metadata: run_metadata: 770 rows where technology = "bulk" and tissue

770 rows where technology = "bulk" and tissue_curation = "Embryo Imprecise"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
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
25188	25188	SRR25670735	SRX21396039	SRS18636197	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 1024cell PAL seq v4	GSM7716868	source name:embryo\|tissue:embryo\|treatment:N1\|geo loc name:missing\|collection date:missing	Fish embryo mRNA 1024cell 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	GSM7716868	GSM7716868: Fish embryo mRNA 1024cell PAL seq v4; Danio rerio; OTHER	GSM7716868 r1	GSM7716868	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_1024cell_PAL_seq_v4_rep1_raw_read1.fastq.gz Fish_embryo_mRNA_1024cell_PAL_seq_v4_rep1_raw_read2.fastq.gz	fastq fastq	2191900794.0	7139742.0	GSM7716868 r1	0:52 1:255	A:571954354;C:551162617;G:572445400;T:490238669;N:6099754	52	255	571954354	551162617	572445400	490238669	6099754	SRX21396039	SRS18636197	SRA1694849	Whitehead Institute	Whitehead Institute	2	0.0011	0.43387	6e-05	0.01058	0.99864	0.99971	0.74576	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	Zygote	Embryo	Embryo Imprecise	All anatomical structures
25189	25189	SRR25670736	SRX21396039	SRS18636197	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 1024cell PAL seq v4	GSM7716868	source name:embryo\|tissue:embryo\|treatment:N1\|geo loc name:missing\|collection date:missing	Fish embryo mRNA 1024cell 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	GSM7716868	GSM7716868: Fish embryo mRNA 1024cell PAL seq v4; Danio rerio; OTHER	GSM7716868 r1	GSM7716868	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_1024cell_PAL_seq_v4_rep2_raw_read1.fastq.gz Fish_embryo_mRNA_1024cell_PAL_seq_v4_rep2_raw_read2.fastq.gz	fastq fastq	3840723193.0	12510499.0	GSM7716868 r2	0:52 1:255	A:985340216;C:991311706;G:1034487140;T:821820974;N:7763157	52	255	985340216	991311706	1034487140	821820974	7763157	SRX21396039	SRS18636197	SRA1694849	Whitehead Institute	Whitehead Institute	2	0.0021	0.0	0.00026	0.0	0.99859	1.0	0.71022		52	255	T	T	mates < 9% mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2023-08-17	Zygote	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
25194	25194	SRR25670741	SRX21396036	SRS18636194	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 1cell PAL seq v4	GSM7716865	source name:embryo\|tissue:embryo\|treatment:N1\|geo loc name:missing\|collection date:missing	Fish embryo mRNA 1cell 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	GSM7716865	GSM7716865: Fish embryo mRNA 1cell PAL seq v4; Danio rerio; OTHER	GSM7716865 r1	GSM7716865	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_1cell_PAL_seq_v4_rep1_raw_read1.fastq.gz Fish_embryo_mRNA_1cell_PAL_seq_v4_rep1_raw_read2.fastq.gz	fastq fastq	2050143851.0	6677993.0	GSM7716865 r1	0:52 1:255	A:536391564;C:527126186;G:557802929;T:422990166;N:5833006	52	255	536391564	527126186	557802929	422990166	5833006	SRX21396036	SRS18636194	SRA1694849	Whitehead Institute	Whitehead Institute	2	0.00016	0.46479	4e-05	0.01408	0.99979	0.99969	0.54545	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	Zygote	Embryo	Embryo Imprecise	All anatomical structures
25195	25195	SRR25670742	SRX21396036	SRS18636194	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 1cell PAL seq v4	GSM7716865	source name:embryo\|tissue:embryo\|treatment:N1\|geo loc name:missing\|collection date:missing	Fish embryo mRNA 1cell 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	GSM7716865	GSM7716865: Fish embryo mRNA 1cell PAL seq v4; Danio rerio; OTHER	GSM7716865 r1	GSM7716865	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_1cell_PAL_seq_v4_rep2_raw_read1.fastq.gz Fish_embryo_mRNA_1cell_PAL_seq_v4_rep2_raw_read2.fastq.gz	fastq fastq	3406093776.0	11094768.0	GSM7716865 r2	0:52 1:255	A:868054279;C:890446070;G:945289336;T:695324057;N:6980034	52	255	868054279	890446070	945289336	695324057	6980034	SRX21396036	SRS18636194	SRA1694849	Whitehead Institute	Whitehead Institute	2	0.00049	0.0	0.00014	0.0	0.99939	1.0	0.58974		52	255	T	T	mates < 9% mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2023-08-17	Zygote	Embryo	Embryo Imprecise	All anatomical structures
28690	28690	SRR26535341	SRX22238472	SRS19292733	SRP468564	PRJNA1032461	A syngeneic spontaneous zebrafish model oftp53 deficient EGFRviii and PI3KCAH1047R driven glioblastoma reveals inhibitory roles for inflammation during tumor initiation and relapsein vivo	GSE246295	Transcriptome Analysis	To build a patient relevantin vivomodel of human glioblastoma we expressed common oncogenic variants including activated human EGFRviii or KRAS and PI3KCAH1047Runder the control of the radial glial specific promoterher4.1in syngeneictp53loss of function mutant zebrafish.Robust tumor formation was observed prior to 45 days of life with a gene expression signature similar to human glioblastoma of the mesenchymal subtype along with a strong inflammatory component. Within early stage tumor lesions and in an intact and endogenous tumor microenvironment we visualized infiltration of phagocytic cells as well as internalization of tumor cells bympeg1.1:GFP+ microglia/macrophages suggesting negative regulatory pressure by pro inflammatory cell types on tumor growth at early stages of glioblastoma initiationin vivo. Furthermore CRISPR/Cas9 mediated gene targeting of master inflammatory transcription factorsirf7andirf8led to increased tumor formation in the primary context while suppression of microglial/macrophage activity led to enhanced tumor cell engraftment following transplantation into otherwise immune competent zebrafish hosts. Altogether we developed a genetically relevant model of aggressive human glioblastoma and harnessed the unique advantages of zebrafish including live imaging high throughput genetic and chemical manipulations to highlight important tumor suppressive roles for the innate immune system on glioblastoma initiation with important future significance for therapeutic discovery and optimizations. Overall design: To capture broad transcriptomic differences in tumor burdened brains versus normal brains we performed bulk RNA sequencing and gene expression analysis of whole brains and sorted cells. EGFRviii derived tumors were induced by microinjection of EGFRviii PI3KCAH1047R and mScarlet constructs defined as EPS. KRAS derived tumors were induced by microinjection of KRAS PI3KCAH1047R GFP constructs defined as KPG. Three whole brains positive for fluorescent tumors EPS 1 3 KPG 1 3 a…	pubmed:39052000	Pooled EPS brains mScarlet ve Sorted Cells	GSM7866396	source name:Sorted Cells\|strain:CG1 p53null\|tissue:Sorted Cells\|geo loc name:missing\|collection date:missing	Pooled EPS brains mScarlet ve Sorted Cells	Raw .fastq data was processed using Salmon quantification of transcripts for each sample. A “decoy aware” index was built with the Danio rerio transcriptome and genome using the GRCz11 assembly with a k mers length of 23 with entries manually added for GFP mScarlet EGFRviii KRAS and PI3KCAH1047R transcripts. Samples were then quantified with the following arguments: r seqBias mp 3 validateMappings rangeFactorizationBins 4. Differential gene expression was compared utilizing DESeq2 and GSEA. Assembly: GRCz11 Supplementary files format and content: Tab delimited .csv file including raw counts for all conditions.	Sorted Cells	Fertilized embryos injected with either EPS or KPG construct mix	Dissected brains or sorted cells were immediately put into Trizol. RNA was then extracted and purified utilizing Monarch RNA Cleanup Kit following manufacturer's recommendations Sequence ready polyA enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina according to manufacturer’s recommendations	Zebrafish were housed and reared following approved animal use protocol	strain:CG1 p53null\|tissue:Sorted Cells	GSM7866396	GSM7866396: Pooled EPS brains mScarlet ve Sorted Cells; Danio rerio; RNA Seq	GSM7866396 r1	GSM7866396	1	Dissected brains or sorted cells were immediately put into Trizol. RNA was then extracted and purified utilizing Monarch RNA Cleanup Kit following manufacturer's recommendations Sequence ready polyA enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina according to manufacturer's recommendations	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP468564	loader:fastq load.py	CS_Neg.fastq.gz	fastq	6384313020.0	63211020.0	GSM7866396 r1	0:101	A:1646899028;C:1504048934;G:1428638008;T:1804712211;N:14839	101		1646899028	1504048934	1428638008	1804712211	14839	SRX22238472	SRS19292733	SRA1740017	Hayes Lab, DSCB, Sickkids Research	Hayes Lab, DSCB, Sickkids Research	1	0.94094		0.14273		0.67416		0.48471		101		B		usable mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	Canada	2023-10-26	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
28691	28691	SRR26535342	SRX22238471	SRS19292732	SRP468564	PRJNA1032461	A syngeneic spontaneous zebrafish model oftp53 deficient EGFRviii and PI3KCAH1047R driven glioblastoma reveals inhibitory roles for inflammation during tumor initiation and relapsein vivo	GSE246295	Transcriptome Analysis	To build a patient relevantin vivomodel of human glioblastoma we expressed common oncogenic variants including activated human EGFRviii or KRAS and PI3KCAH1047Runder the control of the radial glial specific promoterher4.1in syngeneictp53loss of function mutant zebrafish.Robust tumor formation was observed prior to 45 days of life with a gene expression signature similar to human glioblastoma of the mesenchymal subtype along with a strong inflammatory component. Within early stage tumor lesions and in an intact and endogenous tumor microenvironment we visualized infiltration of phagocytic cells as well as internalization of tumor cells bympeg1.1:GFP+ microglia/macrophages suggesting negative regulatory pressure by pro inflammatory cell types on tumor growth at early stages of glioblastoma initiationin vivo. Furthermore CRISPR/Cas9 mediated gene targeting of master inflammatory transcription factorsirf7andirf8led to increased tumor formation in the primary context while suppression of microglial/macrophage activity led to enhanced tumor cell engraftment following transplantation into otherwise immune competent zebrafish hosts. Altogether we developed a genetically relevant model of aggressive human glioblastoma and harnessed the unique advantages of zebrafish including live imaging high throughput genetic and chemical manipulations to highlight important tumor suppressive roles for the innate immune system on glioblastoma initiation with important future significance for therapeutic discovery and optimizations. Overall design: To capture broad transcriptomic differences in tumor burdened brains versus normal brains we performed bulk RNA sequencing and gene expression analysis of whole brains and sorted cells. EGFRviii derived tumors were induced by microinjection of EGFRviii PI3KCAH1047R and mScarlet constructs defined as EPS. KRAS derived tumors were induced by microinjection of KRAS PI3KCAH1047R GFP constructs defined as KPG. Three whole brains positive for fluorescent tumors EPS 1 3 KPG 1 3 a…	pubmed:39052000	Pooled EPS brains mScarlet+ve Sorted Cells	GSM7866395	source name:Sorted Cells\|strain:CG1 p53null\|tissue:Sorted Cells\|geo loc name:missing\|collection date:missing	Pooled EPS brains mScarlet+ve Sorted Cells	Raw .fastq data was processed using Salmon quantification of transcripts for each sample. A “decoy aware” index was built with the Danio rerio transcriptome and genome using the GRCz11 assembly with a k mers length of 23 with entries manually added for GFP mScarlet EGFRviii KRAS and PI3KCAH1047R transcripts. Samples were then quantified with the following arguments: r seqBias mp 3 validateMappings rangeFactorizationBins 4. Differential gene expression was compared utilizing DESeq2 and GSEA. Assembly: GRCz11 Supplementary files format and content: Tab delimited .csv file including raw counts for all conditions.	Sorted Cells	Fertilized embryos injected with either EPS or KPG construct mix	Dissected brains or sorted cells were immediately put into Trizol. RNA was then extracted and purified utilizing Monarch RNA Cleanup Kit following manufacturer's recommendations Sequence ready polyA enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina according to manufacturer’s recommendations	Zebrafish were housed and reared following approved animal use protocol	strain:CG1 p53null\|tissue:Sorted Cells	GSM7866395	GSM7866395: Pooled EPS brains mScarlet+ve Sorted Cells; Danio rerio; RNA Seq	GSM7866395 r1	GSM7866395	1	Dissected brains or sorted cells were immediately put into Trizol. RNA was then extracted and purified utilizing Monarch RNA Cleanup Kit following manufacturer's recommendations Sequence ready polyA enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina according to manufacturer's recommendations	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP468564	loader:fastq load.py	CS_Pos.fastq.gz	fastq	6221936027.0	61603327.0	GSM7866395 r1	0:101	A:1586867899;C:1467436044;G:1398048259;T:1769569401;N:14424	101		1586867899	1467436044	1398048259	1769569401	14424	SRX22238471	SRS19292732	SRA1740017	Hayes Lab, DSCB, Sickkids Research	Hayes Lab, DSCB, Sickkids Research	1	0.88463		0.14567		0.69126		0.48428		101		B		usable mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	Canada	2023-10-26	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
29025	29025	SRR26974567	SRX22668017	SRS19663577	SRP474706	PRJNA1046144	Nlrc3 signaling is required for hematopoietic stem cell emergence by activating Notch signaling in vertebrates	GSE248871	Transcriptome Analysis	Purpose: Since Nlrc3 signaling is imperative for HSPCs production in zebrafish to further determine the regulatory mechanism by which nlrc3 signaling regulates HSPCs. Bulk RNA sequencing analysis is performed to dissect the function and molecular mechanism between the control groups and the nlrc3 morphants groups. Methods: The GFP+ cells in Tgfli1a:eGFP zebrafish embryos at 28 hpf were sorted which is the stage that EHT occurs in the VDA and the site of hemogenic endothelial cells onset. The mRNA profiles of these cells in wild type WT and Nlrc3 knockdown were deep sequencing in triplicate using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner BWA followed by ANOVA ANOVA and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays. Results: Using an optimized data analysis workflow we mapped about 35 million sequence reads per sample and identified 4153 transcripts showing differential expression between the of WT and Nlrc3 morphants with a fold change =1.5 and p value <0.05. Based on the results of RNA seq some signaling pathways essential for the the Nlrc3 regulates the onset of HSPCs in vertebrate are dissected. Including Notch WNT NF kB. Conclusions: Hemogenic endothelial cells mRNA profiles of WT groups and Nlrc3 knockdown groups were deep sequenced and anlysis. Based on the results of RNA seq we performed experiments to validate the up and downstream pathway involved in the the Nlrc3 regulates the onset of HSCPs in vertebrate. Overall design: mRNA profiling by high throughput sequencing to dissect the function and molecular mechanism by which nlrc3 signaling regulates the HSPCs in vertebrate.	pubmed:38172511	samples in nlrc3 MO rep3	GSM7921554	source name:zebrafish embryos\|tissue:GFP+ cells in Tgfli1a:eGFP\|passage:28 hpf embryos\|culture:no culture\|geo loc name:missing\|collection date:missing	samples in nlrc3 MO rep3	Illunima Casava 1.8 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to mm8 whole genome using bowtie v0.12.2 with parameters q p 4 e 100 y a m 10 best strata Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. In short exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Supplementary files format and content: FPKM values for each Sample.	zebrafish embryos		Total RNA was extracted using Trizol reagent Invitrogen CA USA following the manufacturer's procedure. Total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit Agilent CA USA with RIN number >7.0. RNA libraries were prepared for sequencing using standard Illumina protocols		tissue:GFP+ cells in Tgfli1a:eGFP\|passage:28 hpf embryos\|culture:no culture	GSM7921554	GSM7921554: samples in nlrc3 MO rep3; Danio rerio; RNA Seq	GSM7921554 r1	GSM7921554	1	Total RNA was extracted using Trizol reagent Invitrogen CA USA following the manufacturer's procedure. Total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit Agilent CA USA with RIN number >7.0. RNA libraries were prepared for sequencing using standard Illumina protocols	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP474706	loader:fastq load.py	Mo3_Clean_Data2.fq.gz Mo3_Clean_Data1.fq.gz	fastq fastq	5520729146.0	19885310.0	GSM7921554 r1	0:138.82 1:138.81	A:1394113679;C:1363204261;G:1378651437;T:1384757621;N:2148	138	138	1394113679	1363204261	1378651437	1384757621	2148	SRX22668017	SRS19663577	SRA1759375	Zhejiang university	Zhejiang university	2	0.9435	0.94469	0.05163	0.05105	0.7601	0.75958	0.46104	0.46669	141	141	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	bulk	bulk	China	2023-11-28	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
29026	29026	SRR26974568	SRX22668016	SRS19663576	SRP474706	PRJNA1046144	Nlrc3 signaling is required for hematopoietic stem cell emergence by activating Notch signaling in vertebrates	GSE248871	Transcriptome Analysis	Purpose: Since Nlrc3 signaling is imperative for HSPCs production in zebrafish to further determine the regulatory mechanism by which nlrc3 signaling regulates HSPCs. Bulk RNA sequencing analysis is performed to dissect the function and molecular mechanism between the control groups and the nlrc3 morphants groups. Methods: The GFP+ cells in Tgfli1a:eGFP zebrafish embryos at 28 hpf were sorted which is the stage that EHT occurs in the VDA and the site of hemogenic endothelial cells onset. The mRNA profiles of these cells in wild type WT and Nlrc3 knockdown were deep sequencing in triplicate using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner BWA followed by ANOVA ANOVA and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays. Results: Using an optimized data analysis workflow we mapped about 35 million sequence reads per sample and identified 4153 transcripts showing differential expression between the of WT and Nlrc3 morphants with a fold change =1.5 and p value <0.05. Based on the results of RNA seq some signaling pathways essential for the the Nlrc3 regulates the onset of HSPCs in vertebrate are dissected. Including Notch WNT NF kB. Conclusions: Hemogenic endothelial cells mRNA profiles of WT groups and Nlrc3 knockdown groups were deep sequenced and anlysis. Based on the results of RNA seq we performed experiments to validate the up and downstream pathway involved in the the Nlrc3 regulates the onset of HSCPs in vertebrate. Overall design: mRNA profiling by high throughput sequencing to dissect the function and molecular mechanism by which nlrc3 signaling regulates the HSPCs in vertebrate.	pubmed:38172511	samples in nlrc3 MO rep2	GSM7921553	source name:zebrafish embryos\|tissue:GFP+ cells in Tgfli1a:eGFP\|passage:28 hpf embryos\|culture:no culture\|geo loc name:missing\|collection date:missing	samples in nlrc3 MO rep2	Illunima Casava 1.8 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to mm8 whole genome using bowtie v0.12.2 with parameters q p 4 e 100 y a m 10 best strata Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. In short exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Supplementary files format and content: FPKM values for each Sample.	zebrafish embryos		Total RNA was extracted using Trizol reagent Invitrogen CA USA following the manufacturer's procedure. Total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit Agilent CA USA with RIN number >7.0. RNA libraries were prepared for sequencing using standard Illumina protocols		tissue:GFP+ cells in Tgfli1a:eGFP\|passage:28 hpf embryos\|culture:no culture	GSM7921553	GSM7921553: samples in nlrc3 MO rep2; Danio rerio; RNA Seq	GSM7921553 r1	GSM7921553	1	Total RNA was extracted using Trizol reagent Invitrogen CA USA following the manufacturer's procedure. Total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit Agilent CA USA with RIN number >7.0. RNA libraries were prepared for sequencing using standard Illumina protocols	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP474706	loader:fastq load.py	Mo2_Clean_Data1.fq.gz Mo2_Clean_Data2.fq.gz	fastq fastq	6532296488.0	23367662.0	GSM7921553 r1	0:139.78 1:139.77	A:1648685612;C:1610899197;G:1630932563;T:1641776735;N:2381	139	139	1648685612	1610899197	1630932563	1641776735	2381	SRX22668016	SRS19663576	SRA1759375	Zhejiang university	Zhejiang university	2	0.94588	0.94696	0.05065	0.05045	0.75891	0.75854	0.47315	0.47431	141	141	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	bulk	bulk	China	2023-11-28	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
29027	29027	SRR26974569	SRX22668015	SRS19663575	SRP474706	PRJNA1046144	Nlrc3 signaling is required for hematopoietic stem cell emergence by activating Notch signaling in vertebrates	GSE248871	Transcriptome Analysis	Purpose: Since Nlrc3 signaling is imperative for HSPCs production in zebrafish to further determine the regulatory mechanism by which nlrc3 signaling regulates HSPCs. Bulk RNA sequencing analysis is performed to dissect the function and molecular mechanism between the control groups and the nlrc3 morphants groups. Methods: The GFP+ cells in Tgfli1a:eGFP zebrafish embryos at 28 hpf were sorted which is the stage that EHT occurs in the VDA and the site of hemogenic endothelial cells onset. The mRNA profiles of these cells in wild type WT and Nlrc3 knockdown were deep sequencing in triplicate using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner BWA followed by ANOVA ANOVA and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays. Results: Using an optimized data analysis workflow we mapped about 35 million sequence reads per sample and identified 4153 transcripts showing differential expression between the of WT and Nlrc3 morphants with a fold change =1.5 and p value <0.05. Based on the results of RNA seq some signaling pathways essential for the the Nlrc3 regulates the onset of HSPCs in vertebrate are dissected. Including Notch WNT NF kB. Conclusions: Hemogenic endothelial cells mRNA profiles of WT groups and Nlrc3 knockdown groups were deep sequenced and anlysis. Based on the results of RNA seq we performed experiments to validate the up and downstream pathway involved in the the Nlrc3 regulates the onset of HSCPs in vertebrate. Overall design: mRNA profiling by high throughput sequencing to dissect the function and molecular mechanism by which nlrc3 signaling regulates the HSPCs in vertebrate.	pubmed:38172511	samples in nlrc3 MO rep1	GSM7921552	source name:zebrafish embryos\|tissue:GFP+ cells in Tgfli1a:eGFP\|passage:28 hpf embryos\|culture:no culture\|geo loc name:missing\|collection date:missing	samples in nlrc3 MO rep1	Illunima Casava 1.8 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to mm8 whole genome using bowtie v0.12.2 with parameters q p 4 e 100 y a m 10 best strata Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. In short exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Supplementary files format and content: FPKM values for each Sample.	zebrafish embryos		Total RNA was extracted using Trizol reagent Invitrogen CA USA following the manufacturer's procedure. Total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit Agilent CA USA with RIN number >7.0. RNA libraries were prepared for sequencing using standard Illumina protocols		tissue:GFP+ cells in Tgfli1a:eGFP\|passage:28 hpf embryos\|culture:no culture	GSM7921552	GSM7921552: samples in nlrc3 MO rep1; Danio rerio; RNA Seq	GSM7921552 r1	GSM7921552	1	Total RNA was extracted using Trizol reagent Invitrogen CA USA following the manufacturer's procedure. Total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit Agilent CA USA with RIN number >7.0. RNA libraries were prepared for sequencing using standard Illumina protocols	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP474706	loader:fastq load.py	Mo1_Clean_Data1.fq.gz Mo1_Clean_Data2.fq.gz	fastq fastq	5812795813.0	20780108.0	GSM7921552 r1	0:139.86 1:139.87	A:1453223147;C:1447175836;G:1465655085;T:1446739519;N:2226	139	139	1453223147	1447175836	1465655085	1446739519	2226	SRX22668015	SRS19663575	SRA1759375	Zhejiang university	Zhejiang university	2	0.94733	0.94831	0.05436	0.05351	0.76059	0.76063	0.47936	0.47664	141	141	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	bulk	bulk	China	2023-11-28	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
29028	29028	SRR26974570	SRX22668014	SRS19663574	SRP474706	PRJNA1046144	Nlrc3 signaling is required for hematopoietic stem cell emergence by activating Notch signaling in vertebrates	GSE248871	Transcriptome Analysis	Purpose: Since Nlrc3 signaling is imperative for HSPCs production in zebrafish to further determine the regulatory mechanism by which nlrc3 signaling regulates HSPCs. Bulk RNA sequencing analysis is performed to dissect the function and molecular mechanism between the control groups and the nlrc3 morphants groups. Methods: The GFP+ cells in Tgfli1a:eGFP zebrafish embryos at 28 hpf were sorted which is the stage that EHT occurs in the VDA and the site of hemogenic endothelial cells onset. The mRNA profiles of these cells in wild type WT and Nlrc3 knockdown were deep sequencing in triplicate using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner BWA followed by ANOVA ANOVA and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays. Results: Using an optimized data analysis workflow we mapped about 35 million sequence reads per sample and identified 4153 transcripts showing differential expression between the of WT and Nlrc3 morphants with a fold change =1.5 and p value <0.05. Based on the results of RNA seq some signaling pathways essential for the the Nlrc3 regulates the onset of HSPCs in vertebrate are dissected. Including Notch WNT NF kB. Conclusions: Hemogenic endothelial cells mRNA profiles of WT groups and Nlrc3 knockdown groups were deep sequenced and anlysis. Based on the results of RNA seq we performed experiments to validate the up and downstream pathway involved in the the Nlrc3 regulates the onset of HSCPs in vertebrate. Overall design: mRNA profiling by high throughput sequencing to dissect the function and molecular mechanism by which nlrc3 signaling regulates the HSPCs in vertebrate.	pubmed:38172511	samples in control MO rep3	GSM7921551	source name:zebrafish embryos\|tissue:GFP+ cells in Tgfli1a:eGFP\|passage:28 hpf embryos\|culture:no culture\|geo loc name:missing\|collection date:missing	samples in control MO rep3	Illunima Casava 1.8 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to mm8 whole genome using bowtie v0.12.2 with parameters q p 4 e 100 y a m 10 best strata Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. In short exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Supplementary files format and content: FPKM values for each Sample.	zebrafish embryos		Total RNA was extracted using Trizol reagent Invitrogen CA USA following the manufacturer's procedure. Total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit Agilent CA USA with RIN number >7.0. RNA libraries were prepared for sequencing using standard Illumina protocols		tissue:GFP+ cells in Tgfli1a:eGFP\|passage:28 hpf embryos\|culture:no culture	GSM7921551	GSM7921551: samples in control MO rep3; Danio rerio; RNA Seq	GSM7921551 r1	GSM7921551	1	Total RNA was extracted using Trizol reagent Invitrogen CA USA following the manufacturer's procedure. Total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit Agilent CA USA with RIN number >7.0. RNA libraries were prepared for sequencing using standard Illumina protocols	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP474706	loader:fastq load.py	S3_Clean_Data1.fq.gz S3_Clean_Data2.fq.gz	fastq fastq	5643732705.0	20272868.0	GSM7921551 r1	0:139.20 1:139.19	A:1466198749;C:1349499199;G:1367008013;T:1461024521;N:2223	139	139	1466198749	1349499199	1367008013	1461024521	2223	SRX22668014	SRS19663574	SRA1759375	Zhejiang university	Zhejiang university	2	0.95103	0.95208	0.07142	0.07068	0.73428	0.73371	0.47064	0.47197	141	141	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	bulk	bulk	China	2023-11-28	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
29029	29029	SRR26974571	SRX22668013	SRS19663573	SRP474706	PRJNA1046144	Nlrc3 signaling is required for hematopoietic stem cell emergence by activating Notch signaling in vertebrates	GSE248871	Transcriptome Analysis	Purpose: Since Nlrc3 signaling is imperative for HSPCs production in zebrafish to further determine the regulatory mechanism by which nlrc3 signaling regulates HSPCs. Bulk RNA sequencing analysis is performed to dissect the function and molecular mechanism between the control groups and the nlrc3 morphants groups. Methods: The GFP+ cells in Tgfli1a:eGFP zebrafish embryos at 28 hpf were sorted which is the stage that EHT occurs in the VDA and the site of hemogenic endothelial cells onset. The mRNA profiles of these cells in wild type WT and Nlrc3 knockdown were deep sequencing in triplicate using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner BWA followed by ANOVA ANOVA and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays. Results: Using an optimized data analysis workflow we mapped about 35 million sequence reads per sample and identified 4153 transcripts showing differential expression between the of WT and Nlrc3 morphants with a fold change =1.5 and p value <0.05. Based on the results of RNA seq some signaling pathways essential for the the Nlrc3 regulates the onset of HSPCs in vertebrate are dissected. Including Notch WNT NF kB. Conclusions: Hemogenic endothelial cells mRNA profiles of WT groups and Nlrc3 knockdown groups were deep sequenced and anlysis. Based on the results of RNA seq we performed experiments to validate the up and downstream pathway involved in the the Nlrc3 regulates the onset of HSCPs in vertebrate. Overall design: mRNA profiling by high throughput sequencing to dissect the function and molecular mechanism by which nlrc3 signaling regulates the HSPCs in vertebrate.	pubmed:38172511	samples in control MO rep2	GSM7921550	source name:zebrafish embryos\|tissue:GFP+ cells in Tgfli1a:eGFP\|passage:28 hpf embryos\|culture:no culture\|geo loc name:missing\|collection date:missing	samples in control MO rep2	Illunima Casava 1.8 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to mm8 whole genome using bowtie v0.12.2 with parameters q p 4 e 100 y a m 10 best strata Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. In short exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Supplementary files format and content: FPKM values for each Sample.	zebrafish embryos		Total RNA was extracted using Trizol reagent Invitrogen CA USA following the manufacturer's procedure. Total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit Agilent CA USA with RIN number >7.0. RNA libraries were prepared for sequencing using standard Illumina protocols		tissue:GFP+ cells in Tgfli1a:eGFP\|passage:28 hpf embryos\|culture:no culture	GSM7921550	GSM7921550: samples in control MO rep2; Danio rerio; RNA Seq	GSM7921550 r1	GSM7921550	1	Total RNA was extracted using Trizol reagent Invitrogen CA USA following the manufacturer's procedure. Total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit Agilent CA USA with RIN number >7.0. RNA libraries were prepared for sequencing using standard Illumina protocols	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP474706	loader:fastq load.py	S2_Clean_Data1.fq.gz S2_Clean_Data2.fq.gz	fastq fastq	4436220529.0	15923512.0	GSM7921550 r1	0:139.30 1:139.29	A:1152960918;C:1060020216;G:1074069001;T:1149168714;N:1680	139	139	1152960918	1060020216	1074069001	1149168714	1680	SRX22668013	SRS19663573	SRA1759375	Zhejiang university	Zhejiang university	2	0.94868	0.94952	0.07127	0.07083	0.73438	0.73403	0.46822	0.46865	141	141	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	bulk	bulk	China	2023-11-28	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
29030	29030	SRR26974572	SRX22668012	SRS19663572	SRP474706	PRJNA1046144	Nlrc3 signaling is required for hematopoietic stem cell emergence by activating Notch signaling in vertebrates	GSE248871	Transcriptome Analysis	Purpose: Since Nlrc3 signaling is imperative for HSPCs production in zebrafish to further determine the regulatory mechanism by which nlrc3 signaling regulates HSPCs. Bulk RNA sequencing analysis is performed to dissect the function and molecular mechanism between the control groups and the nlrc3 morphants groups. Methods: The GFP+ cells in Tgfli1a:eGFP zebrafish embryos at 28 hpf were sorted which is the stage that EHT occurs in the VDA and the site of hemogenic endothelial cells onset. The mRNA profiles of these cells in wild type WT and Nlrc3 knockdown were deep sequencing in triplicate using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner BWA followed by ANOVA ANOVA and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays. Results: Using an optimized data analysis workflow we mapped about 35 million sequence reads per sample and identified 4153 transcripts showing differential expression between the of WT and Nlrc3 morphants with a fold change =1.5 and p value <0.05. Based on the results of RNA seq some signaling pathways essential for the the Nlrc3 regulates the onset of HSPCs in vertebrate are dissected. Including Notch WNT NF kB. Conclusions: Hemogenic endothelial cells mRNA profiles of WT groups and Nlrc3 knockdown groups were deep sequenced and anlysis. Based on the results of RNA seq we performed experiments to validate the up and downstream pathway involved in the the Nlrc3 regulates the onset of HSCPs in vertebrate. Overall design: mRNA profiling by high throughput sequencing to dissect the function and molecular mechanism by which nlrc3 signaling regulates the HSPCs in vertebrate.	pubmed:38172511	samples in control MO rep1	GSM7921549	source name:zebrafish embryos\|tissue:GFP+ cells in Tgfli1a:eGFP\|passage:28 hpf embryos\|culture:no culture\|geo loc name:missing\|collection date:missing	samples in control MO rep1	Illunima Casava 1.8 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to mm8 whole genome using bowtie v0.12.2 with parameters q p 4 e 100 y a m 10 best strata Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. In short exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Supplementary files format and content: FPKM values for each Sample.	zebrafish embryos		Total RNA was extracted using Trizol reagent Invitrogen CA USA following the manufacturer's procedure. Total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit Agilent CA USA with RIN number >7.0. RNA libraries were prepared for sequencing using standard Illumina protocols		tissue:GFP+ cells in Tgfli1a:eGFP\|passage:28 hpf embryos\|culture:no culture	GSM7921549	GSM7921549: samples in control MO rep1; Danio rerio; RNA Seq	GSM7921549 r1	GSM7921549	1	Total RNA was extracted using Trizol reagent Invitrogen CA USA following the manufacturer's procedure. Total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit Agilent CA USA with RIN number >7.0. RNA libraries were prepared for sequencing using standard Illumina protocols	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP474706	loader:fastq load.py	S1_Clean_Data1.fq.gz S1_Clean_Data2.fq.gz	fastq fastq	6121313766.0	21997860.0	GSM7921549 r1	0:139.14 1:139.13	A:1591232135;C:1462847585;G:1481777440;T:1585450214;N:6392	139	139	1591232135	1462847585	1481777440	1585450214	6392	SRX22668012	SRS19663572	SRA1759375	Zhejiang university	Zhejiang university	2	0.95177	0.95291	0.07145	0.07064	0.73322	0.73306	0.47372	0.47734	141	141	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	bulk	bulk	China	2023-11-28	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
30024	30024	SRR27732020	SRX23397628	SRS20258469	SRP485064	PRJNA1067370	zebrafish embryo for scRNA seq and bulk RNA seq	PRJNA1067370	Other	Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.		wild type 36 hpf embryo	zebrafish embryo 36hpf replicate 1	strain:not applicable\|isolate:not collected\|breed:Danio\|cultivar:not applicable\|ecotype:not applicable\|dev stage:36 hpf\|collection date:2022 10\|geo loc name:not applicable\|sex:not applicable\|tissue:embryo\|genotype:wild type\|sample type:whole organism\|treatment:replicate 1\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: 36hpf embryo	W 13	W 13	bulk RNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485064		WT36h-1_1.fq.gz WT36h-1_2.fq.gz	fastq fastq	7292758500.0	24309195.0	WT36h 1 1.fq.gz	0:150 1:150	A:1908273664;C:1731632674;G:1760624671;T:1892167502;N:59989	150	150	1908273664	1731632674	1760624671	1892167502	59989	SRX23397628	SRS20258469	SRA1791946	Shanghai Ocean University\|College of Fisheries and Life	Shanghai Ocean University	2	0.94269	0.94089	0.07258	0.07222	0.69978	0.70143	0.45682	0.45348	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	China	2024-01-26	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
30025	30025	SRR27732021	SRX23397627	SRS20258468	SRP485064	PRJNA1067370	zebrafish embryo for scRNA seq and bulk RNA seq	PRJNA1067370	Other	Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.		wild type 24 hpf embryo	zebrafish embryo 24hpf replicate 3	strain:not applicable\|isolate:not collected\|breed:Danio\|cultivar:not applicable\|ecotype:not applicable\|dev stage:24 hpf\|collection date:2022 10\|geo loc name:not applicable\|sex:not applicable\|tissue:embryo\|genotype:wild type\|sample type:whole organism\|treatment:replicate 3\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: 24hpf embryo	W 12	W 12	bulk RNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485064		WT24h-3_1.fq.gz WT24h-3_2.fq.gz	fastq fastq	6515838900.0	21719463.0	WT24h 3 1.fq.gz	0:150 1:150	A:1713953613;C:1537571365;G:1564392828;T:1699697009;N:224085	150	150	1713953613	1537571365	1564392828	1699697009	224085	SRX23397627	SRS20258468	SRA1791946	Shanghai Ocean University\|College of Fisheries and Life	Shanghai Ocean University	2	0.93632	0.9362	0.06541	0.06556	0.69992	0.70094	0.46899	0.46674	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	China	2024-01-26	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
30026	30026	SRR27732022	SRX23397626	SRS20258467	SRP485064	PRJNA1067370	zebrafish embryo for scRNA seq and bulk RNA seq	PRJNA1067370	Other	Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.		wild type 24 hpf embryo	zebrafish embryo 24hpf replicate 2	strain:not applicable\|isolate:not collected\|breed:Danio\|cultivar:not applicable\|ecotype:not applicable\|dev stage:24 hpf\|collection date:2022 10\|geo loc name:not applicable\|sex:not applicable\|tissue:embryo\|genotype:wild type\|sample type:whole organism\|treatment:replicate 2\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: 24hpf embryo	W 11	W 11	bulk RNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485064		WT24h-2_1.fq.gz WT24h-2_2.fq.gz	fastq fastq	7161020400.0	23870068.0	WT24h 2 1.fq.gz	0:150 1:150	A:1879362459;C:1692535178;G:1727934369;T:1860947917;N:240477	150	150	1879362459	1692535178	1727934369	1860947917	240477	SRX23397626	SRS20258467	SRA1791946	Shanghai Ocean University\|College of Fisheries and Life	Shanghai Ocean University	2	0.93727	0.93618	0.06477	0.06473	0.69546	0.69534	0.46029	0.46325	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	China	2024-01-26	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
30027	30027	SRR27732023	SRX23397625	SRS20258466	SRP485064	PRJNA1067370	zebrafish embryo for scRNA seq and bulk RNA seq	PRJNA1067370	Other	Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.		wild type 24 hpf embryo	zebrafish embryo 24hpf replicate 1	strain:not applicable\|isolate:not collected\|breed:Danio\|cultivar:not applicable\|ecotype:not applicable\|dev stage:24 hpf\|collection date:2022 10\|geo loc name:not applicable\|sex:not applicable\|tissue:embryo\|genotype:wild type\|sample type:whole organism\|treatment:replicate 1\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: 24hpf embryo	W 10	W 10	bulk RNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485064		WT24h-1_1.fq.gz WT24h-1_2.fq.gz	fastq fastq	6174518700.0	20581729.0	WT24h 1 1.fq.gz	0:150 1:150	A:1622124267;C:1458396393;G:1486147186;T:1607751720;N:99134	150	150	1622124267	1458396393	1486147186	1607751720	99134	SRX23397625	SRS20258466	SRA1791946	Shanghai Ocean University\|College of Fisheries and Life	Shanghai Ocean University	2	0.93835	0.93534	0.06486	0.06373	0.69934	0.70041	0.45483	0.45986	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	China	2024-01-26	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
30028	30028	SRR27732024	SRX23397624	SRS20258465	SRP485064	PRJNA1067370	zebrafish embryo for scRNA seq and bulk RNA seq	PRJNA1067370	Other	Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.		wild type 12 hpf embryo	zebrafish embryo 12hpf replicate 3	strain:not applicable\|isolate:not collected\|breed:Danio\|cultivar:not applicable\|ecotype:not applicable\|dev stage:12 hpf\|collection date:2022 10\|geo loc name:not applicable\|sex:not applicable\|tissue:embryo\|genotype:wild type\|sample type:whole organism\|treatment:replicate 3\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: 12hpf embryo	W 9	W 9	bulk RNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485064		WT12h-3_1.fq.gz WT12h-3_2.fq.gz	fastq fastq	6455561100.0	21518537.0	WT12h 3 1.fq.gz	0:150 1:150	A:1703515693;C:1511743995;G:1560331864;T:1679864521;N:105027	150	150	1703515693	1511743995	1560331864	1679864521	105027	SRX23397624	SRS20258465	SRA1791946	Shanghai Ocean University\|College of Fisheries and Life	Shanghai Ocean University	2	0.94111	0.94086	0.06759	0.06714	0.74383	0.74479	0.46264	0.46309	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	China	2024-01-26	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
30029	30029	SRR27732025	SRX23397623	SRS20258464	SRP485064	PRJNA1067370	zebrafish embryo for scRNA seq and bulk RNA seq	PRJNA1067370	Other	Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.		wild type 12 hpf embryo	zebrafish embryo 12hpf replicate 2	strain:not applicable\|isolate:not collected\|breed:Danio\|cultivar:not applicable\|ecotype:not applicable\|dev stage:12 hpf\|collection date:2022 10\|geo loc name:not applicable\|sex:not applicable\|tissue:embryo\|genotype:wild type\|sample type:whole organism\|treatment:replicate 2\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: 12hpf embryo	W 8	W 8	bulk RNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485064		WT12h-2_1.fq.gz WT12h-2_2.fq.gz	fastq fastq	6161839200.0	20539464.0	WT12h 2 1.fq.gz	0:150 1:150	A:1628002733;C:1440787634;G:1486546983;T:1606403484;N:98366	150	150	1628002733	1440787634	1486546983	1606403484	98366	SRX23397623	SRS20258464	SRA1791946	Shanghai Ocean University\|College of Fisheries and Life	Shanghai Ocean University	2	0.94064	0.93857	0.06897	0.06866	0.7457	0.74621	0.46575	0.46211	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	China	2024-01-26	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
30030	30030	SRR27732026	SRX23397622	SRS20258463	SRP485064	PRJNA1067370	zebrafish embryo for scRNA seq and bulk RNA seq	PRJNA1067370	Other	Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.		wild type 12 hpf embryo	zebrafish embryo 12hpf replicate 1	strain:not applicable\|isolate:not collected\|breed:Danio\|cultivar:not applicable\|ecotype:not applicable\|dev stage:12 hpf\|collection date:2022 10\|geo loc name:not applicable\|sex:not applicable\|tissue:embryo\|genotype:wild type\|sample type:whole organism\|treatment:replicate 1\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: 12hpf embryo	W 7	W 7	bulk RNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485064		WT12h-1_2.fq.gz WT12h-1_1.fq.gz	fastq fastq	6395259000.0	21317530.0	WT12h 1 1.fq.gz	0:150 1:150	A:1700786034;C:1487669685;G:1530455534;T:1676243983;N:103764	150	150	1700786034	1487669685	1530455534	1676243983	103764	SRX23397622	SRS20258463	SRA1791946	Shanghai Ocean University\|College of Fisheries and Life	Shanghai Ocean University	2	0.94192	0.9393	0.07278	0.0714	0.74225	0.74414	0.46258	0.46623	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	China	2024-01-26	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
30031	30031	SRR27732027	SRX23397621	SRS20258462	SRP485064	PRJNA1067370	zebrafish embryo for scRNA seq and bulk RNA seq	PRJNA1067370	Other	Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.		wild type 8 hpf embryo	zebrafish embryo 8hpf replicate 3	strain:not applicable\|isolate:not collected\|breed:Danio\|cultivar:not applicable\|ecotype:not applicable\|dev stage:8 hpf\|collection date:2022 10\|geo loc name:not applicable\|sex:not applicable\|tissue:embryo\|genotype:wild type\|sample type:whole organism\|treatment:replicate 3\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: 8hpf embryo	W 6	W 6	bulk RNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485064		WT8h-3_2.fq.gz WT8h-3_1.fq.gz	fastq fastq	6747267300.0	22490891.0	WT8h 3 1.fq.gz	0:150 1:150	A:1802220913;C:1560718919;G:1610360895;T:1773867706;N:98867	150	150	1802220913	1560718919	1610360895	1773867706	98867	SRX23397621	SRS20258462	SRA1791946	Shanghai Ocean University\|College of Fisheries and Life	Shanghai Ocean University	2	0.94669	0.94524	0.06343	0.06321	0.74517	0.74535	0.46737	0.46861	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	China	2024-01-26	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
30032	30032	SRR27732028	SRX23397620	SRS20258461	SRP485064	PRJNA1067370	zebrafish embryo for scRNA seq and bulk RNA seq	PRJNA1067370	Other	Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.		wild type 72 hpf embryo	zebrafish embryo 72hpf replicate 3	strain:not applicable\|isolate:not collected\|breed:Danio\|cultivar:not applicable\|ecotype:not applicable\|dev stage:72 hpf\|collection date:2022 10\|geo loc name:not applicable\|sex:not applicable\|tissue:embryo\|genotype:wild type\|sample type:whole organism\|treatment:replicate 3\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: 72hpf embryo	W 21	W 21	bulk RNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485064		WT72h-3_1.fq.gz WT72h-3_2.fq.gz	fastq fastq	6611014500.0	22036715.0	WT72h 3 1.fq.gz	0:150 1:150	A:1772431295;C:1528499931;G:1545216909;T:1764783401;N:82964	150	150	1772431295	1528499931	1545216909	1764783401	82964	SRX23397620	SRS20258461	SRA1791946	Shanghai Ocean University\|College of Fisheries and Life	Shanghai Ocean University	2	0.93676	0.9346	0.10556	0.10444	0.66927	0.66991	0.46155	0.46025	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	China	2024-01-26	Larval	Larval	Embryo Imprecise	All anatomical structures
30033	30033	SRR27732029	SRX23397619	SRS20258460	SRP485064	PRJNA1067370	zebrafish embryo for scRNA seq and bulk RNA seq	PRJNA1067370	Other	Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.		wild type 72 hpf embryo	zebrafish embryo 72hpf replicate 2	strain:not applicable\|isolate:not collected\|breed:Danio\|cultivar:not applicable\|ecotype:not applicable\|dev stage:72 hpf\|collection date:2022 10\|geo loc name:not applicable\|sex:not applicable\|tissue:embryo\|genotype:wild type\|sample type:whole organism\|treatment:replicate 2\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: 72hpf embryo	W 20	W 20	bulk RNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485064		WT72h-2_1.fq.gz WT72h-2_2.fq.gz	fastq fastq	5844974100.0	19483247.0	WT72h 2 1.fq.gz	0:150 1:150	A:1570406354;C:1348972192;G:1363229634;T:1562318366;N:47554	150	150	1570406354	1348972192	1363229634	1562318366	47554	SRX23397619	SRS20258460	SRA1791946	Shanghai Ocean University\|College of Fisheries and Life	Shanghai Ocean University	2	0.93927	0.93723	0.10803	0.10754	0.66574	0.66959	0.45443	0.4547	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	China	2024-01-26	Larval	Larval	Embryo Imprecise	All anatomical structures
30034	30034	SRR27732030	SRX23397618	SRS20258459	SRP485064	PRJNA1067370	zebrafish embryo for scRNA seq and bulk RNA seq	PRJNA1067370	Other	Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.		wild type 72 hpf embryo	zebrafish embryo 72hpf replicate 1	strain:not applicable\|isolate:not collected\|breed:Danio\|cultivar:not applicable\|ecotype:not applicable\|dev stage:72 hpf\|collection date:2022 10\|geo loc name:not applicable\|sex:not applicable\|tissue:embryo\|genotype:wild type\|sample type:whole organism\|treatment:replicate 1\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: 72hpf embryo	W 19	W 19	bulk RNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485064		WT72h-1_1.fq.gz WT72h-1_2.fq.gz	fastq fastq	7024123200.0	23413744.0	WT72h 1 1.fq.gz	0:150 1:150	A:1870182203;C:1638926026;G:1656247404;T:1858679271;N:88296	150	150	1870182203	1638926026	1656247404	1858679271	88296	SRX23397618	SRS20258459	SRA1791946	Shanghai Ocean University\|College of Fisheries and Life	Shanghai Ocean University	2	0.93353	0.93369	0.09236	0.09181	0.6674	0.66789	0.44578	0.45563	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	China	2024-01-26	Larval	Larval	Embryo Imprecise	All anatomical structures
30035	30035	SRR27732031	SRX23397617	SRS20258458	SRP485064	PRJNA1067370	zebrafish embryo for scRNA seq and bulk RNA seq	PRJNA1067370	Other	Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.		wild type 48 hpf embryo	zebrafish embryo 48hpf replicate 3	strain:not applicable\|isolate:not collected\|breed:Danio\|cultivar:not applicable\|ecotype:not applicable\|dev stage:48 hpf\|collection date:2022 10\|geo loc name:not applicable\|sex:not applicable\|tissue:embryo\|genotype:wild type\|sample type:whole organism\|treatment:replicate 3\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: 48hpf embryo	W 18	W 18	bulk RNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485064		WT48h-3_1.fq.gz WT48h-3_2.fq.gz	fastq fastq	6520477800.0	21734926.0	WT48h 3 1.fq.gz	0:150 1:150	A:1739928482;C:1516508736;G:1531638319;T:1732180903;N:221360	150	150	1739928482	1516508736	1531638319	1732180903	221360	SRX23397617	SRS20258458	SRA1791946	Shanghai Ocean University\|College of Fisheries and Life	Shanghai Ocean University	2	0.93874	0.93954	0.09485	0.09438	0.67888	0.67913	0.46039	0.46026	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	China	2024-01-26	Hatching	Embryo	Embryo Imprecise	All anatomical structures
30036	30036	SRR27732032	SRX23397616	SRS20258457	SRP485064	PRJNA1067370	zebrafish embryo for scRNA seq and bulk RNA seq	PRJNA1067370	Other	Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.		wild type 48 hpf embryo	zebrafish embryo 48hpf replicate 2	strain:not applicable\|isolate:not collected\|breed:Danio\|cultivar:not applicable\|ecotype:not applicable\|dev stage:48 hpf\|collection date:2022 10\|geo loc name:not applicable\|sex:not applicable\|tissue:embryo\|genotype:wild type\|sample type:whole organism\|treatment:replicate 2\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: 48hpf embryo	W 17	W 17	bulk RNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485064		WT48h-2_2.fq.gz WT48h-2_1.fq.gz	fastq fastq	7046397300.0	23487991.0	WT48h 2 1.fq.gz	0:150 1:150	A:1865031055;C:1655796645;G:1670091105;T:1855237793;N:240702	150	150	1865031055	1655796645	1670091105	1855237793	240702	SRX23397616	SRS20258457	SRA1791946	Shanghai Ocean University\|College of Fisheries and Life	Shanghai Ocean University	2	0.94056	0.93987	0.08562	0.08535	0.68241	0.68288	0.46355	0.46204	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	China	2024-01-26	Hatching	Embryo	Embryo Imprecise	All anatomical structures
30037	30037	SRR27732033	SRX23397615	SRS20258456	SRP485064	PRJNA1067370	zebrafish embryo for scRNA seq and bulk RNA seq	PRJNA1067370	Other	Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.		wild type 48 hpf embryo	zebrafish embryo 48hpf replicate 1	strain:not applicable\|isolate:not collected\|breed:Danio\|cultivar:not applicable\|ecotype:not applicable\|dev stage:48 hpf\|collection date:2022 10\|geo loc name:not applicable\|sex:not applicable\|tissue:embryo\|genotype:wild type\|sample type:whole organism\|treatment:replicate 1\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: 48hpf embryo	W 16	W 16	bulk RNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485064		WT48h-1_1.fq.gz WT48h-1_2.fq.gz	fastq fastq	6851959800.0	22839866.0	WT48h 1 1.fq.gz	0:150 1:150	A:1813160204;C:1610483050;G:1626359291;T:1801871129;N:86126	150	150	1813160204	1610483050	1626359291	1801871129	86126	SRX23397615	SRS20258456	SRA1791946	Shanghai Ocean University\|College of Fisheries and Life	Shanghai Ocean University	2	0.94028	0.93857	0.08526	0.08523	0.68331	0.68477	0.45695	0.45202	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	China	2024-01-26	Hatching	Embryo	Embryo Imprecise	All anatomical structures
30038	30038	SRR27732034	SRX23397614	SRS20258455	SRP485064	PRJNA1067370	zebrafish embryo for scRNA seq and bulk RNA seq	PRJNA1067370	Other	Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.		wild type 36 hpf embryo	zebrafish embryo 36hpf replicate 3	strain:not applicable\|isolate:not collected\|breed:Danio\|cultivar:not applicable\|ecotype:not applicable\|dev stage:36 hpf\|collection date:2022 10\|geo loc name:not applicable\|sex:not applicable\|tissue:embryo\|genotype:wild type\|sample type:whole organism\|treatment:replicate 3\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: 36hpf embryo	W 15	W 15	bulk RNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485064		WT36h-3_1.fq.gz WT36h-3_2.fq.gz	fastq fastq	6607629600.0	22025432.0	WT36h 3 1.fq.gz	0:150 1:150	A:1740033364;C:1558025307;G:1585024036;T:1724491752;N:55141	150	150	1740033364	1558025307	1585024036	1724491752	55141	SRX23397614	SRS20258455	SRA1791946	Shanghai Ocean University\|College of Fisheries and Life	Shanghai Ocean University	2	0.94036	0.93863	0.07395	0.07343	0.69723	0.6994	0.46045	0.46325	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	China	2024-01-26	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
30039	30039	SRR27732035	SRX23397613	SRS20258454	SRP485064	PRJNA1067370	zebrafish embryo for scRNA seq and bulk RNA seq	PRJNA1067370	Other	Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.		wild type 36 hpf embryo	zebrafish embryo 36hpf replicate 2	strain:not applicable\|isolate:not collected\|breed:Danio\|cultivar:not applicable\|ecotype:not applicable\|dev stage:36 hpf\|collection date:2022 10\|geo loc name:not applicable\|sex:not applicable\|tissue:embryo\|genotype:wild type\|sample type:whole organism\|treatment:replicate 2\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: 36hpf embryo	W 14	W 14	bulk RNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485064		WT36h-2_1.fq.gz WT36h-2_2.fq.gz	fastq fastq	7848879900.0	26162933.0	WT36h 2 1.fq.gz	0:150 1:150	A:2065200572;C:1853008494;G:1880402891;T:2050169369;N:98574	150	150	2065200572	1853008494	1880402891	2050169369	98574	SRX23397613	SRS20258454	SRA1791946	Shanghai Ocean University\|College of Fisheries and Life	Shanghai Ocean University	2	0.9395	0.93639	0.07562	0.07383	0.6969	0.69814	0.46478	0.45495	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	China	2024-01-26	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
30040	30040	SRR27732036	SRX23397612	SRS20258453	SRP485064	PRJNA1067370	zebrafish embryo for scRNA seq and bulk RNA seq	PRJNA1067370	Other	Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.		wild type 8 hpf embryo	zebrafish embryo 8hpf replicate 2	strain:not applicable\|isolate:not collected\|breed:Danio\|cultivar:not applicable\|ecotype:not applicable\|dev stage:8 hpf\|collection date:2022 10\|geo loc name:not applicable\|sex:not applicable\|tissue:embryo\|genotype:wild type\|sample type:whole organism\|treatment:replicate 2\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: 8hpf embryo	W 5	W 5	bulk RNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485064		WT8h-2_1.fq.gz WT8h-2_2.fq.gz	fastq fastq	6832373100.0	22774577.0	WT8h 2 1.fq.gz	0:150 1:150	A:1819536066;C:1586031035;G:1634106671;T:1792464818;N:234510	150	150	1819536066	1586031035	1634106671	1792464818	234510	SRX23397612	SRS20258453	SRA1791946	Shanghai Ocean University\|College of Fisheries and Life	Shanghai Ocean University	2	0.94411	0.94402	0.0643	0.06343	0.7472	0.74775	0.47176	0.46993	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	China	2024-01-26	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
30041	30041	SRR27732037	SRX23397611	SRS20258452	SRP485064	PRJNA1067370	zebrafish embryo for scRNA seq and bulk RNA seq	PRJNA1067370	Other	Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.		wild type 8 hpf embryo	zebrafish embryo 8hpf replicate 1	strain:not applicable\|isolate:not collected\|breed:Danio\|cultivar:not applicable\|ecotype:not applicable\|dev stage:8 hpf\|collection date:2022 10\|geo loc name:not applicable\|sex:not applicable\|tissue:embryo\|genotype:wild type\|sample type:whole organism\|treatment:replicate 1\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: 8hpf embryo	W 4	W 4	bulk RNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485064		WT8h-1_1.fq.gz WT8h-1_2.fq.gz	fastq fastq	5792885100.0	19309617.0	WT8h 1 1.fq.gz	0:150 1:150	A:1545377384;C:1341340578;G:1388087015;T:1517986965;N:93158	150	150	1545377384	1341340578	1388087015	1517986965	93158	SRX23397611	SRS20258452	SRA1791946	Shanghai Ocean University\|College of Fisheries and Life	Shanghai Ocean University	2	0.94512	0.9415	0.05988	0.05963	0.74345	0.74582	0.46534	0.46722	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	China	2024-01-26	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
30042	30042	SRR27730705	SRX23396353	SRS20257267	SRP485064	PRJNA1067370	zebrafish embryo for scRNA seq and bulk RNA seq	PRJNA1067370	Other	Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.		hamp / 24 hpf embryo	zebrafish embryo hamp / 24hpf replicate 1	strain:not applicable\|isolate:not collected\|breed:Danio\|cultivar:not applicable\|ecotype:not applicable\|dev stage:24 hpf\|collection date:2022 10\|geo loc name:not applicable\|sex:not applicable\|tissue:embryo\|genotype:hamp / \|sample type:whole organism\|treatment:replicate 1\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: 24hpf embryo	W 31	W 31	bulk RNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485064		hamp24h-1_1.fq.gz hamp24h-1_2.fq.gz	fastq fastq	6643634100.0	22145447.0	hamp24h 1 1.fq.gz	0:150 1:150	A:1742210141;C:1573249075;G:1600079934;T:1727989339;N:105611	150	150	1742210141	1573249075	1600079934	1727989339	105611	SRX23396353	SRS20257267	SRA1791861	Shanghai Ocean University\|College of Fisheries and Life	Shanghai Ocean University	2	0.93899	0.93556	0.06108	0.0602	0.6997	0.70179	0.47261	0.47417	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	China	2024-01-25	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
30043	30043	SRR27730706	SRX23396352	SRS20257266	SRP485064	PRJNA1067370	zebrafish embryo for scRNA seq and bulk RNA seq	PRJNA1067370	Other	Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.		hamp / 12 hpf embryo	zebrafish embryo hamp / 12hpf replicate 3	strain:not applicable\|isolate:not collected\|breed:Danio\|cultivar:not applicable\|ecotype:not applicable\|dev stage:12 hpf\|collection date:2022 10\|geo loc name:not applicable\|sex:not applicable\|tissue:embryo\|genotype:hamp / \|sample type:whole organism\|treatment:replicate 3\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: 12hpf embryo	W 30	W 30	bulk RNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485064		hamp12h-3_1.fq.gz hamp12h-3_2.fq.gz	fastq fastq	6380262000.0	21267540.0	hamp12h 3 1.fq.gz	0:150 1:150	A:1686482981;C:1496556670;G:1525661866;T:1671347887;N:212596	150	150	1686482981	1496556670	1525661866	1671347887	212596	SRX23396352	SRS20257266	SRA1791861	Shanghai Ocean University\|College of Fisheries and Life	Shanghai Ocean University	2	0.93955	0.93782	0.07021	0.07017	0.72541	0.72691	0.4754	0.47596	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	China	2024-01-25	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
30044	30044	SRR27730707	SRX23396351	SRS20257265	SRP485064	PRJNA1067370	zebrafish embryo for scRNA seq and bulk RNA seq	PRJNA1067370	Other	Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.		hamp / 12 hpf embryo	zebrafish embryo hamp / 12hpf replicate 2	strain:not applicable\|isolate:not collected\|breed:Danio\|cultivar:not applicable\|ecotype:not applicable\|dev stage:12 hpf\|collection date:2022 10\|geo loc name:not applicable\|sex:not applicable\|tissue:embryo\|genotype:hamp / \|sample type:whole organism\|treatment:replicate 2\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: 12hpf embryo	W 29	W 29	bulk RNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485064		hamp12h-2_1.fq.gz hamp12h-2_2.fq.gz	fastq fastq	6738373500.0	22461245.0	hamp12h 2 1.fq.gz	0:150 1:150	A:1793407846;C:1570428903;G:1600911780;T:1773421988;N:202983	150	150	1793407846	1570428903	1600911780	1773421988	202983	SRX23396351	SRS20257265	SRA1791861	Shanghai Ocean University\|College of Fisheries and Life	Shanghai Ocean University	2	0.93629	0.93637	0.07013	0.07043	0.72764	0.72912	0.47138	0.47279	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	China	2024-01-25	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
30045	30045	SRR27730708	SRX23396350	SRS20257264	SRP485064	PRJNA1067370	zebrafish embryo for scRNA seq and bulk RNA seq	PRJNA1067370	Other	Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.		hamp / 12 hpf embryo	zebrafish embryo hamp / 12hpf replicate 1	strain:not applicable\|isolate:not collected\|breed:Danio\|cultivar:not applicable\|ecotype:not applicable\|dev stage:12 hpf\|collection date:2022 10\|geo loc name:not applicable\|sex:not applicable\|tissue:embryo\|genotype:hamp / \|sample type:whole organism\|treatment:replicate 1\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: 12hpf embryo	W 28	W 28	bulk RNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485064		hamp12h-1_1.fq.gz hamp12h-1_2.fq.gz	fastq fastq	6882364200.0	22941214.0	hamp12h 1 1.fq.gz	0:150 1:150	A:1816338301;C:1617411981;G:1650700092;T:1797708715;N:205111	150	150	1816338301	1617411981	1650700092	1797708715	205111	SRX23396350	SRS20257264	SRA1791861	Shanghai Ocean University\|College of Fisheries and Life	Shanghai Ocean University	2	0.93465	0.93675	0.06811	0.06816	0.72863	0.72922	0.47838	0.47563	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	China	2024-01-25	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
30046	30046	SRR27730709	SRX23396349	SRS20257263	SRP485064	PRJNA1067370	zebrafish embryo for scRNA seq and bulk RNA seq	PRJNA1067370	Other	Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.		hamp / 8 hpf embryo	zebrafish embryo hamp / 8hpf replicate 3	strain:not applicable\|isolate:not collected\|breed:Danio\|cultivar:not applicable\|ecotype:not applicable\|dev stage:8 hpf\|collection date:2022 10\|geo loc name:not applicable\|sex:not applicable\|tissue:embryo\|genotype:hamp / \|sample type:whole organism\|treatment:replicate 3\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: 8hpf embryo	W 27	W 27	bulk RNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485064		hamp8h-3_1.fq.gz hamp8h-3_2.fq.gz	fastq fastq	6295202100.0	20984007.0	hamp8h 3 1.fq.gz	0:150 1:150	A:1694806329;C:1445372178;G:1488024762;T:1666904080;N:94751	150	150	1694806329	1445372178	1488024762	1666904080	94751	SRX23396349	SRS20257263	SRA1791861	Shanghai Ocean University\|College of Fisheries and Life	Shanghai Ocean University	2	0.94405	0.94297	0.06722	0.06702	0.76627	0.76828	0.48464	0.48699	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	China	2024-01-25	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
30047	30047	SRR27730710	SRX23396348	SRS20257262	SRP485064	PRJNA1067370	zebrafish embryo for scRNA seq and bulk RNA seq	PRJNA1067370	Other	Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.		hamp / 8 hpf embryo	zebrafish embryo hamp / 8hpf replicate 2	strain:not applicable\|isolate:not collected\|breed:Danio\|cultivar:not applicable\|ecotype:not applicable\|dev stage:8 hpf\|collection date:2022 10\|geo loc name:not applicable\|sex:not applicable\|tissue:embryo\|genotype:hamp / \|sample type:whole organism\|treatment:replicate 2\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: 8hpf embryo	W 26	W 26	bulk RNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485064		hamp8h-2_1.fq.gz hamp8h-2_2.fq.gz	fastq fastq	6148660800.0	20495536.0	hamp8h 2 1.fq.gz	0:150 1:150	A:1644992837;C:1420391182;G:1458975922;T:1624091150;N:209709	150	150	1644992837	1420391182	1458975922	1624091150	209709	SRX23396348	SRS20257262	SRA1791861	Shanghai Ocean University\|College of Fisheries and Life	Shanghai Ocean University	2	0.93828	0.93748	0.08438	0.08432	0.74681	0.74732	0.48765	0.48809	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	China	2024-01-25	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
30048	30048	SRR27730711	SRX23396347	SRS20257261	SRP485064	PRJNA1067370	zebrafish embryo for scRNA seq and bulk RNA seq	PRJNA1067370	Other	Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.		hamp / 8 hpf embryo	zebrafish embryo hamp / 8hpf replicate 1	strain:not applicable\|isolate:not collected\|breed:Danio\|cultivar:not applicable\|ecotype:not applicable\|dev stage:8 hpf\|collection date:2022 10\|geo loc name:not applicable\|sex:not applicable\|tissue:embryo\|genotype:hamp / \|sample type:whole organism\|treatment:replicate 1\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: 8hpf embryo	W 25	W 25	bulk RNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485064		hamp8h-1_1.fq.gz hamp8h-1_2.fq.gz	fastq fastq	7443429000.0	24811430.0	hamp8h 1 1.fq.gz	0:150 1:150	A:1989642168;C:1723187805;G:1770726575;T:1959761293;N:111159	150	150	1989642168	1723187805	1770726575	1959761293	111159	SRX23396347	SRS20257261	SRA1791861	Shanghai Ocean University\|College of Fisheries and Life	Shanghai Ocean University	2	0.94417	0.94323	0.06281	0.06203	0.76479	0.76706	0.47849	0.4799	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	China	2024-01-25	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
30049	30049	SRR27730712	SRX23396346	SRS20257260	SRP485064	PRJNA1067370	zebrafish embryo for scRNA seq and bulk RNA seq	PRJNA1067370	Other	Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.		hamp / 72 hpf embryo	zebrafish embryo hamp / 72hpf replicate 3	strain:not applicable\|isolate:not collected\|breed:Danio\|cultivar:not applicable\|ecotype:not applicable\|dev stage:72 hpf\|collection date:2022 10\|geo loc name:not applicable\|sex:not applicable\|tissue:embryo\|genotype:hamp / \|sample type:whole organism\|treatment:replicate 3\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: 72hpf embryo	W 42	W 42	bulk RNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485064		hamp72h-3_1.fq.gz hamp72h-3_2.fq.gz	fastq fastq	7124946000.0	23749820.0	hamp72h 3 1.fq.gz	0:150 1:150	A:1926386901;C:1633268260;G:1649597432;T:1915633812;N:59595	150	150	1926386901	1633268260	1649597432	1915633812	59595	SRX23396346	SRS20257260	SRA1791861	Shanghai Ocean University\|College of Fisheries and Life	Shanghai Ocean University	2	0.9369	0.9352	0.10335	0.10255	0.66703	0.6686	0.47407	0.46796	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	China	2024-01-25	Larval	Larval	Embryo Imprecise	All anatomical structures
30050	30050	SRR27730713	SRX23396345	SRS20257259	SRP485064	PRJNA1067370	zebrafish embryo for scRNA seq and bulk RNA seq	PRJNA1067370	Other	Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.		hamp / 4 hpf embryo	zebrafish embryo hamp / 4hpf replicate 3	strain:not applicable\|isolate:not collected\|breed:Danio\|cultivar:not applicable\|ecotype:not applicable\|dev stage:4 hpf\|collection date:2022 10\|geo loc name:not applicable\|sex:not applicable\|tissue:embryo\|genotype:hamp / \|sample type:whole organism\|treatment:replicate 3\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: 4hpf embryo	W 24	W 24	bulk RNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485064		hamp4h-3_2.fq.gz hamp4h-3_1.fq.gz	fastq fastq	6261088500.0	20870295.0	hamp4h 3 1.fq.gz	0:150 1:150	A:1668720393;C:1449635670;G:1495531397;T:1647100279;N:100761	150	150	1668720393	1449635670	1495531397	1647100279	100761	SRX23396345	SRS20257259	SRA1791861	Shanghai Ocean University\|College of Fisheries and Life	Shanghai Ocean University	2	0.94424	0.94159	0.04146	0.0415	0.75089	0.75201	0.48393	0.48457	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	China	2024-01-25	Blastula	Embryo	Embryo Imprecise	All anatomical structures
30051	30051	SRR27730714	SRX23396344	SRS20257258	SRP485064	PRJNA1067370	zebrafish embryo for scRNA seq and bulk RNA seq	PRJNA1067370	Other	Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.		hamp / 72 hpf embryo	zebrafish embryo hamp / 72hpf replicate 2	strain:not applicable\|isolate:not collected\|breed:Danio\|cultivar:not applicable\|ecotype:not applicable\|dev stage:72 hpf\|collection date:2022 10\|geo loc name:not applicable\|sex:not applicable\|tissue:embryo\|genotype:hamp / \|sample type:whole organism\|treatment:replicate 2\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: 72hpf embryo	W 41	W 41	bulk RNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485064		hamp72h-2_1.fq.gz hamp72h-2_2.fq.gz	fastq fastq	6201979200.0	20673264.0	hamp72h 2 1.fq.gz	0:150 1:150	A:1657650097;C:1440501731;G:1451375517;T:1652374388;N:77467	150	150	1657650097	1440501731	1451375517	1652374388	77467	SRX23396344	SRS20257258	SRA1791861	Shanghai Ocean University\|College of Fisheries and Life	Shanghai Ocean University	2	0.93468	0.9333	0.0972	0.09614	0.66427	0.66588	0.46658	0.46539	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	China	2024-01-25	Larval	Larval	Embryo Imprecise	All anatomical structures
30052	30052	SRR27730715	SRX23396343	SRS20257257	SRP485064	PRJNA1067370	zebrafish embryo for scRNA seq and bulk RNA seq	PRJNA1067370	Other	Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.		hamp / 72 hpf embryo	zebrafish embryo hamp / 72hpf replicate 1	strain:not applicable\|isolate:not collected\|breed:Danio\|cultivar:not applicable\|ecotype:not applicable\|dev stage:72 hpf\|collection date:2022 10\|geo loc name:not applicable\|sex:not applicable\|tissue:embryo\|genotype:hamp / \|sample type:whole organism\|treatment:replicate 1\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: 72hpf embryo	W 40	W 40	bulk RNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485064		hamp72h-1_1.fq.gz hamp72h-1_2.fq.gz	fastq fastq	6432009000.0	21440030.0	hamp72h 1 1.fq.gz	0:150 1:150	A:1734564732;C:1478070668;G:1490938268;T:1728354590;N:80742	150	150	1734564732	1478070668	1490938268	1728354590	80742	SRX23396343	SRS20257257	SRA1791861	Shanghai Ocean University\|College of Fisheries and Life	Shanghai Ocean University	2	0.93382	0.93132	0.10621	0.10453	0.66592	0.66667	0.46409	0.46541	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	China	2024-01-25	Larval	Larval	Embryo Imprecise	All anatomical structures
30053	30053	SRR27730716	SRX23396342	SRS20257256	SRP485064	PRJNA1067370	zebrafish embryo for scRNA seq and bulk RNA seq	PRJNA1067370	Other	Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.		hamp / 48 hpf embryo	zebrafish embryo hamp / 48hpf replicate 3	strain:not applicable\|isolate:not collected\|breed:Danio\|cultivar:not applicable\|ecotype:not applicable\|dev stage:48 hpf\|collection date:2022 10\|geo loc name:not applicable\|sex:not applicable\|tissue:embryo\|genotype:hamp / \|sample type:whole organism\|treatment:replicate 3\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: 48hpf embryo	W 39	W 39	bulk RNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485064		hamp48h-3_1.fq.gz hamp48h-3_2.fq.gz	fastq fastq	7580570700.0	25268569.0	hamp48h 3 1.fq.gz	0:150 1:150	A:2019162299;C:1768225001;G:1782049665;T:2011039613;N:94122	150	150	2019162299	1768225001	1782049665	2011039613	94122	SRX23396342	SRS20257256	SRA1791861	Shanghai Ocean University\|College of Fisheries and Life	Shanghai Ocean University	2	0.93863	0.93681	0.08675	0.08582	0.68394	0.6857	0.46373	0.46321	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	China	2024-01-25	Hatching	Embryo	Embryo Imprecise	All anatomical structures
30054	30054	SRR27730717	SRX23396341	SRS20257255	SRP485064	PRJNA1067370	zebrafish embryo for scRNA seq and bulk RNA seq	PRJNA1067370	Other	Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.		hamp / 48 hpf embryo	zebrafish embryo hamp / 48hpf replicate 2	strain:not applicable\|isolate:not collected\|breed:Danio\|cultivar:not applicable\|ecotype:not applicable\|dev stage:48 hpf\|collection date:2022 10\|geo loc name:not applicable\|sex:not applicable\|tissue:embryo\|genotype:hamp / \|sample type:whole organism\|treatment:replicate 2\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: 48hpf embryo	W 38	W 38	bulk RNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485064		hamp48h-2_1.fq.gz hamp48h-2_2.fq.gz	fastq fastq	7385330400.0	24617768.0	hamp48h 2 1.fq.gz	0:150 1:150	A:1971527478;C:1717463447;G:1738237873;T:1957858394;N:243208	150	150	1971527478	1717463447	1738237873	1957858394	243208	SRX23396341	SRS20257255	SRA1791861	Shanghai Ocean University\|College of Fisheries and Life	Shanghai Ocean University	2	0.93851	0.9369	0.09049	0.08988	0.68274	0.6843	0.45945	0.46042	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	China	2024-01-25	Hatching	Embryo	Embryo Imprecise	All anatomical structures
30055	30055	SRR27730718	SRX23396340	SRS20257254	SRP485064	PRJNA1067370	zebrafish embryo for scRNA seq and bulk RNA seq	PRJNA1067370	Other	Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.		hamp / 48 hpf embryo	zebrafish embryo hamp / 48hpf replicate 1	strain:not applicable\|isolate:not collected\|breed:Danio\|cultivar:not applicable\|ecotype:not applicable\|dev stage:48 hpf\|collection date:2022 10\|geo loc name:not applicable\|sex:not applicable\|tissue:embryo\|genotype:hamp / \|sample type:whole organism\|treatment:replicate 1\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: 48hpf embryo	W 37	W 37	bulk RNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485064		hamp48h-1_1.fq.gz hamp48h-1_2.fq.gz	fastq fastq	6188343000.0	20627810.0	hamp48h 1 1.fq.gz	0:150 1:150	A:1649030143;C:1444577102;G:1461592285;T:1633092294;N:51176	150	150	1649030143	1444577102	1461592285	1633092294	51176	SRX23396340	SRS20257254	SRA1791861	Shanghai Ocean University\|College of Fisheries and Life	Shanghai Ocean University	2	0.94313	0.94006	0.08835	0.08702	0.6859	0.68702	0.45658	0.46001	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	China	2024-01-25	Hatching	Embryo	Embryo Imprecise	All anatomical structures
30056	30056	SRR27730719	SRX23396339	SRS20257253	SRP485064	PRJNA1067370	zebrafish embryo for scRNA seq and bulk RNA seq	PRJNA1067370	Other	Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.		hamp / 36 hpf embryo	zebrafish embryo hamp / 36hpf replicate 3	strain:not applicable\|isolate:not collected\|breed:Danio\|cultivar:not applicable\|ecotype:not applicable\|dev stage:36 hpf\|collection date:2022 10\|geo loc name:not applicable\|sex:not applicable\|tissue:embryo\|genotype:hamp / \|sample type:whole organism\|treatment:replicate 3\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: 36hpf embryo	W 36	W 36	bulk RNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485064		hamp36h-3_1.fq.gz hamp36h-3_2.fq.gz	fastq fastq	6442851300.0	21476171.0	hamp36h 3 1.fq.gz	0:150 1:150	A:1696209844;C:1521086149;G:1542365512;T:1683136288;N:53507	150	150	1696209844	1521086149	1542365512	1683136288	53507	SRX23396339	SRS20257253	SRA1791861	Shanghai Ocean University\|College of Fisheries and Life	Shanghai Ocean University	2	0.9446	0.94399	0.07193	0.07106	0.6955	0.69729	0.46483	0.46399	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	China	2024-01-25	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
30057	30057	SRR27730720	SRX23396338	SRS20257252	SRP485064	PRJNA1067370	zebrafish embryo for scRNA seq and bulk RNA seq	PRJNA1067370	Other	Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.		hamp / 36 hpf embryo	zebrafish embryo hamp / 36hpf replicate 2	strain:not applicable\|isolate:not collected\|breed:Danio\|cultivar:not applicable\|ecotype:not applicable\|dev stage:36 hpf\|collection date:2022 10\|geo loc name:not applicable\|sex:not applicable\|tissue:embryo\|genotype:hamp / \|sample type:whole organism\|treatment:replicate 2\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: 36hpf embryo	W 35	W 35	bulk RNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485064		hamp36h-2_1.fq.gz hamp36h-2_2.fq.gz	fastq fastq	8020366200.0	26734554.0	hamp36h 2 1.fq.gz	0:150 1:150	A:2103699528;C:1897760189;G:1928753070;T:2090039533;N:113880	150	150	2103699528	1897760189	1928753070	2090039533	113880	SRX23396338	SRS20257252	SRA1791861	Shanghai Ocean University\|College of Fisheries and Life	Shanghai Ocean University	2	0.94805	0.94701	0.07022	0.06985	0.69585	0.69777	0.46182	0.45694	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	China	2024-01-25	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
30058	30058	SRR27730721	SRX23396337	SRS20257251	SRP485064	PRJNA1067370	zebrafish embryo for scRNA seq and bulk RNA seq	PRJNA1067370	Other	Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.		hamp / 36 hpf embryo	zebrafish embryo hamp / 36hpf replicate 1	strain:not applicable\|isolate:not collected\|breed:Danio\|cultivar:not applicable\|ecotype:not applicable\|dev stage:36 hpf\|collection date:2022 10\|geo loc name:not applicable\|sex:not applicable\|tissue:embryo\|genotype:hamp / \|sample type:whole organism\|treatment:replicate 1\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: 36hpf embryo	W 34	W 34	bulk RNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485064		hamp36h-1_1.fq.gz hamp36h-1_2.fq.gz	fastq fastq	7319492100.0	24398307.0	hamp36h 1 1.fq.gz	0:150 1:150	A:1924726816;C:1727922135;G:1762476592;T:1904305780;N:60777	150	150	1924726816	1727922135	1762476592	1904305780	60777	SRX23396337	SRS20257251	SRA1791861	Shanghai Ocean University\|College of Fisheries and Life	Shanghai Ocean University	2	0.93938	0.93967	0.07121	0.07085	0.69581	0.69755	0.45448	0.45541	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	China	2024-01-25	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
30059	30059	SRR27730722	SRX23396336	SRS20257250	SRP485064	PRJNA1067370	zebrafish embryo for scRNA seq and bulk RNA seq	PRJNA1067370	Other	Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.		hamp / 24 hpf embryo	zebrafish embryo hamp / 24hpf replicate 3	strain:not applicable\|isolate:not collected\|breed:Danio\|cultivar:not applicable\|ecotype:not applicable\|dev stage:24 hpf\|collection date:2022 10\|geo loc name:not applicable\|sex:not applicable\|tissue:embryo\|genotype:hamp / \|sample type:whole organism\|treatment:replicate 3\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: 24hpf embryo	W 33	W 33	bulk RNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485064		hamp24h-3_1.fq.gz hamp24h-3_2.fq.gz	fastq fastq	6470874300.0	21569581.0	hamp24h 3 1.fq.gz	0:150 1:150	A:1698655936;C:1530916678;G:1555607788;T:1685479625;N:214273	150	150	1698655936	1530916678	1555607788	1685479625	214273	SRX23396336	SRS20257250	SRA1791861	Shanghai Ocean University\|College of Fisheries and Life	Shanghai Ocean University	2	0.93644	0.93637	0.06179	0.06156	0.70011	0.70134	0.47098	0.4709	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	China	2024-01-25	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
30060	30060	SRR27730723	SRX23396335	SRS20257249	SRP485064	PRJNA1067370	zebrafish embryo for scRNA seq and bulk RNA seq	PRJNA1067370	Other	Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.		hamp / 24 hpf embryo	zebrafish embryo hamp / 24hpf replicate 2	strain:not applicable\|isolate:not collected\|breed:Danio\|cultivar:not applicable\|ecotype:not applicable\|dev stage:24 hpf\|collection date:2022 10\|geo loc name:not applicable\|sex:not applicable\|tissue:embryo\|genotype:hamp / \|sample type:whole organism\|treatment:replicate 2\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: 24hpf embryo	W 32	W 32	bulk RNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485064		hamp24h-2_1.fq.gz hamp24h-2_2.fq.gz	fastq fastq	5875188900.0	19583963.0	hamp24h 2 1.fq.gz	0:150 1:150	A:1553428887;C:1379148744;G:1400831429;T:1541584152;N:195688	150	150	1553428887	1379148744	1400831429	1541584152	195688	SRX23396335	SRS20257249	SRA1791861	Shanghai Ocean University\|College of Fisheries and Life	Shanghai Ocean University	2	0.9351	0.93566	0.06624	0.06643	0.69739	0.69875	0.47055	0.47049	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	China	2024-01-25	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
30061	30061	SRR27730724	SRX23396334	SRS20257248	SRP485064	PRJNA1067370	zebrafish embryo for scRNA seq and bulk RNA seq	PRJNA1067370	Other	Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.		hamp / 4 hpf embryo	zebrafish embryo hamp / 4hpf replicate 2	strain:not applicable\|isolate:not collected\|breed:Danio\|cultivar:not applicable\|ecotype:not applicable\|dev stage:4 hpf\|collection date:2022 10\|geo loc name:not applicable\|sex:not applicable\|tissue:embryo\|genotype:hamp / \|sample type:whole organism\|treatment:replicate 2\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: 4hpf embryo	W 23	W 23	bulk RNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485064		hamp4h-2_1.fq.gz hamp4h-2_2.fq.gz	fastq fastq	6140359800.0	20467866.0	hamp4h 2 1.fq.gz	0:150 1:150	A:1622433757;C:1437175847;G:1481587196;T:1599071088;N:91912	150	150	1622433757	1437175847	1481587196	1599071088	91912	SRX23396334	SRS20257248	SRA1791861	Shanghai Ocean University\|College of Fisheries and Life	Shanghai Ocean University	2	0.94763	0.94713	0.03975	0.03948	0.75045	0.75193	0.48915	0.48855	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	China	2024-01-25	Blastula	Embryo	Embryo Imprecise	All anatomical structures
30062	30062	SRR27730725	SRX23396333	SRS20257247	SRP485064	PRJNA1067370	zebrafish embryo for scRNA seq and bulk RNA seq	PRJNA1067370	Other	Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.		hamp / 4 hpf embryo	zebrafish embryo hamp / 4hpf replicate 1	strain:not applicable\|isolate:not collected\|breed:Danio\|cultivar:not applicable\|ecotype:not applicable\|dev stage:4 hpf\|collection date:2022 10\|geo loc name:not applicable\|sex:not applicable\|tissue:embryo\|genotype:hamp / \|sample type:whole organism\|treatment:replicate 1\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: 4hpf embryo	W 22	W 22	bulk RNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485064		hamp4h-1_1.fq.gz hamp4h-1_2.fq.gz	fastq fastq	6482302500.0	21607675.0	hamp4h 1 1.fq.gz	0:150 1:150	A:1723398342;C:1504238189;G:1551942847;T:1702630056;N:93066	150	150	1723398342	1504238189	1551942847	1702630056	93066	SRX23396333	SRS20257247	SRA1791861	Shanghai Ocean University\|College of Fisheries and Life	Shanghai Ocean University	2	0.94434	0.94083	0.04297	0.04235	0.75327	0.75526	0.48487	0.4837	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	China	2024-01-25	Blastula	Embryo	Embryo Imprecise	All anatomical structures
30063	30063	SRR27674233	SRX23341580	SRS20203706	SRP485064	PRJNA1067370	zebrafish embryo for scRNA seq and bulk RNA seq	PRJNA1067370	Other	Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.		wild type 4 phf embryo	zebrafish embryo 4 phf replicate 3	strain:not applicable\|isolate:not collected\|breed:Danio\|cultivar:not applicable\|ecotype:not applicable\|age:4 phf\|dev stage:4 phf\|collection date:2022 10\|geo loc name:not applicable\|sex:not applicable\|tissue:embryo\|genotype:wild type\|sample type:whole organism\|treatment:replicate 3\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: 4hpf embryo	W 3	W 3	bulk RNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485064		WT4h-3_1.fq.gz WT4h-3_2.fq.gz	fastq fastq	5799593100.0	19331977.0	WT4h 3 1.fq.gz	0:150 1:150	A:1543677690;C:1345529657;G:1387996505;T:1522341224;N:48024	150	150	1543677690	1345529657	1387996505	1522341224	48024	SRX23341580	SRS20203706	SRA1789158	Shanghai Ocean University\|College of Fisheries and Life	Shanghai Ocean University	2	0.94823	0.94693	0.0386	0.03884	0.74686	0.74769	0.47863	0.48203	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	China	2024-01-22	Blastula	Embryo	Embryo Imprecise	All anatomical structures
30064	30064	SRR27674234	SRX23341579	SRS20203705	SRP485064	PRJNA1067370	zebrafish embryo for scRNA seq and bulk RNA seq	PRJNA1067370	Other	Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.		wild type 4 phf embryo	zebrafish embryo 4 phf replicate 2	strain:not applicable\|isolate:not collected\|breed:Danio\|cultivar:not applicable\|ecotype:not applicable\|age:4 phf\|dev stage:4 phf\|collection date:2022 10\|geo loc name:not applicable\|sex:not applicable\|tissue:embryo\|genotype:wild type\|sample type:whole organism\|treatment:replicate 2\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: 4hpf embryo	W 2	W 2	bulk RNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485064		WT4h-2_1.fq.gz WT4h-2_2.fq.gz	fastq fastq	6408374700.0	21361249.0	WT4h 2 1.fq.gz	0:150 1:150	A:1700326501;C:1489928909;G:1544130015;T:1673936668;N:52607	150	150	1700326501	1489928909	1544130015	1673936668	52607	SRX23341579	SRS20203705	SRA1789158	Shanghai Ocean University\|College of Fisheries and Life	Shanghai Ocean University	2	0.94833	0.94724	0.03589	0.03528	0.74521	0.74665	0.47991	0.47552	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	China	2024-01-22	Blastula	Embryo	Embryo Imprecise	All anatomical structures
30065	30065	SRR27674235	SRX23341578	SRS20203704	SRP485064	PRJNA1067370	zebrafish embryo for scRNA seq and bulk RNA seq	PRJNA1067370	Other	Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.		wild type 4 phf embryo	zebrafish embryo 4 phf replicate 1	strain:not applicable\|isolate:not collected\|breed:Danio\|cultivar:not applicable\|ecotype:not applicable\|age:4 phf\|dev stage:4 phf\|collection date:2022 10\|geo loc name:not applicable\|sex:not applicable\|tissue:embryo\|genotype:wild type\|sample type:whole organism\|treatment:replicate 1\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: 4hpf embryo	W 1	W 1	bulk RNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485064		WT4h-1_1.fq.gz WT4h-1_2.fq.gz	fastq fastq	6176335500.0	20587785.0	WT4h 1 1.fq.gz	0:150 1:150	A:1639564255;C:1436792246;G:1481775020;T:1618153065;N:50914	150	150	1639564255	1436792246	1481775020	1618153065	50914	SRX23341578	SRS20203704	SRA1789158	Shanghai Ocean University\|College of Fisheries and Life	Shanghai Ocean University	2	0.94837	0.94497	0.03675	0.03629	0.74393	0.74497	0.48332	0.48392	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	China	2024-01-22	Blastula	Embryo	Embryo Imprecise	All anatomical structures
31557	31557	SRR28471021	SRX24074012	SRS20864401	SRP498123	PRJNA1092581	Construction of Danio rerio Asymmetrical Maps DreAM	GSE262578	Transcriptome Analysis	Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally we difined a hox score and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf 12 hpf and 16 hpf.		S16 slice 13	GSM8171995	source name:embryonic cells\|tissue:embryonic cells\|strain:AB\|age:16 hpf\|geo loc name:missing\|collection date:missing	S16 slice 13	Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds files include count matrixes and slice position information post running the processing steps.	embryonic cells	Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	Zebrafish embryos were raised in 0.3x Danieau buffer and were then embedded in OCT at the required developmental stages of 10 hpf 12hpf and 16 hpf.	tissue:embryonic cells\|strain:AB\|age:16 hpf	GSM8171995	GSM8171995: S16 slice 13; Danio rerio; RNA Seq	GSM8171995 r1	GSM8171995	1	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP498123	loader:fastq load.py	S16_2_13-R1.fq.gz S16_2_13-R2.fq.gz	fastq fastq	7021136766.0	24220886.0	GSM8171995 r1	0:143.40 1:146.48	A:1932409729;C:1613003140;G:1510879854;T:1964782006;N:62037	143	146	1932409729	1613003140	1510879854	1964782006	62037	SRX24074012	SRS20864401	SRA1834502	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	China	2024-03-27	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
31558	31558	SRR28471022	SRX24074011	SRS20864400	SRP498123	PRJNA1092581	Construction of Danio rerio Asymmetrical Maps DreAM	GSE262578	Transcriptome Analysis	Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally we difined a hox score and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf 12 hpf and 16 hpf.		S16 slice 12	GSM8171993	source name:embryonic cells\|tissue:embryonic cells\|strain:AB\|age:16 hpf\|geo loc name:missing\|collection date:missing	S16 slice 12	Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds files include count matrixes and slice position information post running the processing steps.	embryonic cells	Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	Zebrafish embryos were raised in 0.3x Danieau buffer and were then embedded in OCT at the required developmental stages of 10 hpf 12hpf and 16 hpf.	tissue:embryonic cells\|strain:AB\|age:16 hpf	GSM8171993	GSM8171993: S16 slice 12; Danio rerio; RNA Seq	GSM8171993 r1	GSM8171993	1	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP498123	loader:fastq load.py	S16_2_12-R1.fq.gz S16_2_12-R2.fq.gz	fastq fastq	6989496704.0	24013496.0	GSM8171993 r1	0:144.73 1:146.34	A:1973063613;C:1539634004;G:1502105630;T:1974633280;N:60177	144	146	1973063613	1539634004	1502105630	1974633280	60177	SRX24074011	SRS20864400	SRA1834502	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	China	2024-03-27	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
31559	31559	SRR28471023	SRX24074010	SRS20864399	SRP498123	PRJNA1092581	Construction of Danio rerio Asymmetrical Maps DreAM	GSE262578	Transcriptome Analysis	Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally we difined a hox score and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf 12 hpf and 16 hpf.		S16 slice 11	GSM8171992	source name:embryonic cells\|tissue:embryonic cells\|strain:AB\|age:16 hpf\|geo loc name:missing\|collection date:missing	S16 slice 11	Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds files include count matrixes and slice position information post running the processing steps.	embryonic cells	Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	Zebrafish embryos were raised in 0.3x Danieau buffer and were then embedded in OCT at the required developmental stages of 10 hpf 12hpf and 16 hpf.	tissue:embryonic cells\|strain:AB\|age:16 hpf	GSM8171992	GSM8171992: S16 slice 11; Danio rerio; RNA Seq	GSM8171992 r1	GSM8171992	1	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP498123	loader:fastq load.py	S16_2_11-R1.fq.gz S16_2_11-R2.fq.gz	fastq fastq	6658580843.0	22968779.0	GSM8171992 r1	0:143.28 1:146.62	A:1850547171;C:1505778383;G:1450300777;T:1851895401;N:59111	143	146	1850547171	1505778383	1450300777	1851895401	59111	SRX24074010	SRS20864399	SRA1834502	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	China	2024-03-27	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
31560	31560	SRR28471024	SRX24074009	SRS20864398	SRP498123	PRJNA1092581	Construction of Danio rerio Asymmetrical Maps DreAM	GSE262578	Transcriptome Analysis	Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally we difined a hox score and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf 12 hpf and 16 hpf.		S16 slice 10	GSM8171991	source name:embryonic cells\|tissue:embryonic cells\|strain:AB\|age:16 hpf\|geo loc name:missing\|collection date:missing	S16 slice 10	Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds files include count matrixes and slice position information post running the processing steps.	embryonic cells	Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	Zebrafish embryos were raised in 0.3x Danieau buffer and were then embedded in OCT at the required developmental stages of 10 hpf 12hpf and 16 hpf.	tissue:embryonic cells\|strain:AB\|age:16 hpf	GSM8171991	GSM8171991: S16 slice 10; Danio rerio; RNA Seq	GSM8171991 r1	GSM8171991	1	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP498123	loader:fastq load.py	S16_2_10-R1.fq.gz S16_2_10-R2.fq.gz	fastq fastq	6764254234.0	23283773.0	GSM8171991 r1	0:143.52 1:146.99	A:1876570759;C:1531892471;G:1478929048;T:1876804139;N:57817	143	146	1876570759	1531892471	1478929048	1876804139	57817	SRX24074009	SRS20864398	SRA1834502	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	China	2024-03-27	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
31561	31561	SRR28471025	SRX24074008	SRS20864397	SRP498123	PRJNA1092581	Construction of Danio rerio Asymmetrical Maps DreAM	GSE262578	Transcriptome Analysis	Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally we difined a hox score and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf 12 hpf and 16 hpf.		S16 slice 9	GSM8171990	source name:embryonic cells\|tissue:embryonic cells\|strain:AB\|age:16 hpf\|geo loc name:missing\|collection date:missing	S16 slice 9	Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds files include count matrixes and slice position information post running the processing steps.	embryonic cells	Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	Zebrafish embryos were raised in 0.3x Danieau buffer and were then embedded in OCT at the required developmental stages of 10 hpf 12hpf and 16 hpf.	tissue:embryonic cells\|strain:AB\|age:16 hpf	GSM8171990	GSM8171990: S16 slice 9; Danio rerio; RNA Seq	GSM8171990 r1	GSM8171990	1	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP498123	loader:fastq load.py	S16_2_09-R1.fq.gz S16_2_09-R2.fq.gz	fastq fastq	6953469676.0	23939332.0	GSM8171990 r1	0:143.01 1:147.45	A:1887466615;C:1613826863;G:1550286679;T:1901843452;N:46067	143	147	1887466615	1613826863	1550286679	1901843452	46067	SRX24074008	SRS20864397	SRA1834502	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	China	2024-03-27	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
31562	31562	SRR28471026	SRX24074007	SRS20864396	SRP498123	PRJNA1092581	Construction of Danio rerio Asymmetrical Maps DreAM	GSE262578	Transcriptome Analysis	Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally we difined a hox score and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf 12 hpf and 16 hpf.		S16 slice 8	GSM8171989	source name:embryonic cells\|tissue:embryonic cells\|strain:AB\|age:16 hpf\|geo loc name:missing\|collection date:missing	S16 slice 8	Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds files include count matrixes and slice position information post running the processing steps.	embryonic cells	Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	Zebrafish embryos were raised in 0.3x Danieau buffer and were then embedded in OCT at the required developmental stages of 10 hpf 12hpf and 16 hpf.	tissue:embryonic cells\|strain:AB\|age:16 hpf	GSM8171989	GSM8171989: S16 slice 8; Danio rerio; RNA Seq	GSM8171989 r1	GSM8171989	1	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP498123	loader:fastq load.py	S16_2_08-R1.fq.gz S16_2_08-R2.fq.gz	fastq fastq	6932164944.0	23736001.0	GSM8171989 r1	0:144.93 1:147.12	A:1878823532;C:1592513147;G:1541045989;T:1919723182;N:59094	144	147	1878823532	1592513147	1541045989	1919723182	59094	SRX24074007	SRS20864396	SRA1834502	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	China	2024-03-27	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
31563	31563	SRR28471027	SRX24074006	SRS20864395	SRP498123	PRJNA1092581	Construction of Danio rerio Asymmetrical Maps DreAM	GSE262578	Transcriptome Analysis	Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally we difined a hox score and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf 12 hpf and 16 hpf.		S16 slice 7	GSM8171987	source name:embryonic cells\|tissue:embryonic cells\|strain:AB\|age:16 hpf\|geo loc name:missing\|collection date:missing	S16 slice 7	Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds files include count matrixes and slice position information post running the processing steps.	embryonic cells	Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	Zebrafish embryos were raised in 0.3x Danieau buffer and were then embedded in OCT at the required developmental stages of 10 hpf 12hpf and 16 hpf.	tissue:embryonic cells\|strain:AB\|age:16 hpf	GSM8171987	GSM8171987: S16 slice 7; Danio rerio; RNA Seq	GSM8171987 r1	GSM8171987	1	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP498123	loader:fastq load.py	S16_2_07-R1.fq.gz S16_2_07-R2.fq.gz	fastq fastq	7175124342.0	24613098.0	GSM8171987 r1	0:144.89 1:146.63	A:1955179901;C:1642901455;G:1556429416;T:2020550025;N:63545	144	146	1955179901	1642901455	1556429416	2020550025	63545	SRX24074006	SRS20864395	SRA1834502	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	China	2024-03-27	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
31564	31564	SRR28471028	SRX24074005	SRS20864394	SRP498123	PRJNA1092581	Construction of Danio rerio Asymmetrical Maps DreAM	GSE262578	Transcriptome Analysis	Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally we difined a hox score and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf 12 hpf and 16 hpf.		S16 slice 6	GSM8171986	source name:embryonic cells\|tissue:embryonic cells\|strain:AB\|age:16 hpf\|geo loc name:missing\|collection date:missing	S16 slice 6	Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds files include count matrixes and slice position information post running the processing steps.	embryonic cells	Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	Zebrafish embryos were raised in 0.3x Danieau buffer and were then embedded in OCT at the required developmental stages of 10 hpf 12hpf and 16 hpf.	tissue:embryonic cells\|strain:AB\|age:16 hpf	GSM8171986	GSM8171986: S16 slice 6; Danio rerio; RNA Seq	GSM8171986 r1	GSM8171986	1	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP498123	loader:fastq load.py	S16_2_06-R1.fq.gz S16_2_06-R2.fq.gz	fastq fastq	7015063214.0	24014594.0	GSM8171986 r1	0:145.26 1:146.86	A:1907017747;C:1603933957;G:1551829473;T:1952222046;N:59991	145	146	1907017747	1603933957	1551829473	1952222046	59991	SRX24074005	SRS20864394	SRA1834502	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	China	2024-03-27	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
31565	31565	SRR28471029	SRX24074004	SRS20864393	SRP498123	PRJNA1092581	Construction of Danio rerio Asymmetrical Maps DreAM	GSE262578	Transcriptome Analysis	Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally we difined a hox score and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf 12 hpf and 16 hpf.		S16 slice 5	GSM8171985	source name:embryonic cells\|tissue:embryonic cells\|strain:AB\|age:16 hpf\|geo loc name:missing\|collection date:missing	S16 slice 5	Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds files include count matrixes and slice position information post running the processing steps.	embryonic cells	Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	Zebrafish embryos were raised in 0.3x Danieau buffer and were then embedded in OCT at the required developmental stages of 10 hpf 12hpf and 16 hpf.	tissue:embryonic cells\|strain:AB\|age:16 hpf	GSM8171985	GSM8171985: S16 slice 5; Danio rerio; RNA Seq	GSM8171985 r1	GSM8171985	1	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP498123	loader:fastq load.py	S16_2_05-R1.fq.gz S16_2_05-R2.fq.gz	fastq fastq	6919538718.0	23740085.0	GSM8171985 r1	0:144.96 1:146.51	A:1882346373;C:1593041314;G:1504597309;T:1939492468;N:61254	144	146	1882346373	1593041314	1504597309	1939492468	61254	SRX24074004	SRS20864393	SRA1834502	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	China	2024-03-27	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
31566	31566	SRR28471030	SRX24074003	SRS20864392	SRP498123	PRJNA1092581	Construction of Danio rerio Asymmetrical Maps DreAM	GSE262578	Transcriptome Analysis	Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally we difined a hox score and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf 12 hpf and 16 hpf.		S16 slice 4	GSM8171984	source name:embryonic cells\|tissue:embryonic cells\|strain:AB\|age:16 hpf\|geo loc name:missing\|collection date:missing	S16 slice 4	Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds files include count matrixes and slice position information post running the processing steps.	embryonic cells	Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	Zebrafish embryos were raised in 0.3x Danieau buffer and were then embedded in OCT at the required developmental stages of 10 hpf 12hpf and 16 hpf.	tissue:embryonic cells\|strain:AB\|age:16 hpf	GSM8171984	GSM8171984: S16 slice 4; Danio rerio; RNA Seq	GSM8171984 r1	GSM8171984	1	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP498123	loader:fastq load.py	S16_2_04-R1.fq.gz S16_2_04-R2.fq.gz	fastq fastq	6868276226.0	23671591.0	GSM8171984 r1	0:144.21 1:145.94	A:1877392790;C:1565333202;G:1481973920;T:1943515595;N:60719	144	145	1877392790	1565333202	1481973920	1943515595	60719	SRX24074003	SRS20864392	SRA1834502	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	China	2024-03-27	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
31567	31567	SRR28471031	SRX24074002	SRS20864391	SRP498123	PRJNA1092581	Construction of Danio rerio Asymmetrical Maps DreAM	GSE262578	Transcriptome Analysis	Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally we difined a hox score and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf 12 hpf and 16 hpf.		S16 slice 3	GSM8171983	source name:embryonic cells\|tissue:embryonic cells\|strain:AB\|age:16 hpf\|geo loc name:missing\|collection date:missing	S16 slice 3	Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds files include count matrixes and slice position information post running the processing steps.	embryonic cells	Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	Zebrafish embryos were raised in 0.3x Danieau buffer and were then embedded in OCT at the required developmental stages of 10 hpf 12hpf and 16 hpf.	tissue:embryonic cells\|strain:AB\|age:16 hpf	GSM8171983	GSM8171983: S16 slice 3; Danio rerio; RNA Seq	GSM8171983 r1	GSM8171983	1	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP498123	loader:fastq load.py	S16_2_03-R1.fq.gz S16_2_03-R2.fq.gz	fastq fastq	6805653527.0	23393184.0	GSM8171983 r1	0:144.38 1:146.54	A:1865258599;C:1547577456;G:1497746987;T:1895011008;N:59477	144	146	1865258599	1547577456	1497746987	1895011008	59477	SRX24074002	SRS20864391	SRA1834502	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	China	2024-03-27	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
31568	31568	SRR28471032	SRX24074001	SRS20864390	SRP498123	PRJNA1092581	Construction of Danio rerio Asymmetrical Maps DreAM	GSE262578	Transcriptome Analysis	Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally we difined a hox score and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf 12 hpf and 16 hpf.		S16 slice 2	GSM8171981	source name:embryonic cells\|tissue:embryonic cells\|strain:AB\|age:16 hpf\|geo loc name:missing\|collection date:missing	S16 slice 2	Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds files include count matrixes and slice position information post running the processing steps.	embryonic cells	Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	Zebrafish embryos were raised in 0.3x Danieau buffer and were then embedded in OCT at the required developmental stages of 10 hpf 12hpf and 16 hpf.	tissue:embryonic cells\|strain:AB\|age:16 hpf	GSM8171981	GSM8171981: S16 slice 2; Danio rerio; RNA Seq	GSM8171981 r1	GSM8171981	1	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP498123	loader:fastq load.py	S16_2_02-R1.fq.gz S16_2_02-R2.fq.gz	fastq fastq	7023963229.0	24162141.0	GSM8171981 r1	0:144.12 1:146.58	A:1918527133;C:1603910134;G:1551695853;T:1949772309;N:57800	144	146	1918527133	1603910134	1551695853	1949772309	57800	SRX24074001	SRS20864390	SRA1834502	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	China	2024-03-27	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
31569	31569	SRR28471033	SRX24074000	SRS20864389	SRP498123	PRJNA1092581	Construction of Danio rerio Asymmetrical Maps DreAM	GSE262578	Transcriptome Analysis	Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally we difined a hox score and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf 12 hpf and 16 hpf.		S16 slice 1	GSM8171980	source name:embryonic cells\|tissue:embryonic cells\|strain:AB\|age:16 hpf\|geo loc name:missing\|collection date:missing	S16 slice 1	Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds files include count matrixes and slice position information post running the processing steps.	embryonic cells	Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	Zebrafish embryos were raised in 0.3x Danieau buffer and were then embedded in OCT at the required developmental stages of 10 hpf 12hpf and 16 hpf.	tissue:embryonic cells\|strain:AB\|age:16 hpf	GSM8171980	GSM8171980: S16 slice 1; Danio rerio; RNA Seq	GSM8171980 r1	GSM8171980	1	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP498123	loader:fastq load.py	S16_2_01-R1.fq.gz S16_2_01-R2.fq.gz	fastq fastq	6619993068.0	22789527.0	GSM8171980 r1	0:143.43 1:147.06	A:1776228931;C:1542516186;G:1481044120;T:1820158687;N:45144	143	147	1776228931	1542516186	1481044120	1820158687	45144	SRX24074000	SRS20864389	SRA1834502	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	China	2024-03-27	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
31570	31570	SRR28471034	SRX24073999	SRS20864388	SRP498123	PRJNA1092581	Construction of Danio rerio Asymmetrical Maps DreAM	GSE262578	Transcriptome Analysis	Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally we difined a hox score and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf 12 hpf and 16 hpf.		S12 slice 12	GSM8171979	source name:embryonic cells\|tissue:embryonic cells\|strain:AB\|age:12 hpf\|geo loc name:missing\|collection date:missing	S12 slice 12	Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds files include count matrixes and slice position information post running the processing steps.	embryonic cells	Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	Zebrafish embryos were raised in 0.3x Danieau buffer and were then embedded in OCT at the required developmental stages of 10 hpf 12hpf and 16 hpf.	tissue:embryonic cells\|strain:AB\|age:12 hpf	GSM8171979	GSM8171979: S12 slice 12; Danio rerio; RNA Seq	GSM8171979 r1	GSM8171979	1	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP498123	loader:fastq load.py	S12_1_12-R1.fq.gz S12_1_12-R2.fq.gz	fastq fastq	6907282671.0	23557012.0	GSM8171979 r1	0:145.54 1:147.68	A:1862944199;C:1601198280;G:1521830219;T:1921292527;N:17446	145	147	1862944199	1601198280	1521830219	1921292527	17446	SRX24073999	SRS20864388	SRA1834502	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	China	2024-03-27	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
31571	31571	SRR28471035	SRX24073998	SRS20864387	SRP498123	PRJNA1092581	Construction of Danio rerio Asymmetrical Maps DreAM	GSE262578	Transcriptome Analysis	Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally we difined a hox score and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf 12 hpf and 16 hpf.		S12 slice 11	GSM8171978	source name:embryonic cells\|tissue:embryonic cells\|strain:AB\|age:12 hpf\|geo loc name:missing\|collection date:missing	S12 slice 11	Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds files include count matrixes and slice position information post running the processing steps.	embryonic cells	Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	Zebrafish embryos were raised in 0.3x Danieau buffer and were then embedded in OCT at the required developmental stages of 10 hpf 12hpf and 16 hpf.	tissue:embryonic cells\|strain:AB\|age:12 hpf	GSM8171978	GSM8171978: S12 slice 11; Danio rerio; RNA Seq	GSM8171978 r1	GSM8171978	1	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP498123	loader:fastq load.py	S12_1_11-R1.fq.gz S12_1_11-R2.fq.gz	fastq fastq	6831871099.0	23334246.0	GSM8171978 r1	0:145.23 1:147.56	A:1841130963;C:1590884839;G:1490156717;T:1909681306;N:17274	145	147	1841130963	1590884839	1490156717	1909681306	17274	SRX24073998	SRS20864387	SRA1834502	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	China	2024-03-27	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
31572	31572	SRR28471036	SRX24073997	SRS20864386	SRP498123	PRJNA1092581	Construction of Danio rerio Asymmetrical Maps DreAM	GSE262578	Transcriptome Analysis	Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally we difined a hox score and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf 12 hpf and 16 hpf.		S12 slice 10	GSM8171977	source name:embryonic cells\|tissue:embryonic cells\|strain:AB\|age:12 hpf\|geo loc name:missing\|collection date:missing	S12 slice 10	Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds files include count matrixes and slice position information post running the processing steps.	embryonic cells	Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	Zebrafish embryos were raised in 0.3x Danieau buffer and were then embedded in OCT at the required developmental stages of 10 hpf 12hpf and 16 hpf.	tissue:embryonic cells\|strain:AB\|age:12 hpf	GSM8171977	GSM8171977: S12 slice 10; Danio rerio; RNA Seq	GSM8171977 r1	GSM8171977	1	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP498123	loader:fastq load.py	S12_1_10-R1.fq.gz S12_1_10-R2.fq.gz	fastq fastq	5783041643.0	19665431.0	GSM8171977 r1	0:146.19 1:147.88	A:1581046379;C:1324978876;G:1248026718;T:1628974699;N:14971	146	147	1581046379	1324978876	1248026718	1628974699	14971	SRX24073997	SRS20864386	SRA1834502	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	China	2024-03-27	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
31573	31573	SRR28471037	SRX24073996	SRS20864385	SRP498123	PRJNA1092581	Construction of Danio rerio Asymmetrical Maps DreAM	GSE262578	Transcriptome Analysis	Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally we difined a hox score and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf 12 hpf and 16 hpf.		S12 slice 9	GSM8171976	source name:embryonic cells\|tissue:embryonic cells\|strain:AB\|age:12 hpf\|geo loc name:missing\|collection date:missing	S12 slice 9	Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds files include count matrixes and slice position information post running the processing steps.	embryonic cells	Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	Zebrafish embryos were raised in 0.3x Danieau buffer and were then embedded in OCT at the required developmental stages of 10 hpf 12hpf and 16 hpf.	tissue:embryonic cells\|strain:AB\|age:12 hpf	GSM8171976	GSM8171976: S12 slice 9; Danio rerio; RNA Seq	GSM8171976 r1	GSM8171976	1	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP498123	loader:fastq load.py	S12_1_09-R1.fq.gz S12_1_09-R2.fq.gz	fastq fastq	7123142895.0	24299296.0	GSM8171976 r1	0:145.49 1:147.66	A:1925297375;C:1659640314;G:1576196761;T:1961990580;N:17865	145	147	1925297375	1659640314	1576196761	1961990580	17865	SRX24073996	SRS20864385	SRA1834502	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	China	2024-03-27	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
31574	31574	SRR28471038	SRX24073995	SRS20864384	SRP498123	PRJNA1092581	Construction of Danio rerio Asymmetrical Maps DreAM	GSE262578	Transcriptome Analysis	Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally we difined a hox score and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf 12 hpf and 16 hpf.		S12 slice 8	GSM8171974	source name:embryonic cells\|tissue:embryonic cells\|strain:AB\|age:12 hpf\|geo loc name:missing\|collection date:missing	S12 slice 8	Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds files include count matrixes and slice position information post running the processing steps.	embryonic cells	Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	Zebrafish embryos were raised in 0.3x Danieau buffer and were then embedded in OCT at the required developmental stages of 10 hpf 12hpf and 16 hpf.	tissue:embryonic cells\|strain:AB\|age:12 hpf	GSM8171974	GSM8171974: S12 slice 8; Danio rerio; RNA Seq	GSM8171974 r1	GSM8171974	1	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP498123	loader:fastq load.py	S12_1_08-R1.fq.gz S12_1_08-R2.fq.gz	fastq fastq	7144819692.0	24316501.0	GSM8171974 r1	0:145.93 1:147.90	A:1915884877;C:1672968137;G:1576641332;T:1979307110;N:18236	145	147	1915884877	1672968137	1576641332	1979307110	18236	SRX24073995	SRS20864384	SRA1834502	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	China	2024-03-27	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
31575	31575	SRR28471039	SRX24073994	SRS20864383	SRP498123	PRJNA1092581	Construction of Danio rerio Asymmetrical Maps DreAM	GSE262578	Transcriptome Analysis	Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally we difined a hox score and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf 12 hpf and 16 hpf.		S12 slice 7	GSM8171973	source name:embryonic cells\|tissue:embryonic cells\|strain:AB\|age:12 hpf\|geo loc name:missing\|collection date:missing	S12 slice 7	Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds files include count matrixes and slice position information post running the processing steps.	embryonic cells	Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	Zebrafish embryos were raised in 0.3x Danieau buffer and were then embedded in OCT at the required developmental stages of 10 hpf 12hpf and 16 hpf.	tissue:embryonic cells\|strain:AB\|age:12 hpf	GSM8171973	GSM8171973: S12 slice 7; Danio rerio; RNA Seq	GSM8171973 r1	GSM8171973	1	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP498123	loader:fastq load.py	S12_1_07-R1.fq.gz S12_1_07-R2.fq.gz	fastq fastq	7379485401.0	25300209.0	GSM8171973 r1	0:143.87 1:147.81	A:1973584695;C:1736374415;G:1654430758;T:2015077010;N:18523	143	147	1973584695	1736374415	1654430758	2015077010	18523	SRX24073994	SRS20864383	SRA1834502	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	China	2024-03-27	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
31576	31576	SRR28471040	SRX24073993	SRS20864382	SRP498123	PRJNA1092581	Construction of Danio rerio Asymmetrical Maps DreAM	GSE262578	Transcriptome Analysis	Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally we difined a hox score and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf 12 hpf and 16 hpf.		S12 slice 6	GSM8171972	source name:embryonic cells\|tissue:embryonic cells\|strain:AB\|age:12 hpf\|geo loc name:missing\|collection date:missing	S12 slice 6	Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds files include count matrixes and slice position information post running the processing steps.	embryonic cells	Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	Zebrafish embryos were raised in 0.3x Danieau buffer and were then embedded in OCT at the required developmental stages of 10 hpf 12hpf and 16 hpf.	tissue:embryonic cells\|strain:AB\|age:12 hpf	GSM8171972	GSM8171972: S12 slice 6; Danio rerio; RNA Seq	GSM8171972 r1	GSM8171972	1	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP498123	loader:fastq load.py	S12_1_06-R1.fq.gz S12_1_06-R2.fq.gz	fastq fastq	6780830499.0	23111786.0	GSM8171972 r1	0:145.59 1:147.80	A:1809593504;C:1599719267;G:1512122288;T:1859381851;N:13589	145	147	1809593504	1599719267	1512122288	1859381851	13589	SRX24073993	SRS20864382	SRA1834502	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	China	2024-03-27	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
31577	31577	SRR28471041	SRX24073992	SRS20864381	SRP498123	PRJNA1092581	Construction of Danio rerio Asymmetrical Maps DreAM	GSE262578	Transcriptome Analysis	Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally we difined a hox score and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf 12 hpf and 16 hpf.		S12 slice 5	GSM8171971	source name:embryonic cells\|tissue:embryonic cells\|strain:AB\|age:12 hpf\|geo loc name:missing\|collection date:missing	S12 slice 5	Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds files include count matrixes and slice position information post running the processing steps.	embryonic cells	Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	Zebrafish embryos were raised in 0.3x Danieau buffer and were then embedded in OCT at the required developmental stages of 10 hpf 12hpf and 16 hpf.	tissue:embryonic cells\|strain:AB\|age:12 hpf	GSM8171971	GSM8171971: S12 slice 5; Danio rerio; RNA Seq	GSM8171971 r1	GSM8171971	1	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP498123	loader:fastq load.py	S12_1_05-R1.fq.gz S12_1_05-R2.fq.gz	fastq fastq	6959350050.0	23769190.0	GSM8171971 r1	0:145.06 1:147.72	A:1875092128;C:1615063748;G:1550970555;T:1918160024;N:63595	145	147	1875092128	1615063748	1550970555	1918160024	63595	SRX24073992	SRS20864381	SRA1834502	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	China	2024-03-27	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
31578	31578	SRR28471042	SRX24073991	SRS20864380	SRP498123	PRJNA1092581	Construction of Danio rerio Asymmetrical Maps DreAM	GSE262578	Transcriptome Analysis	Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally we difined a hox score and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf 12 hpf and 16 hpf.		S12 slice 4	GSM8171970	source name:embryonic cells\|tissue:embryonic cells\|strain:AB\|age:12 hpf\|geo loc name:missing\|collection date:missing	S12 slice 4	Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds files include count matrixes and slice position information post running the processing steps.	embryonic cells	Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	Zebrafish embryos were raised in 0.3x Danieau buffer and were then embedded in OCT at the required developmental stages of 10 hpf 12hpf and 16 hpf.	tissue:embryonic cells\|strain:AB\|age:12 hpf	GSM8171970	GSM8171970: S12 slice 4; Danio rerio; RNA Seq	GSM8171970 r1	GSM8171970	1	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP498123	loader:fastq load.py	S12_1_04-R1.fq.gz S12_1_04-R2.fq.gz	fastq fastq	7016331930.0	23929575.0	GSM8171970 r1	0:145.36 1:147.85	A:1883672645;C:1639902329;G:1566256062;T:1926486960;N:13934	145	147	1883672645	1639902329	1566256062	1926486960	13934	SRX24073991	SRS20864380	SRA1834502	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	China	2024-03-27	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
31579	31579	SRR28471043	SRX24073990	SRS20864379	SRP498123	PRJNA1092581	Construction of Danio rerio Asymmetrical Maps DreAM	GSE262578	Transcriptome Analysis	Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally we difined a hox score and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf 12 hpf and 16 hpf.		S12 slice 3	GSM8171968	source name:embryonic cells\|tissue:embryonic cells\|strain:AB\|age:12 hpf\|geo loc name:missing\|collection date:missing	S12 slice 3	Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds files include count matrixes and slice position information post running the processing steps.	embryonic cells	Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	Zebrafish embryos were raised in 0.3x Danieau buffer and were then embedded in OCT at the required developmental stages of 10 hpf 12hpf and 16 hpf.	tissue:embryonic cells\|strain:AB\|age:12 hpf	GSM8171968	GSM8171968: S12 slice 3; Danio rerio; RNA Seq	GSM8171968 r1	GSM8171968	1	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP498123	loader:fastq load.py	S12_1_03-R1.fq.gz S12_1_03-R2.fq.gz	fastq fastq	7014757897.0	23928375.0	GSM8171968 r1	0:145.38 1:147.78	A:1893627672;C:1629188725;G:1555319202;T:1936558222;N:64076	145	147	1893627672	1629188725	1555319202	1936558222	64076	SRX24073990	SRS20864379	SRA1834502	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	China	2024-03-27	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
31580	31580	SRR28471044	SRX24073989	SRS20864378	SRP498123	PRJNA1092581	Construction of Danio rerio Asymmetrical Maps DreAM	GSE262578	Transcriptome Analysis	Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally we difined a hox score and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf 12 hpf and 16 hpf.		S12 slice 2	GSM8171967	source name:embryonic cells\|tissue:embryonic cells\|strain:AB\|age:12 hpf\|geo loc name:missing\|collection date:missing	S12 slice 2	Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds files include count matrixes and slice position information post running the processing steps.	embryonic cells	Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	Zebrafish embryos were raised in 0.3x Danieau buffer and were then embedded in OCT at the required developmental stages of 10 hpf 12hpf and 16 hpf.	tissue:embryonic cells\|strain:AB\|age:12 hpf	GSM8171967	GSM8171967: S12 slice 2; Danio rerio; RNA Seq	GSM8171967 r1	GSM8171967	1	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP498123	loader:fastq load.py	S12_1_02-R1.fq.gz S12_1_02-R2.fq.gz	fastq fastq	6840908671.0	23398529.0	GSM8171967 r1	0:144.87 1:147.50	A:1887167845;C:1555902053;G:1495740904;T:1902033708;N:64161	144	147	1887167845	1555902053	1495740904	1902033708	64161	SRX24073989	SRS20864378	SRA1834502	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	China	2024-03-27	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
31581	31581	SRR28471045	SRX24073988	SRS20864376	SRP498123	PRJNA1092581	Construction of Danio rerio Asymmetrical Maps DreAM	GSE262578	Transcriptome Analysis	Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally we difined a hox score and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf 12 hpf and 16 hpf.		S12 slice 1	GSM8171966	source name:embryonic cells\|tissue:embryonic cells\|strain:AB\|age:12 hpf\|geo loc name:missing\|collection date:missing	S12 slice 1	Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds files include count matrixes and slice position information post running the processing steps.	embryonic cells	Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	Zebrafish embryos were raised in 0.3x Danieau buffer and were then embedded in OCT at the required developmental stages of 10 hpf 12hpf and 16 hpf.	tissue:embryonic cells\|strain:AB\|age:12 hpf	GSM8171966	GSM8171966: S12 slice 1; Danio rerio; RNA Seq	GSM8171966 r1	GSM8171966	1	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP498123	loader:fastq load.py	S12_1_01-R1.fq.gz S12_1_01-R2.fq.gz	fastq fastq	7278647579.0	24915967.0	GSM8171966 r1	0:144.68 1:147.45	A:1978225177;C:1677337831;G:1598910902;T:2024108056;N:65613	144	147	1978225177	1677337831	1598910902	2024108056	65613	SRX24073988	SRS20864376	SRA1834502	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	China	2024-03-27	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
31582	31582	SRR28471046	SRX24073987	SRS20864375	SRP498123	PRJNA1092581	Construction of Danio rerio Asymmetrical Maps DreAM	GSE262578	Transcriptome Analysis	Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally we difined a hox score and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf 12 hpf and 16 hpf.		S10 slice 28	GSM8171965	source name:embryonic cells\|tissue:embryonic cells\|strain:AB\|age:10 hpf\|geo loc name:missing\|collection date:missing	S10 slice 28	Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds files include count matrixes and slice position information post running the processing steps.	embryonic cells	Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	Zebrafish embryos were raised in 0.3x Danieau buffer and were then embedded in OCT at the required developmental stages of 10 hpf 12hpf and 16 hpf.	tissue:embryonic cells\|strain:AB\|age:10 hpf	GSM8171965	GSM8171965: S10 slice 28; Danio rerio; RNA Seq	GSM8171965 r1	GSM8171965	1	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP498123	loader:fastq load.py	S10_2_28-R1.fq.gz S10_2_28-R2.fq.gz	fastq fastq	759288186.0	2615807.0	GSM8171965 r1	0:143.73 1:146.54	A:205364809;C:175246978;G:163844785;T:214825556;N:6058	143	146	205364809	175246978	163844785	214825556	6058	SRX24073987	SRS20864375	SRA1834502	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	China	2024-03-27	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
31583	31583	SRR28471047	SRX24073986	SRS20864377	SRP498123	PRJNA1092581	Construction of Danio rerio Asymmetrical Maps DreAM	GSE262578	Transcriptome Analysis	Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally we difined a hox score and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf 12 hpf and 16 hpf.		S10 slice 27	GSM8171964	source name:embryonic cells\|tissue:embryonic cells\|strain:AB\|age:10 hpf\|geo loc name:missing\|collection date:missing	S10 slice 27	Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds files include count matrixes and slice position information post running the processing steps.	embryonic cells	Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	Zebrafish embryos were raised in 0.3x Danieau buffer and were then embedded in OCT at the required developmental stages of 10 hpf 12hpf and 16 hpf.	tissue:embryonic cells\|strain:AB\|age:10 hpf	GSM8171964	GSM8171964: S10 slice 27; Danio rerio; RNA Seq	GSM8171964 r1	GSM8171964	1	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP498123	loader:fastq load.py	S10_2_27-R1.fq.gz S10_2_27-R2.fq.gz	fastq fastq	6581985394.0	22700834.0	GSM8171964 r1	0:143.52 1:146.42	A:1794301951;C:1513541111;G:1430119165;T:1844015897;N:7270	143	146	1794301951	1513541111	1430119165	1844015897	7270	SRX24073986	SRS20864377	SRA1834502	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	China	2024-03-27	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
31584	31584	SRR28471048	SRX24073985	SRS20864373	SRP498123	PRJNA1092581	Construction of Danio rerio Asymmetrical Maps DreAM	GSE262578	Transcriptome Analysis	Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally we difined a hox score and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf 12 hpf and 16 hpf.		S10 slice 26	GSM8171962	source name:embryonic cells\|tissue:embryonic cells\|strain:AB\|age:10 hpf\|geo loc name:missing\|collection date:missing	S10 slice 26	Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds files include count matrixes and slice position information post running the processing steps.	embryonic cells	Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	Zebrafish embryos were raised in 0.3x Danieau buffer and were then embedded in OCT at the required developmental stages of 10 hpf 12hpf and 16 hpf.	tissue:embryonic cells\|strain:AB\|age:10 hpf	GSM8171962	GSM8171962: S10 slice 26; Danio rerio; RNA Seq	GSM8171962 r1	GSM8171962	1	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP498123	loader:fastq load.py	S10_2_26-R1.fq.gz S10_2_26-R2.fq.gz	fastq fastq	7222374349.0	24651582.0	GSM8171962 r1	0:145.51 1:147.47	A:1979954857;C:1642503990;G:1569784440;T:2030123197;N:7865	145	147	1979954857	1642503990	1569784440	2030123197	7865	SRX24073985	SRS20864373	SRA1834502	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	China	2024-03-27	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
31585	31585	SRR28471049	SRX24073984	SRS20864374	SRP498123	PRJNA1092581	Construction of Danio rerio Asymmetrical Maps DreAM	GSE262578	Transcriptome Analysis	Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally we difined a hox score and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf 12 hpf and 16 hpf.		S10 slice 25	GSM8171961	source name:embryonic cells\|tissue:embryonic cells\|strain:AB\|age:10 hpf\|geo loc name:missing\|collection date:missing	S10 slice 25	Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds files include count matrixes and slice position information post running the processing steps.	embryonic cells	Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	Zebrafish embryos were raised in 0.3x Danieau buffer and were then embedded in OCT at the required developmental stages of 10 hpf 12hpf and 16 hpf.	tissue:embryonic cells\|strain:AB\|age:10 hpf	GSM8171961	GSM8171961: S10 slice 25; Danio rerio; RNA Seq	GSM8171961 r1	GSM8171961	1	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP498123	loader:fastq load.py	S10_2_25-R1.fq.gz S10_2_25-R2.fq.gz	fastq fastq	6912437288.0	23704050.0	GSM8171961 r1	0:144.17 1:147.45	A:1886377008;C:1583136289;G:1524973541;T:1917942644;N:7806	144	147	1886377008	1583136289	1524973541	1917942644	7806	SRX24073984	SRS20864374	SRA1834502	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	China	2024-03-27	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
31586	31586	SRR28471050	SRX24073983	SRS20864372	SRP498123	PRJNA1092581	Construction of Danio rerio Asymmetrical Maps DreAM	GSE262578	Transcriptome Analysis	Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally we difined a hox score and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf 12 hpf and 16 hpf.		S10 slice 24	GSM8171960	source name:embryonic cells\|tissue:embryonic cells\|strain:AB\|age:10 hpf\|geo loc name:missing\|collection date:missing	S10 slice 24	Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds files include count matrixes and slice position information post running the processing steps.	embryonic cells	Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	Zebrafish embryos were raised in 0.3x Danieau buffer and were then embedded in OCT at the required developmental stages of 10 hpf 12hpf and 16 hpf.	tissue:embryonic cells\|strain:AB\|age:10 hpf	GSM8171960	GSM8171960: S10 slice 24; Danio rerio; RNA Seq	GSM8171960 r1	GSM8171960	1	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP498123	loader:fastq load.py	S10_2_24-R1.fq.gz S10_2_24-R2.fq.gz	fastq fastq	6839477961.0	23381494.0	GSM8171960 r1	0:145.10 1:147.42	A:1878952639;C:1564093766;G:1477542759;T:1918881626;N:7171	145	147	1878952639	1564093766	1477542759	1918881626	7171	SRX24073983	SRS20864372	SRA1834502	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	China	2024-03-27	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
31587	31587	SRR28471051	SRX24073982	SRS20864371	SRP498123	PRJNA1092581	Construction of Danio rerio Asymmetrical Maps DreAM	GSE262578	Transcriptome Analysis	Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally we difined a hox score and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf 12 hpf and 16 hpf.		S10 slice 23	GSM8171959	source name:embryonic cells\|tissue:embryonic cells\|strain:AB\|age:10 hpf\|geo loc name:missing\|collection date:missing	S10 slice 23	Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds files include count matrixes and slice position information post running the processing steps.	embryonic cells	Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	Zebrafish embryos were raised in 0.3x Danieau buffer and were then embedded in OCT at the required developmental stages of 10 hpf 12hpf and 16 hpf.	tissue:embryonic cells\|strain:AB\|age:10 hpf	GSM8171959	GSM8171959: S10 slice 23; Danio rerio; RNA Seq	GSM8171959 r1	GSM8171959	1	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP498123	loader:fastq load.py	S10_2_23-R1.fq.gz S10_2_23-R2.fq.gz	fastq fastq	7167273237.0	24443101.0	GSM8171959 r1	0:145.85 1:147.38	A:1939464339;C:1670904264;G:1550365240;T:2006531554;N:7840	145	147	1939464339	1670904264	1550365240	2006531554	7840	SRX24073982	SRS20864371	SRA1834502	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	China	2024-03-27	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
31588	31588	SRR28471052	SRX24073981	SRS20864369	SRP498123	PRJNA1092581	Construction of Danio rerio Asymmetrical Maps DreAM	GSE262578	Transcriptome Analysis	Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally we difined a hox score and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf 12 hpf and 16 hpf.		S10 slice 22	GSM8171958	source name:embryonic cells\|tissue:embryonic cells\|strain:AB\|age:10 hpf\|geo loc name:missing\|collection date:missing	S10 slice 22	Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds files include count matrixes and slice position information post running the processing steps.	embryonic cells	Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	Zebrafish embryos were raised in 0.3x Danieau buffer and were then embedded in OCT at the required developmental stages of 10 hpf 12hpf and 16 hpf.	tissue:embryonic cells\|strain:AB\|age:10 hpf	GSM8171958	GSM8171958: S10 slice 22; Danio rerio; RNA Seq	GSM8171958 r1	GSM8171958	1	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP498123	loader:fastq load.py	S10_2_22-R1.fq.gz S10_2_22-R2.fq.gz	fastq fastq	7201833997.0	24595383.0	GSM8171958 r1	0:145.55 1:147.26	A:1961492345;C:1657551460;G:1566181731;T:2016600464;N:7997	145	147	1961492345	1657551460	1566181731	2016600464	7997	SRX24073981	SRS20864369	SRA1834502	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	China	2024-03-27	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
31589	31589	SRR28471053	SRX24073980	SRS20864370	SRP498123	PRJNA1092581	Construction of Danio rerio Asymmetrical Maps DreAM	GSE262578	Transcriptome Analysis	Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally we difined a hox score and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf 12 hpf and 16 hpf.		S10 slice 21	GSM8171957	source name:embryonic cells\|tissue:embryonic cells\|strain:AB\|age:10 hpf\|geo loc name:missing\|collection date:missing	S10 slice 21	Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds files include count matrixes and slice position information post running the processing steps.	embryonic cells	Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	Zebrafish embryos were raised in 0.3x Danieau buffer and were then embedded in OCT at the required developmental stages of 10 hpf 12hpf and 16 hpf.	tissue:embryonic cells\|strain:AB\|age:10 hpf	GSM8171957	GSM8171957: S10 slice 21; Danio rerio; RNA Seq	GSM8171957 r1	GSM8171957	1	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP498123	loader:fastq load.py	S10_2_21-R1.fq.gz S10_2_21-R2.fq.gz	fastq fastq	7200671307.0	24658175.0	GSM8171957 r1	0:145.00 1:147.02	A:1952177571;C:1673984272;G:1548414880;T:2026087466;N:7118	145	147	1952177571	1673984272	1548414880	2026087466	7118	SRX24073980	SRS20864370	SRA1834502	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	China	2024-03-27	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
31590	31590	SRR28471054	SRX24073979	SRS20864368	SRP498123	PRJNA1092581	Construction of Danio rerio Asymmetrical Maps DreAM	GSE262578	Transcriptome Analysis	Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally we difined a hox score and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf 12 hpf and 16 hpf.		S10 slice 20	GSM8171955	source name:embryonic cells\|tissue:embryonic cells\|strain:AB\|age:10 hpf\|geo loc name:missing\|collection date:missing	S10 slice 20	Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds files include count matrixes and slice position information post running the processing steps.	embryonic cells	Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	Zebrafish embryos were raised in 0.3x Danieau buffer and were then embedded in OCT at the required developmental stages of 10 hpf 12hpf and 16 hpf.	tissue:embryonic cells\|strain:AB\|age:10 hpf	GSM8171955	GSM8171955: S10 slice 20; Danio rerio; RNA Seq	GSM8171955 r1	GSM8171955	1	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP498123	loader:fastq load.py	S10_2_20-R1.fq.gz S10_2_20-R2.fq.gz	fastq fastq	7029384198.0	24038713.0	GSM8171955 r1	0:145.27 1:147.15	A:1927499291;C:1610291489;G:1509165690;T:1982420962;N:6766	145	147	1927499291	1610291489	1509165690	1982420962	6766	SRX24073979	SRS20864368	SRA1834502	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	China	2024-03-27	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
31591	31591	SRR28471055	SRX24073978	SRS20864367	SRP498123	PRJNA1092581	Construction of Danio rerio Asymmetrical Maps DreAM	GSE262578	Transcriptome Analysis	Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally we difined a hox score and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf 12 hpf and 16 hpf.		S10 slice 19	GSM8171954	source name:embryonic cells\|tissue:embryonic cells\|strain:AB\|age:10 hpf\|geo loc name:missing\|collection date:missing	S10 slice 19	Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds files include count matrixes and slice position information post running the processing steps.	embryonic cells	Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	Zebrafish embryos were raised in 0.3x Danieau buffer and were then embedded in OCT at the required developmental stages of 10 hpf 12hpf and 16 hpf.	tissue:embryonic cells\|strain:AB\|age:10 hpf	GSM8171954	GSM8171954: S10 slice 19; Danio rerio; RNA Seq	GSM8171954 r1	GSM8171954	1	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP498123	loader:fastq load.py	S10_2_19-R1.fq.gz S10_2_19-R2.fq.gz	fastq fastq	6805088018.0	23209224.0	GSM8171954 r1	0:145.80 1:147.41	A:1868791398;C:1559085219;G:1478313464;T:1898890630;N:7307	145	147	1868791398	1559085219	1478313464	1898890630	7307	SRX24073978	SRS20864367	SRA1834502	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	China	2024-03-27	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
31592	31592	SRR28471056	SRX24073977	SRS20864366	SRP498123	PRJNA1092581	Construction of Danio rerio Asymmetrical Maps DreAM	GSE262578	Transcriptome Analysis	Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally we difined a hox score and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf 12 hpf and 16 hpf.		S10 slice 18	GSM8171953	source name:embryonic cells\|tissue:embryonic cells\|strain:AB\|age:10 hpf\|geo loc name:missing\|collection date:missing	S10 slice 18	Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds files include count matrixes and slice position information post running the processing steps.	embryonic cells	Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	Zebrafish embryos were raised in 0.3x Danieau buffer and were then embedded in OCT at the required developmental stages of 10 hpf 12hpf and 16 hpf.	tissue:embryonic cells\|strain:AB\|age:10 hpf	GSM8171953	GSM8171953: S10 slice 18; Danio rerio; RNA Seq	GSM8171953 r1	GSM8171953	1	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP498123	loader:fastq load.py	S10_2_18-R1.fq.gz S10_2_18-R2.fq.gz	fastq fastq	6840069197.0	23337475.0	GSM8171953 r1	0:145.70 1:147.40	A:1857694353;C:1583014737;G:1489270628;T:1910082435;N:7044	145	147	1857694353	1583014737	1489270628	1910082435	7044	SRX24073977	SRS20864366	SRA1834502	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	China	2024-03-27	Gastrula	Embryo	Embryo Imprecise	All anatomical structures

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