the tube 30 times and pipetting the mixture 10 times through a 200 µl tip. Cells were then transported into a clear Petri dish and GFP labeled PGCs were manually picked under fluorescence microscope with mouth pipette. GFP nanos1 3’UTR mRNA was injected into WT and pigu / zygotes respectively to label PGCs. Then the embryos at shield or bud stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 µl PBS. Dissections were performed for up to 5 min. The volume of PBS containing embryos was adjusted to 200 µl and then cells were mechanically dissociated by flicking the tube 30 times and pipetting the mixture 10 times through a 200 µl tip. Cells were then transported into a clear Petri dish and GFP labeled PGCs were manually picked under fluorescence microscope with mouth pipette.	Total RNA of oocytes were purified using RNeasy Mini kit QIAGEN 74104 as recommended protocols. Total RNA 5 μg was DNase I Fermentas EN0521 treated at 37°C for 1 h. Poly A tailed mRNA was collected using DynabeadsTM mRNA Purification Kit Invitrogen 61006. RNA seq was carried out with the SMART seq2 protocol as previously described and subjected to paired end sequencing on the Nextseq 500 Illumina platform according to the manufacturer’s instructions. Notably SMART seq2 of low input RNA seq relies on polyA based amplification.	The wild type Tuebingen Tu and India strains were used throughout the experiments. The transgenic line Tgkop:EGFP nanos 3’UTR citation was described before. Unless stated all embryos were raised in Holtfreter’s solution at 28.5°C and staged as described previously.	tissue:embryo\|cell line:germ cell\|cell type:PGCs\|genotype:pigu homo	GSM8193367	GSM8193367: pigu homo bud PGCs RNA rep1; Danio rerio; RNA Seq	GSM8193367 r1	GSM8193367	1	Total RNA of oocytes were purified using RNeasy Mini kit QIAGEN 74104 as recommended protocols. Total RNA 5 μg was DNase I Fermentas EN0521 treated at 37°C for 1 h. Poly A tailed mRNA was collected using DynabeadsTM mRNA Purification Kit Invitrogen 61006. RNA seq was carried out with the SMART seq2 protocol as previously described and subjected to paired end sequencing on the Nextseq 500 Illumina platform according to the manufacturer's instructions. Notably SMART seq2 of low input RNA seq relies on polyA based amplification.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP500320			pigu_homo_bud_PGCs_RNA_rep1_r1.fq.gz pigu_homo_bud_PGCs_RNA_rep1_r2.fq.gz	fastq fastq	2734187100.0	9113957.0	GSM8193367 r1	0:150 1:150	A:729072634;C:614811431;G:644751435;T:745548063;N:3537	150	150	729072634	614811431	644751435	745548063	3537	SRX24189490	SRS20963513	SRA1842063	Tsinghua University	Tsinghua University	2	0.94018	0.93763	0.11685	0.1143	0.77749	0.78204	0.50988	0.50832	150	150	B	B	biological fallback assumption	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_plate	smartseq	China	2024-04-08	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
33008	33008	SRR29632270	SRX25138332	SRS21830414	SRP516621	PRJNA1129168	in vitro construction of an embryonic caudal organizer	GSE270989	Other	Purpose: Characterization of cell types in bmp4 explants and BMP4 induced human embryoids. Methods: Single cell transcriptomes of bmp4 explants were harvested at 6 hpf 8 hpf 10 hpf 12 hpf 18 hpf and 24 hpf. Single cell transcriptomes of BMP4 induced human embryoids were harvested at Day 5 and Day 6. Libraries were prepared using Single Cell three primeLibrary & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer's protocol for 10000 cell recovery. Results: paraxial mesoderm lateral plate mesoderm and their derivatives were detected in bmp4 explants and NMP somite and neural cell fates were detected in bmp4 induced human embryoids. Conclusions: A well organized caudal like structure was induced in bmp4 explants and caudal cell fates were specified in BMP4 induced human embryoids. Overall design: bmp4 injected zebrafish explants or BMP4 induced human embryoids were harvested for scRNA seq.				Bmp4 explant 24h	GSM8366755		source name:embryonic\|tissue:embryonic\|cell line:zebrafish embryonic stem cells\|cell type:stem cell\|geo loc name:missing\|collection date:missing	Bmp4 explant 24h	Illumina sequencing reads were aligned to the zebrafish GRCz11 or human mRNA reference genome GRCh38 using the 10x Genomics CellRanger pipeline version 3.0.2 with default parameters. Assembly: GRCz11 GRCh38 Supplementary files format and content: tar archive includes filtered gene bc matrices post running CellRanger pipeline	embryonic	To generate bmp4 explants bmp4 8 10 pg mRNA was injected into one animal pole blastomere at the 128 cell stage. Then the animal pole region was explanted and raised to 24hpf. To generate BMP4 induced human embryoids human embryonic stem cells hESCs of the H9 line were grown on Matrigel coated 12 well plates for a period ranging from 48 to 72 hours utilizing them when they reached an approximate confluence of 70%. On the initial day of the experiment both wild type H9 cells and ihBmp4 cells were treated with accutase to facilitate their dissociation. They were then transferred to 96 well U bottom low attachment plates for culture. The seeding density was adjusted to 1300 cells per well for H9 cells and 400 cells per well for ihBmp4 cells using 50 μl of an aggregation medium based on TeSR E6 and supplemented with the ROCK inhibitor 10μM Y27632. post a 24 hour incubation period both types of cells formed embryoid bodies EBs in their respective wells. These H9 and ihBmp4 EBs were then co cultured in the same well with 80 μl of the TeSR E6 based medium to encourage fusion. Between days 2 and 4 of the culture period the EBs were subjected to an induction process to enhance Bmp4 expression which initiated the morphogenesis phase. The culture medium was replaced with a fresh TeSR E6 medium that included 75 ng ml 1 Doxycycline and 50 ng ml 1 FGF2 to stimulate these processes. Starting from day 4 the Doxycycline and FGF2 were omitted from the culture medium. The EBs were then maintained in a TeSR E6 based medium for continued growth and development.	Single cell RNA of each sample was extracted by following the Chromium Controller and Chromium Single Cell 30 Library & Gel Bead Kit v3.110x Genomics PN 1000121 protocol. Libraries were prepared using Single Cell 3′Library & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer’s protocol for 10000 cell recovery.	Bmp4 explants were cultured in Dulbecco's modified Eagle’s medium DMEM/F 12 with 10 mM HEPES 1x MEM with non essential amino acids 7 mM CaCl2 1 mM sodium pyruvate 50 μg/ml gentamycin 100 μM 2 mercaptoethanol 1× antibiotic antimycotic 10% serum replacement and kept at 28.5℃.BMP4 induced human embryoids were cultured in a 96 well U shaped ultra low plate with culture medium TeSR E6 medium supplemented with 0.5% N2 and 0.5% B27 to support cell growth. Small molecule compounds and recombinant proteins inducing differentiation were added according to the treatment protocol. Samples were collected on day 5 and 6 of differentiation.	tissue:embryonic\|cell line:zebrafish embryonic stem cells\|cell type:stem cell	GSM8366755	GSM8366755: Bmp4 explant 24h; Danio rerio; RNA Seq	GSM8366755 r1	GSM8366755	1	Single cell RNA of each sample was extracted by following the Chromium Controller and Chromium Single Cell 30 Library & Gel Bead Kit v3.110x Genomics PN 1000121 protocol. Libraries were prepared using Single Cell 3′Library & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer's protocol for 10000 cell recovery.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP516621			Bmp4_24h_S1_L001_R1_001.fastq.gz Bmp4_24h_S1_L001_R2_001.fastq.gz	fastq fastq	49098784294.0	412594826.0	GSM8366755 r1	0:28 1:91	A:13643133254;C:11126085942;G:11676909916;T:12651522663;N:1132519	28	91	13643133254	11126085942	11676909916	12651522663	1132519	SRX25138332	SRS21830414	SRA1911917	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2024-06-27	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
33009	33009	SRR29632271	SRX25138331	SRS21830413	SRP516621	PRJNA1129168	in vitro construction of an embryonic caudal organizer	GSE270989	Other	Purpose: Characterization of cell types in bmp4 explants and BMP4 induced human embryoids. Methods: Single cell transcriptomes of bmp4 explants were harvested at 6 hpf 8 hpf 10 hpf 12 hpf 18 hpf and 24 hpf. Single cell transcriptomes of BMP4 induced human embryoids were harvested at Day 5 and Day 6. Libraries were prepared using Single Cell three primeLibrary & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer's protocol for 10000 cell recovery. Results: paraxial mesoderm lateral plate mesoderm and their derivatives were detected in bmp4 explants and NMP somite and neural cell fates were detected in bmp4 induced human embryoids. Conclusions: A well organized caudal like structure was induced in bmp4 explants and caudal cell fates were specified in BMP4 induced human embryoids. Overall design: bmp4 injected zebrafish explants or BMP4 induced human embryoids were harvested for scRNA seq.				Bmp4 explant 18h	GSM8366754		source name:embryonic\|tissue:embryonic\|cell line:zebrafish embryonic stem cells\|cell type:stem cell\|geo loc name:missing\|collection date:missing	Bmp4 explant 18h	Illumina sequencing reads were aligned to the zebrafish GRCz11 or human mRNA reference genome GRCh38 using the 10x Genomics CellRanger pipeline version 3.0.2 with default parameters. Assembly: GRCz11 GRCh38 Supplementary files format and content: tar archive includes filtered gene bc matrices post running CellRanger pipeline	embryonic	To generate bmp4 explants bmp4 8 10 pg mRNA was injected into one animal pole blastomere at the 128 cell stage. Then the animal pole region was explanted and raised to 24hpf. To generate BMP4 induced human embryoids human embryonic stem cells hESCs of the H9 line were grown on Matrigel coated 12 well plates for a period ranging from 48 to 72 hours utilizing them when they reached an approximate confluence of 70%. On the initial day of the experiment both wild type H9 cells and ihBmp4 cells were treated with accutase to facilitate their dissociation. They were then transferred to 96 well U bottom low attachment plates for culture. The seeding density was adjusted to 1300 cells per well for H9 cells and 400 cells per well for ihBmp4 cells using 50 μl of an aggregation medium based on TeSR E6 and supplemented with the ROCK inhibitor 10μM Y27632. post a 24 hour incubation period both types of cells formed embryoid bodies EBs in their respective wells. These H9 and ihBmp4 EBs were then co cultured in the same well with 80 μl of the TeSR E6 based medium to encourage fusion. Between days 2 and 4 of the culture period the EBs were subjected to an induction process to enhance Bmp4 expression which initiated the morphogenesis phase. The culture medium was replaced with a fresh TeSR E6 medium that included 75 ng ml 1 Doxycycline and 50 ng ml 1 FGF2 to stimulate these processes. Starting from day 4 the Doxycycline and FGF2 were omitted from the culture medium. The EBs were then maintained in a TeSR E6 based medium for continued growth and development.	Single cell RNA of each sample was extracted by following the Chromium Controller and Chromium Single Cell 30 Library & Gel Bead Kit v3.110x Genomics PN 1000121 protocol. Libraries were prepared using Single Cell 3′Library & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer’s protocol for 10000 cell recovery.	Bmp4 explants were cultured in Dulbecco's modified Eagle’s medium DMEM/F 12 with 10 mM HEPES 1x MEM with non essential amino acids 7 mM CaCl2 1 mM sodium pyruvate 50 μg/ml gentamycin 100 μM 2 mercaptoethanol 1× antibiotic antimycotic 10% serum replacement and kept at 28.5℃.BMP4 induced human embryoids were cultured in a 96 well U shaped ultra low plate with culture medium TeSR E6 medium supplemented with 0.5% N2 and 0.5% B27 to support cell growth. Small molecule compounds and recombinant proteins inducing differentiation were added according to the treatment protocol. Samples were collected on day 5 and 6 of differentiation.	tissue:embryonic\|cell line:zebrafish embryonic stem cells\|cell type:stem cell	GSM8366754	GSM8366754: Bmp4 explant 18h; Danio rerio; RNA Seq	GSM8366754 r1	GSM8366754	1	Single cell RNA of each sample was extracted by following the Chromium Controller and Chromium Single Cell 30 Library & Gel Bead Kit v3.110x Genomics PN 1000121 protocol. Libraries were prepared using Single Cell 3′Library & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer's protocol for 10000 cell recovery.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP516621			Bmp4_18h_S1_L001_R1_001.fastq.gz Bmp4_18h_S1_L001_R2_001.fastq.gz	fastq fastq	44863080801.0	377000679.0	GSM8366754 r1	0:28 1:91	A:12441486571;C:10199111519;G:10790306255;T:11430847129;N:1329327	28	91	12441486571	10199111519	10790306255	11430847129	1329327	SRX25138331	SRS21830413	SRA1911917	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2024-06-27	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
33010	33010	SRR29632272	SRX25138330	SRS21830412	SRP516621	PRJNA1129168	in vitro construction of an embryonic caudal organizer	GSE270989	Other	Purpose: Characterization of cell types in bmp4 explants and BMP4 induced human embryoids. Methods: Single cell transcriptomes of bmp4 explants were harvested at 6 hpf 8 hpf 10 hpf 12 hpf 18 hpf and 24 hpf. Single cell transcriptomes of BMP4 induced human embryoids were harvested at Day 5 and Day 6. Libraries were prepared using Single Cell three primeLibrary & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer's protocol for 10000 cell recovery. Results: paraxial mesoderm lateral plate mesoderm and their derivatives were detected in bmp4 explants and NMP somite and neural cell fates were detected in bmp4 induced human embryoids. Conclusions: A well organized caudal like structure was induced in bmp4 explants and caudal cell fates were specified in BMP4 induced human embryoids. Overall design: bmp4 injected zebrafish explants or BMP4 induced human embryoids were harvested for scRNA seq.				Bmp4 explant 12h	GSM8366753		source name:embryonic\|tissue:embryonic\|cell line:zebrafish embryonic stem cells\|cell type:stem cell\|geo loc name:missing\|collection date:missing	Bmp4 explant 12h	Illumina sequencing reads were aligned to the zebrafish GRCz11 or human mRNA reference genome GRCh38 using the 10x Genomics CellRanger pipeline version 3.0.2 with default parameters. Assembly: GRCz11 GRCh38 Supplementary files format and content: tar archive includes filtered gene bc matrices post running CellRanger pipeline	embryonic	To generate bmp4 explants bmp4 8 10 pg mRNA was injected into one animal pole blastomere at the 128 cell stage. Then the animal pole region was explanted and raised to 24hpf. To generate BMP4 induced human embryoids human embryonic stem cells hESCs of the H9 line were grown on Matrigel coated 12 well plates for a period ranging from 48 to 72 hours utilizing them when they reached an approximate confluence of 70%. On the initial day of the experiment both wild type H9 cells and ihBmp4 cells were treated with accutase to facilitate their dissociation. They were then transferred to 96 well U bottom low attachment plates for culture. The seeding density was adjusted to 1300 cells per well for H9 cells and 400 cells per well for ihBmp4 cells using 50 μl of an aggregation medium based on TeSR E6 and supplemented with the ROCK inhibitor 10μM Y27632. post a 24 hour incubation period both types of cells formed embryoid bodies EBs in their respective wells. These H9 and ihBmp4 EBs were then co cultured in the same well with 80 μl of the TeSR E6 based medium to encourage fusion. Between days 2 and 4 of the culture period the EBs were subjected to an induction process to enhance Bmp4 expression which initiated the morphogenesis phase. The culture medium was replaced with a fresh TeSR E6 medium that included 75 ng ml 1 Doxycycline and 50 ng ml 1 FGF2 to stimulate these processes. Starting from day 4 the Doxycycline and FGF2 were omitted from the culture medium. The EBs were then maintained in a TeSR E6 based medium for continued growth and development.	Single cell RNA of each sample was extracted by following the Chromium Controller and Chromium Single Cell 30 Library & Gel Bead Kit v3.110x Genomics PN 1000121 protocol. Libraries were prepared using Single Cell 3′Library & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer’s protocol for 10000 cell recovery.	Bmp4 explants were cultured in Dulbecco's modified Eagle’s medium DMEM/F 12 with 10 mM HEPES 1x MEM with non essential amino acids 7 mM CaCl2 1 mM sodium pyruvate 50 μg/ml gentamycin 100 μM 2 mercaptoethanol 1× antibiotic antimycotic 10% serum replacement and kept at 28.5℃.BMP4 induced human embryoids were cultured in a 96 well U shaped ultra low plate with culture medium TeSR E6 medium supplemented with 0.5% N2 and 0.5% B27 to support cell growth. Small molecule compounds and recombinant proteins inducing differentiation were added according to the treatment protocol. Samples were collected on day 5 and 6 of differentiation.	tissue:embryonic\|cell line:zebrafish embryonic stem cells\|cell type:stem cell	GSM8366753	GSM8366753: Bmp4 explant 12h; Danio rerio; RNA Seq	GSM8366753 r1	GSM8366753	1	Single cell RNA of each sample was extracted by following the Chromium Controller and Chromium Single Cell 30 Library & Gel Bead Kit v3.110x Genomics PN 1000121 protocol. Libraries were prepared using Single Cell 3′Library & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer's protocol for 10000 cell recovery.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP516621			Bmp4_12h_S1_L001_R1_001.fastq.gz Bmp4_12h_S1_L001_R2_001.fastq.gz	fastq fastq	50138128747.0	421328813.0	GSM8366753 r1	0:28 1:91	A:14089229753;C:10936347905;G:11403388741;T:13708020723;N:1141625	28	91	14089229753	10936347905	11403388741	13708020723	1141625	SRX25138330	SRS21830412	SRA1911917	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2024-06-27	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
33011	33011	SRR29632273	SRX25138329	SRS21830410	SRP516621	PRJNA1129168	in vitro construction of an embryonic caudal organizer	GSE270989	Other	Purpose: Characterization of cell types in bmp4 explants and BMP4 induced human embryoids. Methods: Single cell transcriptomes of bmp4 explants were harvested at 6 hpf 8 hpf 10 hpf 12 hpf 18 hpf and 24 hpf. Single cell transcriptomes of BMP4 induced human embryoids were harvested at Day 5 and Day 6. Libraries were prepared using Single Cell three primeLibrary & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer's protocol for 10000 cell recovery. Results: paraxial mesoderm lateral plate mesoderm and their derivatives were detected in bmp4 explants and NMP somite and neural cell fates were detected in bmp4 induced human embryoids. Conclusions: A well organized caudal like structure was induced in bmp4 explants and caudal cell fates were specified in BMP4 induced human embryoids. Overall design: bmp4 injected zebrafish explants or BMP4 induced human embryoids were harvested for scRNA seq.				Bmp4 explant 10h	GSM8366752		source name:embryonic\|tissue:embryonic\|cell line:zebrafish embryonic stem cells\|cell type:stem cell\|geo loc name:missing\|collection date:missing	Bmp4 explant 10h	Illumina sequencing reads were aligned to the zebrafish GRCz11 or human mRNA reference genome GRCh38 using the 10x Genomics CellRanger pipeline version 3.0.2 with default parameters. Assembly: GRCz11 GRCh38 Supplementary files format and content: tar archive includes filtered gene bc matrices post running CellRanger pipeline	embryonic	To generate bmp4 explants bmp4 8 10 pg mRNA was injected into one animal pole blastomere at the 128 cell stage. Then the animal pole region was explanted and raised to 24hpf. To generate BMP4 induced human embryoids human embryonic stem cells hESCs of the H9 line were grown on Matrigel coated 12 well plates for a period ranging from 48 to 72 hours utilizing them when they reached an approximate confluence of 70%. On the initial day of the experiment both wild type H9 cells and ihBmp4 cells were treated with accutase to facilitate their dissociation. They were then transferred to 96 well U bottom low attachment plates for culture. The seeding density was adjusted to 1300 cells per well for H9 cells and 400 cells per well for ihBmp4 cells using 50 μl of an aggregation medium based on TeSR E6 and supplemented with the ROCK inhibitor 10μM Y27632. post a 24 hour incubation period both types of cells formed embryoid bodies EBs in their respective wells. These H9 and ihBmp4 EBs were then co cultured in the same well with 80 μl of the TeSR E6 based medium to encourage fusion. Between days 2 and 4 of the culture period the EBs were subjected to an induction process to enhance Bmp4 expression which initiated the morphogenesis phase. The culture medium was replaced with a fresh TeSR E6 medium that included 75 ng ml 1 Doxycycline and 50 ng ml 1 FGF2 to stimulate these processes. Starting from day 4 the Doxycycline and FGF2 were omitted from the culture medium. The EBs were then maintained in a TeSR E6 based medium for continued growth and development.	Single cell RNA of each sample was extracted by following the Chromium Controller and Chromium Single Cell 30 Library & Gel Bead Kit v3.110x Genomics PN 1000121 protocol. Libraries were prepared using Single Cell 3′Library & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer’s protocol for 10000 cell recovery.	Bmp4 explants were cultured in Dulbecco's modified Eagle’s medium DMEM/F 12 with 10 mM HEPES 1x MEM with non essential amino acids 7 mM CaCl2 1 mM sodium pyruvate 50 μg/ml gentamycin 100 μM 2 mercaptoethanol 1× antibiotic antimycotic 10% serum replacement and kept at 28.5℃.BMP4 induced human embryoids were cultured in a 96 well U shaped ultra low plate with culture medium TeSR E6 medium supplemented with 0.5% N2 and 0.5% B27 to support cell growth. Small molecule compounds and recombinant proteins inducing differentiation were added according to the treatment protocol. Samples were collected on day 5 and 6 of differentiation.	tissue:embryonic\|cell line:zebrafish embryonic stem cells\|cell type:stem cell	GSM8366752	GSM8366752: Bmp4 explant 10h; Danio rerio; RNA Seq	GSM8366752 r1	GSM8366752	1	Single cell RNA of each sample was extracted by following the Chromium Controller and Chromium Single Cell 30 Library & Gel Bead Kit v3.110x Genomics PN 1000121 protocol. Libraries were prepared using Single Cell 3′Library & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer's protocol for 10000 cell recovery.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP516621			Bmp4-10h_S1_L001_R1_001.fastq.gz Bmp4-10h_S1_L001_R2_001.fastq.gz	fastq fastq	149164547700.0	497215159.0	GSM8366752 r1	0:150 1:150	A:44020073879;C:31344780625;G:29505876494;T:44289819189;N:3997513	150	150	44020073879	31344780625	29505876494	44289819189	3997513	SRX25138329	SRS21830410	SRA1911917	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University												T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2024-06-27	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
33012	33012	SRR29632274	SRX25138328	SRS21830409	SRP516621	PRJNA1129168	in vitro construction of an embryonic caudal organizer	GSE270989	Other	Purpose: Characterization of cell types in bmp4 explants and BMP4 induced human embryoids. Methods: Single cell transcriptomes of bmp4 explants were harvested at 6 hpf 8 hpf 10 hpf 12 hpf 18 hpf and 24 hpf. Single cell transcriptomes of BMP4 induced human embryoids were harvested at Day 5 and Day 6. Libraries were prepared using Single Cell three primeLibrary & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer's protocol for 10000 cell recovery. Results: paraxial mesoderm lateral plate mesoderm and their derivatives were detected in bmp4 explants and NMP somite and neural cell fates were detected in bmp4 induced human embryoids. Conclusions: A well organized caudal like structure was induced in bmp4 explants and caudal cell fates were specified in BMP4 induced human embryoids. Overall design: bmp4 injected zebrafish explants or BMP4 induced human embryoids were harvested for scRNA seq.				Bmp4 explant 8h	GSM8366751		source name:embryonic\|tissue:embryonic\|cell line:zebrafish embryonic stem cells\|cell type:stem cell\|geo loc name:missing\|collection date:missing	Bmp4 explant 8h	Illumina sequencing reads were aligned to the zebrafish GRCz11 or human mRNA reference genome GRCh38 using the 10x Genomics CellRanger pipeline version 3.0.2 with default parameters. Assembly: GRCz11 GRCh38 Supplementary files format and content: tar archive includes filtered gene bc matrices post running CellRanger pipeline	embryonic	To generate bmp4 explants bmp4 8 10 pg mRNA was injected into one animal pole blastomere at the 128 cell stage. Then the animal pole region was explanted and raised to 24hpf. To generate BMP4 induced human embryoids human embryonic stem cells hESCs of the H9 line were grown on Matrigel coated 12 well plates for a period ranging from 48 to 72 hours utilizing them when they reached an approximate confluence of 70%. On the initial day of the experiment both wild type H9 cells and ihBmp4 cells were treated with accutase to facilitate their dissociation. They were then transferred to 96 well U bottom low attachment plates for culture. The seeding density was adjusted to 1300 cells per well for H9 cells and 400 cells per well for ihBmp4 cells using 50 μl of an aggregation medium based on TeSR E6 and supplemented with the ROCK inhibitor 10μM Y27632. post a 24 hour incubation period both types of cells formed embryoid bodies EBs in their respective wells. These H9 and ihBmp4 EBs were then co cultured in the same well with 80 μl of the TeSR E6 based medium to encourage fusion. Between days 2 and 4 of the culture period the EBs were subjected to an induction process to enhance Bmp4 expression which initiated the morphogenesis phase. The culture medium was replaced with a fresh TeSR E6 medium that included 75 ng ml 1 Doxycycline and 50 ng ml 1 FGF2 to stimulate these processes. Starting from day 4 the Doxycycline and FGF2 were omitted from the culture medium. The EBs were then maintained in a TeSR E6 based medium for continued growth and development.	Single cell RNA of each sample was extracted by following the Chromium Controller and Chromium Single Cell 30 Library & Gel Bead Kit v3.110x Genomics PN 1000121 protocol. Libraries were prepared using Single Cell 3′Library & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer’s protocol for 10000 cell recovery.	Bmp4 explants were cultured in Dulbecco's modified Eagle’s medium DMEM/F 12 with 10 mM HEPES 1x MEM with non essential amino acids 7 mM CaCl2 1 mM sodium pyruvate 50 μg/ml gentamycin 100 μM 2 mercaptoethanol 1× antibiotic antimycotic 10% serum replacement and kept at 28.5℃.BMP4 induced human embryoids were cultured in a 96 well U shaped ultra low plate with culture medium TeSR E6 medium supplemented with 0.5% N2 and 0.5% B27 to support cell growth. Small molecule compounds and recombinant proteins inducing differentiation were added according to the treatment protocol. Samples were collected on day 5 and 6 of differentiation.	tissue:embryonic\|cell line:zebrafish embryonic stem cells\|cell type:stem cell	GSM8366751	GSM8366751: Bmp4 explant 8h; Danio rerio; RNA Seq	GSM8366751 r1	GSM8366751	1	Single cell RNA of each sample was extracted by following the Chromium Controller and Chromium Single Cell 30 Library & Gel Bead Kit v3.110x Genomics PN 1000121 protocol. Libraries were prepared using Single Cell 3′Library & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer's protocol for 10000 cell recovery.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP516621			Bmp4-8h_S1_L001_R1_001.fastq.gz Bmp4-8h_S1_L001_R2_001.fastq.gz	fastq fastq	118709118600.0	395697062.0	GSM8366751 r1	0:150 1:150	A:35474636770;C:23305712896;G:22894585568;T:37031410017;N:2773349	150	150	35474636770	23305712896	22894585568	37031410017	2773349	SRX25138328	SRS21830409	SRA1911917	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University												B	B	mate1-mate2 similar by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2024-06-27	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
33013	33013	SRR29632275	SRX25138327	SRS21830411	SRP516621	PRJNA1129168	in vitro construction of an embryonic caudal organizer	GSE270989	Other	Purpose: Characterization of cell types in bmp4 explants and BMP4 induced human embryoids. Methods: Single cell transcriptomes of bmp4 explants were harvested at 6 hpf 8 hpf 10 hpf 12 hpf 18 hpf and 24 hpf. Single cell transcriptomes of BMP4 induced human embryoids were harvested at Day 5 and Day 6. Libraries were prepared using Single Cell three primeLibrary & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer's protocol for 10000 cell recovery. Results: paraxial mesoderm lateral plate mesoderm and their derivatives were detected in bmp4 explants and NMP somite and neural cell fates were detected in bmp4 induced human embryoids. Conclusions: A well organized caudal like structure was induced in bmp4 explants and caudal cell fates were specified in BMP4 induced human embryoids. Overall design: bmp4 injected zebrafish explants or BMP4 induced human embryoids were harvested for scRNA seq.				Bmp4 explant 6h	GSM8366750		source name:embryonic\|tissue:embryonic\|cell line:zebrafish embryonic stem cells\|cell type:stem cell\|geo loc name:missing\|collection date:missing	Bmp4 explant 6h	Illumina sequencing reads were aligned to the zebrafish GRCz11 or human mRNA reference genome GRCh38 using the 10x Genomics CellRanger pipeline version 3.0.2 with default parameters. Assembly: GRCz11 GRCh38 Supplementary files format and content: tar archive includes filtered gene bc matrices post running CellRanger pipeline	embryonic	To generate bmp4 explants bmp4 8 10 pg mRNA was injected into one animal pole blastomere at the 128 cell stage. Then the animal pole region was explanted and raised to 24hpf. To generate BMP4 induced human embryoids human embryonic stem cells hESCs of the H9 line were grown on Matrigel coated 12 well plates for a period ranging from 48 to 72 hours utilizing them when they reached an approximate confluence of 70%. On the initial day of the experiment both wild type H9 cells and ihBmp4 cells were treated with accutase to facilitate their dissociation. They were then transferred to 96 well U bottom low attachment plates for culture. The seeding density was adjusted to 1300 cells per well for H9 cells and 400 cells per well for ihBmp4 cells using 50 μl of an aggregation medium based on TeSR E6 and supplemented with the ROCK inhibitor 10μM Y27632. post a 24 hour incubation period both types of cells formed embryoid bodies EBs in their respective wells. These H9 and ihBmp4 EBs were then co cultured in the same well with 80 μl of the TeSR E6 based medium to encourage fusion. Between days 2 and 4 of the culture period the EBs were subjected to an induction process to enhance Bmp4 expression which initiated the morphogenesis phase. The culture medium was replaced with a fresh TeSR E6 medium that included 75 ng ml 1 Doxycycline and 50 ng ml 1 FGF2 to stimulate these processes. Starting from day 4 the Doxycycline and FGF2 were omitted from the culture medium. The EBs were then maintained in a TeSR E6 based medium for continued growth and development.	Single cell RNA of each sample was extracted by following the Chromium Controller and Chromium Single Cell 30 Library & Gel Bead Kit v3.110x Genomics PN 1000121 protocol. Libraries were prepared using Single Cell 3′Library & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer’s protocol for 10000 cell recovery.	Bmp4 explants were cultured in Dulbecco's modified Eagle’s medium DMEM/F 12 with 10 mM HEPES 1x MEM with non essential amino acids 7 mM CaCl2 1 mM sodium pyruvate 50 μg/ml gentamycin 100 μM 2 mercaptoethanol 1× antibiotic antimycotic 10% serum replacement and kept at 28.5℃.BMP4 induced human embryoids were cultured in a 96 well U shaped ultra low plate with culture medium TeSR E6 medium supplemented with 0.5% N2 and 0.5% B27 to support cell growth. Small molecule compounds and recombinant proteins inducing differentiation were added according to the treatment protocol. Samples were collected on day 5 and 6 of differentiation.	tissue:embryonic\|cell line:zebrafish embryonic stem cells\|cell type:stem cell	GSM8366750	GSM8366750: Bmp4 explant 6h; Danio rerio; RNA Seq	GSM8366750 r1	GSM8366750	1	Single cell RNA of each sample was extracted by following the Chromium Controller and Chromium Single Cell 30 Library & Gel Bead Kit v3.110x Genomics PN 1000121 protocol. Libraries were prepared using Single Cell 3′Library & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer's protocol for 10000 cell recovery.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP516621			Bmp4_6h_S1_L001_R1_001.fastq.gz Bmp4_6h_S1_L001_R2_001.fastq.gz	fastq fastq	52586645972.0	441904588.0	GSM8366750 r1	0:28 1:91	A:14755432217;C:11271293276;G:11858476334;T:14700289448;N:1154697	28	91	14755432217	11271293276	11858476334	14700289448	1154697	SRX25138327	SRS21830411	SRA1911917	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2024-06-27	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
33722	33722	SRR30640695	SRX26062515	SRS22631699	SRP532179	PRJNA1159911	Peri Centriolar Material 1 regulates polarized endosome dynamics and neural progenitor fate	PRJNA1159911	Other	RNA seq was performed on control and maternal zygotic developmentally defective pcm1 morphants MO and pcm1 knock out KO zebrafish embryos at 24 hpf.					WT24hpfcontrol1		breed:natural spawning of AB adults\|age:24hpf\|dev stage:adult\|collection date:2021 03 19\|geo loc name:USA:San Francisco\|sex:not determined\|tissue:WT24hpfcontrol1 embryo\|BioSampleModel:Model organism or animal									RNA seq of Wild type zebrafish : 12 embryos in total 2 3mg	WT24hpfcontrol1 R	WT24hpfcontrol1 R	Wild type zebrafish			RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED	ILLUMINA	Illumina HiSeq 1000	SRP532179			WT24hpfcontrol1_R1.clean.fq.gz WT24hpfcontrol1_R2.clean.fq.gz	fastq fastq	6761688309.0	27496581.0	WT24hpfcontrol1 R1.clean.fq.gz	0:122.99 1:122.92	A:1946719560;C:1442103403;G:1451347536;T:1921456727;N:61083	122	122	1946719560	1442103403	1451347536	1921456727	61083	SRX26062515	SRS22631699	SRA1970017	Huazhong Agricultural University, China\|Department of Neurosurgery	Huazhong Agricultural University, China												B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2024-09-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
33723	33723	SRR30640696	SRX26062514	SRS22631698	SRP532179	PRJNA1159911	Peri Centriolar Material 1 regulates polarized endosome dynamics and neural progenitor fate	PRJNA1159911	Other	RNA seq was performed on control and maternal zygotic developmentally defective pcm1 morphants MO and pcm1 knock out KO zebrafish embryos at 24 hpf.					PCM1MOMutant3		breed:Tg [ef1:Myr Tdtomato]\|age:24hpf\|dev stage:adult\|collection date:2021 03 19\|geo loc name:USA:San Francisco\|sex:not determined\|tissue:PCM1MOMutant3 embryo\|BioSampleModel:Model organism or animal									RNA seq of MO morphants zebrafish : 12 embryos in total 2 5mg	PCM1MOMutant3 R	PCM1MOMutant3 R	MO morphants zebrafish			RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED	ILLUMINA	Illumina HiSeq 1000	SRP532179			PCM1MOMutant3_R1.clean.fq.gz PCM1MOMutant3_R2.clean.fq.gz	fastq fastq	6356420208.0	23407180.0	PCM1MOMutant3 R1.clean.fq.gz	0:135.78 1:135.78	A:1742323782;C:1448163439;G:1451783264;T:1714090084;N:59639	135	135	1742323782	1448163439	1451783264	1714090084	59639	SRX26062514	SRS22631698	SRA1970017	Huazhong Agricultural University, China\|Department of Neurosurgery	Huazhong Agricultural University, China												B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2024-09-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
33724	33724	SRR30640697	SRX26062513	SRS22631697	SRP532179	PRJNA1159911	Peri Centriolar Material 1 regulates polarized endosome dynamics and neural progenitor fate	PRJNA1159911	Other	RNA seq was performed on control and maternal zygotic developmentally defective pcm1 morphants MO and pcm1 knock out KO zebrafish embryos at 24 hpf.					PCM1MOMutant2		breed:Tg [ef1:Myr Tdtomato]\|age:24hpf\|dev stage:adult\|collection date:2021 03 19\|geo loc name:USA:San Francisco\|sex:not determined\|tissue:PCM1MOMutant2 embryo\|BioSampleModel:Model organism or animal									RNA seq of MO morphants zebrafish : 12 embryos in total 2 4mg	PCM1MOMutant2 R	PCM1MOMutant2 R	MO morphants zebrafish			RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED	ILLUMINA	Illumina HiSeq 1000	SRP532179			PCM1MOMutant2_R1.clean.fq.gz PCM1MOMutant2_R2.clean.fq.gz	fastq fastq	6146772469.0	22703012.0	PCM1MOMutant2 R1.clean.fq.gz	0:135.37 1:135.37	A:1647298308;C:1435201745;G:1438871965;T:1625343182;N:57269	135	135	1647298308	1435201745	1438871965	1625343182	57269	SRX26062513	SRS22631697	SRA1970017	Huazhong Agricultural University, China\|Department of Neurosurgery	Huazhong Agricultural University, China												B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2024-09-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
33725	33725	SRR30640698	SRX26062512	SRS22631696	SRP532179	PRJNA1159911	Peri Centriolar Material 1 regulates polarized endosome dynamics and neural progenitor fate	PRJNA1159911	Other	RNA seq was performed on control and maternal zygotic developmentally defective pcm1 morphants MO and pcm1 knock out KO zebrafish embryos at 24 hpf.					PCM1MOMutant1		breed:Tg [ef1:Myr Tdtomato]\|age:24hpf\|dev stage:adult\|collection date:2021 03 19\|geo loc name:USA:San Francisco\|sex:not determined\|tissue:PCM1MOMutant1 embryo\|BioSampleModel:Model organism or animal									RNA seq of MO morphants zebrafish : 12 embryos in total 2 3mg	PCM1MOMutant1 R	PCM1MOMutant1 R	MO morphants zebrafish			RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED	ILLUMINA	Illumina HiSeq 1000	SRP532179			PCM1MOMutant1_R1.clean.fq.gz PCM1MOMutant1_R2.clean.fq.gz	fastq fastq	5701775379.0	21587297.0	PCM1MOMutant1 R1.clean.fq.gz	0:132.06 1:132.06	A:1578153876;C:1282130829;G:1284978375;T:1556460380;N:51919	132	132	1578153876	1282130829	1284978375	1556460380	51919	SRX26062512	SRS22631696	SRA1970017	Huazhong Agricultural University, China\|Department of Neurosurgery	Huazhong Agricultural University, China												B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2024-09-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
33726	33726	SRR30640699	SRX26062511	SRS22631695	SRP532179	PRJNA1159911	Peri Centriolar Material 1 regulates polarized endosome dynamics and neural progenitor fate	PRJNA1159911	Other	RNA seq was performed on control and maternal zygotic developmentally defective pcm1 morphants MO and pcm1 knock out KO zebrafish embryos at 24 hpf.					PCM1KOmutant3		breed:Tg [ef1:Myr Tdtomato]\|age:24hpf\|dev stage:adult\|collection date:2021 03 19\|geo loc name:USA:San Francisco\|sex:not determined\|tissue:PCM1KOmutant3 embryo\|BioSampleModel:Model organism or animal									RNA seq of pcm1 KO mutant zebrafish : 12 embryos in total 2 5mg	PCM1KOmutant3 R	PCM1KOmutant3 R	pcm1 KO mutant zebrafish			RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED	ILLUMINA	Illumina HiSeq 1000	SRP532179			PCM1KOmutant3_R1.clean.fq.gz PCM1KOmutant3_R2.clean.fq.gz	fastq fastq	4673179612.0	17529406.0	PCM1KOmutant3 R1.clean.fq.gz	0:133.29 1:133.30	A:1266929858;C:1078407007;G:1080490713;T:1247307342;N:44692	133	133	1266929858	1078407007	1080490713	1247307342	44692	SRX26062511	SRS22631695	SRA1970017	Huazhong Agricultural University, China\|Department of Neurosurgery	Huazhong Agricultural University, China												B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2024-09-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
33727	33727	SRR30640700	SRX26062510	SRS22631694	SRP532179	PRJNA1159911	Peri Centriolar Material 1 regulates polarized endosome dynamics and neural progenitor fate	PRJNA1159911	Other	RNA seq was performed on control and maternal zygotic developmentally defective pcm1 morphants MO and pcm1 knock out KO zebrafish embryos at 24 hpf.					PCM1KOmutant2		breed:Tg [ef1:Myr Tdtomato]\|age:24hpf\|dev stage:adult\|collection date:2021 03 19\|geo loc name:USA:San Francisco\|sex:not determined\|tissue:PCM1KOmutant2 embryo\|BioSampleModel:Model organism or animal									RNA seq of pcm1 KO mutant zebrafish : 12 embryos in total 2 4mg	PCM1KOmutant2 R	PCM1KOmutant2 R	pcm1 KO mutant zebrafish			RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED	ILLUMINA	Illumina HiSeq 1000	SRP532179			PCM1KOmutant2_R1.clean.fq.gz PCM1KOmutant2_R2.clean.fq.gz	fastq fastq	6073820902.0	23767661.0	PCM1KOmutant2 R1.clean.fq.gz	0:127.78 1:127.77	A:1691243395;C:1356197711;G:1357868249;T:1668456939;N:54608	127	127	1691243395	1356197711	1357868249	1668456939	54608	SRX26062510	SRS22631694	SRA1970017	Huazhong Agricultural University, China\|Department of Neurosurgery	Huazhong Agricultural University, China												B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2024-09-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
33728	33728	SRR30640701	SRX26062509	SRS22631693	SRP532179	PRJNA1159911	Peri Centriolar Material 1 regulates polarized endosome dynamics and neural progenitor fate	PRJNA1159911	Other	RNA seq was performed on control and maternal zygotic developmentally defective pcm1 morphants MO and pcm1 knock out KO zebrafish embryos at 24 hpf.					PCM1KOmutant1		breed:Tg [ef1:Myr Tdtomato]\|age:24hpf\|dev stage:adult\|collection date:2021 03 19\|geo loc name:USA:San Francisco\|sex:not determined\|tissue:PCM1KOmutant1 embryo\|BioSampleModel:Model organism or animal									RNA seq of pcm1 KO mutant zebrafish : 12 embryos in total 2 3mg	PCM1KOmutant1 R	PCM1KOmutant1 R	KO mutant zebrafish			RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED	ILLUMINA	Illumina HiSeq 1000	SRP532179			PCM1KOmutant1_R1.clean.fq.gz PCM1KOmutant1_R2.clean.fq.gz	fastq fastq	6040589500.0	23826027.0	PCM1KOmutant1 R1.clean.fq.gz	0:126.76 1:126.76	A:1733588631;C:1297359473;G:1301151829;T:1708434373;N:55194	126	126	1733588631	1297359473	1301151829	1708434373	55194	SRX26062509	SRS22631693	SRA1970017	Huazhong Agricultural University, China\|Department of Neurosurgery	Huazhong Agricultural University, China												B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2024-09-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
33729	33729	SRR30640702	SRX26062508	SRS22631692	SRP532179	PRJNA1159911	Peri Centriolar Material 1 regulates polarized endosome dynamics and neural progenitor fate	PRJNA1159911	Other	RNA seq was performed on control and maternal zygotic developmentally defective pcm1 morphants MO and pcm1 knock out KO zebrafish embryos at 24 hpf.					PCM1KOcompensate3		breed:Tg [HuC:GFP\|age:24hpf\|dev stage:adult\|collection date:2021 03 19\|geo loc name:USA:San Francisco\|sex:not determined\|tissue:PCM1KOcompensate3 embryo\|BioSampleModel:Model organism or animal									RNA seq of pcm1 KO compensate zebrafish : 12 embryos in total 2 5mg	PCM1KOcompensate3 R	PCM1KOcompensate3 R	pcm1 KO compensate zebrafish			RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED	ILLUMINA	Illumina HiSeq 1000	SRP532179			PCM1KOcompensate3_R1.clean.fq.gz PCM1KOcompensate3_R2.clean.fq.gz	fastq fastq	5632945620.0	21351897.0	PCM1KOcompensate3 R1.clean.fq.gz	0:131.92 1:131.90	A:1561604697;C:1264380828;G:1267746178;T:1539161674;N:52243	131	131	1561604697	1264380828	1267746178	1539161674	52243	SRX26062508	SRS22631692	SRA1970017	Huazhong Agricultural University, China\|Department of Neurosurgery	Huazhong Agricultural University, China												B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2024-09-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
33730	33730	SRR30640703	SRX26062507	SRS22631691	SRP532179	PRJNA1159911	Peri Centriolar Material 1 regulates polarized endosome dynamics and neural progenitor fate	PRJNA1159911	Other	RNA seq was performed on control and maternal zygotic developmentally defective pcm1 morphants MO and pcm1 knock out KO zebrafish embryos at 24 hpf.					WT24hpfcontrol3		breed:natural spawning of AB adults\|age:24hpf\|dev stage:adult\|collection date:2021 03 19\|geo loc name:USA:San Francisco\|sex:not determined\|tissue:WT24hpfcontrol3 embryo\|BioSampleModel:Model organism or animal									RNA seq of Wild type zebrafish : 12 embryos in total 2 5mg	WT24hpfcontrol3 R	WT24hpfcontrol3 R	Wild type zebrafish			RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED	ILLUMINA	Illumina HiSeq 1000	SRP532179			WT24hpfcontrol3_R1.clean.fq.gz WT24hpfcontrol3_R2.clean.fq.gz	fastq fastq	5047867453.0	19837417.0	WT24hpfcontrol3 R1.clean.fq.gz	0:127.23 1:127.23	A:1412463929;C:1119657233;G:1121642146;T:1394058438;N:45707	127	127	1412463929	1119657233	1121642146	1394058438	45707	SRX26062507	SRS22631691	SRA1970017	Huazhong Agricultural University, China\|Department of Neurosurgery	Huazhong Agricultural University, China												B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2024-09-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
33731	33731	SRR30640704	SRX26062506	SRS22631690	SRP532179	PRJNA1159911	Peri Centriolar Material 1 regulates polarized endosome dynamics and neural progenitor fate	PRJNA1159911	Other	RNA seq was performed on control and maternal zygotic developmentally defective pcm1 morphants MO and pcm1 knock out KO zebrafish embryos at 24 hpf.					WT24hpfcontrol2		breed:natural spawning of AB adults\|age:24hpf\|dev stage:adult\|collection date:2021 03 19\|geo loc name:USA:San Francisco\|sex:not determined\|tissue:WT24hpfcontrol2 embryo\|BioSampleModel:Model organism or animal									RNA seq of Wild type zebrafish : 12 embryos in total 2 4mg	WT24hpfcontrol2 R	WT24hpfcontrol2 R	Wild type zebrafish			RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED	ILLUMINA	Illumina HiSeq 1000	SRP532179			WT24hpfcontrol2_R1.clean.fq.gz WT24hpfcontrol2_R2.clean.fq.gz	fastq fastq	5408273952.0	21601107.0	WT24hpfcontrol2 R1.clean.fq.gz	0:125.19 1:125.18	A:1510365712;C:1201646307;G:1204419555;T:1491793767;N:48611	125	125	1510365712	1201646307	1204419555	1491793767	48611	SRX26062506	SRS22631690	SRA1970017	Huazhong Agricultural University, China\|Department of Neurosurgery	Huazhong Agricultural University, China												B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2024-09-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
33732	33732	SRR30640705	SRX26062505	SRS22631689	SRP532179	PRJNA1159911	Peri Centriolar Material 1 regulates polarized endosome dynamics and neural progenitor fate	PRJNA1159911	Other	RNA seq was performed on control and maternal zygotic developmentally defective pcm1 morphants MO and pcm1 knock out KO zebrafish embryos at 24 hpf.					PCM1KOcompensate2		breed:Tg [HuC:GFP\|age:24hpf\|dev stage:adult\|collection date:2021 03 19\|geo loc name:USA:San Francisco\|sex:not determined\|tissue:PCM1KOcompensate2 embryo\|BioSampleModel:Model organism or animal									RNA seq of pcm1 KO compensate zebrafish : 12 embryos in total 2 4mg	PCM1KOcompensate2 R	PCM1KOcompensate2 R	pcm1 KO compensate zebrafish			RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED	ILLUMINA	Illumina HiSeq 1000	SRP532179			PCM1KOcompensate2_R1.clean.fq.gz PCM1KOcompensate2_R2.clean.fq.gz	fastq fastq	5996379188.0	22765993.0	PCM1KOcompensate2 R1.clean.fq.gz	0:131.70 1:131.70	A:1669800521;C:1339211911;G:1342418096;T:1644890999;N:57661	131	131	1669800521	1339211911	1342418096	1644890999	57661	SRX26062505	SRS22631689	SRA1970017	Huazhong Agricultural University, China\|Department of Neurosurgery	Huazhong Agricultural University, China												B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2024-09-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
33733	33733	SRR30640706	SRX26062504	SRS22631688	SRP532179	PRJNA1159911	Peri Centriolar Material 1 regulates polarized endosome dynamics and neural progenitor fate	PRJNA1159911	Other	RNA seq was performed on control and maternal zygotic developmentally defective pcm1 morphants MO and pcm1 knock out KO zebrafish embryos at 24 hpf.					PCM1KOcompensate1		breed:Tg [HuC:GFP\|age:24hpf\|dev stage:adult\|collection date:2021 03 19\|geo loc name:USA:San Francisco\|sex:not determined\|tissue:PCM1KOcompensate1 embryo\|BioSampleModel:Model organism or animal									RNA seq of pcm1 KO compensate zebrafish : 12 embryos in total 2 3mg	PCM1KOcompensate1 R	PCM1KOcompensate1 R	pcm1 KO compensate zebrafish			RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED	ILLUMINA	Illumina HiSeq 1000	SRP532179			PCM1KOcompensate1_R1.clean.fq.gz PCM1KOcompensate1_R2.clean.fq.gz	fastq fastq	5594219881.0	21191291.0	PCM1KOcompensate1 R1.clean.fq.gz	0:131.99 1:131.99	A:1594003450;C:1214578517;G:1215705001;T:1569880851;N:52062	131	131	1594003450	1214578517	1215705001	1569880851	52062	SRX26062504	SRS22631688	SRA1970017	Huazhong Agricultural University, China\|Department of Neurosurgery	Huazhong Agricultural University, China												B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2024-09-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
34688	34688	SRR32217622	SRX27557938	SRS23971739	SRP561364	PRJNA1218816	p21 ccng1 foxo3b and fbxw7 contribute to p53 dependent cell cycle arrest [MPNP timecross]	GSE288666	Transcriptome Analysis	p53 is a transcription factor that plays a critical role in cancer prevention. However the mechanisms by which p53 exerts its tumor suppressive function is still unclear. While PUMA/BBC3 and NOXA/PMAIP1 are known to be important in p53 dependent apoptosis and p21/CDKN1A is crucial for p53 dependent cell cycle arrest we demonstrate that zebrafish lacking puma noxa and p21 do not show a predisposition to cancer. This suggests that additional p53 transcriptional targets are sufficient for its tumor suppressive function. Contrary to the prevailing belief that p21 is the key regulator of p53 dependent cell cycle arrest we provide evidence that p53 can still induce cell cycle arrest in the absence of p21 following DNA damage or loss of mdm2 p53 activation in the absence of stress. This implies the involvement of other p53 transcriptional targets in mediating p53 dependent cell cycle arrest. Since p53 tumor suppression is conserved across multiple vertebrate species we conducted a cross species comparative analysis of p53 dependent transcriptional profiles to identify a conserved set of 136 p53 upregulated transcripts. Our analysis stresses the importance of ortholog to paralog analysis across species since in many cases the paralog but not ortholog in differing species is p53 dependent. Additionally we performed a CRISPR/Cas9 G0 “crispant” screen in a genetic background lacking mdm2 puma noxa and p21 to identify key components involved in p53 dependent cell cycle arrest. Our findings revealed that ccng1 fbxw7 and foxo3b play an important role in this process. Overall design: RNA sequencing was performed on zebrafish of un genotyped progeny from mdm2+/ ; pnp / intercrosses at various developmental stages 8 10 12 14 16 hpf as the mutant group N=50 embryos for each group referred to as MPNP. While this approach generated a dilution of RNA transcripts since only approxmiately ¼ of the embryos were mpnp / it nonetheless allowed us to glimpse at the dynamics of p53 target gene induction in mpnp / anim…		pubmed:40487439		Zebrafish PNP 16hpf 2	GSM8772774		source name:16 hpf embryos\|tissue:16 hpf embryos\|genotype:puma / ; noxa / ; p21 / \|geo loc name:missing\|collection date:missing	Zebrafish PNP 16hpf 2	Raw sequencing reads were aligned to the Danio rerio GRCz11 genome assemblies using STAR version 2.7.3a GCC 6.4.0 2.28 with default setting. Following alignment raw read counts were generated using HTSeq version 0.12.3 foss 2018b Python 3.6.6. The corresponding gene annotation files used in HTSeq were Danio rerio.GRCz11.102.chr.gtf for zebrafish samples. Differentially expressed genes DEGs were identified using DESeq2 version 1.42.1 in R version 4.3.3. Normalized counts were obtained using RSEM version 1.3.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes TPM values for each samples	16 hpf embryos		Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit QIAGEN #74134 according to the manufacturer’s instructions. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared using the Illumina RNA kit with PolyA selection. Sequencing was performed on the Illumina HiSeq platform generating 2x150 bp paired end reads and was conducted by Genewiz from Azenta Life Sciences.	The fertilization windown was set to 15 minutes. All embryos were cleaned approximately 6 hpf with approximately 30 embryos pooled in each Petri dish.	tissue:16 hpf embryos\|genotype:puma / ; noxa / ; p21 /	GSM8772774	GSM8772774: Zebrafish PNP 16hpf 2; Danio rerio; RNA Seq	GSM8772774 r1	GSM8772774	1	Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit QIAGEN #74134 according to the manufacturer's instructions. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared using the Illumina RNA kit with PolyA selection. Sequencing was performed on the Illumina HiSeq platform generating 2x150 bp paired end reads and was conducted by Genewiz from Azenta Life Sciences.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP561364			PNP-16hpf-R2_R1_001.fastq.gz PNP-16hpf-R2_R2_001.fastq.gz	fastq fastq	10535154600.0	35117182.0	GSM8772774 r1	0:150 1:150	A:2785456121;C:2485921943;G:2549544461;T:2712941662;N:1290413	150	150	2785456121	2485921943	2549544461	2712941662	1290413	SRX27557938	SRS23971739	SRA2069214	University of Alabama at Birmingham	University of Alabama at Birmingham												B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2025-02-03	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
34689	34689	SRR32217623	SRX27557937	SRS23971738	SRP561364	PRJNA1218816	p21 ccng1 foxo3b and fbxw7 contribute to p53 dependent cell cycle arrest [MPNP timecross]	GSE288666	Transcriptome Analysis	p53 is a transcription factor that plays a critical role in cancer prevention. However the mechanisms by which p53 exerts its tumor suppressive function is still unclear. While PUMA/BBC3 and NOXA/PMAIP1 are known to be important in p53 dependent apoptosis and p21/CDKN1A is crucial for p53 dependent cell cycle arrest we demonstrate that zebrafish lacking puma noxa and p21 do not show a predisposition to cancer. This suggests that additional p53 transcriptional targets are sufficient for its tumor suppressive function. Contrary to the prevailing belief that p21 is the key regulator of p53 dependent cell cycle arrest we provide evidence that p53 can still induce cell cycle arrest in the absence of p21 following DNA damage or loss of mdm2 p53 activation in the absence of stress. This implies the involvement of other p53 transcriptional targets in mediating p53 dependent cell cycle arrest. Since p53 tumor suppression is conserved across multiple vertebrate species we conducted a cross species comparative analysis of p53 dependent transcriptional profiles to identify a conserved set of 136 p53 upregulated transcripts. Our analysis stresses the importance of ortholog to paralog analysis across species since in many cases the paralog but not ortholog in differing species is p53 dependent. Additionally we performed a CRISPR/Cas9 G0 “crispant” screen in a genetic background lacking mdm2 puma noxa and p21 to identify key components involved in p53 dependent cell cycle arrest. Our findings revealed that ccng1 fbxw7 and foxo3b play an important role in this process. Overall design: RNA sequencing was performed on zebrafish of un genotyped progeny from mdm2+/ ; pnp / intercrosses at various developmental stages 8 10 12 14 16 hpf as the mutant group N=50 embryos for each group referred to as MPNP. While this approach generated a dilution of RNA transcripts since only approxmiately ¼ of the embryos were mpnp / it nonetheless allowed us to glimpse at the dynamics of p53 target gene induction in mpnp / anim…		pubmed:40487439		Zebrafish PNP 16hpf 1	GSM8772773		source name:16 hpf embryos\|tissue:16 hpf embryos\|genotype:puma / ; noxa / ; p21 / \|geo loc name:missing\|collection date:missing	Zebrafish PNP 16hpf 1	Raw sequencing reads were aligned to the Danio rerio GRCz11 genome assemblies using STAR version 2.7.3a GCC 6.4.0 2.28 with default setting. Following alignment raw read counts were generated using HTSeq version 0.12.3 foss 2018b Python 3.6.6. The corresponding gene annotation files used in HTSeq were Danio rerio.GRCz11.102.chr.gtf for zebrafish samples. Differentially expressed genes DEGs were identified using DESeq2 version 1.42.1 in R version 4.3.3. Normalized counts were obtained using RSEM version 1.3.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes TPM values for each samples	16 hpf embryos		Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit QIAGEN #74134 according to the manufacturer’s instructions. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared using the Illumina RNA kit with PolyA selection. Sequencing was performed on the Illumina HiSeq platform generating 2x150 bp paired end reads and was conducted by Genewiz from Azenta Life Sciences.	The fertilization windown was set to 15 minutes. All embryos were cleaned approximately 6 hpf with approximately 30 embryos pooled in each Petri dish.	tissue:16 hpf embryos\|genotype:puma / ; noxa / ; p21 /	GSM8772773	GSM8772773: Zebrafish PNP 16hpf 1; Danio rerio; RNA Seq	GSM8772773 r1	GSM8772773	1	Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit QIAGEN #74134 according to the manufacturer's instructions. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared using the Illumina RNA kit with PolyA selection. Sequencing was performed on the Illumina HiSeq platform generating 2x150 bp paired end reads and was conducted by Genewiz from Azenta Life Sciences.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP561364			PNP-16hpf-R1-LCM9111_L3_R1_001.fastq.gz PNP-16hpf-R1-LCM9111_L3_R2_001.fastq.gz	fastq fastq	10601406000.0	35338020.0	GSM8772773 r1	0:150 1:150	A:2680198721;C:2624253376;G:2633457482;T:2663407541;N:88880	150	150	2680198721	2624253376	2633457482	2663407541	88880	SRX27557937	SRS23971738	SRA2069214	University of Alabama at Birmingham	University of Alabama at Birmingham												B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2025-02-03	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
34690	34690	SRR32217624	SRX27557936	SRS23971737	SRP561364	PRJNA1218816	p21 ccng1 foxo3b and fbxw7 contribute to p53 dependent cell cycle arrest [MPNP timecross]	GSE288666	Transcriptome Analysis	p53 is a transcription factor that plays a critical role in cancer prevention. However the mechanisms by which p53 exerts its tumor suppressive function is still unclear. While PUMA/BBC3 and NOXA/PMAIP1 are known to be important in p53 dependent apoptosis and p21/CDKN1A is crucial for p53 dependent cell cycle arrest we demonstrate that zebrafish lacking puma noxa and p21 do not show a predisposition to cancer. This suggests that additional p53 transcriptional targets are sufficient for its tumor suppressive function. Contrary to the prevailing belief that p21 is the key regulator of p53 dependent cell cycle arrest we provide evidence that p53 can still induce cell cycle arrest in the absence of p21 following DNA damage or loss of mdm2 p53 activation in the absence of stress. This implies the involvement of other p53 transcriptional targets in mediating p53 dependent cell cycle arrest. Since p53 tumor suppression is conserved across multiple vertebrate species we conducted a cross species comparative analysis of p53 dependent transcriptional profiles to identify a conserved set of 136 p53 upregulated transcripts. Our analysis stresses the importance of ortholog to paralog analysis across species since in many cases the paralog but not ortholog in differing species is p53 dependent. Additionally we performed a CRISPR/Cas9 G0 “crispant” screen in a genetic background lacking mdm2 puma noxa and p21 to identify key components involved in p53 dependent cell cycle arrest. Our findings revealed that ccng1 fbxw7 and foxo3b play an important role in this process. Overall design: RNA sequencing was performed on zebrafish of un genotyped progeny from mdm2+/ ; pnp / intercrosses at various developmental stages 8 10 12 14 16 hpf as the mutant group N=50 embryos for each group referred to as MPNP. While this approach generated a dilution of RNA transcripts since only approxmiately ¼ of the embryos were mpnp / it nonetheless allowed us to glimpse at the dynamics of p53 target gene induction in mpnp / anim…		pubmed:40487439		Zebrafish MPNP 16hpf 2	GSM8772772		source name:16 hpf embryos\|tissue:16 hpf embryos\|genotype:mdm2 / or mdm2+/+ mdm2+/ ; puma / ; noxa / ; p21 / \|geo loc name:missing\|collection date:missing	Zebrafish MPNP 16hpf 2	Raw sequencing reads were aligned to the Danio rerio GRCz11 genome assemblies using STAR version 2.7.3a GCC 6.4.0 2.28 with default setting. Following alignment raw read counts were generated using HTSeq version 0.12.3 foss 2018b Python 3.6.6. The corresponding gene annotation files used in HTSeq were Danio rerio.GRCz11.102.chr.gtf for zebrafish samples. Differentially expressed genes DEGs were identified using DESeq2 version 1.42.1 in R version 4.3.3. Normalized counts were obtained using RSEM version 1.3.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes TPM values for each samples	16 hpf embryos		Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit QIAGEN #74134 according to the manufacturer’s instructions. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared using the Illumina RNA kit with PolyA selection. Sequencing was performed on the Illumina HiSeq platform generating 2x150 bp paired end reads and was conducted by Genewiz from Azenta Life Sciences.	The fertilization windown was set to 15 minutes. All embryos were cleaned approximately 6 hpf with approximately 30 embryos pooled in each Petri dish.	tissue:16 hpf embryos\|genotype:mdm2 / or mdm2+/+ mdm2+/ ; puma / ; noxa / ; p21 /	GSM8772772	GSM8772772: Zebrafish MPNP 16hpf 2; Danio rerio; RNA Seq	GSM8772772 r1	GSM8772772	1	Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit QIAGEN #74134 according to the manufacturer's instructions. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared using the Illumina RNA kit with PolyA selection. Sequencing was performed on the Illumina HiSeq platform generating 2x150 bp paired end reads and was conducted by Genewiz from Azenta Life Sciences.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP561364			MPNP-16hpf-R2_R1_001.fastq.gz MPNP-16hpf-R2_R2_001.fastq.gz	fastq fastq	14701359300.0	49004531.0	GSM8772772 r1	0:150 1:150	A:3947459353;C:3409168557;G:3472564779;T:3870403810;N:1762801	150	150	3947459353	3409168557	3472564779	3870403810	1762801	SRX27557936	SRS23971737	SRA2069214	University of Alabama at Birmingham	University of Alabama at Birmingham												B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2025-02-03	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
34691	34691	SRR32217625	SRX27557935	SRS23971736	SRP561364	PRJNA1218816	p21 ccng1 foxo3b and fbxw7 contribute to p53 dependent cell cycle arrest [MPNP timecross]	GSE288666	Transcriptome Analysis	p53 is a transcription factor that plays a critical role in cancer prevention. However the mechanisms by which p53 exerts its tumor suppressive function is still unclear. While PUMA/BBC3 and NOXA/PMAIP1 are known to be important in p53 dependent apoptosis and p21/CDKN1A is crucial for p53 dependent cell cycle arrest we demonstrate that zebrafish lacking puma noxa and p21 do not show a predisposition to cancer. This suggests that additional p53 transcriptional targets are sufficient for its tumor suppressive function. Contrary to the prevailing belief that p21 is the key regulator of p53 dependent cell cycle arrest we provide evidence that p53 can still induce cell cycle arrest in the absence of p21 following DNA damage or loss of mdm2 p53 activation in the absence of stress. This implies the involvement of other p53 transcriptional targets in mediating p53 dependent cell cycle arrest. Since p53 tumor suppression is conserved across multiple vertebrate species we conducted a cross species comparative analysis of p53 dependent transcriptional profiles to identify a conserved set of 136 p53 upregulated transcripts. Our analysis stresses the importance of ortholog to paralog analysis across species since in many cases the paralog but not ortholog in differing species is p53 dependent. Additionally we performed a CRISPR/Cas9 G0 “crispant” screen in a genetic background lacking mdm2 puma noxa and p21 to identify key components involved in p53 dependent cell cycle arrest. Our findings revealed that ccng1 fbxw7 and foxo3b play an important role in this process. Overall design: RNA sequencing was performed on zebrafish of un genotyped progeny from mdm2+/ ; pnp / intercrosses at various developmental stages 8 10 12 14 16 hpf as the mutant group N=50 embryos for each group referred to as MPNP. While this approach generated a dilution of RNA transcripts since only approxmiately ¼ of the embryos were mpnp / it nonetheless allowed us to glimpse at the dynamics of p53 target gene induction in mpnp / anim…		pubmed:40487439		Zebrafish MPNP 16hpf 1	GSM8772771		source name:16 hpf embryos\|tissue:16 hpf embryos\|genotype:mdm2 / or mdm2+/+ mdm2+/ ; puma / ; noxa / ; p21 / \|geo loc name:missing\|collection date:missing	Zebrafish MPNP 16hpf 1	Raw sequencing reads were aligned to the Danio rerio GRCz11 genome assemblies using STAR version 2.7.3a GCC 6.4.0 2.28 with default setting. Following alignment raw read counts were generated using HTSeq version 0.12.3 foss 2018b Python 3.6.6. The corresponding gene annotation files used in HTSeq were Danio rerio.GRCz11.102.chr.gtf for zebrafish samples. Differentially expressed genes DEGs were identified using DESeq2 version 1.42.1 in R version 4.3.3. Normalized counts were obtained using RSEM version 1.3.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes TPM values for each samples	16 hpf embryos		Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit QIAGEN #74134 according to the manufacturer’s instructions. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared using the Illumina RNA kit with PolyA selection. Sequencing was performed on the Illumina HiSeq platform generating 2x150 bp paired end reads and was conducted by Genewiz from Azenta Life Sciences.	The fertilization windown was set to 15 minutes. All embryos were cleaned approximately 6 hpf with approximately 30 embryos pooled in each Petri dish.	tissue:16 hpf embryos\|genotype:mdm2 / or mdm2+/+ mdm2+/ ; puma / ; noxa / ; p21 /	GSM8772771	GSM8772771: Zebrafish MPNP 16hpf 1; Danio rerio; RNA Seq	GSM8772771 r1	GSM8772771	1	Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit QIAGEN #74134 according to the manufacturer's instructions. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared using the Illumina RNA kit with PolyA selection. Sequencing was performed on the Illumina HiSeq platform generating 2x150 bp paired end reads and was conducted by Genewiz from Azenta Life Sciences.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP561364			MPNP-16hpf-R1-LCM9110_L3_R1_001.fastq.gz MPNP-16hpf-R1-LCM9110_L3_R2_001.fastq.gz	fastq fastq	10235183700.0	34117279.0	GSM8772771 r1	0:150 1:150	A:2570056156;C:2549706468;G:2564252810;T:2551084265;N:84001	150	150	2570056156	2549706468	2564252810	2551084265	84001	SRX27557935	SRS23971736	SRA2069214	University of Alabama at Birmingham	University of Alabama at Birmingham												B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2025-02-03	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
34692	34692	SRR32217629	SRX27557934	SRS23971735	SRP561364	PRJNA1218816	p21 ccng1 foxo3b and fbxw7 contribute to p53 dependent cell cycle arrest [MPNP timecross]	GSE288666	Transcriptome Analysis	p53 is a transcription factor that plays a critical role in cancer prevention. However the mechanisms by which p53 exerts its tumor suppressive function is still unclear. While PUMA/BBC3 and NOXA/PMAIP1 are known to be important in p53 dependent apoptosis and p21/CDKN1A is crucial for p53 dependent cell cycle arrest we demonstrate that zebrafish lacking puma noxa and p21 do not show a predisposition to cancer. This suggests that additional p53 transcriptional targets are sufficient for its tumor suppressive function. Contrary to the prevailing belief that p21 is the key regulator of p53 dependent cell cycle arrest we provide evidence that p53 can still induce cell cycle arrest in the absence of p21 following DNA damage or loss of mdm2 p53 activation in the absence of stress. This implies the involvement of other p53 transcriptional targets in mediating p53 dependent cell cycle arrest. Since p53 tumor suppression is conserved across multiple vertebrate species we conducted a cross species comparative analysis of p53 dependent transcriptional profiles to identify a conserved set of 136 p53 upregulated transcripts. Our analysis stresses the importance of ortholog to paralog analysis across species since in many cases the paralog but not ortholog in differing species is p53 dependent. Additionally we performed a CRISPR/Cas9 G0 “crispant” screen in a genetic background lacking mdm2 puma noxa and p21 to identify key components involved in p53 dependent cell cycle arrest. Our findings revealed that ccng1 fbxw7 and foxo3b play an important role in this process. Overall design: RNA sequencing was performed on zebrafish of un genotyped progeny from mdm2+/ ; pnp / intercrosses at various developmental stages 8 10 12 14 16 hpf as the mutant group N=50 embryos for each group referred to as MPNP. While this approach generated a dilution of RNA transcripts since only approxmiately ¼ of the embryos were mpnp / it nonetheless allowed us to glimpse at the dynamics of p53 target gene induction in mpnp / anim…		pubmed:40487439		Zebrafish PNP 14hpf 2	GSM8772770		source name:14 hpf embryos\|tissue:14 hpf embryos\|genotype:puma / ; noxa / ; p21 / \|geo loc name:missing\|collection date:missing	Zebrafish PNP 14hpf 2	Raw sequencing reads were aligned to the Danio rerio GRCz11 genome assemblies using STAR version 2.7.3a GCC 6.4.0 2.28 with default setting. Following alignment raw read counts were generated using HTSeq version 0.12.3 foss 2018b Python 3.6.6. The corresponding gene annotation files used in HTSeq were Danio rerio.GRCz11.102.chr.gtf for zebrafish samples. Differentially expressed genes DEGs were identified using DESeq2 version 1.42.1 in R version 4.3.3. Normalized counts were obtained using RSEM version 1.3.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes TPM values for each samples	14 hpf embryos		Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit QIAGEN #74134 according to the manufacturer’s instructions. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared using the Illumina RNA kit with PolyA selection. Sequencing was performed on the Illumina HiSeq platform generating 2x150 bp paired end reads and was conducted by Genewiz from Azenta Life Sciences.	The fertilization windown was set to 15 minutes. All embryos were cleaned approximately 6 hpf with approximately 30 embryos pooled in each Petri dish.	tissue:14 hpf embryos\|genotype:puma / ; noxa / ; p21 /	GSM8772770	GSM8772770: Zebrafish PNP 14hpf 2; Danio rerio; RNA Seq	GSM8772770 r1	GSM8772770	1	Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit QIAGEN #74134 according to the manufacturer's instructions. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared using the Illumina RNA kit with PolyA selection. Sequencing was performed on the Illumina HiSeq platform generating 2x150 bp paired end reads and was conducted by Genewiz from Azenta Life Sciences.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP561364			PNP-14hpf-R2_R1_001.fastq.gz PNP-14hpf-R2_R2_001.fastq.gz	fastq fastq	5414434800.0	18048116.0	GSM8772770 r1	0:150 1:150	A:1444381230;C:1263354350;G:1292187383;T:1413874437;N:637400	150	150	1444381230	1263354350	1292187383	1413874437	637400	SRX27557934	SRS23971735	SRA2069214	University of Alabama at Birmingham	University of Alabama at Birmingham												B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2025-02-03	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
34693	34693	SRR32217626	SRX27557933	SRS23971734	SRP561364	PRJNA1218816	p21 ccng1 foxo3b and fbxw7 contribute to p53 dependent cell cycle arrest [MPNP timecross]	GSE288666	Transcriptome Analysis	p53 is a transcription factor that plays a critical role in cancer prevention. However the mechanisms by which p53 exerts its tumor suppressive function is still unclear. While PUMA/BBC3 and NOXA/PMAIP1 are known to be important in p53 dependent apoptosis and p21/CDKN1A is crucial for p53 dependent cell cycle arrest we demonstrate that zebrafish lacking puma noxa and p21 do not show a predisposition to cancer. This suggests that additional p53 transcriptional targets are sufficient for its tumor suppressive function. Contrary to the prevailing belief that p21 is the key regulator of p53 dependent cell cycle arrest we provide evidence that p53 can still induce cell cycle arrest in the absence of p21 following DNA damage or loss of mdm2 p53 activation in the absence of stress. This implies the involvement of other p53 transcriptional targets in mediating p53 dependent cell cycle arrest. Since p53 tumor suppression is conserved across multiple vertebrate species we conducted a cross species comparative analysis of p53 dependent transcriptional profiles to identify a conserved set of 136 p53 upregulated transcripts. Our analysis stresses the importance of ortholog to paralog analysis across species since in many cases the paralog but not ortholog in differing species is p53 dependent. Additionally we performed a CRISPR/Cas9 G0 “crispant” screen in a genetic background lacking mdm2 puma noxa and p21 to identify key components involved in p53 dependent cell cycle arrest. Our findings revealed that ccng1 fbxw7 and foxo3b play an important role in this process. Overall design: RNA sequencing was performed on zebrafish of un genotyped progeny from mdm2+/ ; pnp / intercrosses at various developmental stages 8 10 12 14 16 hpf as the mutant group N=50 embryos for each group referred to as MPNP. While this approach generated a dilution of RNA transcripts since only approxmiately ¼ of the embryos were mpnp / it nonetheless allowed us to glimpse at the dynamics of p53 target gene induction in mpnp / anim…		pubmed:40487439		Zebrafish PNP 14hpf 1	GSM8772769		source name:14 hpf embryos\|tissue:14 hpf embryos\|genotype:puma / ; noxa / ; p21 / \|geo loc name:missing\|collection date:missing	Zebrafish PNP 14hpf 1	Raw sequencing reads were aligned to the Danio rerio GRCz11 genome assemblies using STAR version 2.7.3a GCC 6.4.0 2.28 with default setting. Following alignment raw read counts were generated using HTSeq version 0.12.3 foss 2018b Python 3.6.6. The corresponding gene annotation files used in HTSeq were Danio rerio.GRCz11.102.chr.gtf for zebrafish samples. Differentially expressed genes DEGs were identified using DESeq2 version 1.42.1 in R version 4.3.3. Normalized counts were obtained using RSEM version 1.3.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes TPM values for each samples	14 hpf embryos		Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit QIAGEN #74134 according to the manufacturer’s instructions. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared using the Illumina RNA kit with PolyA selection. Sequencing was performed on the Illumina HiSeq platform generating 2x150 bp paired end reads and was conducted by Genewiz from Azenta Life Sciences.	The fertilization windown was set to 15 minutes. All embryos were cleaned approximately 6 hpf with approximately 30 embryos pooled in each Petri dish.	tissue:14 hpf embryos\|genotype:puma / ; noxa / ; p21 /	GSM8772769	GSM8772769: Zebrafish PNP 14hpf 1; Danio rerio; RNA Seq	GSM8772769 r1	GSM8772769	1	Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit QIAGEN #74134 according to the manufacturer's instructions. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared using the Illumina RNA kit with PolyA selection. Sequencing was performed on the Illumina HiSeq platform generating 2x150 bp paired end reads and was conducted by Genewiz from Azenta Life Sciences.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP561364			PNP-14hpf-R1-LCM9109_L3_R1_001.fastq.gz PNP-14hpf-R1-LCM9109_L3_R2_001.fastq.gz	fastq fastq	9851333400.0	32837778.0	GSM8772769 r1	0:150 1:150	A:2483678308;C:2443272708;G:2457808801;T:2466491868;N:81715	150	150	2483678308	2443272708	2457808801	2466491868	81715	SRX27557933	SRS23971734	SRA2069214	University of Alabama at Birmingham	University of Alabama at Birmingham												B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2025-02-03	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
34694	34694	SRR32217627	SRX27557932	SRS23971733	SRP561364	PRJNA1218816	p21 ccng1 foxo3b and fbxw7 contribute to p53 dependent cell cycle arrest [MPNP timecross]	GSE288666	Transcriptome Analysis	p53 is a transcription factor that plays a critical role in cancer prevention. However the mechanisms by which p53 exerts its tumor suppressive function is still unclear. While PUMA/BBC3 and NOXA/PMAIP1 are known to be important in p53 dependent apoptosis and p21/CDKN1A is crucial for p53 dependent cell cycle arrest we demonstrate that zebrafish lacking puma noxa and p21 do not show a predisposition to cancer. This suggests that additional p53 transcriptional targets are sufficient for its tumor suppressive function. Contrary to the prevailing belief that p21 is the key regulator of p53 dependent cell cycle arrest we provide evidence that p53 can still induce cell cycle arrest in the absence of p21 following DNA damage or loss of mdm2 p53 activation in the absence of stress. This implies the involvement of other p53 transcriptional targets in mediating p53 dependent cell cycle arrest. Since p53 tumor suppression is conserved across multiple vertebrate species we conducted a cross species comparative analysis of p53 dependent transcriptional profiles to identify a conserved set of 136 p53 upregulated transcripts. Our analysis stresses the importance of ortholog to paralog analysis across species since in many cases the paralog but not ortholog in differing species is p53 dependent. Additionally we performed a CRISPR/Cas9 G0 “crispant” screen in a genetic background lacking mdm2 puma noxa and p21 to identify key components involved in p53 dependent cell cycle arrest. Our findings revealed that ccng1 fbxw7 and foxo3b play an important role in this process. Overall design: RNA sequencing was performed on zebrafish of un genotyped progeny from mdm2+/ ; pnp / intercrosses at various developmental stages 8 10 12 14 16 hpf as the mutant group N=50 embryos for each group referred to as MPNP. While this approach generated a dilution of RNA transcripts since only approxmiately ¼ of the embryos were mpnp / it nonetheless allowed us to glimpse at the dynamics of p53 target gene induction in mpnp / anim…		pubmed:40487439		Zebrafish MPNP 14hpf 2	GSM8772768		source name:14 hpf embryos\|tissue:14 hpf embryos\|genotype:mdm2 / or mdm2+/+ mdm2+/ ; puma / ; noxa / ; p21 / \|geo loc name:missing\|collection date:missing	Zebrafish MPNP 14hpf 2	Raw sequencing reads were aligned to the Danio rerio GRCz11 genome assemblies using STAR version 2.7.3a GCC 6.4.0 2.28 with default setting. Following alignment raw read counts were generated using HTSeq version 0.12.3 foss 2018b Python 3.6.6. The corresponding gene annotation files used in HTSeq were Danio rerio.GRCz11.102.chr.gtf for zebrafish samples. Differentially expressed genes DEGs were identified using DESeq2 version 1.42.1 in R version 4.3.3. Normalized counts were obtained using RSEM version 1.3.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes TPM values for each samples	14 hpf embryos		Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit QIAGEN #74134 according to the manufacturer’s instructions. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared using the Illumina RNA kit with PolyA selection. Sequencing was performed on the Illumina HiSeq platform generating 2x150 bp paired end reads and was conducted by Genewiz from Azenta Life Sciences.	The fertilization windown was set to 15 minutes. All embryos were cleaned approximately 6 hpf with approximately 30 embryos pooled in each Petri dish.	tissue:14 hpf embryos\|genotype:mdm2 / or mdm2+/+ mdm2+/ ; puma / ; noxa / ; p21 /	GSM8772768	GSM8772768: Zebrafish MPNP 14hpf 2; Danio rerio; RNA Seq	GSM8772768 r1	GSM8772768	1	Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit QIAGEN #74134 according to the manufacturer's instructions. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared using the Illumina RNA kit with PolyA selection. Sequencing was performed on the Illumina HiSeq platform generating 2x150 bp paired end reads and was conducted by Genewiz from Azenta Life Sciences.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP561364			MPNP-14hpf-R2_R1_001.fastq.gz MPNP-14hpf-R2_R2_001.fastq.gz	fastq fastq	5953892700.0	19846309.0	GSM8772768 r1	0:150 1:150	A:1597853468;C:1382446019;G:1420097871;T:1552767183;N:728159	150	150	1597853468	1382446019	1420097871	1552767183	728159	SRX27557932	SRS23971733	SRA2069214	University of Alabama at Birmingham	University of Alabama at Birmingham												B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2025-02-03	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
34695	34695	SRR32217628	SRX27557931	SRS23971732	SRP561364	PRJNA1218816	p21 ccng1 foxo3b and fbxw7 contribute to p53 dependent cell cycle arrest [MPNP timecross]	GSE288666	Transcriptome Analysis	p53 is a transcription factor that plays a critical role in cancer prevention. However the mechanisms by which p53 exerts its tumor suppressive function is still unclear. While PUMA/BBC3 and NOXA/PMAIP1 are known to be important in p53 dependent apoptosis and p21/CDKN1A is crucial for p53 dependent cell cycle arrest we demonstrate that zebrafish lacking puma noxa and p21 do not show a predisposition to cancer. This suggests that additional p53 transcriptional targets are sufficient for its tumor suppressive function. Contrary to the prevailing belief that p21 is the key regulator of p53 dependent cell cycle arrest we provide evidence that p53 can still induce cell cycle arrest in the absence of p21 following DNA damage or loss of mdm2 p53 activation in the absence of stress. This implies the involvement of other p53 transcriptional targets in mediating p53 dependent cell cycle arrest. Since p53 tumor suppression is conserved across multiple vertebrate species we conducted a cross species comparative analysis of p53 dependent transcriptional profiles to identify a conserved set of 136 p53 upregulated transcripts. Our analysis stresses the importance of ortholog to paralog analysis across species since in many cases the paralog but not ortholog in differing species is p53 dependent. Additionally we performed a CRISPR/Cas9 G0 “crispant” screen in a genetic background lacking mdm2 puma noxa and p21 to identify key components involved in p53 dependent cell cycle arrest. Our findings revealed that ccng1 fbxw7 and foxo3b play an important role in this process. Overall design: RNA sequencing was performed on zebrafish of un genotyped progeny from mdm2+/ ; pnp / intercrosses at various developmental stages 8 10 12 14 16 hpf as the mutant group N=50 embryos for each group referred to as MPNP. While this approach generated a dilution of RNA transcripts since only approxmiately ¼ of the embryos were mpnp / it nonetheless allowed us to glimpse at the dynamics of p53 target gene induction in mpnp / anim…		pubmed:40487439		Zebrafish MPNP 14hpf 1	GSM8772767		source name:14 hpf embryos\|tissue:14 hpf embryos\|genotype:mdm2 / or mdm2+/+ mdm2+/ ; puma / ; noxa / ; p21 / \|geo loc name:missing\|collection date:missing	Zebrafish MPNP 14hpf 1	Raw sequencing reads were aligned to the Danio rerio GRCz11 genome assemblies using STAR version 2.7.3a GCC 6.4.0 2.28 with default setting. Following alignment raw read counts were generated using HTSeq version 0.12.3 foss 2018b Python 3.6.6. The corresponding gene annotation files used in HTSeq were Danio rerio.GRCz11.102.chr.gtf for zebrafish samples. Differentially expressed genes DEGs were identified using DESeq2 version 1.42.1 in R version 4.3.3. Normalized counts were obtained using RSEM version 1.3.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes TPM values for each samples	14 hpf embryos		Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit QIAGEN #74134 according to the manufacturer’s instructions. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared using the Illumina RNA kit with PolyA selection. Sequencing was performed on the Illumina HiSeq platform generating 2x150 bp paired end reads and was conducted by Genewiz from Azenta Life Sciences.	The fertilization windown was set to 15 minutes. All embryos were cleaned approximately 6 hpf with approximately 30 embryos pooled in each Petri dish.	tissue:14 hpf embryos\|genotype:mdm2 / or mdm2+/+ mdm2+/ ; puma / ; noxa / ; p21 /	GSM8772767	GSM8772767: Zebrafish MPNP 14hpf 1; Danio rerio; RNA Seq	GSM8772767 r1	GSM8772767	1	Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit QIAGEN #74134 according to the manufacturer's instructions. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared using the Illumina RNA kit with PolyA selection. Sequencing was performed on the Illumina HiSeq platform generating 2x150 bp paired end reads and was conducted by Genewiz from Azenta Life Sciences.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP561364			MPNP-14hpf-R1-LCM9108_L3_R1_001.fastq.gz MPNP-14hpf-R1-LCM9108_L3_R2_001.fastq.gz	fastq fastq	11636365200.0	38787884.0	GSM8772767 r1	0:150 1:150	A:2939300419;C:2879587889;G:2900004636;T:2917376468;N:95788	150	150	2939300419	2879587889	2900004636	2917376468	95788	SRX27557931	SRS23971732	SRA2069214	University of Alabama at Birmingham	University of Alabama at Birmingham												B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2025-02-03	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
34696	34696	SRR32217630	SRX27557930	SRS23971731	SRP561364	PRJNA1218816	p21 ccng1 foxo3b and fbxw7 contribute to p53 dependent cell cycle arrest [MPNP timecross]	GSE288666	Transcriptome Analysis	p53 is a transcription factor that plays a critical role in cancer prevention. However the mechanisms by which p53 exerts its tumor suppressive function is still unclear. While PUMA/BBC3 and NOXA/PMAIP1 are known to be important in p53 dependent apoptosis and p21/CDKN1A is crucial for p53 dependent cell cycle arrest we demonstrate that zebrafish lacking puma noxa and p21 do not show a predisposition to cancer. This suggests that additional p53 transcriptional targets are sufficient for its tumor suppressive function. Contrary to the prevailing belief that p21 is the key regulator of p53 dependent cell cycle arrest we provide evidence that p53 can still induce cell cycle arrest in the absence of p21 following DNA damage or loss of mdm2 p53 activation in the absence of stress. This implies the involvement of other p53 transcriptional targets in mediating p53 dependent cell cycle arrest. Since p53 tumor suppression is conserved across multiple vertebrate species we conducted a cross species comparative analysis of p53 dependent transcriptional profiles to identify a conserved set of 136 p53 upregulated transcripts. Our analysis stresses the importance of ortholog to paralog analysis across species since in many cases the paralog but not ortholog in differing species is p53 dependent. Additionally we performed a CRISPR/Cas9 G0 “crispant” screen in a genetic background lacking mdm2 puma noxa and p21 to identify key components involved in p53 dependent cell cycle arrest. Our findings revealed that ccng1 fbxw7 and foxo3b play an important role in this process. Overall design: RNA sequencing was performed on zebrafish of un genotyped progeny from mdm2+/ ; pnp / intercrosses at various developmental stages 8 10 12 14 16 hpf as the mutant group N=50 embryos for each group referred to as MPNP. While this approach generated a dilution of RNA transcripts since only approxmiately ¼ of the embryos were mpnp / it nonetheless allowed us to glimpse at the dynamics of p53 target gene induction in mpnp / anim…		pubmed:40487439		Zebrafish PNP 12hpf 2	GSM8772766		source name:12 hpf embryos\|tissue:12 hpf embryos\|genotype:puma / ; noxa / ; p21 / \|geo loc name:missing\|collection date:missing	Zebrafish PNP 12hpf 2	Raw sequencing reads were aligned to the Danio rerio GRCz11 genome assemblies using STAR version 2.7.3a GCC 6.4.0 2.28 with default setting. Following alignment raw read counts were generated using HTSeq version 0.12.3 foss 2018b Python 3.6.6. The corresponding gene annotation files used in HTSeq were Danio rerio.GRCz11.102.chr.gtf for zebrafish samples. Differentially expressed genes DEGs were identified using DESeq2 version 1.42.1 in R version 4.3.3. Normalized counts were obtained using RSEM version 1.3.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes TPM values for each samples	12 hpf embryos		Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit QIAGEN #74134 according to the manufacturer’s instructions. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared using the Illumina RNA kit with PolyA selection. Sequencing was performed on the Illumina HiSeq platform generating 2x150 bp paired end reads and was conducted by Genewiz from Azenta Life Sciences.	The fertilization windown was set to 15 minutes. All embryos were cleaned approximately 6 hpf with approximately 30 embryos pooled in each Petri dish.	tissue:12 hpf embryos\|genotype:puma / ; noxa / ; p21 /	GSM8772766	GSM8772766: Zebrafish PNP 12hpf 2; Danio rerio; RNA Seq	GSM8772766 r1	GSM8772766	1	Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit QIAGEN #74134 according to the manufacturer's instructions. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared using the Illumina RNA kit with PolyA selection. Sequencing was performed on the Illumina HiSeq platform generating 2x150 bp paired end reads and was conducted by Genewiz from Azenta Life Sciences.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP561364			PNP-12hpf-R2_R1_001.fastq.gz PNP-12hpf-R2_R2_001.fastq.gz	fastq fastq	11432631000.0	38108770.0	GSM8772766 r1	0:150 1:150	A:3080886583;C:2644530522;G:2728628121;T:2977190031;N:1395743	150	150	3080886583	2644530522	2728628121	2977190031	1395743	SRX27557930	SRS23971731	SRA2069214	University of Alabama at Birmingham	University of Alabama at Birmingham												B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2025-02-03	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
34697	34697	SRR32217631	SRX27557929	SRS23971730	SRP561364	PRJNA1218816	p21 ccng1 foxo3b and fbxw7 contribute to p53 dependent cell cycle arrest [MPNP timecross]	GSE288666	Transcriptome Analysis	p53 is a transcription factor that plays a critical role in cancer prevention. However the mechanisms by which p53 exerts its tumor suppressive function is still unclear. While PUMA/BBC3 and NOXA/PMAIP1 are known to be important in p53 dependent apoptosis and p21/CDKN1A is crucial for p53 dependent cell cycle arrest we demonstrate that zebrafish lacking puma noxa and p21 do not show a predisposition to cancer. This suggests that additional p53 transcriptional targets are sufficient for its tumor suppressive function. Contrary to the prevailing belief that p21 is the key regulator of p53 dependent cell cycle arrest we provide evidence that p53 can still induce cell cycle arrest in the absence of p21 following DNA damage or loss of mdm2 p53 activation in the absence of stress. This implies the involvement of other p53 transcriptional targets in mediating p53 dependent cell cycle arrest. Since p53 tumor suppression is conserved across multiple vertebrate species we conducted a cross species comparative analysis of p53 dependent transcriptional profiles to identify a conserved set of 136 p53 upregulated transcripts. Our analysis stresses the importance of ortholog to paralog analysis across species since in many cases the paralog but not ortholog in differing species is p53 dependent. Additionally we performed a CRISPR/Cas9 G0 “crispant” screen in a genetic background lacking mdm2 puma noxa and p21 to identify key components involved in p53 dependent cell cycle arrest. Our findings revealed that ccng1 fbxw7 and foxo3b play an important role in this process. Overall design: RNA sequencing was performed on zebrafish of un genotyped progeny from mdm2+/ ; pnp / intercrosses at various developmental stages 8 10 12 14 16 hpf as the mutant group N=50 embryos for each group referred to as MPNP. While this approach generated a dilution of RNA transcripts since only approxmiately ¼ of the embryos were mpnp / it nonetheless allowed us to glimpse at the dynamics of p53 target gene induction in mpnp / anim…		pubmed:40487439		Zebrafish PNP 12hpf 1	GSM8772765		source name:12 hpf embryos\|tissue:12 hpf embryos\|genotype:puma / ; noxa / ; p21 / \|geo loc name:missing\|collection date:missing	Zebrafish PNP 12hpf 1	Raw sequencing reads were aligned to the Danio rerio GRCz11 genome assemblies using STAR version 2.7.3a GCC 6.4.0 2.28 with default setting. Following alignment raw read counts were generated using HTSeq version 0.12.3 foss 2018b Python 3.6.6. The corresponding gene annotation files used in HTSeq were Danio rerio.GRCz11.102.chr.gtf for zebrafish samples. Differentially expressed genes DEGs were identified using DESeq2 version 1.42.1 in R version 4.3.3. Normalized counts were obtained using RSEM version 1.3.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes TPM values for each samples	12 hpf embryos		Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit QIAGEN #74134 according to the manufacturer’s instructions. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared using the Illumina RNA kit with PolyA selection. Sequencing was performed on the Illumina HiSeq platform generating 2x150 bp paired end reads and was conducted by Genewiz from Azenta Life Sciences.	The fertilization windown was set to 15 minutes. All embryos were cleaned approximately 6 hpf with approximately 30 embryos pooled in each Petri dish.	tissue:12 hpf embryos\|genotype:puma / ; noxa / ; p21 /	GSM8772765	GSM8772765: Zebrafish PNP 12hpf 1; Danio rerio; RNA Seq	GSM8772765 r1	GSM8772765	1	Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit QIAGEN #74134 according to the manufacturer's instructions. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared using the Illumina RNA kit with PolyA selection. Sequencing was performed on the Illumina HiSeq platform generating 2x150 bp paired end reads and was conducted by Genewiz from Azenta Life Sciences.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP561364			PNP-12hpf-R1-LCM9107_L3_R1_001.fastq.gz PNP-12hpf-R1-LCM9107_L3_R2_001.fastq.gz	fastq fastq	10479699900.0	34932333.0	GSM8772765 r1	0:150 1:150	A:2633044362;C:2608423365;G:2628903024;T:2609268781;N:60368	150	150	2633044362	2608423365	2628903024	2609268781	60368	SRX27557929	SRS23971730	SRA2069214	University of Alabama at Birmingham	University of Alabama at Birmingham												B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2025-02-03	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
34698	34698	SRR32217632	SRX27557928	SRS23971729	SRP561364	PRJNA1218816	p21 ccng1 foxo3b and fbxw7 contribute to p53 dependent cell cycle arrest [MPNP timecross]	GSE288666	Transcriptome Analysis	p53 is a transcription factor that plays a critical role in cancer prevention. However the mechanisms by which p53 exerts its tumor suppressive function is still unclear. While PUMA/BBC3 and NOXA/PMAIP1 are known to be important in p53 dependent apoptosis and p21/CDKN1A is crucial for p53 dependent cell cycle arrest we demonstrate that zebrafish lacking puma noxa and p21 do not show a predisposition to cancer. This suggests that additional p53 transcriptional targets are sufficient for its tumor suppressive function. Contrary to the prevailing belief that p21 is the key regulator of p53 dependent cell cycle arrest we provide evidence that p53 can still induce cell cycle arrest in the absence of p21 following DNA damage or loss of mdm2 p53 activation in the absence of stress. This implies the involvement of other p53 transcriptional targets in mediating p53 dependent cell cycle arrest. Since p53 tumor suppression is conserved across multiple vertebrate species we conducted a cross species comparative analysis of p53 dependent transcriptional profiles to identify a conserved set of 136 p53 upregulated transcripts. Our analysis stresses the importance of ortholog to paralog analysis across species since in many cases the paralog but not ortholog in differing species is p53 dependent. Additionally we performed a CRISPR/Cas9 G0 “crispant” screen in a genetic background lacking mdm2 puma noxa and p21 to identify key components involved in p53 dependent cell cycle arrest. Our findings revealed that ccng1 fbxw7 and foxo3b play an important role in this process. Overall design: RNA sequencing was performed on zebrafish of un genotyped progeny from mdm2+/ ; pnp / intercrosses at various developmental stages 8 10 12 14 16 hpf as the mutant group N=50 embryos for each group referred to as MPNP. While this approach generated a dilution of RNA transcripts since only approxmiately ¼ of the embryos were mpnp / it nonetheless allowed us to glimpse at the dynamics of p53 target gene induction in mpnp / anim…		pubmed:40487439		Zebrafish MPNP 12hpf 2	GSM8772764		source name:12 hpf embryos\|tissue:12 hpf embryos\|genotype:mdm2 / or mdm2+/+ mdm2+/ ; puma / ; noxa / ; p21 / \|geo loc name:missing\|collection date:missing	Zebrafish MPNP 12hpf 2	Raw sequencing reads were aligned to the Danio rerio GRCz11 genome assemblies using STAR version 2.7.3a GCC 6.4.0 2.28 with default setting. Following alignment raw read counts were generated using HTSeq version 0.12.3 foss 2018b Python 3.6.6. The corresponding gene annotation files used in HTSeq were Danio rerio.GRCz11.102.chr.gtf for zebrafish samples. Differentially expressed genes DEGs were identified using DESeq2 version 1.42.1 in R version 4.3.3. Normalized counts were obtained using RSEM version 1.3.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes TPM values for each samples	12 hpf embryos		Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit QIAGEN #74134 according to the manufacturer’s instructions. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared using the Illumina RNA kit with PolyA selection. Sequencing was performed on the Illumina HiSeq platform generating 2x150 bp paired end reads and was conducted by Genewiz from Azenta Life Sciences.	The fertilization windown was set to 15 minutes. All embryos were cleaned approximately 6 hpf with approximately 30 embryos pooled in each Petri dish.	tissue:12 hpf embryos\|genotype:mdm2 / or mdm2+/+ mdm2+/ ; puma / ; noxa / ; p21 /	GSM8772764	GSM8772764: Zebrafish MPNP 12hpf 2; Danio rerio; RNA Seq	GSM8772764 r1	GSM8772764	1	Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit QIAGEN #74134 according to the manufacturer's instructions. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared using the Illumina RNA kit with PolyA selection. Sequencing was performed on the Illumina HiSeq platform generating 2x150 bp paired end reads and was conducted by Genewiz from Azenta Life Sciences.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP561364			MPNP-12hpf-R2_R1_001.fastq.gz MPNP-12hpf-R2_R2_001.fastq.gz	fastq fastq	13955378700.0	46517929.0	GSM8772764 r1	0:150 1:150	A:3763427959;C:3222562735;G:3362175176;T:3605511213;N:1701617	150	150	3763427959	3222562735	3362175176	3605511213	1701617	SRX27557928	SRS23971729	SRA2069214	University of Alabama at Birmingham	University of Alabama at Birmingham												B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2025-02-03	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
34699	34699	SRR32217633	SRX27557927	SRS23971728	SRP561364	PRJNA1218816	p21 ccng1 foxo3b and fbxw7 contribute to p53 dependent cell cycle arrest [MPNP timecross]	GSE288666	Transcriptome Analysis	p53 is a transcription factor that plays a critical role in cancer prevention. However the mechanisms by which p53 exerts its tumor suppressive function is still unclear. While PUMA/BBC3 and NOXA/PMAIP1 are known to be important in p53 dependent apoptosis and p21/CDKN1A is crucial for p53 dependent cell cycle arrest we demonstrate that zebrafish lacking puma noxa and p21 do not show a predisposition to cancer. This suggests that additional p53 transcriptional targets are sufficient for its tumor suppressive function. Contrary to the prevailing belief that p21 is the key regulator of p53 dependent cell cycle arrest we provide evidence that p53 can still induce cell cycle arrest in the absence of p21 following DNA damage or loss of mdm2 p53 activation in the absence of stress. This implies the involvement of other p53 transcriptional targets in mediating p53 dependent cell cycle arrest. Since p53 tumor suppression is conserved across multiple vertebrate species we conducted a cross species comparative analysis of p53 dependent transcriptional profiles to identify a conserved set of 136 p53 upregulated transcripts. Our analysis stresses the importance of ortholog to paralog analysis across species since in many cases the paralog but not ortholog in differing species is p53 dependent. Additionally we performed a CRISPR/Cas9 G0 “crispant” screen in a genetic background lacking mdm2 puma noxa and p21 to identify key components involved in p53 dependent cell cycle arrest. Our findings revealed that ccng1 fbxw7 and foxo3b play an important role in this process. Overall design: RNA sequencing was performed on zebrafish of un genotyped progeny from mdm2+/ ; pnp / intercrosses at various developmental stages 8 10 12 14 16 hpf as the mutant group N=50 embryos for each group referred to as MPNP. While this approach generated a dilution of RNA transcripts since only approxmiately ¼ of the embryos were mpnp / it nonetheless allowed us to glimpse at the dynamics of p53 target gene induction in mpnp / anim…		pubmed:40487439		Zebrafish MPNP 12hpf 1	GSM8772763		source name:12 hpf embryos\|tissue:12 hpf embryos\|genotype:mdm2 / or mdm2+/+ mdm2+/ ; puma / ; noxa / ; p21 / \|geo loc name:missing\|collection date:missing	Zebrafish MPNP 12hpf 1	Raw sequencing reads were aligned to the Danio rerio GRCz11 genome assemblies using STAR version 2.7.3a GCC 6.4.0 2.28 with default setting. Following alignment raw read counts were generated using HTSeq version 0.12.3 foss 2018b Python 3.6.6. The corresponding gene annotation files used in HTSeq were Danio rerio.GRCz11.102.chr.gtf for zebrafish samples. Differentially expressed genes DEGs were identified using DESeq2 version 1.42.1 in R version 4.3.3. Normalized counts were obtained using RSEM version 1.3.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes TPM values for each samples	12 hpf embryos		Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit QIAGEN #74134 according to the manufacturer’s instructions. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared using the Illumina RNA kit with PolyA selection. Sequencing was performed on the Illumina HiSeq platform generating 2x150 bp paired end reads and was conducted by Genewiz from Azenta Life Sciences.	The fertilization windown was set to 15 minutes. All embryos were cleaned approximately 6 hpf with approximately 30 embryos pooled in each Petri dish.	tissue:12 hpf embryos\|genotype:mdm2 / or mdm2+/+ mdm2+/ ; puma / ; noxa / ; p21 /	GSM8772763	GSM8772763: Zebrafish MPNP 12hpf 1; Danio rerio; RNA Seq	GSM8772763 r1	GSM8772763	1	Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit QIAGEN #74134 according to the manufacturer's instructions. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared using the Illumina RNA kit with PolyA selection. Sequencing was performed on the Illumina HiSeq platform generating 2x150 bp paired end reads and was conducted by Genewiz from Azenta Life Sciences.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP561364			MPNP-12hpf-R1-LCM9106_L3_R1_001.fastq.gz MPNP-12hpf-R1-LCM9106_L3_R2_001.fastq.gz	fastq fastq	10563368700.0	35211229.0	GSM8772763 r1	0:150 1:150	A:2677547502;C:2602743506;G:2625615434;T:2657374696;N:87562	150	150	2677547502	2602743506	2625615434	2657374696	87562	SRX27557927	SRS23971728	SRA2069214	University of Alabama at Birmingham	University of Alabama at Birmingham												B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2025-02-03	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
34708	34708	SRR32217642	SRX27557942	SRS23971743	SRP561365	PRJNA1218818	p21 ccng1 foxo3b and fbxw7 contribute to p53 dependent cell cycle arrest [MPNP 18hpf]	GSE288667	Transcriptome Analysis	p53 is a transcription factor that plays a critical role in cancer prevention. However the mechanisms by which p53 exerts its tumor suppressive function is still unclear. While PUMA/BBC3 and NOXA/PMAIP1 are known to be important in p53 dependent apoptosis and p21/CDKN1A is crucial for p53 dependent cell cycle arrest we demonstrate that zebrafish lacking puma noxa and p21 do not show a predisposition to cancer. This suggests that additional p53 transcriptional targets are sufficient for its tumor suppressive function. Contrary to the prevailing belief that p21 is the key regulator of p53 dependent cell cycle arrest we provide evidence that p53 can still induce cell cycle arrest in the absence of p21 following DNA damage or loss of mdm2 p53 activation in the absence of stress. This implies the involvement of other p53 transcriptional targets in mediating p53 dependent cell cycle arrest. Since p53 tumor suppression is conserved across multiple vertebrate species we conducted a cross species comparative analysis of p53 dependent transcriptional profiles to identify a conserved set of 136 p53 upregulated transcripts. Our analysis stresses the importance of ortholog to paralog analysis across species since in many cases the paralog but not ortholog in differing species is p53 dependent. Additionally we performed a CRISPR/Cas9 G0 “crispant” screen in a genetic background lacking mdm2 puma noxa and p21 to identify key components involved in p53 dependent cell cycle arrest. Our findings revealed that ccng1 fbxw7 and foxo3b play an important role in this process. Overall design: RNA sequencing was performed on zebrafish quadruple knockouts of mdm2 puma noxa and p21 at 18 hpf Sibling controls from the same batch including mdm2+/ or mdm2+/+; puma / ; noxa / ; and p21 / embryos were also harvested to extract RNA for comparison.		pubmed:40487439		Zebrafish Normal PNP 18hpf 2	GSM8772778		source name:30 hpf embryos\|tissue:30 hpf embryos\|genotype:mdm2+/ or mdm2+/+; puma / ; noxa / ; p21 / \|geo loc name:missing\|collection date:missing	Zebrafish Normal PNP 18hpf 2	Raw sequencing reads were aligned to the Danio rerio GRCz11 genome assemblies using STAR version 2.7.3a GCC 6.4.0 2.28 with default setting. Following alignment raw read counts were generated using HTSeq version 0.12.3 foss 2018b Python 3.6.6. The corresponding gene annotation files used in HTSeq were Danio rerio.GRCz11.102.chr.gtf for zebrafish samples. Differentially expressed genes DEGs were identified using DESeq2 version 1.42.1 in R version 4.3.3. Normalized counts were obtained using RSEM version 1.3.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes TPM values for each samples	30 hpf embryos		Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit QIAGEN #74134 according to the manufacturer’s instructions. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared using the Illumina RNA kit with PolyA selection. Sequencing was performed on the Illumina HiSeq platform generating 2x150 bp paired end reads and was conducted by Genewiz from Azenta Life Sciences.	The fertilization windown was set to 15 minutes. All embryos were cleaned approximately 6 hpf with approximately 30 embryos pooled in each Petri dish.	tissue:30 hpf embryos\|genotype:mdm2+/ or mdm2+/+; puma / ; noxa / ; p21 /	GSM8772778	GSM8772778: Zebrafish Normal PNP 18hpf 2; Danio rerio; RNA Seq	GSM8772778 r1	GSM8772778	1	Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit QIAGEN #74134 according to the manufacturer's instructions. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared using the Illumina RNA kit with PolyA selection. Sequencing was performed on the Illumina HiSeq platform generating 2x150 bp paired end reads and was conducted by Genewiz from Azenta Life Sciences.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP561365			PNP-18hpf-R2-LCM9117_L3_R1_001 PNP-18hpf-R2-LCM9117_L3_R2_001	fastq fastq	11448228300.0	38160761.0	GSM8772778 r1	0:150 1:150	A:2869273191;C:2853873509;G:2871650417;T:2853336221;N:94962	150	150	2869273191	2853873509	2871650417	2853336221	94962	SRX27557942	SRS23971743	SRA2069215	University of Alabama at Birmingham	University of Alabama at Birmingham												B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2025-02-03	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
34709	34709	SRR32217643	SRX27557941	SRS23971742	SRP561365	PRJNA1218818	p21 ccng1 foxo3b and fbxw7 contribute to p53 dependent cell cycle arrest [MPNP 18hpf]	GSE288667	Transcriptome Analysis	p53 is a transcription factor that plays a critical role in cancer prevention. However the mechanisms by which p53 exerts its tumor suppressive function is still unclear. While PUMA/BBC3 and NOXA/PMAIP1 are known to be important in p53 dependent apoptosis and p21/CDKN1A is crucial for p53 dependent cell cycle arrest we demonstrate that zebrafish lacking puma noxa and p21 do not show a predisposition to cancer. This suggests that additional p53 transcriptional targets are sufficient for its tumor suppressive function. Contrary to the prevailing belief that p21 is the key regulator of p53 dependent cell cycle arrest we provide evidence that p53 can still induce cell cycle arrest in the absence of p21 following DNA damage or loss of mdm2 p53 activation in the absence of stress. This implies the involvement of other p53 transcriptional targets in mediating p53 dependent cell cycle arrest. Since p53 tumor suppression is conserved across multiple vertebrate species we conducted a cross species comparative analysis of p53 dependent transcriptional profiles to identify a conserved set of 136 p53 upregulated transcripts. Our analysis stresses the importance of ortholog to paralog analysis across species since in many cases the paralog but not ortholog in differing species is p53 dependent. Additionally we performed a CRISPR/Cas9 G0 “crispant” screen in a genetic background lacking mdm2 puma noxa and p21 to identify key components involved in p53 dependent cell cycle arrest. Our findings revealed that ccng1 fbxw7 and foxo3b play an important role in this process. Overall design: RNA sequencing was performed on zebrafish quadruple knockouts of mdm2 puma noxa and p21 at 18 hpf Sibling controls from the same batch including mdm2+/ or mdm2+/+; puma / ; noxa / ; and p21 / embryos were also harvested to extract RNA for comparison.		pubmed:40487439		Zebrafish Normal PNP 18hpf 1	GSM8772777		source name:30 hpf embryos\|tissue:30 hpf embryos\|genotype:mdm2+/ or mdm2+/+; puma / ; noxa / ; p21 / \|geo loc name:missing\|collection date:missing	Zebrafish Normal PNP 18hpf 1	Raw sequencing reads were aligned to the Danio rerio GRCz11 genome assemblies using STAR version 2.7.3a GCC 6.4.0 2.28 with default setting. Following alignment raw read counts were generated using HTSeq version 0.12.3 foss 2018b Python 3.6.6. The corresponding gene annotation files used in HTSeq were Danio rerio.GRCz11.102.chr.gtf for zebrafish samples. Differentially expressed genes DEGs were identified using DESeq2 version 1.42.1 in R version 4.3.3. Normalized counts were obtained using RSEM version 1.3.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes TPM values for each samples	30 hpf embryos		Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit QIAGEN #74134 according to the manufacturer’s instructions. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared using the Illumina RNA kit with PolyA selection. Sequencing was performed on the Illumina HiSeq platform generating 2x150 bp paired end reads and was conducted by Genewiz from Azenta Life Sciences.	The fertilization windown was set to 15 minutes. All embryos were cleaned approximately 6 hpf with approximately 30 embryos pooled in each Petri dish.	tissue:30 hpf embryos\|genotype:mdm2+/ or mdm2+/+; puma / ; noxa / ; p21 /	GSM8772777	GSM8772777: Zebrafish Normal PNP 18hpf 1; Danio rerio; RNA Seq	GSM8772777 r1	GSM8772777	1	Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit QIAGEN #74134 according to the manufacturer's instructions. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared using the Illumina RNA kit with PolyA selection. Sequencing was performed on the Illumina HiSeq platform generating 2x150 bp paired end reads and was conducted by Genewiz from Azenta Life Sciences.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP561365			PNP-18hpf-R1-LCM9116_L3_R1_001 PNP-18hpf-R1-LCM9116_L3_R2_001	fastq fastq	10028796900.0	33429323.0	GSM8772777 r1	0:150 1:150	A:2522600143;C:2493920962;G:2504259374;T:2507933554;N:82867	150	150	2522600143	2493920962	2504259374	2507933554	82867	SRX27557941	SRS23971742	SRA2069215	University of Alabama at Birmingham	University of Alabama at Birmingham												B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2025-02-03	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
34710	34710	SRR32217644	SRX27557940	SRS23971741	SRP561365	PRJNA1218818	p21 ccng1 foxo3b and fbxw7 contribute to p53 dependent cell cycle arrest [MPNP 18hpf]	GSE288667	Transcriptome Analysis	p53 is a transcription factor that plays a critical role in cancer prevention. However the mechanisms by which p53 exerts its tumor suppressive function is still unclear. While PUMA/BBC3 and NOXA/PMAIP1 are known to be important in p53 dependent apoptosis and p21/CDKN1A is crucial for p53 dependent cell cycle arrest we demonstrate that zebrafish lacking puma noxa and p21 do not show a predisposition to cancer. This suggests that additional p53 transcriptional targets are sufficient for its tumor suppressive function. Contrary to the prevailing belief that p21 is the key regulator of p53 dependent cell cycle arrest we provide evidence that p53 can still induce cell cycle arrest in the absence of p21 following DNA damage or loss of mdm2 p53 activation in the absence of stress. This implies the involvement of other p53 transcriptional targets in mediating p53 dependent cell cycle arrest. Since p53 tumor suppression is conserved across multiple vertebrate species we conducted a cross species comparative analysis of p53 dependent transcriptional profiles to identify a conserved set of 136 p53 upregulated transcripts. Our analysis stresses the importance of ortholog to paralog analysis across species since in many cases the paralog but not ortholog in differing species is p53 dependent. Additionally we performed a CRISPR/Cas9 G0 “crispant” screen in a genetic background lacking mdm2 puma noxa and p21 to identify key components involved in p53 dependent cell cycle arrest. Our findings revealed that ccng1 fbxw7 and foxo3b play an important role in this process. Overall design: RNA sequencing was performed on zebrafish quadruple knockouts of mdm2 puma noxa and p21 at 18 hpf Sibling controls from the same batch including mdm2+/ or mdm2+/+; puma / ; noxa / ; and p21 / embryos were also harvested to extract RNA for comparison.		pubmed:40487439		Zebrafish Abnormal MPNP 18hpf 2	GSM8772776		source name:30 hpf embryos\|tissue:30 hpf embryos\|genotype:mdm2 / ; puma / ; noxa / ; p21 / \|geo loc name:missing\|collection date:missing	Zebrafish Abnormal MPNP 18hpf 2	Raw sequencing reads were aligned to the Danio rerio GRCz11 genome assemblies using STAR version 2.7.3a GCC 6.4.0 2.28 with default setting. Following alignment raw read counts were generated using HTSeq version 0.12.3 foss 2018b Python 3.6.6. The corresponding gene annotation files used in HTSeq were Danio rerio.GRCz11.102.chr.gtf for zebrafish samples. Differentially expressed genes DEGs were identified using DESeq2 version 1.42.1 in R version 4.3.3. Normalized counts were obtained using RSEM version 1.3.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes TPM values for each samples	30 hpf embryos		Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit QIAGEN #74134 according to the manufacturer’s instructions. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared using the Illumina RNA kit with PolyA selection. Sequencing was performed on the Illumina HiSeq platform generating 2x150 bp paired end reads and was conducted by Genewiz from Azenta Life Sciences.	The fertilization windown was set to 15 minutes. All embryos were cleaned approximately 6 hpf with approximately 30 embryos pooled in each Petri dish.	tissue:30 hpf embryos\|genotype:mdm2 / ; puma / ; noxa / ; p21 /	GSM8772776	GSM8772776: Zebrafish Abnormal MPNP 18hpf 2; Danio rerio; RNA Seq	GSM8772776 r1	GSM8772776	1	Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit QIAGEN #74134 according to the manufacturer's instructions. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared using the Illumina RNA kit with PolyA selection. Sequencing was performed on the Illumina HiSeq platform generating 2x150 bp paired end reads and was conducted by Genewiz from Azenta Life Sciences.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP561365			MPNP-Abnor-18hpf-R2-LCM9115_L3_R1_001 MPNP-Abnor-18hpf-R2-LCM9115_L3_R2_001	fastq fastq	9458944500.0	31529815.0	GSM8772776 r1	0:150 1:150	A:2402362356;C:2327441574;G:2341949851;T:2387110941;N:79778	150	150	2402362356	2327441574	2341949851	2387110941	79778	SRX27557940	SRS23971741	SRA2069215	University of Alabama at Birmingham	University of Alabama at Birmingham												B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2025-02-03	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
34711	34711	SRR32217645	SRX27557939	SRS23971740	SRP561365	PRJNA1218818	p21 ccng1 foxo3b and fbxw7 contribute to p53 dependent cell cycle arrest [MPNP 18hpf]	GSE288667	Transcriptome Analysis	p53 is a transcription factor that plays a critical role in cancer prevention. However the mechanisms by which p53 exerts its tumor suppressive function is still unclear. While PUMA/BBC3 and NOXA/PMAIP1 are known to be important in p53 dependent apoptosis and p21/CDKN1A is crucial for p53 dependent cell cycle arrest we demonstrate that zebrafish lacking puma noxa and p21 do not show a predisposition to cancer. This suggests that additional p53 transcriptional targets are sufficient for its tumor suppressive function. Contrary to the prevailing belief that p21 is the key regulator of p53 dependent cell cycle arrest we provide evidence that p53 can still induce cell cycle arrest in the absence of p21 following DNA damage or loss of mdm2 p53 activation in the absence of stress. This implies the involvement of other p53 transcriptional targets in mediating p53 dependent cell cycle arrest. Since p53 tumor suppression is conserved across multiple vertebrate species we conducted a cross species comparative analysis of p53 dependent transcriptional profiles to identify a conserved set of 136 p53 upregulated transcripts. Our analysis stresses the importance of ortholog to paralog analysis across species since in many cases the paralog but not ortholog in differing species is p53 dependent. Additionally we performed a CRISPR/Cas9 G0 “crispant” screen in a genetic background lacking mdm2 puma noxa and p21 to identify key components involved in p53 dependent cell cycle arrest. Our findings revealed that ccng1 fbxw7 and foxo3b play an important role in this process. Overall design: RNA sequencing was performed on zebrafish quadruple knockouts of mdm2 puma noxa and p21 at 18 hpf Sibling controls from the same batch including mdm2+/ or mdm2+/+; puma / ; noxa / ; and p21 / embryos were also harvested to extract RNA for comparison.		pubmed:40487439		Zebrafish Abnormal MPNP 18hpf 1	GSM8772775		source name:30 hpf embryos\|tissue:30 hpf embryos\|genotype:mdm2 / ; puma / ; noxa / ; p21 / \|geo loc name:missing\|collection date:missing	Zebrafish Abnormal MPNP 18hpf 1	Raw sequencing reads were aligned to the Danio rerio GRCz11 genome assemblies using STAR version 2.7.3a GCC 6.4.0 2.28 with default setting. Following alignment raw read counts were generated using HTSeq version 0.12.3 foss 2018b Python 3.6.6. The corresponding gene annotation files used in HTSeq were Danio rerio.GRCz11.102.chr.gtf for zebrafish samples. Differentially expressed genes DEGs were identified using DESeq2 version 1.42.1 in R version 4.3.3. Normalized counts were obtained using RSEM version 1.3.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes TPM values for each samples	30 hpf embryos		Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit QIAGEN #74134 according to the manufacturer’s instructions. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared using the Illumina RNA kit with PolyA selection. Sequencing was performed on the Illumina HiSeq platform generating 2x150 bp paired end reads and was conducted by Genewiz from Azenta Life Sciences.	The fertilization windown was set to 15 minutes. All embryos were cleaned approximately 6 hpf with approximately 30 embryos pooled in each Petri dish.	tissue:30 hpf embryos\|genotype:mdm2 / ; puma / ; noxa / ; p21 /	GSM8772775	GSM8772775: Zebrafish Abnormal MPNP 18hpf 1; Danio rerio; RNA Seq	GSM8772775 r1	GSM8772775	1	Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit QIAGEN #74134 according to the manufacturer's instructions. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared using the Illumina RNA kit with PolyA selection. Sequencing was performed on the Illumina HiSeq platform generating 2x150 bp paired end reads and was conducted by Genewiz from Azenta Life Sciences.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP561365			MPNP-Abnor-18hpf-R1-LCM9114_L3_R1_001 MPNP-Abnor-18hpf-R1-LCM9114_L3_R2_001	fastq fastq	10085728800.0	33619096.0	GSM8772775 r1	0:150 1:150	A:2514952200;C:2527390008;G:2540349801;T:2502952120;N:84671	150	150	2514952200	2527390008	2540349801	2502952120	84671	SRX27557939	SRS23971740	SRA2069215	University of Alabama at Birmingham	University of Alabama at Birmingham												B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2025-02-03	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
35389	35389	SRR32737834	SRX28024098	SRS24385653	SRP570947	PRJNA1237347	Developmental opioid exposure results in lasting transcriptome alterations in zebrafish Danio rerio embryos	GSE292183	Transcriptome Analysis	The opioid epidemic has introduced significant public health challenges with little knowledge regarding the consequences of opioid exposure during embryonic development. While neurobehavioral effects of developmental opioid exposure are well documented early effects of exposure remain largely unexplored. We investigated the effects of oxycodone and fentanyl exposure on gene expression in zebrafish Danio rerio embryos using whole embryo RNA sequencing. Embryos were exposed to environmentally relevant Oxycodone HCl 10.6pg/mL and Fentanyl Citrate 0.629pg/mL and therapeutically relevant Oxycodone HCl 35.14ng/mL and Fentanyl Citrate 3.14ng/mL from 2 hpf to 24 hpf followed by another 24hrs of opioid free development. RNA sequencing at 48hpf revealed dose and drug specific gene expression changes. Lower doses of oxycodone and fentanyl both induced more differentially expressed genes DEGs than higher doses potentially indicative of opioid receptor desensitization occurring at higher concentrations. In total 892 DEGs were identified across all conditions indicating continued differential gene expression well post cessation of opioid exposure. Gene ontology analysis revealed changes in gene expression relating to extracellular matrix ECM organization cell adhesion and visual and nervous system formation. Key pathways include axon guidance synapse formation and ECM biosynthesis/remodeling all of which have potential implications on neural connectivity and sensory development. These findings demonstrate that developmental exposure to opioids induced persistent transcriptomic changes which may have lasting implications for structural integrity and function in vertebrate nervous systems providing insights into the molecular mechanisms of opioid induced alterations during development. Overall design: Zebrafish embryos were exposed to one of the following conditions: fentanyl effluent FE; 0.629 pg/mL fentanyl therapeutic FT; 3.14 ng/mL oxycodone effluent OE; 10.6 pg/mL and oxycodone therapeutic OT; 35.14 ng/mL. Opioi…		pubmed:40429979		replicate 5 oxycod1 therapeutic exposed 0 24hpf total RNA at xxx hpf	GSM8851836		source name:Total embryo 50 embryo homogenate\|tissue:Total embryo 50 embryo homogenate\|genotype:WT\|treatment:35.14ng/mL oxycod1\|batch:3/25/2024\|geo loc name:missing\|collection date:missing	replicate 5 oxycod1 therapeutic exposed 0 24hpf total RNA at xxx hpf	Sequenced by NovaGene via Novaseq X Plus Platform paired end reads Raw reads are available as the fq.gz files Trimmed via trimmomatic and ran through rCorrector then mapped to GRCz11 ensemble constructed reference library via Salmon. The aggregated count matrixes for each condition are availible as the txt files Assembly: These are raw reads from Novaseq X plus seqeuncing and count matrixes as txt files Supplementary files format and content: txt files of aggregated count matrixes see above Supplementary files format and content: the counts derived from Salmon	Total embryo 50 embryo homogenate	one of the following conditions: fentanyl effluent FE; 0.629 pg/mL fentanyl therapeutic FT; 3.14 ng/mL oxycodone effluent OE; 10.6 pg/mL oxycodone therapeutic OT; 35.14 ng/mL Control. Opioid exposed embryos were exposed from xxx ttwo xxx hpf. At 24 hpf embryos were washed to remove opioids and allowed to develop normally until 48 hpf.	Trizol Chloroform extraction of total RNA followed by Dnase I treatment and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003	zebrafish embryos were maintained in 0.3x Danieau solution at 28.5C	tissue:Total embryo 50 embryo homogenate\|genotype:WT\|treatment:35.14ng/mL oxycod1\|batch:3/25/2024	GSM8851836	GSM8851836: replicate 5 oxycod1 therapeutic exposed 0 24hpf total RNA at xxx hpf; Danio rerio; RNA Seq	GSM8851836 r1	GSM8851836	1	Trizol Chloroform extraction of total RNA followed by Dnase I treatment and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq X Plus	SRP570947			R7OT_CKDL240008774-1A_22KFGHLT3_L3_1.fq.gz R7OT_CKDL240008774-1A_22KFGHLT3_L3_2.fq.gz	fastq fastq	18969663600.0	63232212.0	GSM8851836 r1	0:150 1:150	A:5368170604;C:4078596357;G:4113230716;T:5408149968;N:1515955	150	150	5368170604	4078596357	4113230716	5408149968	1515955	SRX28024098	SRS24385653	SRA2094947	Merzdorf, MCB, Montana State University	Merzdorf, MCB, Montana State University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	bulk	bulk	United States	2025-03-17	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
35390	35390	SRR32737835	SRX28024097	SRS24385650	SRP570947	PRJNA1237347	Developmental opioid exposure results in lasting transcriptome alterations in zebrafish Danio rerio embryos	GSE292183	Transcriptome Analysis	The opioid epidemic has introduced significant public health challenges with little knowledge regarding the consequences of opioid exposure during embryonic development. While neurobehavioral effects of developmental opioid exposure are well documented early effects of exposure remain largely unexplored. We investigated the effects of oxycodone and fentanyl exposure on gene expression in zebrafish Danio rerio embryos using whole embryo RNA sequencing. Embryos were exposed to environmentally relevant Oxycodone HCl 10.6pg/mL and Fentanyl Citrate 0.629pg/mL and therapeutically relevant Oxycodone HCl 35.14ng/mL and Fentanyl Citrate 3.14ng/mL from 2 hpf to 24 hpf followed by another 24hrs of opioid free development. RNA sequencing at 48hpf revealed dose and drug specific gene expression changes. Lower doses of oxycodone and fentanyl both induced more differentially expressed genes DEGs than higher doses potentially indicative of opioid receptor desensitization occurring at higher concentrations. In total 892 DEGs were identified across all conditions indicating continued differential gene expression well post cessation of opioid exposure. Gene ontology analysis revealed changes in gene expression relating to extracellular matrix ECM organization cell adhesion and visual and nervous system formation. Key pathways include axon guidance synapse formation and ECM biosynthesis/remodeling all of which have potential implications on neural connectivity and sensory development. These findings demonstrate that developmental exposure to opioids induced persistent transcriptomic changes which may have lasting implications for structural integrity and function in vertebrate nervous systems providing insights into the molecular mechanisms of opioid induced alterations during development. Overall design: Zebrafish embryos were exposed to one of the following conditions: fentanyl effluent FE; 0.629 pg/mL fentanyl therapeutic FT; 3.14 ng/mL oxycodone effluent OE; 10.6 pg/mL and oxycodone therapeutic OT; 35.14 ng/mL. Opioi…		pubmed:40429979		replicate 4 oxycod1 therapeutic exposed 0 24hpf total RNA at xxx hpf	GSM8851835		source name:Total embryo 50 embryo homogenate\|tissue:Total embryo 50 embryo homogenate\|genotype:WT\|treatment:35.14ng/mL oxycod1\|batch:3/25/2024\|geo loc name:missing\|collection date:missing	replicate 4 oxycod1 therapeutic exposed 0 24hpf total RNA at xxx hpf	Sequenced by NovaGene via Novaseq X Plus Platform paired end reads Raw reads are available as the fq.gz files Trimmed via trimmomatic and ran through rCorrector then mapped to GRCz11 ensemble constructed reference library via Salmon. The aggregated count matrixes for each condition are availible as the txt files Assembly: These are raw reads from Novaseq X plus seqeuncing and count matrixes as txt files Supplementary files format and content: txt files of aggregated count matrixes see above Supplementary files format and content: the counts derived from Salmon	Total embryo 50 embryo homogenate	one of the following conditions: fentanyl effluent FE; 0.629 pg/mL fentanyl therapeutic FT; 3.14 ng/mL oxycodone effluent OE; 10.6 pg/mL oxycodone therapeutic OT; 35.14 ng/mL Control. Opioid exposed embryos were exposed from xxx ttwo xxx hpf. At 24 hpf embryos were washed to remove opioids and allowed to develop normally until 48 hpf.	Trizol Chloroform extraction of total RNA followed by Dnase I treatment and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003	zebrafish embryos were maintained in 0.3x Danieau solution at 28.5C	tissue:Total embryo 50 embryo homogenate\|genotype:WT\|treatment:35.14ng/mL oxycod1\|batch:3/25/2024	GSM8851835	GSM8851835: replicate 4 oxycod1 therapeutic exposed 0 24hpf total RNA at xxx hpf; Danio rerio; RNA Seq	GSM8851835 r1	GSM8851835	1	Trizol Chloroform extraction of total RNA followed by Dnase I treatment and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq X Plus	SRP570947			R5OT_CKDL240008774-1A_22KFGHLT3_L3_1.fq.gz R5OT_CKDL240008774-1A_22KFGHLT3_L3_2.fq.gz	fastq fastq	19589608200.0	65298694.0	GSM8851835 r1	0:150 1:150	A:5414548081;C:4374558112;G:4362382403;T:5436601325;N:1518279	150	150	5414548081	4374558112	4362382403	5436601325	1518279	SRX28024097	SRS24385650	SRA2094947	Merzdorf, MCB, Montana State University	Merzdorf, MCB, Montana State University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	bulk	bulk	United States	2025-03-17	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
35391	35391	SRR32737836	SRX28024096	SRS24385649	SRP570947	PRJNA1237347	Developmental opioid exposure results in lasting transcriptome alterations in zebrafish Danio rerio embryos	GSE292183	Transcriptome Analysis	The opioid epidemic has introduced significant public health challenges with little knowledge regarding the consequences of opioid exposure during embryonic development. While neurobehavioral effects of developmental opioid exposure are well documented early effects of exposure remain largely unexplored. We investigated the effects of oxycodone and fentanyl exposure on gene expression in zebrafish Danio rerio embryos using whole embryo RNA sequencing. Embryos were exposed to environmentally relevant Oxycodone HCl 10.6pg/mL and Fentanyl Citrate 0.629pg/mL and therapeutically relevant Oxycodone HCl 35.14ng/mL and Fentanyl Citrate 3.14ng/mL from 2 hpf to 24 hpf followed by another 24hrs of opioid free development. RNA sequencing at 48hpf revealed dose and drug specific gene expression changes. Lower doses of oxycodone and fentanyl both induced more differentially expressed genes DEGs than higher doses potentially indicative of opioid receptor desensitization occurring at higher concentrations. In total 892 DEGs were identified across all conditions indicating continued differential gene expression well post cessation of opioid exposure. Gene ontology analysis revealed changes in gene expression relating to extracellular matrix ECM organization cell adhesion and visual and nervous system formation. Key pathways include axon guidance synapse formation and ECM biosynthesis/remodeling all of which have potential implications on neural connectivity and sensory development. These findings demonstrate that developmental exposure to opioids induced persistent transcriptomic changes which may have lasting implications for structural integrity and function in vertebrate nervous systems providing insights into the molecular mechanisms of opioid induced alterations during development. Overall design: Zebrafish embryos were exposed to one of the following conditions: fentanyl effluent FE; 0.629 pg/mL fentanyl therapeutic FT; 3.14 ng/mL oxycodone effluent OE; 10.6 pg/mL and oxycodone therapeutic OT; 35.14 ng/mL. Opioi…		pubmed:40429979		replicate 3 oxycod1 therapeutic exposed 0 24hpf total RNA at xxx hpf	GSM8851834		source name:Total embryo 50 embryo homogenate\|tissue:Total embryo 50 embryo homogenate\|genotype:WT\|treatment:35.14ng/mL oxycod1\|batch:3/25/2024\|geo loc name:missing\|collection date:missing	replicate 3 oxycod1 therapeutic exposed 0 24hpf total RNA at xxx hpf	Sequenced by NovaGene via Novaseq X Plus Platform paired end reads Raw reads are available as the fq.gz files Trimmed via trimmomatic and ran through rCorrector then mapped to GRCz11 ensemble constructed reference library via Salmon. The aggregated count matrixes for each condition are availible as the txt files Assembly: These are raw reads from Novaseq X plus seqeuncing and count matrixes as txt files Supplementary files format and content: txt files of aggregated count matrixes see above Supplementary files format and content: the counts derived from Salmon	Total embryo 50 embryo homogenate	one of the following conditions: fentanyl effluent FE; 0.629 pg/mL fentanyl therapeutic FT; 3.14 ng/mL oxycodone effluent OE; 10.6 pg/mL oxycodone therapeutic OT; 35.14 ng/mL Control. Opioid exposed embryos were exposed from xxx ttwo xxx hpf. At 24 hpf embryos were washed to remove opioids and allowed to develop normally until 48 hpf.	Trizol Chloroform extraction of total RNA followed by Dnase I treatment and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003	zebrafish embryos were maintained in 0.3x Danieau solution at 28.5C	tissue:Total embryo 50 embryo homogenate\|genotype:WT\|treatment:35.14ng/mL oxycod1\|batch:3/25/2024	GSM8851834	GSM8851834: replicate 3 oxycod1 therapeutic exposed 0 24hpf total RNA at xxx hpf; Danio rerio; RNA Seq	GSM8851834 r1	GSM8851834	1	Trizol Chloroform extraction of total RNA followed by Dnase I treatment and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq X Plus	SRP570947			R4OT_CKDL240008774-1A_22KFGHLT3_L3_1.fq.gz R4OT_CKDL240008774-1A_22KFGHLT3_L3_2.fq.gz	fastq fastq	19946087100.0	66486957.0	GSM8851834 r1	0:150 1:150	A:5380413495;C:4584083127;G:4577230707;T:5402765142;N:1594629	150	150	5380413495	4584083127	4577230707	5402765142	1594629	SRX28024096	SRS24385649	SRA2094947	Merzdorf, MCB, Montana State University	Merzdorf, MCB, Montana State University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	bulk	bulk	United States	2025-03-17	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
35392	35392	SRR32737837	SRX28024095	SRS24385647	SRP570947	PRJNA1237347	Developmental opioid exposure results in lasting transcriptome alterations in zebrafish Danio rerio embryos	GSE292183	Transcriptome Analysis	The opioid epidemic has introduced significant public health challenges with little knowledge regarding the consequences of opioid exposure during embryonic development. While neurobehavioral effects of developmental opioid exposure are well documented early effects of exposure remain largely unexplored. We investigated the effects of oxycodone and fentanyl exposure on gene expression in zebrafish Danio rerio embryos using whole embryo RNA sequencing. Embryos were exposed to environmentally relevant Oxycodone HCl 10.6pg/mL and Fentanyl Citrate 0.629pg/mL and therapeutically relevant Oxycodone HCl 35.14ng/mL and Fentanyl Citrate 3.14ng/mL from 2 hpf to 24 hpf followed by another 24hrs of opioid free development. RNA sequencing at 48hpf revealed dose and drug specific gene expression changes. Lower doses of oxycodone and fentanyl both induced more differentially expressed genes DEGs than higher doses potentially indicative of opioid receptor desensitization occurring at higher concentrations. In total 892 DEGs were identified across all conditions indicating continued differential gene expression well post cessation of opioid exposure. Gene ontology analysis revealed changes in gene expression relating to extracellular matrix ECM organization cell adhesion and visual and nervous system formation. Key pathways include axon guidance synapse formation and ECM biosynthesis/remodeling all of which have potential implications on neural connectivity and sensory development. These findings demonstrate that developmental exposure to opioids induced persistent transcriptomic changes which may have lasting implications for structural integrity and function in vertebrate nervous systems providing insights into the molecular mechanisms of opioid induced alterations during development. Overall design: Zebrafish embryos were exposed to one of the following conditions: fentanyl effluent FE; 0.629 pg/mL fentanyl therapeutic FT; 3.14 ng/mL oxycodone effluent OE; 10.6 pg/mL and oxycodone therapeutic OT; 35.14 ng/mL. Opioi…		pubmed:40429979		replicate 2 oxycod1 therapeutic exposed 0 24hpf total RNA at xxx hpf	GSM8851833		source name:Total embryo 50 embryo homogenate\|tissue:Total embryo 50 embryo homogenate\|genotype:WT\|treatment:35.14ng/mL oxycod1\|batch:3/25/2024\|geo loc name:missing\|collection date:missing	replicate 2 oxycod1 therapeutic exposed 0 24hpf total RNA at xxx hpf	Sequenced by NovaGene via Novaseq X Plus Platform paired end reads Raw reads are available as the fq.gz files Trimmed via trimmomatic and ran through rCorrector then mapped to GRCz11 ensemble constructed reference library via Salmon. The aggregated count matrixes for each condition are availible as the txt files Assembly: These are raw reads from Novaseq X plus seqeuncing and count matrixes as txt files Supplementary files format and content: txt files of aggregated count matrixes see above Supplementary files format and content: the counts derived from Salmon	Total embryo 50 embryo homogenate	one of the following conditions: fentanyl effluent FE; 0.629 pg/mL fentanyl therapeutic FT; 3.14 ng/mL oxycodone effluent OE; 10.6 pg/mL oxycodone therapeutic OT; 35.14 ng/mL Control. Opioid exposed embryos were exposed from xxx ttwo xxx hpf. At 24 hpf embryos were washed to remove opioids and allowed to develop normally until 48 hpf.	Trizol Chloroform extraction of total RNA followed by Dnase I treatment and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003	zebrafish embryos were maintained in 0.3x Danieau solution at 28.5C	tissue:Total embryo 50 embryo homogenate\|genotype:WT\|treatment:35.14ng/mL oxycod1\|batch:3/25/2024	GSM8851833	GSM8851833: replicate 2 oxycod1 therapeutic exposed 0 24hpf total RNA at xxx hpf; Danio rerio; RNA Seq	GSM8851833 r1	GSM8851833	1	Trizol Chloroform extraction of total RNA followed by Dnase I treatment and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq X Plus	SRP570947			R2OT_CKDL240008774-1A_22KFGHLT3_L3_1.fq.gz R2OT_CKDL240008774-1A_22KFGHLT3_L3_2.fq.gz	fastq fastq	12448266300.0	41494221.0	GSM8851833 r1	0:150 1:150	A:3395623757;C:2824144586;G:2822937408;T:3404571425;N:989124	150	150	3395623757	2824144586	2822937408	3404571425	989124	SRX28024095	SRS24385647	SRA2094947	Merzdorf, MCB, Montana State University	Merzdorf, MCB, Montana State University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	bulk	bulk	United States	2025-03-17	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
35393	35393	SRR32737838	SRX28024094	SRS24385648	SRP570947	PRJNA1237347	Developmental opioid exposure results in lasting transcriptome alterations in zebrafish Danio rerio embryos	GSE292183	Transcriptome Analysis	The opioid epidemic has introduced significant public health challenges with little knowledge regarding the consequences of opioid exposure during embryonic development. While neurobehavioral effects of developmental opioid exposure are well documented early effects of exposure remain largely unexplored. We investigated the effects of oxycodone and fentanyl exposure on gene expression in zebrafish Danio rerio embryos using whole embryo RNA sequencing. Embryos were exposed to environmentally relevant Oxycodone HCl 10.6pg/mL and Fentanyl Citrate 0.629pg/mL and therapeutically relevant Oxycodone HCl 35.14ng/mL and Fentanyl Citrate 3.14ng/mL from 2 hpf to 24 hpf followed by another 24hrs of opioid free development. RNA sequencing at 48hpf revealed dose and drug specific gene expression changes. Lower doses of oxycodone and fentanyl both induced more differentially expressed genes DEGs than higher doses potentially indicative of opioid receptor desensitization occurring at higher concentrations. In total 892 DEGs were identified across all conditions indicating continued differential gene expression well post cessation of opioid exposure. Gene ontology analysis revealed changes in gene expression relating to extracellular matrix ECM organization cell adhesion and visual and nervous system formation. Key pathways include axon guidance synapse formation and ECM biosynthesis/remodeling all of which have potential implications on neural connectivity and sensory development. These findings demonstrate that developmental exposure to opioids induced persistent transcriptomic changes which may have lasting implications for structural integrity and function in vertebrate nervous systems providing insights into the molecular mechanisms of opioid induced alterations during development. Overall design: Zebrafish embryos were exposed to one of the following conditions: fentanyl effluent FE; 0.629 pg/mL fentanyl therapeutic FT; 3.14 ng/mL oxycodone effluent OE; 10.6 pg/mL and oxycodone therapeutic OT; 35.14 ng/mL. Opioi…		pubmed:40429979		replicate 1 oxycod1 therapeutic exposed 0 24hpf total RNA at xxx hpf	GSM8851832		source name:Total embryo 50 embryo homogenate\|tissue:Total embryo 50 embryo homogenate\|genotype:WT\|treatment:35.14ng/mL oxycod1\|batch:3/25/2024\|geo loc name:missing\|collection date:missing	replicate 1 oxycod1 therapeutic exposed 0 24hpf total RNA at xxx hpf	Sequenced by NovaGene via Novaseq X Plus Platform paired end reads Raw reads are available as the fq.gz files Trimmed via trimmomatic and ran through rCorrector then mapped to GRCz11 ensemble constructed reference library via Salmon. The aggregated count matrixes for each condition are availible as the txt files Assembly: These are raw reads from Novaseq X plus seqeuncing and count matrixes as txt files Supplementary files format and content: txt files of aggregated count matrixes see above Supplementary files format and content: the counts derived from Salmon	Total embryo 50 embryo homogenate	one of the following conditions: fentanyl effluent FE; 0.629 pg/mL fentanyl therapeutic FT; 3.14 ng/mL oxycodone effluent OE; 10.6 pg/mL oxycodone therapeutic OT; 35.14 ng/mL Control. Opioid exposed embryos were exposed from xxx ttwo xxx hpf. At 24 hpf embryos were washed to remove opioids and allowed to develop normally until 48 hpf.	Trizol Chloroform extraction of total RNA followed by Dnase I treatment and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003	zebrafish embryos were maintained in 0.3x Danieau solution at 28.5C	tissue:Total embryo 50 embryo homogenate\|genotype:WT\|treatment:35.14ng/mL oxycod1\|batch:3/25/2024	GSM8851832	GSM8851832: replicate 1 oxycod1 therapeutic exposed 0 24hpf total RNA at xxx hpf; Danio rerio; RNA Seq	GSM8851832 r1	GSM8851832	1	Trizol Chloroform extraction of total RNA followed by Dnase I treatment and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq X Plus	SRP570947			R1OT_CKDL240008774-1A_22KFGHLT3_L3_1.fq.gz R1OT_CKDL240008774-1A_22KFGHLT3_L3_2.fq.gz	fastq fastq	19798955700.0	65996519.0	GSM8851832 r1	0:150 1:150	A:5229008693;C:4668558136;G:4674407786;T:5225398568;N:1582517	150	150	5229008693	4668558136	4674407786	5225398568	1582517	SRX28024094	SRS24385648	SRA2094947	Merzdorf, MCB, Montana State University	Merzdorf, MCB, Montana State University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	bulk	bulk	United States	2025-03-17	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
35394	35394	SRR32737842	SRX28024093	SRS24385646	SRP570947	PRJNA1237347	Developmental opioid exposure results in lasting transcriptome alterations in zebrafish Danio rerio embryos	GSE292183	Transcriptome Analysis	The opioid epidemic has introduced significant public health challenges with little knowledge regarding the consequences of opioid exposure during embryonic development. While neurobehavioral effects of developmental opioid exposure are well documented early effects of exposure remain largely unexplored. We investigated the effects of oxycodone and fentanyl exposure on gene expression in zebrafish Danio rerio embryos using whole embryo RNA sequencing. Embryos were exposed to environmentally relevant Oxycodone HCl 10.6pg/mL and Fentanyl Citrate 0.629pg/mL and therapeutically relevant Oxycodone HCl 35.14ng/mL and Fentanyl Citrate 3.14ng/mL from 2 hpf to 24 hpf followed by another 24hrs of opioid free development. RNA sequencing at 48hpf revealed dose and drug specific gene expression changes. Lower doses of oxycodone and fentanyl both induced more differentially expressed genes DEGs than higher doses potentially indicative of opioid receptor desensitization occurring at higher concentrations. In total 892 DEGs were identified across all conditions indicating continued differential gene expression well post cessation of opioid exposure. Gene ontology analysis revealed changes in gene expression relating to extracellular matrix ECM organization cell adhesion and visual and nervous system formation. Key pathways include axon guidance synapse formation and ECM biosynthesis/remodeling all of which have potential implications on neural connectivity and sensory development. These findings demonstrate that developmental exposure to opioids induced persistent transcriptomic changes which may have lasting implications for structural integrity and function in vertebrate nervous systems providing insights into the molecular mechanisms of opioid induced alterations during development. Overall design: Zebrafish embryos were exposed to one of the following conditions: fentanyl effluent FE; 0.629 pg/mL fentanyl therapeutic FT; 3.14 ng/mL oxycodone effluent OE; 10.6 pg/mL and oxycodone therapeutic OT; 35.14 ng/mL. Opioi…		pubmed:40429979		replicate 5 oxycod1 effluent exposed 0 24hpf total RNA at xxxhpf	GSM8851831		source name:Total embryo 50 embryo homogenate\|tissue:Total embryo 50 embryo homogenate\|genotype:WT\|treatment:10.6pg/mL oxycod1\|batch:3/25/2024\|geo loc name:missing\|collection date:missing	replicate 5 oxycod1 effluent exposed 0 24hpf total RNA at xxxhpf	Sequenced by NovaGene via Novaseq X Plus Platform paired end reads Raw reads are available as the fq.gz files Trimmed via trimmomatic and ran through rCorrector then mapped to GRCz11 ensemble constructed reference library via Salmon. The aggregated count matrixes for each condition are availible as the txt files Assembly: These are raw reads from Novaseq X plus seqeuncing and count matrixes as txt files Supplementary files format and content: txt files of aggregated count matrixes see above Supplementary files format and content: the counts derived from Salmon	Total embryo 50 embryo homogenate	one of the following conditions: fentanyl effluent FE; 0.629 pg/mL fentanyl therapeutic FT; 3.14 ng/mL oxycodone effluent OE; 10.6 pg/mL oxycodone therapeutic OT; 35.14 ng/mL Control. Opioid exposed embryos were exposed from xxx ttwo xxx hpf. At 24 hpf embryos were washed to remove opioids and allowed to develop normally until 48 hpf.	Trizol Chloroform extraction of total RNA followed by Dnase I treatment and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003	zebrafish embryos were maintained in 0.3x Danieau solution at 28.5C	tissue:Total embryo 50 embryo homogenate\|genotype:WT\|treatment:10.6pg/mL oxycod1\|batch:3/25/2024	GSM8851831	GSM8851831: replicate 5 oxycod1 effluent exposed 0 24hpf total RNA at xxxhpf; Danio rerio; RNA Seq	GSM8851831 r1	GSM8851831	1	Trizol Chloroform extraction of total RNA followed by Dnase I treatment and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq X Plus	SRP570947			R6OE_CKDL240008774-1A_22KFGHLT3_L3_1.fq.gz R6OE_CKDL240008774-1A_22KFGHLT3_L3_2.fq.gz	fastq fastq	18130666800.0	60435556.0	GSM8851831 r1	0:150 1:150	A:4966144411;C:4092769735;G:4085294185;T:4985017148;N:1441321	150	150	4966144411	4092769735	4085294185	4985017148	1441321	SRX28024093	SRS24385646	SRA2094947	Merzdorf, MCB, Montana State University	Merzdorf, MCB, Montana State University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	bulk	bulk	United States	2025-03-17	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
35395	35395	SRR32737839	SRX28024092	SRS24385645	SRP570947	PRJNA1237347	Developmental opioid exposure results in lasting transcriptome alterations in zebrafish Danio rerio embryos	GSE292183	Transcriptome Analysis	The opioid epidemic has introduced significant public health challenges with little knowledge regarding the consequences of opioid exposure during embryonic development. While neurobehavioral effects of developmental opioid exposure are well documented early effects of exposure remain largely unexplored. We investigated the effects of oxycodone and fentanyl exposure on gene expression in zebrafish Danio rerio embryos using whole embryo RNA sequencing. Embryos were exposed to environmentally relevant Oxycodone HCl 10.6pg/mL and Fentanyl Citrate 0.629pg/mL and therapeutically relevant Oxycodone HCl 35.14ng/mL and Fentanyl Citrate 3.14ng/mL from 2 hpf to 24 hpf followed by another 24hrs of opioid free development. RNA sequencing at 48hpf revealed dose and drug specific gene expression changes. Lower doses of oxycodone and fentanyl both induced more differentially expressed genes DEGs than higher doses potentially indicative of opioid receptor desensitization occurring at higher concentrations. In total 892 DEGs were identified across all conditions indicating continued differential gene expression well post cessation of opioid exposure. Gene ontology analysis revealed changes in gene expression relating to extracellular matrix ECM organization cell adhesion and visual and nervous system formation. Key pathways include axon guidance synapse formation and ECM biosynthesis/remodeling all of which have potential implications on neural connectivity and sensory development. These findings demonstrate that developmental exposure to opioids induced persistent transcriptomic changes which may have lasting implications for structural integrity and function in vertebrate nervous systems providing insights into the molecular mechanisms of opioid induced alterations during development. Overall design: Zebrafish embryos were exposed to one of the following conditions: fentanyl effluent FE; 0.629 pg/mL fentanyl therapeutic FT; 3.14 ng/mL oxycodone effluent OE; 10.6 pg/mL and oxycodone therapeutic OT; 35.14 ng/mL. Opioi…		pubmed:40429979		replicate 4 oxycod1 effluent exposed 0 24hpf total RNA at xxxhpf	GSM8851830		source name:Total embryo 50 embryo homogenate\|tissue:Total embryo 50 embryo homogenate\|genotype:WT\|treatment:10.6pg/mL oxycod1\|batch:3/25/2024\|geo loc name:missing\|collection date:missing	replicate 4 oxycod1 effluent exposed 0 24hpf total RNA at xxxhpf	Sequenced by NovaGene via Novaseq X Plus Platform paired end reads Raw reads are available as the fq.gz files Trimmed via trimmomatic and ran through rCorrector then mapped to GRCz11 ensemble constructed reference library via Salmon. The aggregated count matrixes for each condition are availible as the txt files Assembly: These are raw reads from Novaseq X plus seqeuncing and count matrixes as txt files Supplementary files format and content: txt files of aggregated count matrixes see above Supplementary files format and content: the counts derived from Salmon	Total embryo 50 embryo homogenate	one of the following conditions: fentanyl effluent FE; 0.629 pg/mL fentanyl therapeutic FT; 3.14 ng/mL oxycodone effluent OE; 10.6 pg/mL oxycodone therapeutic OT; 35.14 ng/mL Control. Opioid exposed embryos were exposed from xxx ttwo xxx hpf. At 24 hpf embryos were washed to remove opioids and allowed to develop normally until 48 hpf.	Trizol Chloroform extraction of total RNA followed by Dnase I treatment and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003	zebrafish embryos were maintained in 0.3x Danieau solution at 28.5C	tissue:Total embryo 50 embryo homogenate\|genotype:WT\|treatment:10.6pg/mL oxycod1\|batch:3/25/2024	GSM8851830	GSM8851830: replicate 4 oxycod1 effluent exposed 0 24hpf total RNA at xxxhpf; Danio rerio; RNA Seq	GSM8851830 r1	GSM8851830	1	Trizol Chloroform extraction of total RNA followed by Dnase I treatment and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq X Plus	SRP570947			R4OE_CKDL240008774-1A_22KFGHLT3_L3_1.fq.gz R4OE_CKDL240008774-1A_22KFGHLT3_L3_2.fq.gz	fastq fastq	19991640600.0	66638802.0	GSM8851830 r1	0:150 1:150	A:5447335535;C:4526376231;G:4535727704;T:5480632098;N:1569032	150	150	5447335535	4526376231	4535727704	5480632098	1569032	SRX28024092	SRS24385645	SRA2094947	Merzdorf, MCB, Montana State University	Merzdorf, MCB, Montana State University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	bulk	bulk	United States	2025-03-17	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
35396	35396	SRR32737840	SRX28024091	SRS24385644	SRP570947	PRJNA1237347	Developmental opioid exposure results in lasting transcriptome alterations in zebrafish Danio rerio embryos	GSE292183	Transcriptome Analysis	The opioid epidemic has introduced significant public health challenges with little knowledge regarding the consequences of opioid exposure during embryonic development. While neurobehavioral effects of developmental opioid exposure are well documented early effects of exposure remain largely unexplored. We investigated the effects of oxycodone and fentanyl exposure on gene expression in zebrafish Danio rerio embryos using whole embryo RNA sequencing. Embryos were exposed to environmentally relevant Oxycodone HCl 10.6pg/mL and Fentanyl Citrate 0.629pg/mL and therapeutically relevant Oxycodone HCl 35.14ng/mL and Fentanyl Citrate 3.14ng/mL from 2 hpf to 24 hpf followed by another 24hrs of opioid free development. RNA sequencing at 48hpf revealed dose and drug specific gene expression changes. Lower doses of oxycodone and fentanyl both induced more differentially expressed genes DEGs than higher doses potentially indicative of opioid receptor desensitization occurring at higher concentrations. In total 892 DEGs were identified across all conditions indicating continued differential gene expression well post cessation of opioid exposure. Gene ontology analysis revealed changes in gene expression relating to extracellular matrix ECM organization cell adhesion and visual and nervous system formation. Key pathways include axon guidance synapse formation and ECM biosynthesis/remodeling all of which have potential implications on neural connectivity and sensory development. These findings demonstrate that developmental exposure to opioids induced persistent transcriptomic changes which may have lasting implications for structural integrity and function in vertebrate nervous systems providing insights into the molecular mechanisms of opioid induced alterations during development. Overall design: Zebrafish embryos were exposed to one of the following conditions: fentanyl effluent FE; 0.629 pg/mL fentanyl therapeutic FT; 3.14 ng/mL oxycodone effluent OE; 10.6 pg/mL and oxycodone therapeutic OT; 35.14 ng/mL. Opioi…		pubmed:40429979		replicate 3 oxycod1 effluent exposed 0 24hpf total RNA at xxxhpf	GSM8851829		source name:Total embryo 50 embryo homogenate\|tissue:Total embryo 50 embryo homogenate\|genotype:WT\|treatment:10.6pg/mL oxycod1\|batch:3/25/2024\|geo loc name:missing\|collection date:missing	replicate 3 oxycod1 effluent exposed 0 24hpf total RNA at xxxhpf	Sequenced by NovaGene via Novaseq X Plus Platform paired end reads Raw reads are available as the fq.gz files Trimmed via trimmomatic and ran through rCorrector then mapped to GRCz11 ensemble constructed reference library via Salmon. The aggregated count matrixes for each condition are availible as the txt files Assembly: These are raw reads from Novaseq X plus seqeuncing and count matrixes as txt files Supplementary files format and content: txt files of aggregated count matrixes see above Supplementary files format and content: the counts derived from Salmon	Total embryo 50 embryo homogenate	one of the following conditions: fentanyl effluent FE; 0.629 pg/mL fentanyl therapeutic FT; 3.14 ng/mL oxycodone effluent OE; 10.6 pg/mL oxycodone therapeutic OT; 35.14 ng/mL Control. Opioid exposed embryos were exposed from xxx ttwo xxx hpf. At 24 hpf embryos were washed to remove opioids and allowed to develop normally until 48 hpf.	Trizol Chloroform extraction of total RNA followed by Dnase I treatment and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003	zebrafish embryos were maintained in 0.3x Danieau solution at 28.5C	tissue:Total embryo 50 embryo homogenate\|genotype:WT\|treatment:10.6pg/mL oxycod1\|batch:3/25/2024	GSM8851829	GSM8851829: replicate 3 oxycod1 effluent exposed 0 24hpf total RNA at xxxhpf; Danio rerio; RNA Seq	GSM8851829 r1	GSM8851829	1	Trizol Chloroform extraction of total RNA followed by Dnase I treatment and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq X Plus	SRP570947			R3OE_CKDL240008774-1A_22KFGHLT3_L3_1.fq.gz R3OE_CKDL240008774-1A_22KFGHLT3_L3_2.fq.gz	fastq fastq	22065261900.0	73550873.0	GSM8851829 r1	0:150 1:150	A:5991325177;C:5034454094;G:5016024645;T:6021738394;N:1719590	150	150	5991325177	5034454094	5016024645	6021738394	1719590	SRX28024091	SRS24385644	SRA2094947	Merzdorf, MCB, Montana State University	Merzdorf, MCB, Montana State University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	bulk	bulk	United States	2025-03-17	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
35397	35397	SRR32737841	SRX28024090	SRS24385643	SRP570947	PRJNA1237347	Developmental opioid exposure results in lasting transcriptome alterations in zebrafish Danio rerio embryos	GSE292183	Transcriptome Analysis	The opioid epidemic has introduced significant public health challenges with little knowledge regarding the consequences of opioid exposure during embryonic development. While neurobehavioral effects of developmental opioid exposure are well documented early effects of exposure remain largely unexplored. We investigated the effects of oxycodone and fentanyl exposure on gene expression in zebrafish Danio rerio embryos using whole embryo RNA sequencing. Embryos were exposed to environmentally relevant Oxycodone HCl 10.6pg/mL and Fentanyl Citrate 0.629pg/mL and therapeutically relevant Oxycodone HCl 35.14ng/mL and Fentanyl Citrate 3.14ng/mL from 2 hpf to 24 hpf followed by another 24hrs of opioid free development. RNA sequencing at 48hpf revealed dose and drug specific gene expression changes. Lower doses of oxycodone and fentanyl both induced more differentially expressed genes DEGs than higher doses potentially indicative of opioid receptor desensitization occurring at higher concentrations. In total 892 DEGs were identified across all conditions indicating continued differential gene expression well post cessation of opioid exposure. Gene ontology analysis revealed changes in gene expression relating to extracellular matrix ECM organization cell adhesion and visual and nervous system formation. Key pathways include axon guidance synapse formation and ECM biosynthesis/remodeling all of which have potential implications on neural connectivity and sensory development. These findings demonstrate that developmental exposure to opioids induced persistent transcriptomic changes which may have lasting implications for structural integrity and function in vertebrate nervous systems providing insights into the molecular mechanisms of opioid induced alterations during development. Overall design: Zebrafish embryos were exposed to one of the following conditions: fentanyl effluent FE; 0.629 pg/mL fentanyl therapeutic FT; 3.14 ng/mL oxycodone effluent OE; 10.6 pg/mL and oxycodone therapeutic OT; 35.14 ng/mL. Opioi…		pubmed:40429979		replicate 2 oxycod1 effluent exposed 0 24hpf total RNA at xxxhpf	GSM8851828		source name:Total embryo 50 embryo homogenate\|tissue:Total embryo 50 embryo homogenate\|genotype:WT\|treatment:10.6pg/mL oxycod1\|batch:3/25/2024\|geo loc name:missing\|collection date:missing	replicate 2 oxycod1 effluent exposed 0 24hpf total RNA at xxxhpf	Sequenced by NovaGene via Novaseq X Plus Platform paired end reads Raw reads are available as the fq.gz files Trimmed via trimmomatic and ran through rCorrector then mapped to GRCz11 ensemble constructed reference library via Salmon. The aggregated count matrixes for each condition are availible as the txt files Assembly: These are raw reads from Novaseq X plus seqeuncing and count matrixes as txt files Supplementary files format and content: txt files of aggregated count matrixes see above Supplementary files format and content: the counts derived from Salmon	Total embryo 50 embryo homogenate	one of the following conditions: fentanyl effluent FE; 0.629 pg/mL fentanyl therapeutic FT; 3.14 ng/mL oxycodone effluent OE; 10.6 pg/mL oxycodone therapeutic OT; 35.14 ng/mL Control. Opioid exposed embryos were exposed from xxx ttwo xxx hpf. At 24 hpf embryos were washed to remove opioids and allowed to develop normally until 48 hpf.	Trizol Chloroform extraction of total RNA followed by Dnase I treatment and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003	zebrafish embryos were maintained in 0.3x Danieau solution at 28.5C	tissue:Total embryo 50 embryo homogenate\|genotype:WT\|treatment:10.6pg/mL oxycod1\|batch:3/25/2024	GSM8851828	GSM8851828: replicate 2 oxycod1 effluent exposed 0 24hpf total RNA at xxxhpf; Danio rerio; RNA Seq	GSM8851828 r1	GSM8851828	1	Trizol Chloroform extraction of total RNA followed by Dnase I treatment and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq X Plus	SRP570947			R2OE_CKDL240008774-1A_22KFGHLT3_L3_1.fq.gz R2OE_CKDL240008774-1A_22KFGHLT3_L3_2.fq.gz	fastq fastq	14038941600.0	46796472.0	GSM8851828 r1	0:150 1:150	A:3916268130;C:3079070561;G:3101493441;T:3941005195;N:1104273	150	150	3916268130	3079070561	3101493441	3941005195	1104273	SRX28024090	SRS24385643	SRA2094947	Merzdorf, MCB, Montana State University	Merzdorf, MCB, Montana State University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	bulk	bulk	United States	2025-03-17	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
35398	35398	SRR32737843	SRX28024089	SRS24385641	SRP570947	PRJNA1237347	Developmental opioid exposure results in lasting transcriptome alterations in zebrafish Danio rerio embryos	GSE292183	Transcriptome Analysis	The opioid epidemic has introduced significant public health challenges with little knowledge regarding the consequences of opioid exposure during embryonic development. While neurobehavioral effects of developmental opioid exposure are well documented early effects of exposure remain largely unexplored. We investigated the effects of oxycodone and fentanyl exposure on gene expression in zebrafish Danio rerio embryos using whole embryo RNA sequencing. Embryos were exposed to environmentally relevant Oxycodone HCl 10.6pg/mL and Fentanyl Citrate 0.629pg/mL and therapeutically relevant Oxycodone HCl 35.14ng/mL and Fentanyl Citrate 3.14ng/mL from 2 hpf to 24 hpf followed by another 24hrs of opioid free development. RNA sequencing at 48hpf revealed dose and drug specific gene expression changes. Lower doses of oxycodone and fentanyl both induced more differentially expressed genes DEGs than higher doses potentially indicative of opioid receptor desensitization occurring at higher concentrations. In total 892 DEGs were identified across all conditions indicating continued differential gene expression well post cessation of opioid exposure. Gene ontology analysis revealed changes in gene expression relating to extracellular matrix ECM organization cell adhesion and visual and nervous system formation. Key pathways include axon guidance synapse formation and ECM biosynthesis/remodeling all of which have potential implications on neural connectivity and sensory development. These findings demonstrate that developmental exposure to opioids induced persistent transcriptomic changes which may have lasting implications for structural integrity and function in vertebrate nervous systems providing insights into the molecular mechanisms of opioid induced alterations during development. Overall design: Zebrafish embryos were exposed to one of the following conditions: fentanyl effluent FE; 0.629 pg/mL fentanyl therapeutic FT; 3.14 ng/mL oxycodone effluent OE; 10.6 pg/mL and oxycodone therapeutic OT; 35.14 ng/mL. Opioi…		pubmed:40429979		replicate 1 oxycod1 effluent exposed 0 24hpf total RNA at xxxhpf	GSM8851827		source name:Total embryo 50 embryo homogenate\|tissue:Total embryo 50 embryo homogenate\|genotype:WT\|treatment:10.6pg/mL oxycod1\|batch:3/25/2024\|geo loc name:missing\|collection date:missing	replicate 1 oxycod1 effluent exposed 0 24hpf total RNA at xxxhpf	Sequenced by NovaGene via Novaseq X Plus Platform paired end reads Raw reads are available as the fq.gz files Trimmed via trimmomatic and ran through rCorrector then mapped to GRCz11 ensemble constructed reference library via Salmon. The aggregated count matrixes for each condition are availible as the txt files Assembly: These are raw reads from Novaseq X plus seqeuncing and count matrixes as txt files Supplementary files format and content: txt files of aggregated count matrixes see above Supplementary files format and content: the counts derived from Salmon	Total embryo 50 embryo homogenate	one of the following conditions: fentanyl effluent FE; 0.629 pg/mL fentanyl therapeutic FT; 3.14 ng/mL oxycodone effluent OE; 10.6 pg/mL oxycodone therapeutic OT; 35.14 ng/mL Control. Opioid exposed embryos were exposed from xxx ttwo xxx hpf. At 24 hpf embryos were washed to remove opioids and allowed to develop normally until 48 hpf.	Trizol Chloroform extraction of total RNA followed by Dnase I treatment and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003	zebrafish embryos were maintained in 0.3x Danieau solution at 28.5C	tissue:Total embryo 50 embryo homogenate\|genotype:WT\|treatment:10.6pg/mL oxycod1\|batch:3/25/2024	GSM8851827	GSM8851827: replicate 1 oxycod1 effluent exposed 0 24hpf total RNA at xxxhpf; Danio rerio; RNA Seq	GSM8851827 r1	GSM8851827	1	Trizol Chloroform extraction of total RNA followed by Dnase I treatment and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq X Plus	SRP570947			R1OE_CKDL240008774-1A_22KFGHLT3_L3_1.fq.gz R1OE_CKDL240008774-1A_22KFGHLT3_L3_2.fq.gz	fastq fastq	13386761100.0	44622537.0	GSM8851827 r1	0:150 1:150	A:3794190335;C:2871376272;G:2905470401;T:3814688762;N:1035330	150	150	3794190335	2871376272	2905470401	3814688762	1035330	SRX28024089	SRS24385641	SRA2094947	Merzdorf, MCB, Montana State University	Merzdorf, MCB, Montana State University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	bulk	bulk	United States	2025-03-17	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
35399	35399	SRR32737844	SRX28024088	SRS24385642	SRP570947	PRJNA1237347	Developmental opioid exposure results in lasting transcriptome alterations in zebrafish Danio rerio embryos	GSE292183	Transcriptome Analysis	The opioid epidemic has introduced significant public health challenges with little knowledge regarding the consequences of opioid exposure during embryonic development. While neurobehavioral effects of developmental opioid exposure are well documented early effects of exposure remain largely unexplored. We investigated the effects of oxycodone and fentanyl exposure on gene expression in zebrafish Danio rerio embryos using whole embryo RNA sequencing. Embryos were exposed to environmentally relevant Oxycodone HCl 10.6pg/mL and Fentanyl Citrate 0.629pg/mL and therapeutically relevant Oxycodone HCl 35.14ng/mL and Fentanyl Citrate 3.14ng/mL from 2 hpf to 24 hpf followed by another 24hrs of opioid free development. RNA sequencing at 48hpf revealed dose and drug specific gene expression changes. Lower doses of oxycodone and fentanyl both induced more differentially expressed genes DEGs than higher doses potentially indicative of opioid receptor desensitization occurring at higher concentrations. In total 892 DEGs were identified across all conditions indicating continued differential gene expression well post cessation of opioid exposure. Gene ontology analysis revealed changes in gene expression relating to extracellular matrix ECM organization cell adhesion and visual and nervous system formation. Key pathways include axon guidance synapse formation and ECM biosynthesis/remodeling all of which have potential implications on neural connectivity and sensory development. These findings demonstrate that developmental exposure to opioids induced persistent transcriptomic changes which may have lasting implications for structural integrity and function in vertebrate nervous systems providing insights into the molecular mechanisms of opioid induced alterations during development. Overall design: Zebrafish embryos were exposed to one of the following conditions: fentanyl effluent FE; 0.629 pg/mL fentanyl therapeutic FT; 3.14 ng/mL oxycodone effluent OE; 10.6 pg/mL and oxycodone therapeutic OT; 35.14 ng/mL. Opioi…		pubmed:40429979		replicate 5 fentanyl therapeutic exposed 0 24hpf total RNA at xxxhpf	GSM8851826		source name:Total embryo 50 embryo homogenate\|tissue:Total embryo 50 embryo homogenate\|genotype:WT\|treatment:3.14 ng/mL fentanyl\|batch:3/25/2024\|geo loc name:missing\|collection date:missing	replicate 5 fentanyl therapeutic exposed 0 24hpf total RNA at xxxhpf	Sequenced by NovaGene via Novaseq X Plus Platform paired end reads Raw reads are available as the fq.gz files Trimmed via trimmomatic and ran through rCorrector then mapped to GRCz11 ensemble constructed reference library via Salmon. The aggregated count matrixes for each condition are availible as the txt files Assembly: These are raw reads from Novaseq X plus seqeuncing and count matrixes as txt files Supplementary files format and content: txt files of aggregated count matrixes see above Supplementary files format and content: the counts derived from Salmon	Total embryo 50 embryo homogenate	one of the following conditions: fentanyl effluent FE; 0.629 pg/mL fentanyl therapeutic FT; 3.14 ng/mL oxycodone effluent OE; 10.6 pg/mL oxycodone therapeutic OT; 35.14 ng/mL Control. Opioid exposed embryos were exposed from xxx ttwo xxx hpf. At 24 hpf embryos were washed to remove opioids and allowed to develop normally until 48 hpf.	Trizol Chloroform extraction of total RNA followed by Dnase I treatment and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003	zebrafish embryos were maintained in 0.3x Danieau solution at 28.5C	tissue:Total embryo 50 embryo homogenate\|genotype:WT\|treatment:3.14 ng/mL fentanyl\|batch:3/25/2024	GSM8851826	GSM8851826: replicate 5 fentanyl therapeutic exposed 0 24hpf total RNA at xxxhpf; Danio rerio; RNA Seq	GSM8851826 r1	GSM8851826	1	Trizol Chloroform extraction of total RNA followed by Dnase I treatment and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq X Plus	SRP570947			R6FT_CKDL240008774-1A_22KFGHLT3_L3_1.fq.gz R6FT_CKDL240008774-1A_22KFGHLT3_L3_2.fq.gz	fastq fastq	21105961200.0	70353204.0	GSM8851826 r1	0:150 1:150	A:5809999918;C:4738287088;G:4727306148;T:5828688062;N:1679984	150	150	5809999918	4738287088	4727306148	5828688062	1679984	SRX28024088	SRS24385642	SRA2094947	Merzdorf, MCB, Montana State University	Merzdorf, MCB, Montana State University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	bulk	bulk	United States	2025-03-17	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
35400	35400	SRR32737845	SRX28024087	SRS24385640	SRP570947	PRJNA1237347	Developmental opioid exposure results in lasting transcriptome alterations in zebrafish Danio rerio embryos	GSE292183	Transcriptome Analysis	The opioid epidemic has introduced significant public health challenges with little knowledge regarding the consequences of opioid exposure during embryonic development. While neurobehavioral effects of developmental opioid exposure are well documented early effects of exposure remain largely unexplored. We investigated the effects of oxycodone and fentanyl exposure on gene expression in zebrafish Danio rerio embryos using whole embryo RNA sequencing. Embryos were exposed to environmentally relevant Oxycodone HCl 10.6pg/mL and Fentanyl Citrate 0.629pg/mL and therapeutically relevant Oxycodone HCl 35.14ng/mL and Fentanyl Citrate 3.14ng/mL from 2 hpf to 24 hpf followed by another 24hrs of opioid free development. RNA sequencing at 48hpf revealed dose and drug specific gene expression changes. Lower doses of oxycodone and fentanyl both induced more differentially expressed genes DEGs than higher doses potentially indicative of opioid receptor desensitization occurring at higher concentrations. In total 892 DEGs were identified across all conditions indicating continued differential gene expression well post cessation of opioid exposure. Gene ontology analysis revealed changes in gene expression relating to extracellular matrix ECM organization cell adhesion and visual and nervous system formation. Key pathways include axon guidance synapse formation and ECM biosynthesis/remodeling all of which have potential implications on neural connectivity and sensory development. These findings demonstrate that developmental exposure to opioids induced persistent transcriptomic changes which may have lasting implications for structural integrity and function in vertebrate nervous systems providing insights into the molecular mechanisms of opioid induced alterations during development. Overall design: Zebrafish embryos were exposed to one of the following conditions: fentanyl effluent FE; 0.629 pg/mL fentanyl therapeutic FT; 3.14 ng/mL oxycodone effluent OE; 10.6 pg/mL and oxycodone therapeutic OT; 35.14 ng/mL. Opioi…		pubmed:40429979		replicate 4 fentanyl therapeutic exposed 0 24hpf total RNA at xxxhpf	GSM8851825		source name:Total embryo 50 embryo homogenate\|tissue:Total embryo 50 embryo homogenate\|genotype:WT\|treatment:3.14 ng/mL fentanyl\|batch:3/25/2024\|geo loc name:missing\|collection date:missing	replicate 4 fentanyl therapeutic exposed 0 24hpf total RNA at xxxhpf	Sequenced by NovaGene via Novaseq X Plus Platform paired end reads Raw reads are available as the fq.gz files Trimmed via trimmomatic and ran through rCorrector then mapped to GRCz11 ensemble constructed reference library via Salmon. The aggregated count matrixes for each condition are availible as the txt files Assembly: These are raw reads from Novaseq X plus seqeuncing and count matrixes as txt files Supplementary files format and content: txt files of aggregated count matrixes see above Supplementary files format and content: the counts derived from Salmon	Total embryo 50 embryo homogenate	one of the following conditions: fentanyl effluent FE; 0.629 pg/mL fentanyl therapeutic FT; 3.14 ng/mL oxycodone effluent OE; 10.6 pg/mL oxycodone therapeutic OT; 35.14 ng/mL Control. Opioid exposed embryos were exposed from xxx ttwo xxx hpf. At 24 hpf embryos were washed to remove opioids and allowed to develop normally until 48 hpf.	Trizol Chloroform extraction of total RNA followed by Dnase I treatment and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003	zebrafish embryos were maintained in 0.3x Danieau solution at 28.5C	tissue:Total embryo 50 embryo homogenate\|genotype:WT\|treatment:3.14 ng/mL fentanyl\|batch:3/25/2024	GSM8851825	GSM8851825: replicate 4 fentanyl therapeutic exposed 0 24hpf total RNA at xxxhpf; Danio rerio; RNA Seq	GSM8851825 r1	GSM8851825	1	Trizol Chloroform extraction of total RNA followed by Dnase I treatment and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq X Plus	SRP570947			R5FT_CKDL240008774-1A_22KFGHLT3_L3_1.fq.gz R5FT_CKDL240008774-1A_22KFGHLT3_L3_2.fq.gz	fastq fastq	23123472900.0	77078243.0	GSM8851825 r1	0:150 1:150	A:6076414910;C:5484056288;G:5478904909;T:6082279094;N:1817699	150	150	6076414910	5484056288	5478904909	6082279094	1817699	SRX28024087	SRS24385640	SRA2094947	Merzdorf, MCB, Montana State University	Merzdorf, MCB, Montana State University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	bulk	bulk	United States	2025-03-17	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
35401	35401	SRR32737846	SRX28024086	SRS24385638	SRP570947	PRJNA1237347	Developmental opioid exposure results in lasting transcriptome alterations in zebrafish Danio rerio embryos	GSE292183	Transcriptome Analysis	The opioid epidemic has introduced significant public health challenges with little knowledge regarding the consequences of opioid exposure during embryonic development. While neurobehavioral effects of developmental opioid exposure are well documented early effects of exposure remain largely unexplored. We investigated the effects of oxycodone and fentanyl exposure on gene expression in zebrafish Danio rerio embryos using whole embryo RNA sequencing. Embryos were exposed to environmentally relevant Oxycodone HCl 10.6pg/mL and Fentanyl Citrate 0.629pg/mL and therapeutically relevant Oxycodone HCl 35.14ng/mL and Fentanyl Citrate 3.14ng/mL from 2 hpf to 24 hpf followed by another 24hrs of opioid free development. RNA sequencing at 48hpf revealed dose and drug specific gene expression changes. Lower doses of oxycodone and fentanyl both induced more differentially expressed genes DEGs than higher doses potentially indicative of opioid receptor desensitization occurring at higher concentrations. In total 892 DEGs were identified across all conditions indicating continued differential gene expression well post cessation of opioid exposure. Gene ontology analysis revealed changes in gene expression relating to extracellular matrix ECM organization cell adhesion and visual and nervous system formation. Key pathways include axon guidance synapse formation and ECM biosynthesis/remodeling all of which have potential implications on neural connectivity and sensory development. These findings demonstrate that developmental exposure to opioids induced persistent transcriptomic changes which may have lasting implications for structural integrity and function in vertebrate nervous systems providing insights into the molecular mechanisms of opioid induced alterations during development. Overall design: Zebrafish embryos were exposed to one of the following conditions: fentanyl effluent FE; 0.629 pg/mL fentanyl therapeutic FT; 3.14 ng/mL oxycodone effluent OE; 10.6 pg/mL and oxycodone therapeutic OT; 35.14 ng/mL. Opioi…		pubmed:40429979		replicate 3 fentanyl therapeutic exposed 0 24hpf total RNA at xxxhpf	GSM8851824		source name:Total embryo 50 embryo homogenate\|tissue:Total embryo 50 embryo homogenate\|genotype:WT\|treatment:3.14 ng/mL fentanyl\|batch:3/25/2024\|geo loc name:missing\|collection date:missing	replicate 3 fentanyl therapeutic exposed 0 24hpf total RNA at xxxhpf	Sequenced by NovaGene via Novaseq X Plus Platform paired end reads Raw reads are available as the fq.gz files Trimmed via trimmomatic and ran through rCorrector then mapped to GRCz11 ensemble constructed reference library via Salmon. The aggregated count matrixes for each condition are availible as the txt files Assembly: These are raw reads from Novaseq X plus seqeuncing and count matrixes as txt files Supplementary files format and content: txt files of aggregated count matrixes see above Supplementary files format and content: the counts derived from Salmon	Total embryo 50 embryo homogenate	one of the following conditions: fentanyl effluent FE; 0.629 pg/mL fentanyl therapeutic FT; 3.14 ng/mL oxycodone effluent OE; 10.6 pg/mL oxycodone therapeutic OT; 35.14 ng/mL Control. Opioid exposed embryos were exposed from xxx ttwo xxx hpf. At 24 hpf embryos were washed to remove opioids and allowed to develop normally until 48 hpf.	Trizol Chloroform extraction of total RNA followed by Dnase I treatment and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003	zebrafish embryos were maintained in 0.3x Danieau solution at 28.5C	tissue:Total embryo 50 embryo homogenate\|genotype:WT\|treatment:3.14 ng/mL fentanyl\|batch:3/25/2024	GSM8851824	GSM8851824: replicate 3 fentanyl therapeutic exposed 0 24hpf total RNA at xxxhpf; Danio rerio; RNA Seq	GSM8851824 r1	GSM8851824	1	Trizol Chloroform extraction of total RNA followed by Dnase I treatment and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq X Plus	SRP570947			R4FT_CKDL240008774-1A_22KFGHLT3_L3_1.fq.gz R4FT_CKDL240008774-1A_22KFGHLT3_L3_2.fq.gz	fastq fastq	21177911700.0	70593039.0	GSM8851824 r1	0:150 1:150	A:5565860585;C:5018913046;G:5013238014;T:5578213850;N:1686205	150	150	5565860585	5018913046	5013238014	5578213850	1686205	SRX28024086	SRS24385638	SRA2094947	Merzdorf, MCB, Montana State University	Merzdorf, MCB, Montana State University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	bulk	bulk	United States	2025-03-17	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
35402	35402	SRR32737850	SRX28024085	SRS24385639	SRP570947	PRJNA1237347	Developmental opioid exposure results in lasting transcriptome alterations in zebrafish Danio rerio embryos	GSE292183	Transcriptome Analysis	The opioid epidemic has introduced significant public health challenges with little knowledge regarding the consequences of opioid exposure during embryonic development. While neurobehavioral effects of developmental opioid exposure are well documented early effects of exposure remain largely unexplored. We investigated the effects of oxycodone and fentanyl exposure on gene expression in zebrafish Danio rerio embryos using whole embryo RNA sequencing. Embryos were exposed to environmentally relevant Oxycodone HCl 10.6pg/mL and Fentanyl Citrate 0.629pg/mL and therapeutically relevant Oxycodone HCl 35.14ng/mL and Fentanyl Citrate 3.14ng/mL from 2 hpf to 24 hpf followed by another 24hrs of opioid free development. RNA sequencing at 48hpf revealed dose and drug specific gene expression changes. Lower doses of oxycodone and fentanyl both induced more differentially expressed genes DEGs than higher doses potentially indicative of opioid receptor desensitization occurring at higher concentrations. In total 892 DEGs were identified across all conditions indicating continued differential gene expression well post cessation of opioid exposure. Gene ontology analysis revealed changes in gene expression relating to extracellular matrix ECM organization cell adhesion and visual and nervous system formation. Key pathways include axon guidance synapse formation and ECM biosynthesis/remodeling all of which have potential implications on neural connectivity and sensory development. These findings demonstrate that developmental exposure to opioids induced persistent transcriptomic changes which may have lasting implications for structural integrity and function in vertebrate nervous systems providing insights into the molecular mechanisms of opioid induced alterations during development. Overall design: Zebrafish embryos were exposed to one of the following conditions: fentanyl effluent FE; 0.629 pg/mL fentanyl therapeutic FT; 3.14 ng/mL oxycodone effluent OE; 10.6 pg/mL and oxycodone therapeutic OT; 35.14 ng/mL. Opioi…		pubmed:40429979		replicate 2 fentanyl therapeutic exposed 0 24hpf total RNA at xxxhpf	GSM8851823		source name:Total embryo 50 embryo homogenate\|tissue:Total embryo 50 embryo homogenate\|genotype:WT\|treatment:3.14 ng/mL fentanyl\|batch:3/25/2024\|geo loc name:missing\|collection date:missing	replicate 2 fentanyl therapeutic exposed 0 24hpf total RNA at xxxhpf	Sequenced by NovaGene via Novaseq X Plus Platform paired end reads Raw reads are available as the fq.gz files Trimmed via trimmomatic and ran through rCorrector then mapped to GRCz11 ensemble constructed reference library via Salmon. The aggregated count matrixes for each condition are availible as the txt files Assembly: These are raw reads from Novaseq X plus seqeuncing and count matrixes as txt files Supplementary files format and content: txt files of aggregated count matrixes see above Supplementary files format and content: the counts derived from Salmon	Total embryo 50 embryo homogenate	one of the following conditions: fentanyl effluent FE; 0.629 pg/mL fentanyl therapeutic FT; 3.14 ng/mL oxycodone effluent OE; 10.6 pg/mL oxycodone therapeutic OT; 35.14 ng/mL Control. Opioid exposed embryos were exposed from xxx ttwo xxx hpf. At 24 hpf embryos were washed to remove opioids and allowed to develop normally until 48 hpf.	Trizol Chloroform extraction of total RNA followed by Dnase I treatment and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003	zebrafish embryos were maintained in 0.3x Danieau solution at 28.5C	tissue:Total embryo 50 embryo homogenate\|genotype:WT\|treatment:3.14 ng/mL fentanyl\|batch:3/25/2024	GSM8851823	GSM8851823: replicate 2 fentanyl therapeutic exposed 0 24hpf total RNA at xxxhpf; Danio rerio; RNA Seq	GSM8851823 r1	GSM8851823	1	Trizol Chloroform extraction of total RNA followed by Dnase I treatment and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq X Plus	SRP570947			R2FT_CKDL240008774-1A_22KFGHLT3_L3_1.fq.gz R2FT_CKDL240008774-1A_22KFGHLT3_L3_2.fq.gz	fastq fastq	23561164500.0	78537215.0	GSM8851823 r1	0:150 1:150	A:7284568054;C:4438434312;G:4560720005;T:7275566382;N:1875747	150	150	7284568054	4438434312	4560720005	7275566382	1875747	SRX28024085	SRS24385639	SRA2094947	Merzdorf, MCB, Montana State University	Merzdorf, MCB, Montana State University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	bulk	bulk	United States	2025-03-17	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
35403	35403	SRR32737847	SRX28024084	SRS24385637	SRP570947	PRJNA1237347	Developmental opioid exposure results in lasting transcriptome alterations in zebrafish Danio rerio embryos	GSE292183	Transcriptome Analysis	The opioid epidemic has introduced significant public health challenges with little knowledge regarding the consequences of opioid exposure during embryonic development. While neurobehavioral effects of developmental opioid exposure are well documented early effects of exposure remain largely unexplored. We investigated the effects of oxycodone and fentanyl exposure on gene expression in zebrafish Danio rerio embryos using whole embryo RNA sequencing. Embryos were exposed to environmentally relevant Oxycodone HCl 10.6pg/mL and Fentanyl Citrate 0.629pg/mL and therapeutically relevant Oxycodone HCl 35.14ng/mL and Fentanyl Citrate 3.14ng/mL from 2 hpf to 24 hpf followed by another 24hrs of opioid free development. RNA sequencing at 48hpf revealed dose and drug specific gene expression changes. Lower doses of oxycodone and fentanyl both induced more differentially expressed genes DEGs than higher doses potentially indicative of opioid receptor desensitization occurring at higher concentrations. In total 892 DEGs were identified across all conditions indicating continued differential gene expression well post cessation of opioid exposure. Gene ontology analysis revealed changes in gene expression relating to extracellular matrix ECM organization cell adhesion and visual and nervous system formation. Key pathways include axon guidance synapse formation and ECM biosynthesis/remodeling all of which have potential implications on neural connectivity and sensory development. These findings demonstrate that developmental exposure to opioids induced persistent transcriptomic changes which may have lasting implications for structural integrity and function in vertebrate nervous systems providing insights into the molecular mechanisms of opioid induced alterations during development. Overall design: Zebrafish embryos were exposed to one of the following conditions: fentanyl effluent FE; 0.629 pg/mL fentanyl therapeutic FT; 3.14 ng/mL oxycodone effluent OE; 10.6 pg/mL and oxycodone therapeutic OT; 35.14 ng/mL. Opioi…		pubmed:40429979		replicate 1 fentanyl therapeutic exposed 0 24hpf total RNA at xxxhpf	GSM8851822		source name:Total embryo 50 embryo homogenate\|tissue:Total embryo 50 embryo homogenate\|genotype:WT\|treatment:3.14 ng/mL fentanyl\|batch:3/25/2024\|geo loc name:missing\|collection date:missing	replicate 1 fentanyl therapeutic exposed 0 24hpf total RNA at xxxhpf	Sequenced by NovaGene via Novaseq X Plus Platform paired end reads Raw reads are available as the fq.gz files Trimmed via trimmomatic and ran through rCorrector then mapped to GRCz11 ensemble constructed reference library via Salmon. The aggregated count matrixes for each condition are availible as the txt files Assembly: These are raw reads from Novaseq X plus seqeuncing and count matrixes as txt files Supplementary files format and content: txt files of aggregated count matrixes see above Supplementary files format and content: the counts derived from Salmon	Total embryo 50 embryo homogenate	one of the following conditions: fentanyl effluent FE; 0.629 pg/mL fentanyl therapeutic FT; 3.14 ng/mL oxycodone effluent OE; 10.6 pg/mL oxycodone therapeutic OT; 35.14 ng/mL Control. Opioid exposed embryos were exposed from xxx ttwo xxx hpf. At 24 hpf embryos were washed to remove opioids and allowed to develop normally until 48 hpf.	Trizol Chloroform extraction of total RNA followed by Dnase I treatment and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003	zebrafish embryos were maintained in 0.3x Danieau solution at 28.5C	tissue:Total embryo 50 embryo homogenate\|genotype:WT\|treatment:3.14 ng/mL fentanyl\|batch:3/25/2024	GSM8851822	GSM8851822: replicate 1 fentanyl therapeutic exposed 0 24hpf total RNA at xxxhpf; Danio rerio; RNA Seq	GSM8851822 r1	GSM8851822	1	Trizol Chloroform extraction of total RNA followed by Dnase I treatment and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq X Plus	SRP570947			R1FT_CKDL240008774-1A_22KFGHLT3_L3_1.fq.gz R1FT_CKDL240008774-1A_22KFGHLT3_L3_2.fq.gz	fastq fastq	11262181200.0	37540604.0	GSM8851822 r1	0:150 1:150	A:3084661516;C:2546033080;G:2544910194;T:3085685271;N:891139	150	150	3084661516	2546033080	2544910194	3085685271	891139	SRX28024084	SRS24385637	SRA2094947	Merzdorf, MCB, Montana State University	Merzdorf, MCB, Montana State University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	bulk	bulk	United States	2025-03-17	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
35404	35404	SRR32737848	SRX28024083	SRS24385636	SRP570947	PRJNA1237347	Developmental opioid exposure results in lasting transcriptome alterations in zebrafish Danio rerio embryos	GSE292183	Transcriptome Analysis	The opioid epidemic has introduced significant public health challenges with little knowledge regarding the consequences of opioid exposure during embryonic development. While neurobehavioral effects of developmental opioid exposure are well documented early effects of exposure remain largely unexplored. We investigated the effects of oxycodone and fentanyl exposure on gene expression in zebrafish Danio rerio embryos using whole embryo RNA sequencing. Embryos were exposed to environmentally relevant Oxycodone HCl 10.6pg/mL and Fentanyl Citrate 0.629pg/mL and therapeutically relevant Oxycodone HCl 35.14ng/mL and Fentanyl Citrate 3.14ng/mL from 2 hpf to 24 hpf followed by another 24hrs of opioid free development. RNA sequencing at 48hpf revealed dose and drug specific gene expression changes. Lower doses of oxycodone and fentanyl both induced more differentially expressed genes DEGs than higher doses potentially indicative of opioid receptor desensitization occurring at higher concentrations. In total 892 DEGs were identified across all conditions indicating continued differential gene expression well post cessation of opioid exposure. Gene ontology analysis revealed changes in gene expression relating to extracellular matrix ECM organization cell adhesion and visual and nervous system formation. Key pathways include axon guidance synapse formation and ECM biosynthesis/remodeling all of which have potential implications on neural connectivity and sensory development. These findings demonstrate that developmental exposure to opioids induced persistent transcriptomic changes which may have lasting implications for structural integrity and function in vertebrate nervous systems providing insights into the molecular mechanisms of opioid induced alterations during development. Overall design: Zebrafish embryos were exposed to one of the following conditions: fentanyl effluent FE; 0.629 pg/mL fentanyl therapeutic FT; 3.14 ng/mL oxycodone effluent OE; 10.6 pg/mL and oxycodone therapeutic OT; 35.14 ng/mL. Opioi…		pubmed:40429979		replicate 5 fentanyl effluent exposed 0 24hpf total RNA at xxxhpf	GSM8851821		source name:Total embryo 50 embryo homogenate\|tissue:Total embryo 50 embryo homogenate\|genotype:WT\|treatment:0.629pg/mL fentanyl\|batch:3/25/2024\|geo loc name:missing\|collection date:missing	replicate 5 fentanyl effluent exposed 0 24hpf total RNA at xxxhpf	Sequenced by NovaGene via Novaseq X Plus Platform paired end reads Raw reads are available as the fq.gz files Trimmed via trimmomatic and ran through rCorrector then mapped to GRCz11 ensemble constructed reference library via Salmon. The aggregated count matrixes for each condition are availible as the txt files Assembly: These are raw reads from Novaseq X plus seqeuncing and count matrixes as txt files Supplementary files format and content: txt files of aggregated count matrixes see above Supplementary files format and content: the counts derived from Salmon	Total embryo 50 embryo homogenate	one of the following conditions: fentanyl effluent FE; 0.629 pg/mL fentanyl therapeutic FT; 3.14 ng/mL oxycodone effluent OE; 10.6 pg/mL oxycodone therapeutic OT; 35.14 ng/mL Control. Opioid exposed embryos were exposed from xxx ttwo xxx hpf. At 24 hpf embryos were washed to remove opioids and allowed to develop normally until 48 hpf.	Trizol Chloroform extraction of total RNA followed by Dnase I treatment and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003	zebrafish embryos were maintained in 0.3x Danieau solution at 28.5C	tissue:Total embryo 50 embryo homogenate\|genotype:WT\|treatment:0.629pg/mL fentanyl\|batch:3/25/2024	GSM8851821	GSM8851821: replicate 5 fentanyl effluent exposed 0 24hpf total RNA at xxxhpf; Danio rerio; RNA Seq	GSM8851821 r1	GSM8851821	1	Trizol Chloroform extraction of total RNA followed by Dnase I treatment and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq X Plus	SRP570947			R7FE_CKDL240008774-1A_22KFGHLT3_L3_1.fq.gz R7FE_CKDL240008774-1A_22KFGHLT3_L3_2.fq.gz	fastq fastq	15368398200.0	51227994.0	GSM8851821 r1	0:150 1:150	A:4439560630;C:3205670434;G:3245419161;T:4476535407;N:1212568	150	150	4439560630	3205670434	3245419161	4476535407	1212568	SRX28024083	SRS24385636	SRA2094947	Merzdorf, MCB, Montana State University	Merzdorf, MCB, Montana State University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	bulk	bulk	United States	2025-03-17	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures

Advanced export

JSON shape: default, array, newline-delimited

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");;