metadata: run_metadata: 25 rows where devstage_curation = "Cleavage" and experiment.library

25 rows where devstage_curation = "Cleavage" and experiment.library_strategy = "RIP-Seq"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
32033	32033	SRR28976522	SRX24505963	SRS21254128	SRP506702	PRJNA1109723	rbm24a is an organizer component of germ plasm to determine germ cell fate	GSE267086	Other	The formation of germ cells is a critical issue for the continuation of species. A large group of animals follow a preformation strategy to generate their primordial germ cells PGCs. They produce a set of localized maternal mRNAs and proteins to form phase separated germ plasm that functions as the PGC determinants but the mechanisms underlying the assembly of germ plasm is poorly understood. This study identifies Rbm24a as an enssential localized germ plasm protein component that controls the formation of large and functional germ plasm granules. Rbm24a is complexed with Buc and interacts with germ plasm mRNAs which determines the specific grasp of germ plasm mRNAs into the phase separated aggregates. Rbm24a absent granules fail to undergo kinesin dependent transport towards the cleavage furrows where small particles fuse into large ones. The loss of maternal rbm24a causes the complete degradation of germ plasm components and the disappearance of PGCs resulting in totally sterile animals. Our work establishes that Rbm24 is a critical nucleating organizer component of germ plasm highlighting an emerging common mechanism to read and recruit RNA component into phase separated condensates. Overall design: To elucidate the comprehensive RNA binding landscape of Rbm24a in zebrafish we employed RIP seq analysis on both rbm24a GFP knock in and wild type zebrafish.			Zebrafish RIP seq Rbm24a Knock in IP	GSM8259538	source name:whole embryo\|tissue:whole embryo\|developmental stage:4 cell stage\|cell type:embryonic cell\|genotype:Rbm24a Knock in\|antibody:GFP\|geo loc name:missing\|collection date:missing	Zebrafish RIP seq Rbm24a Knock in IP	Each library was amplified by a 15 cycle PCR and 150 bp paired end sequencing was subjected to Illumina Nova seq 6000 to obtain the raw data. Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: Bigwig file for each Sample	whole embryo	Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA and RIP IP RNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina Nova seq 6000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer’s instructions.	Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C	tissue:whole embryo\|developmental stage:4 cell stage\|cell type:embryonic cell\|genotype:Rbm24a Knock in\|antibody:GFP	GSM8259538	GSM8259538: Zebrafish RIP seq Rbm24a Knock in IP; Danio rerio; RIP Seq	GSM8259538 r1	GSM8259538	1	Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA and RIP IP RNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina Nova seq 6000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions.		RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP506702		RIP_KI_IP_R2.fq.gz RIP_KI_IP_R1.fq.gz	fastq fastq	6457893104.0	21383752.0	GSM8259538 r1	0:151 1:151	A:975588225;C:2019180290;G:2469634919;T:992947702;N:541968	151	151	975588225	2019180290	2469634919	992947702	541968	SRX24505963	SRS21254128	SRA1863578	Ang Li, College of Life Sciences, shandong university	Ang Li, College of Life Sciences, shandong university	2	0.90304	0.86018	0.20083	0.20471	0.96382	0.96743	0.96102	0.98876	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	China	2024-05-09	Cleavage	Embryo	Whole Organism	All anatomical structures
32034	32034	SRR28976523	SRX24505962	SRS21254127	SRP506702	PRJNA1109723	rbm24a is an organizer component of germ plasm to determine germ cell fate	GSE267086	Other	The formation of germ cells is a critical issue for the continuation of species. A large group of animals follow a preformation strategy to generate their primordial germ cells PGCs. They produce a set of localized maternal mRNAs and proteins to form phase separated germ plasm that functions as the PGC determinants but the mechanisms underlying the assembly of germ plasm is poorly understood. This study identifies Rbm24a as an enssential localized germ plasm protein component that controls the formation of large and functional germ plasm granules. Rbm24a is complexed with Buc and interacts with germ plasm mRNAs which determines the specific grasp of germ plasm mRNAs into the phase separated aggregates. Rbm24a absent granules fail to undergo kinesin dependent transport towards the cleavage furrows where small particles fuse into large ones. The loss of maternal rbm24a causes the complete degradation of germ plasm components and the disappearance of PGCs resulting in totally sterile animals. Our work establishes that Rbm24 is a critical nucleating organizer component of germ plasm highlighting an emerging common mechanism to read and recruit RNA component into phase separated condensates. Overall design: To elucidate the comprehensive RNA binding landscape of Rbm24a in zebrafish we employed RIP seq analysis on both rbm24a GFP knock in and wild type zebrafish.			Zebrafish RIP seq wild type IP	GSM8259537	source name:whole embryo\|tissue:whole embryo\|developmental stage:4 cell stage\|cell type:embryonic cell\|genotype:wild type\|antibody:GFP\|geo loc name:missing\|collection date:missing	Zebrafish RIP seq wild type IP	Each library was amplified by a 15 cycle PCR and 150 bp paired end sequencing was subjected to Illumina Nova seq 6000 to obtain the raw data. Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: Bigwig file for each Sample	whole embryo	Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA and RIP IP RNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina Nova seq 6000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer’s instructions.	Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C	tissue:whole embryo\|developmental stage:4 cell stage\|cell type:embryonic cell\|genotype:wild type\|antibody:GFP	GSM8259537	GSM8259537: Zebrafish RIP seq wild type IP; Danio rerio; RIP Seq	GSM8259537 r1	GSM8259537	1	Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA and RIP IP RNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina Nova seq 6000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions.		RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP506702		RIP_WT_IP_R2.fq.gz RIP_WT_IP_R1.fq.gz	fastq fastq	4501412680.0	14905340.0	GSM8259537 r1	0:151 1:151	A:651609366;C:1285679784;G:1901211768;T:662533141;N:378621	151	151	651609366	1285679784	1901211768	662533141	378621	SRX24505962	SRS21254127	SRA1863578	Ang Li, College of Life Sciences, shandong university	Ang Li, College of Life Sciences, shandong university	2	0.96426	0.81361	0.26579	0.2253	0.97784	0.97806	0.8699	0.93379	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	China	2024-05-09	Cleavage	Embryo	Whole Organism	All anatomical structures
32035	32035	SRR28976524	SRX24505961	SRS21254126	SRP506702	PRJNA1109723	rbm24a is an organizer component of germ plasm to determine germ cell fate	GSE267086	Other	The formation of germ cells is a critical issue for the continuation of species. A large group of animals follow a preformation strategy to generate their primordial germ cells PGCs. They produce a set of localized maternal mRNAs and proteins to form phase separated germ plasm that functions as the PGC determinants but the mechanisms underlying the assembly of germ plasm is poorly understood. This study identifies Rbm24a as an enssential localized germ plasm protein component that controls the formation of large and functional germ plasm granules. Rbm24a is complexed with Buc and interacts with germ plasm mRNAs which determines the specific grasp of germ plasm mRNAs into the phase separated aggregates. Rbm24a absent granules fail to undergo kinesin dependent transport towards the cleavage furrows where small particles fuse into large ones. The loss of maternal rbm24a causes the complete degradation of germ plasm components and the disappearance of PGCs resulting in totally sterile animals. Our work establishes that Rbm24 is a critical nucleating organizer component of germ plasm highlighting an emerging common mechanism to read and recruit RNA component into phase separated condensates. Overall design: To elucidate the comprehensive RNA binding landscape of Rbm24a in zebrafish we employed RIP seq analysis on both rbm24a GFP knock in and wild type zebrafish.			Zebrafish RIP seq Rbm24a Knock in input	GSM8259536	source name:whole embryo\|tissue:whole embryo\|developmental stage:4 cell stage\|cell type:embryonic cell\|genotype:Rbm24a Knock in\|antibody:input\|geo loc name:missing\|collection date:missing	Zebrafish RIP seq Rbm24a Knock in input	Each library was amplified by a 15 cycle PCR and 150 bp paired end sequencing was subjected to Illumina Nova seq 6000 to obtain the raw data. Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: Bigwig file for each Sample	whole embryo	Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA and RIP IP RNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina Nova seq 6000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer’s instructions.	Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C	tissue:whole embryo\|developmental stage:4 cell stage\|cell type:embryonic cell\|genotype:Rbm24a Knock in\|antibody:input	GSM8259536	GSM8259536: Zebrafish RIP seq Rbm24a Knock in input; Danio rerio; RIP Seq	GSM8259536 r1	GSM8259536	1	Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA and RIP IP RNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina Nova seq 6000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions.		RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP506702		RIP_KI_Input_R2.fq.gz RIP_KI_Input_R1.fq.gz	fastq fastq	9539398726.0	31587413.0	GSM8259536 r1	0:151 1:151	A:2233069830;C:2078359171;G:3009942870;T:2217201959;N:824896	151	151	2233069830	2078359171	3009942870	2217201959	824896	SRX24505961	SRS21254126	SRA1863578	Ang Li, College of Life Sciences, shandong university	Ang Li, College of Life Sciences, shandong university	2	0.90112	0.81448	0.02415	0.01993	0.79287	0.79807	0.47884	0.48186	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	China	2024-05-09	Cleavage	Embryo	Whole Organism	All anatomical structures
32036	32036	SRR28976525	SRX24505960	SRS21254125	SRP506702	PRJNA1109723	rbm24a is an organizer component of germ plasm to determine germ cell fate	GSE267086	Other	The formation of germ cells is a critical issue for the continuation of species. A large group of animals follow a preformation strategy to generate their primordial germ cells PGCs. They produce a set of localized maternal mRNAs and proteins to form phase separated germ plasm that functions as the PGC determinants but the mechanisms underlying the assembly of germ plasm is poorly understood. This study identifies Rbm24a as an enssential localized germ plasm protein component that controls the formation of large and functional germ plasm granules. Rbm24a is complexed with Buc and interacts with germ plasm mRNAs which determines the specific grasp of germ plasm mRNAs into the phase separated aggregates. Rbm24a absent granules fail to undergo kinesin dependent transport towards the cleavage furrows where small particles fuse into large ones. The loss of maternal rbm24a causes the complete degradation of germ plasm components and the disappearance of PGCs resulting in totally sterile animals. Our work establishes that Rbm24 is a critical nucleating organizer component of germ plasm highlighting an emerging common mechanism to read and recruit RNA component into phase separated condensates. Overall design: To elucidate the comprehensive RNA binding landscape of Rbm24a in zebrafish we employed RIP seq analysis on both rbm24a GFP knock in and wild type zebrafish.			Zebrafish RIP seq wild type input	GSM8259535	source name:whole embryo\|tissue:whole embryo\|developmental stage:4 cell stage\|cell type:embryonic cell\|genotype:wild type\|antibody:input\|geo loc name:missing\|collection date:missing	Zebrafish RIP seq wild type input	Each library was amplified by a 15 cycle PCR and 150 bp paired end sequencing was subjected to Illumina Nova seq 6000 to obtain the raw data. Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: Bigwig file for each Sample	whole embryo	Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA and RIP IP RNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina Nova seq 6000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer’s instructions.	Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C	tissue:whole embryo\|developmental stage:4 cell stage\|cell type:embryonic cell\|genotype:wild type\|antibody:input	GSM8259535	GSM8259535: Zebrafish RIP seq wild type input; Danio rerio; RIP Seq	GSM8259535 r1	GSM8259535	1	Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA and RIP IP RNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina Nova seq 6000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions.		RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP506702		RIP_WT_Input_R2.fq.gz RIP_WT_Input_R1.fq.gz	fastq fastq	14180410302.0	46955001.0	GSM8259535 r1	0:151 1:151	A:3380011534;C:2883841476;G:4593876270;T:3321465622;N:1215400	151	151	3380011534	2883841476	4593876270	3321465622	1215400	SRX24505960	SRS21254125	SRA1863578	Ang Li, College of Life Sciences, shandong university	Ang Li, College of Life Sciences, shandong university	2	0.86497	0.64685	0.04432	0.02854	0.79324	0.8031	0.52927	0.53304	151	151	B	B	mate2-mate1 similar by mapping diff	illumina	novaseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	China	2024-05-09	Cleavage	Embryo	Whole Organism	All anatomical structures
41556	41556	SRR5017067	SRX2345562	SRS1796129	SRP093295	PRJNA353372	N6 methyladenosine dynamics during early vertebrate embryogenesis	GSE89815	Other	Early vertebrate embryogenesis is characterized by extensive post transcriptional regulation during the maternal to zygotic transition. The N6 methyladenosine m6A modifications on mRNA has been shown to affect both translation and stability of transcripts. Here we investigate the m6A topology during early vertebrate embryogenesis and its association with RNA stability translation efficiency and effect on miR 430 degradation kinetics. Notably we find a strong association of m6A with cytoplasmic polyadenylation and translational efficiency prior to zygotic genome activation. Genes required for zygotic genome activation such as nanog and pou5f3 display dynamic m6A levels. post zygotic genome activation m6A is associated with improved stability and dampens the effect of miR 430 mediated degradation. Through sequence analyses we identified enrichment of motifs for RNA binding proteins involved in translational regulation and RNA degradation. We propose a role for m6A in multiple mRNA regulatory mechanisms for the first time in an in vivo system and improve our understanding of the combinatorial code behind the complex post transcriptional regulation of reprogramming during early vertebrate development. Overall design: Examination of m6A in four different developmental stages			input 64cell rep2	GSM2390020	tissue:Embryos\|developmental stage:64 cell embryos\|strain:AB wild type	input 64cell rep2	Base calling The sequencing output from each of the 4 lanes the sequencing run was trimmed 7 nucleotides in the 5’end and de multiplexed 4 samples in each lane. Reads were mapped to Zv10 using the STAR aligner Dobin et al. 2013 with options seedSearchStartLmax 15 clip3pNbases 10 clip5pNbases 10 outFilterMultimapNmax 20 outFilterMismatchNoverLmax 0.05 outFilterMatchNminOverLread 0.0 outFilterMatchNmin 15 outFilterScoreMinOverLread 0.0. We performed peak calling and detection of differentially methylated genes using ExomePeak Meng et al. 2013. Genome build: Zv10 Supplementary files format and content: Bed files with enriched regions from each developmental stage and txt file with raw and normalized read counts for each gene using the input samples	Embryos	We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization 2 4 and 6 hpf in batches of 200 embryos using TRIzol Invitrogen cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads® mRNA Purification Kit Ambion #61006. The m6A RIP experiment was carried out as previously described Ke et al. 2015 and the protocol can be found in supplementary file 1. Briefly polyA+ enriched RNA was partially fragmented by alkaline hydrolysis ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies # 10008D conjugated anti m6A antibody Synaptic systems # 202003. post stringent washing the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich # M2780 ethanol precipitated and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3’pre adenylated DNA liker ligation with T4 RNA ligase2 truncated KQ NEB #M0373L at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014 with improved RT primers indicated in Ke et al. 2015.	Embryos from the AB wild type strain were obtained from the NMBU zebrafish facility where the zebrafish were kept at 28±1°C on a 14 10 hour light dark cycle at a density of 5 10 fish/L. System water SW was prepared from particle and active charcoal filtrated tap water deionized by reverse osmosis RO and kept sterile by UV irradiation. The water was conditioned to a conductivity of 500µS/cm general hardness GH 4 5 and pH 7.5 by addition of 155g synthetic sea salt Instant Ocean Blacksburg USA 53g sodium carbonate and 15g calcium chloride Sigma Aldrich per liter RO water. Adult fish were fed with Gemma Micro 300 Skretting Stavanger Norway dry feed twice a day and live artemia Scanbur Karlslunde Denmark once a day. Health monitoring was by daily inspection use of sentinel fish sent for pathology ZIRC Eugene Oregon and water microbiology analysis NMBU Vetbio Oslo every six month. Adult fish were allowed to mate for 30 minutes in standard 1L breeding tanks Aquatic Habitats Apopka FL. Harvested embryos were kept in autoclaved SW at 28 °C harvested by snap freezing liquid nitrogen and visually controlled for stage and lack of abnormalities at the selected time points. All experiments were performed according to Norwegian Animal Welfare Act 2009 the EU Directive 2010/63.	developmental stage:64 cell embryos\|strain:AB wild type	GSM2390020	GSM2390020: input 64cell rep2; Danio rerio; RIP Seq	GSM2390020		1	We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization 2 4 and 6 hpf in batches of 200 embryos using TRIzol Invitrogen cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads® mRNA Purification Kit Ambion #61006. The m6A RIP experiment was carried out as previously described Ke et al. 2015 and the protocol can be found in supplementary file 1. Briefly polyA+ enriched RNA was partially fragmented by alkaline hydrolysis ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies # 10008D conjugated anti m6A antibody Synaptic systems # 202003. post stringent washing the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich # M2780 ethanol precipitated and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3’pre adenylated DNA liker ligation with T4 RNA ligase2 truncated KQ NEB #M0373L at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014 with improved RT primers indicated in Ke et al. 2015.	GEO Accession:GSM2390020	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP093295		input_64cell_rep2.fastq.gz	fastq	3598782386.0	38284919.0	GSM2390020 r1	0:94	A:953869445;C:864903757;G:875832539;T:903947732;N:228913	94		953869445	864903757	875832539	903947732	228913	SRX2345562	SRS1796129	SRA492943	GEO	Klungland Lab, Dept of microbiology, Oslo University Hospital	1	0.04289		0.00757		0.9418		0.6078		94		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Norway	2016-11-14	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
41557	41557	SRR5017066	SRX2345561	SRS1796141	SRP093295	PRJNA353372	N6 methyladenosine dynamics during early vertebrate embryogenesis	GSE89815	Other	Early vertebrate embryogenesis is characterized by extensive post transcriptional regulation during the maternal to zygotic transition. The N6 methyladenosine m6A modifications on mRNA has been shown to affect both translation and stability of transcripts. Here we investigate the m6A topology during early vertebrate embryogenesis and its association with RNA stability translation efficiency and effect on miR 430 degradation kinetics. Notably we find a strong association of m6A with cytoplasmic polyadenylation and translational efficiency prior to zygotic genome activation. Genes required for zygotic genome activation such as nanog and pou5f3 display dynamic m6A levels. post zygotic genome activation m6A is associated with improved stability and dampens the effect of miR 430 mediated degradation. Through sequence analyses we identified enrichment of motifs for RNA binding proteins involved in translational regulation and RNA degradation. We propose a role for m6A in multiple mRNA regulatory mechanisms for the first time in an in vivo system and improve our understanding of the combinatorial code behind the complex post transcriptional regulation of reprogramming during early vertebrate development. Overall design: Examination of m6A in four different developmental stages			input 64cell rep1	GSM2390019	tissue:Embryos\|developmental stage:64 cell embryos\|strain:AB wild type	input 64cell rep1	Base calling The sequencing output from each of the 4 lanes the sequencing run was trimmed 7 nucleotides in the 5’end and de multiplexed 4 samples in each lane. Reads were mapped to Zv10 using the STAR aligner Dobin et al. 2013 with options seedSearchStartLmax 15 clip3pNbases 10 clip5pNbases 10 outFilterMultimapNmax 20 outFilterMismatchNoverLmax 0.05 outFilterMatchNminOverLread 0.0 outFilterMatchNmin 15 outFilterScoreMinOverLread 0.0. We performed peak calling and detection of differentially methylated genes using ExomePeak Meng et al. 2013. Genome build: Zv10 Supplementary files format and content: Bed files with enriched regions from each developmental stage and txt file with raw and normalized read counts for each gene using the input samples	Embryos	We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization 2 4 and 6 hpf in batches of 200 embryos using TRIzol Invitrogen cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads® mRNA Purification Kit Ambion #61006. The m6A RIP experiment was carried out as previously described Ke et al. 2015 and the protocol can be found in supplementary file 1. Briefly polyA+ enriched RNA was partially fragmented by alkaline hydrolysis ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies # 10008D conjugated anti m6A antibody Synaptic systems # 202003. post stringent washing the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich # M2780 ethanol precipitated and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3’pre adenylated DNA liker ligation with T4 RNA ligase2 truncated KQ NEB #M0373L at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014 with improved RT primers indicated in Ke et al. 2015.	Embryos from the AB wild type strain were obtained from the NMBU zebrafish facility where the zebrafish were kept at 28±1°C on a 14 10 hour light dark cycle at a density of 5 10 fish/L. System water SW was prepared from particle and active charcoal filtrated tap water deionized by reverse osmosis RO and kept sterile by UV irradiation. The water was conditioned to a conductivity of 500µS/cm general hardness GH 4 5 and pH 7.5 by addition of 155g synthetic sea salt Instant Ocean Blacksburg USA 53g sodium carbonate and 15g calcium chloride Sigma Aldrich per liter RO water. Adult fish were fed with Gemma Micro 300 Skretting Stavanger Norway dry feed twice a day and live artemia Scanbur Karlslunde Denmark once a day. Health monitoring was by daily inspection use of sentinel fish sent for pathology ZIRC Eugene Oregon and water microbiology analysis NMBU Vetbio Oslo every six month. Adult fish were allowed to mate for 30 minutes in standard 1L breeding tanks Aquatic Habitats Apopka FL. Harvested embryos were kept in autoclaved SW at 28 °C harvested by snap freezing liquid nitrogen and visually controlled for stage and lack of abnormalities at the selected time points. All experiments were performed according to Norwegian Animal Welfare Act 2009 the EU Directive 2010/63.	developmental stage:64 cell embryos\|strain:AB wild type	GSM2390019	GSM2390019: input 64cell rep1; Danio rerio; RIP Seq	GSM2390019		1	We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization 2 4 and 6 hpf in batches of 200 embryos using TRIzol Invitrogen cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads® mRNA Purification Kit Ambion #61006. The m6A RIP experiment was carried out as previously described Ke et al. 2015 and the protocol can be found in supplementary file 1. Briefly polyA+ enriched RNA was partially fragmented by alkaline hydrolysis ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies # 10008D conjugated anti m6A antibody Synaptic systems # 202003. post stringent washing the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich # M2780 ethanol precipitated and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3’pre adenylated DNA liker ligation with T4 RNA ligase2 truncated KQ NEB #M0373L at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014 with improved RT primers indicated in Ke et al. 2015.	GEO Accession:GSM2390019	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP093295		input_64cell_rep1.fastq.gz	fastq	3538898746.0	37647859.0	GSM2390019 r1	0:94	A:916878511;C:870431252;G:873611680;T:877750503;N:226800	94		916878511	870431252	873611680	877750503	226800	SRX2345561	SRS1796141	SRA492943	GEO	Klungland Lab, Dept of microbiology, Oslo University Hospital	1	0.03397		0.00616		0.95268		0.62545		94		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Norway	2016-11-14	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
41558	41558	SRR5017065	SRX2345560	SRS1796153	SRP093295	PRJNA353372	N6 methyladenosine dynamics during early vertebrate embryogenesis	GSE89815	Other	Early vertebrate embryogenesis is characterized by extensive post transcriptional regulation during the maternal to zygotic transition. The N6 methyladenosine m6A modifications on mRNA has been shown to affect both translation and stability of transcripts. Here we investigate the m6A topology during early vertebrate embryogenesis and its association with RNA stability translation efficiency and effect on miR 430 degradation kinetics. Notably we find a strong association of m6A with cytoplasmic polyadenylation and translational efficiency prior to zygotic genome activation. Genes required for zygotic genome activation such as nanog and pou5f3 display dynamic m6A levels. post zygotic genome activation m6A is associated with improved stability and dampens the effect of miR 430 mediated degradation. Through sequence analyses we identified enrichment of motifs for RNA binding proteins involved in translational regulation and RNA degradation. We propose a role for m6A in multiple mRNA regulatory mechanisms for the first time in an in vivo system and improve our understanding of the combinatorial code behind the complex post transcriptional regulation of reprogramming during early vertebrate development. Overall design: Examination of m6A in four different developmental stages			ip 64cell rep2	GSM2390018	tissue:Embryos\|developmental stage:64 cell embryos\|strain:AB wild type	ip 64cell rep2	Base calling The sequencing output from each of the 4 lanes the sequencing run was trimmed 7 nucleotides in the 5’end and de multiplexed 4 samples in each lane. Reads were mapped to Zv10 using the STAR aligner Dobin et al. 2013 with options seedSearchStartLmax 15 clip3pNbases 10 clip5pNbases 10 outFilterMultimapNmax 20 outFilterMismatchNoverLmax 0.05 outFilterMatchNminOverLread 0.0 outFilterMatchNmin 15 outFilterScoreMinOverLread 0.0. We performed peak calling and detection of differentially methylated genes using ExomePeak Meng et al. 2013. Genome build: Zv10 Supplementary files format and content: Bed files with enriched regions from each developmental stage and txt file with raw and normalized read counts for each gene using the input samples	Embryos	We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization 2 4 and 6 hpf in batches of 200 embryos using TRIzol Invitrogen cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads® mRNA Purification Kit Ambion #61006. The m6A RIP experiment was carried out as previously described Ke et al. 2015 and the protocol can be found in supplementary file 1. Briefly polyA+ enriched RNA was partially fragmented by alkaline hydrolysis ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies # 10008D conjugated anti m6A antibody Synaptic systems # 202003. post stringent washing the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich # M2780 ethanol precipitated and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3’pre adenylated DNA liker ligation with T4 RNA ligase2 truncated KQ NEB #M0373L at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014 with improved RT primers indicated in Ke et al. 2015.	Embryos from the AB wild type strain were obtained from the NMBU zebrafish facility where the zebrafish were kept at 28±1°C on a 14 10 hour light dark cycle at a density of 5 10 fish/L. System water SW was prepared from particle and active charcoal filtrated tap water deionized by reverse osmosis RO and kept sterile by UV irradiation. The water was conditioned to a conductivity of 500µS/cm general hardness GH 4 5 and pH 7.5 by addition of 155g synthetic sea salt Instant Ocean Blacksburg USA 53g sodium carbonate and 15g calcium chloride Sigma Aldrich per liter RO water. Adult fish were fed with Gemma Micro 300 Skretting Stavanger Norway dry feed twice a day and live artemia Scanbur Karlslunde Denmark once a day. Health monitoring was by daily inspection use of sentinel fish sent for pathology ZIRC Eugene Oregon and water microbiology analysis NMBU Vetbio Oslo every six month. Adult fish were allowed to mate for 30 minutes in standard 1L breeding tanks Aquatic Habitats Apopka FL. Harvested embryos were kept in autoclaved SW at 28 °C harvested by snap freezing liquid nitrogen and visually controlled for stage and lack of abnormalities at the selected time points. All experiments were performed according to Norwegian Animal Welfare Act 2009 the EU Directive 2010/63.	developmental stage:64 cell embryos\|strain:AB wild type	GSM2390018	GSM2390018: ip 64cell rep2; Danio rerio; RIP Seq	GSM2390018		1	We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization 2 4 and 6 hpf in batches of 200 embryos using TRIzol Invitrogen cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads® mRNA Purification Kit Ambion #61006. The m6A RIP experiment was carried out as previously described Ke et al. 2015 and the protocol can be found in supplementary file 1. Briefly polyA+ enriched RNA was partially fragmented by alkaline hydrolysis ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies # 10008D conjugated anti m6A antibody Synaptic systems # 202003. post stringent washing the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich # M2780 ethanol precipitated and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3’pre adenylated DNA liker ligation with T4 RNA ligase2 truncated KQ NEB #M0373L at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014 with improved RT primers indicated in Ke et al. 2015.	GEO Accession:GSM2390018	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP093295		ip_64cell_rep2.fastq.gz	fastq	3530677976.0	37560404.0	GSM2390018 r1	0:94	A:966880666;C:841411144;G:858285224;T:862983808;N:1117134	94		966880666	841411144	858285224	862983808	1117134	SRX2345560	SRS1796153	SRA492943	GEO	Klungland Lab, Dept of microbiology, Oslo University Hospital	1	0.04775		0.00421		0.92845		0.5748		94		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Norway	2016-11-14	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
41559	41559	SRR5017064	SRX2345559	SRS1796135	SRP093295	PRJNA353372	N6 methyladenosine dynamics during early vertebrate embryogenesis	GSE89815	Other	Early vertebrate embryogenesis is characterized by extensive post transcriptional regulation during the maternal to zygotic transition. The N6 methyladenosine m6A modifications on mRNA has been shown to affect both translation and stability of transcripts. Here we investigate the m6A topology during early vertebrate embryogenesis and its association with RNA stability translation efficiency and effect on miR 430 degradation kinetics. Notably we find a strong association of m6A with cytoplasmic polyadenylation and translational efficiency prior to zygotic genome activation. Genes required for zygotic genome activation such as nanog and pou5f3 display dynamic m6A levels. post zygotic genome activation m6A is associated with improved stability and dampens the effect of miR 430 mediated degradation. Through sequence analyses we identified enrichment of motifs for RNA binding proteins involved in translational regulation and RNA degradation. We propose a role for m6A in multiple mRNA regulatory mechanisms for the first time in an in vivo system and improve our understanding of the combinatorial code behind the complex post transcriptional regulation of reprogramming during early vertebrate development. Overall design: Examination of m6A in four different developmental stages			ip 64cell rep1	GSM2390017	tissue:Embryos\|developmental stage:64 cell embryos\|strain:AB wild type	ip 64cell rep1	Base calling The sequencing output from each of the 4 lanes the sequencing run was trimmed 7 nucleotides in the 5’end and de multiplexed 4 samples in each lane. Reads were mapped to Zv10 using the STAR aligner Dobin et al. 2013 with options seedSearchStartLmax 15 clip3pNbases 10 clip5pNbases 10 outFilterMultimapNmax 20 outFilterMismatchNoverLmax 0.05 outFilterMatchNminOverLread 0.0 outFilterMatchNmin 15 outFilterScoreMinOverLread 0.0. We performed peak calling and detection of differentially methylated genes using ExomePeak Meng et al. 2013. Genome build: Zv10 Supplementary files format and content: Bed files with enriched regions from each developmental stage and txt file with raw and normalized read counts for each gene using the input samples	Embryos	We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization 2 4 and 6 hpf in batches of 200 embryos using TRIzol Invitrogen cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads® mRNA Purification Kit Ambion #61006. The m6A RIP experiment was carried out as previously described Ke et al. 2015 and the protocol can be found in supplementary file 1. Briefly polyA+ enriched RNA was partially fragmented by alkaline hydrolysis ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies # 10008D conjugated anti m6A antibody Synaptic systems # 202003. post stringent washing the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich # M2780 ethanol precipitated and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3’pre adenylated DNA liker ligation with T4 RNA ligase2 truncated KQ NEB #M0373L at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014 with improved RT primers indicated in Ke et al. 2015.	Embryos from the AB wild type strain were obtained from the NMBU zebrafish facility where the zebrafish were kept at 28±1°C on a 14 10 hour light dark cycle at a density of 5 10 fish/L. System water SW was prepared from particle and active charcoal filtrated tap water deionized by reverse osmosis RO and kept sterile by UV irradiation. The water was conditioned to a conductivity of 500µS/cm general hardness GH 4 5 and pH 7.5 by addition of 155g synthetic sea salt Instant Ocean Blacksburg USA 53g sodium carbonate and 15g calcium chloride Sigma Aldrich per liter RO water. Adult fish were fed with Gemma Micro 300 Skretting Stavanger Norway dry feed twice a day and live artemia Scanbur Karlslunde Denmark once a day. Health monitoring was by daily inspection use of sentinel fish sent for pathology ZIRC Eugene Oregon and water microbiology analysis NMBU Vetbio Oslo every six month. Adult fish were allowed to mate for 30 minutes in standard 1L breeding tanks Aquatic Habitats Apopka FL. Harvested embryos were kept in autoclaved SW at 28 °C harvested by snap freezing liquid nitrogen and visually controlled for stage and lack of abnormalities at the selected time points. All experiments were performed according to Norwegian Animal Welfare Act 2009 the EU Directive 2010/63.	developmental stage:64 cell embryos\|strain:AB wild type	GSM2390017	GSM2390017: ip 64cell rep1; Danio rerio; RIP Seq	GSM2390017		1	We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization 2 4 and 6 hpf in batches of 200 embryos using TRIzol Invitrogen cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads® mRNA Purification Kit Ambion #61006. The m6A RIP experiment was carried out as previously described Ke et al. 2015 and the protocol can be found in supplementary file 1. Briefly polyA+ enriched RNA was partially fragmented by alkaline hydrolysis ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies # 10008D conjugated anti m6A antibody Synaptic systems # 202003. post stringent washing the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich # M2780 ethanol precipitated and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3’pre adenylated DNA liker ligation with T4 RNA ligase2 truncated KQ NEB #M0373L at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014 with improved RT primers indicated in Ke et al. 2015.	GEO Accession:GSM2390017	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP093295		ip_64cell_rep1.fastq.gz	fastq	3912003734.0	41617061.0	GSM2390017 r1	0:94	A:1040276279;C:945311584;G:953598043;T:971589029;N:1228799	94		1040276279	945311584	953598043	971589029	1228799	SRX2345559	SRS1796135	SRA492943	GEO	Klungland Lab, Dept of microbiology, Oslo University Hospital	1	0.03544		0.00268		0.93914		0.53712		94		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Norway	2016-11-14	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
49539	49539	SRR8937005	SRX5717518	SRS4655938	SRP162876	PRJNA493828	Ybx1 binding sites and Ybx1 binding m5C sites in zebrafish embryo sample.	GSE120646	Other	The maternal to zygotic transition MZT is a conserved and fundamental process during which the embryo undergoes dramatic reprogramming to convert maternal environment to embryonic driven programing. However how the maternally supplied transcripts are dynamically regulated during MZT remains largely unknown. Herein through genome wide profiling of RNA 5 methylcytosine m5C in zebrafish early embryos we show that m5C methylated maternal mRNAs display higher stability during MZT. We identify that the Y box binding protein 1 Ybx1 prefers to recognizing m5C modified mRNAs through p p interaction with a key residue Trp45 in its cold shock domain CSD which plays essential roles in maternal mRNA stability and early embryogenesis of zebrafish. Cooperated with an mRNA stabilizer Pabpc1a Ybx1 promotes the stability of its target mRNAs in an m5C dependent manner. Our study demonstrates a novel mechanism of RNA m5C methylation regulated maternal mRNA stability during zebrafish MZT highlighting the critical role of m5C mRNA methylation in early development. Overall design: Examination of Ybx1 binding sites and Ybx1 binding m5C sites in zebrafish embryo. RIP seq: Briefly 500 zebrafish embryos at shield stage 4 hpf were resuspended with 2 ml lysis buffer 150 mM KCl 10 mM HEPES pH 7.6 2 mM EDTA 0.5% NP 40 0.5 mM DTT 1:100 protease inhibitor cocktail 0.4 U/Î¼l RNasin by rotating at 4Â°C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4Â°C for 1 h. 50 Î¼l pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax China and 30 Î¼l Protein A Dynabeads for 4 h at 4Â°C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl 50 mM HEPES pH 7.6 2 mM EDTA 0.05% NP 40 0.5 mM DTT 0.4U/Âµl RNasin for eight times and once with 1ml ice cold 1Ã— PK buffer 100 mM Tris HCl pH 7.4 50 mM NaCl 10 mM EDTA 0.2% SDS the beads was treated i…	parent bioproject:PRJNA534030		RIP INPUT 2hpf rep2	GSM3732425	source name:RIP INPUT 2hpf\|strain:AB strain\|age:2 hpf\|tissue:whole embryo	RIP INPUT 2hpf rep2	Reads were aligned to the zv9 genome assembly using TopHat v2.1.1. MACS2 v2.1.1 were used for the peak calling and peaks were annotated by applying BEDTools’ intersectBed. Genome build: zv9 Supplementary files format and content: Ybx1 binding sites in two biological replicates.	RIP INPUT 2hpf	Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA BisSeq library construction. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode creating reads with a length of 150 bp.		strain:AB strain\|age:2 hpf\|tissue:whole embryo	GSM3732425	GSM3732425: RIP INPUT 2hpf rep2; Danio rerio; RIP Seq	GSM3732425		1	Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA BisSeq library construction. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode creating reads with a length of 150 bp.	GEO Accession:GSM3732425	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP162876		RIP-INPUT_2hpf_rep2_R1.fastq.gz RIP-INPUT_2hpf_rep2_R2.fastq.gz	fastq fastq	16388119500.0	54627065.0	GSM3732425 r1	0:150 1:150	A:3232127065;C:4976385987;G:5052844082;T:3122288663;N:4473703	150	150	3232127065	4976385987	5052844082	3122288663	4473703	SRX5717518	SRS4655938	SRA786939	GEO	Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)	2	0.98209	0.9812	0.33332	0.33565	0.93811	0.94186	0.95153	0.95984	150	150	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	smarter	bulk	clip	iclip	China	2019-04-22	Cleavage	Embryo	Whole Organism	All anatomical structures
49540	49540	SRR8937004	SRX5717517	SRS4655937	SRP162876	PRJNA493828	Ybx1 binding sites and Ybx1 binding m5C sites in zebrafish embryo sample.	GSE120646	Other	The maternal to zygotic transition MZT is a conserved and fundamental process during which the embryo undergoes dramatic reprogramming to convert maternal environment to embryonic driven programing. However how the maternally supplied transcripts are dynamically regulated during MZT remains largely unknown. Herein through genome wide profiling of RNA 5 methylcytosine m5C in zebrafish early embryos we show that m5C methylated maternal mRNAs display higher stability during MZT. We identify that the Y box binding protein 1 Ybx1 prefers to recognizing m5C modified mRNAs through p p interaction with a key residue Trp45 in its cold shock domain CSD which plays essential roles in maternal mRNA stability and early embryogenesis of zebrafish. Cooperated with an mRNA stabilizer Pabpc1a Ybx1 promotes the stability of its target mRNAs in an m5C dependent manner. Our study demonstrates a novel mechanism of RNA m5C methylation regulated maternal mRNA stability during zebrafish MZT highlighting the critical role of m5C mRNA methylation in early development. Overall design: Examination of Ybx1 binding sites and Ybx1 binding m5C sites in zebrafish embryo. RIP seq: Briefly 500 zebrafish embryos at shield stage 4 hpf were resuspended with 2 ml lysis buffer 150 mM KCl 10 mM HEPES pH 7.6 2 mM EDTA 0.5% NP 40 0.5 mM DTT 1:100 protease inhibitor cocktail 0.4 U/Î¼l RNasin by rotating at 4Â°C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4Â°C for 1 h. 50 Î¼l pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax China and 30 Î¼l Protein A Dynabeads for 4 h at 4Â°C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl 50 mM HEPES pH 7.6 2 mM EDTA 0.05% NP 40 0.5 mM DTT 0.4U/Âµl RNasin for eight times and once with 1ml ice cold 1Ã— PK buffer 100 mM Tris HCl pH 7.4 50 mM NaCl 10 mM EDTA 0.2% SDS the beads was treated i…	parent bioproject:PRJNA534030		RIP INPUT 2hpf rep1	GSM3732424	source name:RIP INPUT 2hpf\|strain:AB strain\|age:2 hpf\|tissue:whole embryo	RIP INPUT 2hpf rep1	Reads were aligned to the zv9 genome assembly using TopHat v2.1.1. MACS2 v2.1.1 were used for the peak calling and peaks were annotated by applying BEDTools’ intersectBed. Genome build: zv9 Supplementary files format and content: Ybx1 binding sites in two biological replicates.	RIP INPUT 2hpf	Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA BisSeq library construction. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode creating reads with a length of 150 bp.		strain:AB strain\|age:2 hpf\|tissue:whole embryo	GSM3732424	GSM3732424: RIP INPUT 2hpf rep1; Danio rerio; RIP Seq	GSM3732424		1	Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA BisSeq library construction. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode creating reads with a length of 150 bp.	GEO Accession:GSM3732424	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP162876		RIP-INPUT_2hpf_rep1_R1.fastq.gz RIP-INPUT_2hpf_rep1_R2.fastq.gz	fastq fastq	18857336400.0	62857788.0	GSM3732424 r1	0:150 1:150	A:3116761123;C:6239715125;G:6450542871;T:3049605751;N:711530	150	150	3116761123	6239715125	6450542871	3049605751	711530	SRX5717517	SRS4655937	SRA786939	GEO	Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)	2	0.97874	0.96891	0.03494	0.03355	0.92693	0.93456	0.9502	0.94986	150	150	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	smarter	bulk	clip	iclip	China	2019-04-22	Cleavage	Embryo	Whole Organism	All anatomical structures
49543	49543	SRR8937001	SRX5717514	SRS4655934	SRP162876	PRJNA493828	Ybx1 binding sites and Ybx1 binding m5C sites in zebrafish embryo sample.	GSE120646	Other	The maternal to zygotic transition MZT is a conserved and fundamental process during which the embryo undergoes dramatic reprogramming to convert maternal environment to embryonic driven programing. However how the maternally supplied transcripts are dynamically regulated during MZT remains largely unknown. Herein through genome wide profiling of RNA 5 methylcytosine m5C in zebrafish early embryos we show that m5C methylated maternal mRNAs display higher stability during MZT. We identify that the Y box binding protein 1 Ybx1 prefers to recognizing m5C modified mRNAs through p p interaction with a key residue Trp45 in its cold shock domain CSD which plays essential roles in maternal mRNA stability and early embryogenesis of zebrafish. Cooperated with an mRNA stabilizer Pabpc1a Ybx1 promotes the stability of its target mRNAs in an m5C dependent manner. Our study demonstrates a novel mechanism of RNA m5C methylation regulated maternal mRNA stability during zebrafish MZT highlighting the critical role of m5C mRNA methylation in early development. Overall design: Examination of Ybx1 binding sites and Ybx1 binding m5C sites in zebrafish embryo. RIP seq: Briefly 500 zebrafish embryos at shield stage 4 hpf were resuspended with 2 ml lysis buffer 150 mM KCl 10 mM HEPES pH 7.6 2 mM EDTA 0.5% NP 40 0.5 mM DTT 1:100 protease inhibitor cocktail 0.4 U/Î¼l RNasin by rotating at 4Â°C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4Â°C for 1 h. 50 Î¼l pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax China and 30 Î¼l Protein A Dynabeads for 4 h at 4Â°C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl 50 mM HEPES pH 7.6 2 mM EDTA 0.05% NP 40 0.5 mM DTT 0.4U/Âµl RNasin for eight times and once with 1ml ice cold 1Ã— PK buffer 100 mM Tris HCl pH 7.4 50 mM NaCl 10 mM EDTA 0.2% SDS the beads was treated i…	parent bioproject:PRJNA534030		RIP 2hpf rep2	GSM3732421	source name:RIP 2hpf\|strain:AB strain\|age:2 hpf\|tissue:whole embryo\|rip antibody:rabbit polyclonal anti Ybx1 antibody	RIP 2hpf rep2	Reads were aligned to the zv9 genome assembly using TopHat v2.1.1. MACS2 v2.1.1 were used for the peak calling and peaks were annotated by applying BEDTools’ intersectBed. Genome build: zv9 Supplementary files format and content: Ybx1 binding sites in two biological replicates.	RIP 2hpf	Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA BisSeq library construction. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode creating reads with a length of 150 bp.		strain:AB strain\|age:2 hpf\|tissue:whole embryo\|rip antibody:rabbit polyclonal anti Ybx1 antibody	GSM3732421	GSM3732421: RIP 2hpf rep2; Danio rerio; RIP Seq	GSM3732421		1	Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA BisSeq library construction. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode creating reads with a length of 150 bp.	GEO Accession:GSM3732421	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP162876		RIP_2hpf_rep2_R1.fastq.gz RIP_2hpf_rep2_R2.fastq.gz	fastq fastq	17557024800.0	58523416.0	GSM3732421 r1	0:150 1:150	A:4454737772;C:4407385601;G:4364085079;T:4328962997;N:1853351	150	150	4454737772	4407385601	4364085079	4328962997	1853351	SRX5717514	SRS4655934	SRA786939	GEO	Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)	2	0.96216	0.96226	0.08174	0.08009	0.76907	0.77693	0.68824	0.65939	150	150	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	smarter	bulk	clip	iclip	China	2019-04-22	Cleavage	Embryo	Whole Organism	All anatomical structures
49544	49544	SRR8937000	SRX5717513	SRS4655933	SRP162876	PRJNA493828	Ybx1 binding sites and Ybx1 binding m5C sites in zebrafish embryo sample.	GSE120646	Other	The maternal to zygotic transition MZT is a conserved and fundamental process during which the embryo undergoes dramatic reprogramming to convert maternal environment to embryonic driven programing. However how the maternally supplied transcripts are dynamically regulated during MZT remains largely unknown. Herein through genome wide profiling of RNA 5 methylcytosine m5C in zebrafish early embryos we show that m5C methylated maternal mRNAs display higher stability during MZT. We identify that the Y box binding protein 1 Ybx1 prefers to recognizing m5C modified mRNAs through p p interaction with a key residue Trp45 in its cold shock domain CSD which plays essential roles in maternal mRNA stability and early embryogenesis of zebrafish. Cooperated with an mRNA stabilizer Pabpc1a Ybx1 promotes the stability of its target mRNAs in an m5C dependent manner. Our study demonstrates a novel mechanism of RNA m5C methylation regulated maternal mRNA stability during zebrafish MZT highlighting the critical role of m5C mRNA methylation in early development. Overall design: Examination of Ybx1 binding sites and Ybx1 binding m5C sites in zebrafish embryo. RIP seq: Briefly 500 zebrafish embryos at shield stage 4 hpf were resuspended with 2 ml lysis buffer 150 mM KCl 10 mM HEPES pH 7.6 2 mM EDTA 0.5% NP 40 0.5 mM DTT 1:100 protease inhibitor cocktail 0.4 U/Î¼l RNasin by rotating at 4Â°C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4Â°C for 1 h. 50 Î¼l pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax China and 30 Î¼l Protein A Dynabeads for 4 h at 4Â°C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl 50 mM HEPES pH 7.6 2 mM EDTA 0.05% NP 40 0.5 mM DTT 0.4U/Âµl RNasin for eight times and once with 1ml ice cold 1Ã— PK buffer 100 mM Tris HCl pH 7.4 50 mM NaCl 10 mM EDTA 0.2% SDS the beads was treated i…	parent bioproject:PRJNA534030		RIP 2hpf rep1	GSM3732420	source name:RIP 2hpf\|strain:AB strain\|age:2 hpf\|tissue:whole embryo\|rip antibody:rabbit polyclonal anti Ybx1 antibody	RIP 2hpf rep1	Reads were aligned to the zv9 genome assembly using TopHat v2.1.1. MACS2 v2.1.1 were used for the peak calling and peaks were annotated by applying BEDTools’ intersectBed. Genome build: zv9 Supplementary files format and content: Ybx1 binding sites in two biological replicates.	RIP 2hpf	Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA BisSeq library construction. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode creating reads with a length of 150 bp.		strain:AB strain\|age:2 hpf\|tissue:whole embryo\|rip antibody:rabbit polyclonal anti Ybx1 antibody	GSM3732420	GSM3732420: RIP 2hpf rep1; Danio rerio; RIP Seq	GSM3732420		1	Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA BisSeq library construction. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode creating reads with a length of 150 bp.	GEO Accession:GSM3732420	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP162876		RIP_2hpf_rep1_R1.fastq.gz RIP_2hpf_rep1_R2.fastq.gz	fastq fastq	5656083600.0	18853612.0	GSM3732420 r1	0:150 1:150	A:1244757394;C:1581273853;G:1666307178;T:1162885398;N:859777	150	150	1244757394	1581273853	1666307178	1162885398	859777	SRX5717513	SRS4655933	SRA786939	GEO	Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)	2	0.80705	0.80575	0.2454	0.24923	0.85478	0.85644	0.83319	0.80065	150	150	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	smarter	bulk	clip	iclip	China	2019-04-22	Cleavage	Embryo	Whole Organism	All anatomical structures
63732	63732	SRR13998080	SRX10375446	SRS8490052	SRP311218	PRJNA715461	RIP seq for Ddx3xb in zebrafish embryos	GSE169161	Other	We show that liquid liquid phase separation LLPS mediated zebrafish Ddx3xb condensation facilitates MZT through promoting maternal mRNAs translation. Ddx3xb forms condensates via its N terminal intrinsically disordered regions IDRs and the gradually increased ATP concentration post fertilization promotes its aggregation capability. Ddx3xb deficiency decelerates the decay of maternal mRNAs and impedes zygotic genome activation further leading to developmental defect. The phenotype in Ddx3xb deficiency embryos can be efficiently rescued by condensed Ddx3xb but not the Ddx3xb without xxx ability. Mechanistically the condensation of Ddx3xb is vital for its RNA helicase activity which is critical for involved in promoting translation efficiency of maternal mRNAs through opening five prime UTR structures during the MZT process. Our study demonstrates that the condensation of Ddx3xb promotes maternal mRNAs translation via its RNA unwinding activity and further facilitates MZT highlighting the critical role of protein phase separation in translational control and animal early development. Overall design: RIP seq of 4 samples from Ddx3xb mRNA injected zebrafish embryos at xxx and 4 hpf including two biological replicates	parent bioproject:PRJNA715459	pubmed:35661831	rip 2h WT rep2	GSM5179332	source name:control 2h RIP seq rep2\|tissue:zebrafish embryos\|genotype:wild type\|age:2 hpf	rip 2h WT rep2	low quality bases were trimmed and filtered by cutadapt V 1.13 and Trimmomatic V 0.36. Processed reads were mapped to zebrafish rRNA transcriptome using bowtie and retain unmapped reads. Processed reads were mapped to zebrafish rRNA transcriptome using bowtie and retain unmapped reads. The remaining reads were mapped to zebrafish genome Zv9 using TopHat v2.1.1 with ‘‘–bowtie1’’. The target binding regions of Ddx3xb were identified using MACS2 software version 2.0.10 with options ‘–nomodel’ keep dup and gsize=1.4e9 and using RNA seq data as input. A stringent cutoff threshold for P value of 1 × 10−2 was used to obtain target genes of Ddx3xb. The target genes were annotated based on Ensembl release 79 gene annotation information by applying BEDTools’ intersectBed version 2.16.2. Genome build: Zv9 Supplementary files format and content: binding peaks for Ddx3xb protein	control 2h RIP seq rep2	flag ddx3xb mRNA injected embryos were collected at xxx hpf or 4 hpf and lysed in NETN lysis buffer 150 mM NaCl 0.5% NP 40 50 mM Tris HCl pH 7.4. Ddx3xb RIP was carried out following a published protocol but with some modifications. Lysate was incubated with anti FLAG M2 Magnetic Beads Merck M8823 for 4 h at 4C. RNA was extracted and subjected to library construction using the SMARTer smRNA Seq kit Clontech 635031. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Clontech Laboratories Inc.		tissue:zebrafish embryos\|genotype:wild type\|age:2 hpf	GSM5179332	GSM5179332: rip 2h WT rep2; Danio rerio; RIP Seq	GSM5179332		1	RIP was carried out as previously described Despic et al. 2017. flag ddx3xb mRNA injected embryos were collected at xxx hpf and 6 hpf. 400 zebrafish embryos were irradiated twice with 0.8 J/cm2 Stratalinker 2400 Stratagene lysed and subjected to mild RNA fragmentation. Crosslinked RNA proteins complexes were immunopurified using Anti FLAG M2 Magnetic Beads Merck M8823 for 4 h. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Clontech Laboratories Inc	GEO Accession:GSM5179332	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP311218	loader:fastq load.py	rip_2h_WT2.fq.gz	fastq	12320805000.0	82138700.0	GSM5179332 r1	0:150	A:3686415626;C:2826613772;G:3732955088;T:2073945227;N:875287	150		3686415626	2826613772	3732955088	2073945227	875287	SRX10375446	SRS8490052	SRA1207702	GEO	Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)	1	0.1848		0.11194		0.9669		0.82171		150		B		usable mapping rate	illumina	novaseq_era	full_length	other	smarter	bulk	unknown	unknown	China	2021-03-18	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
63733	63733	SRR13998079	SRX10375445	SRS8490051	SRP311218	PRJNA715461	RIP seq for Ddx3xb in zebrafish embryos	GSE169161	Other	We show that liquid liquid phase separation LLPS mediated zebrafish Ddx3xb condensation facilitates MZT through promoting maternal mRNAs translation. Ddx3xb forms condensates via its N terminal intrinsically disordered regions IDRs and the gradually increased ATP concentration post fertilization promotes its aggregation capability. Ddx3xb deficiency decelerates the decay of maternal mRNAs and impedes zygotic genome activation further leading to developmental defect. The phenotype in Ddx3xb deficiency embryos can be efficiently rescued by condensed Ddx3xb but not the Ddx3xb without xxx ability. Mechanistically the condensation of Ddx3xb is vital for its RNA helicase activity which is critical for involved in promoting translation efficiency of maternal mRNAs through opening five prime UTR structures during the MZT process. Our study demonstrates that the condensation of Ddx3xb promotes maternal mRNAs translation via its RNA unwinding activity and further facilitates MZT highlighting the critical role of protein phase separation in translational control and animal early development. Overall design: RIP seq of 4 samples from Ddx3xb mRNA injected zebrafish embryos at xxx and 4 hpf including two biological replicates	parent bioproject:PRJNA715459	pubmed:35661831	rip 2h WT rep1	GSM5179331	source name:control 2h RIP seq rep1\|tissue:zebrafish embryos\|genotype:wild type\|age:2 hpf	rip 2h WT rep1	low quality bases were trimmed and filtered by cutadapt V 1.13 and Trimmomatic V 0.36. Processed reads were mapped to zebrafish rRNA transcriptome using bowtie and retain unmapped reads. Processed reads were mapped to zebrafish rRNA transcriptome using bowtie and retain unmapped reads. The remaining reads were mapped to zebrafish genome Zv9 using TopHat v2.1.1 with ‘‘–bowtie1’’. The target binding regions of Ddx3xb were identified using MACS2 software version 2.0.10 with options ‘–nomodel’ keep dup and gsize=1.4e9 and using RNA seq data as input. A stringent cutoff threshold for P value of 1 × 10−2 was used to obtain target genes of Ddx3xb. The target genes were annotated based on Ensembl release 79 gene annotation information by applying BEDTools’ intersectBed version 2.16.2. Genome build: Zv9 Supplementary files format and content: binding peaks for Ddx3xb protein	control 2h RIP seq rep1	flag ddx3xb mRNA injected embryos were collected at xxx hpf or 4 hpf and lysed in NETN lysis buffer 150 mM NaCl 0.5% NP 40 50 mM Tris HCl pH 7.4. Ddx3xb RIP was carried out following a published protocol but with some modifications. Lysate was incubated with anti FLAG M2 Magnetic Beads Merck M8823 for 4 h at 4C. RNA was extracted and subjected to library construction using the SMARTer smRNA Seq kit Clontech 635031. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Clontech Laboratories Inc.		tissue:zebrafish embryos\|genotype:wild type\|age:2 hpf	GSM5179331	GSM5179331: rip 2h WT rep1; Danio rerio; RIP Seq	GSM5179331		1	RIP was carried out as previously described Despic et al. 2017. flag ddx3xb mRNA injected embryos were collected at xxx hpf and 6 hpf. 400 zebrafish embryos were irradiated twice with 0.8 J/cm2 Stratalinker 2400 Stratagene lysed and subjected to mild RNA fragmentation. Crosslinked RNA proteins complexes were immunopurified using Anti FLAG M2 Magnetic Beads Merck M8823 for 4 h. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Clontech Laboratories Inc	GEO Accession:GSM5179331	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP311218	loader:fastq load.py	rip_2h_WT1.fq.gz	fastq	8787958800.0	58586392.0	GSM5179331 r1	0:150	A:2671043775;C:2046825976;G:2545406298;T:1524056303;N:626448	150		2671043775	2046825976	2545406298	1524056303	626448	SRX10375445	SRS8490051	SRA1207702	GEO	Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)	1	0.30731		0.17665		0.94117		0.79653		150		B		usable mapping rate	illumina	novaseq_era	full_length	other	smarter	bulk	unknown	unknown	China	2021-03-18	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
75633	75633	SRR24746216	SRX20523363	SRS17832951	SRP439774	PRJNA976671	RNA seq of RNAs immunoprecipitated with eIF4E1c and eiF4E1c in early zebrafish embryos	GSE233570	Other	To investigate the mRNAs that are bound by eIF4E1b and eIF4E1c we performed RNA immunoprecipitation RIP experiments using anti GFP beads and transgenic embryos expressing GFP eIF4E1b or GFP eIF4E1c at the 8 cell stage. Overall design: We performed differential expression gene analyses of eIF4E1b n = 3 biological replicates versus eIF4E1c n = 2 biological replciates RIP and input samples.		pubmed:38177902	eIF4E1c input biol rep 3	GSM7430668	source name:Whole embryo lysate\|tissue:Whole embryo lysate\|cell type:8 cell stage\|genotype:tgactb2:3xflag sfGFP eIF4E1c\|geo loc name:missing\|collection date:missing	eIF4E1c input biol rep 3	RNA seq reads were trimmed using trim galore v0.5.0 and reads mapping to abundant sequences Dr mitochondrial chromosome SILVA Dr ribosomal RNA phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts with parameter s 0 for unstranded analysis subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts	Whole embryo lysate	RNA Clean & Concentrator kit Zymo Research of RIP and input samples SMARTerStrandedRNA library Ribo Zero for input samples; SMARTer ultra low RNA kit for RIP samples RNA Seq RIP and ssRNA seq Ribo Ziro		tissue:Whole embryo lysate\|cell type:8 cell stage\|genotype:tgactb2:3xflag sfGFP eIF4E1c	GSM7430668	GSM7430668: eIF4E1c input biol rep 3; Danio rerio; RIP Seq	GSM7430668 r1	GSM7430668	1	RNA Clean & Concentrator kit Zymo Research of RIP and input samples SMARTerStrandedRNA library Ribo Zero for input samples; SMARTer ultra low RNA kit for RIP samples RNA Seq RIP and ssRNA seq Ribo Ziro		RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP439774	loader:fastq load.py	e1c-RIP_input_3_1.fastq.gz e1c-RIP_input_3_2.fastq.gz	fastq fastq	3690634738.0	18270469.0	GSM7430668 r1	0:101 1:101	A:844997958;C:941209221;G:1016802233;T:887576626;N:48700	101	101	844997958	941209221	1016802233	887576626	48700	SRX20523363	SRS17832951	SRA1645065	IMP	IMP	2	0.88478	0.85242	0.07667	0.0787	0.77354	0.77636	0.54943	0.5474	101	101	B	B	biological fallback assumption	illumina	novaseq_era	full_length	rrna_depletion	ribozero	bulk	unknown	unknown	Austria	2023-05-26	Cleavage	Embryo	Whole Organism	All anatomical structures
75634	75634	SRR24746217	SRX20523362	SRS17832949	SRP439774	PRJNA976671	RNA seq of RNAs immunoprecipitated with eIF4E1c and eiF4E1c in early zebrafish embryos	GSE233570	Other	To investigate the mRNAs that are bound by eIF4E1b and eIF4E1c we performed RNA immunoprecipitation RIP experiments using anti GFP beads and transgenic embryos expressing GFP eIF4E1b or GFP eIF4E1c at the 8 cell stage. Overall design: We performed differential expression gene analyses of eIF4E1b n = 3 biological replicates versus eIF4E1c n = 2 biological replciates RIP and input samples.		pubmed:38177902	eIF4E1c input biol rep 2	GSM7430667	source name:Whole embryo lysate\|tissue:Whole embryo lysate\|cell type:8 cell stage\|genotype:tgactb2:3xflag sfGFP eIF4E1c\|geo loc name:missing\|collection date:missing	eIF4E1c input biol rep 2	RNA seq reads were trimmed using trim galore v0.5.0 and reads mapping to abundant sequences Dr mitochondrial chromosome SILVA Dr ribosomal RNA phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts with parameter s 0 for unstranded analysis subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts	Whole embryo lysate	RNA Clean & Concentrator kit Zymo Research of RIP and input samples SMARTerStrandedRNA library Ribo Zero for input samples; SMARTer ultra low RNA kit for RIP samples RNA Seq RIP and ssRNA seq Ribo Ziro		tissue:Whole embryo lysate\|cell type:8 cell stage\|genotype:tgactb2:3xflag sfGFP eIF4E1c	GSM7430667	GSM7430667: eIF4E1c input biol rep 2; Danio rerio; RIP Seq	GSM7430667 r1	GSM7430667	1	RNA Clean & Concentrator kit Zymo Research of RIP and input samples SMARTerStrandedRNA library Ribo Zero for input samples; SMARTer ultra low RNA kit for RIP samples RNA Seq RIP and ssRNA seq Ribo Ziro		RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP439774	loader:fastq load.py	e1c-RIP_input_2_1.fastq.gz e1c-RIP_input_2_2.fastq.gz	fastq fastq	3698444058.0	18309129.0	GSM7430667 r1	0:101 1:101	A:882466312;C:908503385;G:987657378;T:919768451;N:48532	101	101	882466312	908503385	987657378	919768451	48532	SRX20523362	SRS17832949	SRA1645065	IMP	IMP	2	0.89236	0.88681	0.06986	0.07322	0.76897	0.77037	0.53302	0.53232	101	101	B	B	biological fallback assumption	illumina	novaseq_era	full_length	rrna_depletion	ribozero	bulk	unknown	unknown	Austria	2023-05-26	Cleavage	Embryo	Whole Organism	All anatomical structures
75635	75635	SRR24746218	SRX20523361	SRS17832950	SRP439774	PRJNA976671	RNA seq of RNAs immunoprecipitated with eIF4E1c and eiF4E1c in early zebrafish embryos	GSE233570	Other	To investigate the mRNAs that are bound by eIF4E1b and eIF4E1c we performed RNA immunoprecipitation RIP experiments using anti GFP beads and transgenic embryos expressing GFP eIF4E1b or GFP eIF4E1c at the 8 cell stage. Overall design: We performed differential expression gene analyses of eIF4E1b n = 3 biological replicates versus eIF4E1c n = 2 biological replciates RIP and input samples.		pubmed:38177902	eIF4E1c input biol rep 1	GSM7430666	source name:Whole embryo lysate\|tissue:Whole embryo lysate\|cell type:8 cell stage\|genotype:tgactb2:3xflag sfGFP eIF4E1c\|geo loc name:missing\|collection date:missing	eIF4E1c input biol rep 1	RNA seq reads were trimmed using trim galore v0.5.0 and reads mapping to abundant sequences Dr mitochondrial chromosome SILVA Dr ribosomal RNA phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts with parameter s 0 for unstranded analysis subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts	Whole embryo lysate	RNA Clean & Concentrator kit Zymo Research of RIP and input samples SMARTerStrandedRNA library Ribo Zero for input samples; SMARTer ultra low RNA kit for RIP samples RNA Seq RIP and ssRNA seq Ribo Ziro		tissue:Whole embryo lysate\|cell type:8 cell stage\|genotype:tgactb2:3xflag sfGFP eIF4E1c	GSM7430666	GSM7430666: eIF4E1c input biol rep 1; Danio rerio; RIP Seq	GSM7430666 r1	GSM7430666	1	RNA Clean & Concentrator kit Zymo Research of RIP and input samples SMARTerStrandedRNA library Ribo Zero for input samples; SMARTer ultra low RNA kit for RIP samples RNA Seq RIP and ssRNA seq Ribo Ziro		RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP439774	loader:fastq load.py	e1c-RIP_input_1_1.fastq.gz e1c-RIP_input_1_2.fastq.gz	fastq fastq	3259312622.0	16135211.0	GSM7430666 r1	0:101 1:101	A:725034304;C:851812248;G:940759649;T:741654528;N:51893	101	101	725034304	851812248	940759649	741654528	51893	SRX20523361	SRS17832950	SRA1645065	IMP	IMP	2	0.82557	0.81479	0.09862	0.09133	0.78309	0.78368	0.5647	0.47779	101	101	B	B	biological fallback assumption	illumina	novaseq_era	full_length	rrna_depletion	ribozero	bulk	unknown	unknown	Austria	2023-05-26	Cleavage	Embryo	Whole Organism	All anatomical structures
75636	75636	SRR24746219	SRX20523360	SRS17832944	SRP439774	PRJNA976671	RNA seq of RNAs immunoprecipitated with eIF4E1c and eiF4E1c in early zebrafish embryos	GSE233570	Other	To investigate the mRNAs that are bound by eIF4E1b and eIF4E1c we performed RNA immunoprecipitation RIP experiments using anti GFP beads and transgenic embryos expressing GFP eIF4E1b or GFP eIF4E1c at the 8 cell stage. Overall design: We performed differential expression gene analyses of eIF4E1b n = 3 biological replicates versus eIF4E1c n = 2 biological replciates RIP and input samples.		pubmed:38177902	eIF4E1b input biol rep 3	GSM7430665	source name:Whole embryo lysate\|tissue:Whole embryo lysate\|cell type:8 cell stage\|genotype:tgactb2:3xflag sfGFP eIF4E1b\|geo loc name:missing\|collection date:missing	eIF4E1b input biol rep 3	RNA seq reads were trimmed using trim galore v0.5.0 and reads mapping to abundant sequences Dr mitochondrial chromosome SILVA Dr ribosomal RNA phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts with parameter s 0 for unstranded analysis subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts	Whole embryo lysate	RNA Clean & Concentrator kit Zymo Research of RIP and input samples SMARTerStrandedRNA library Ribo Zero for input samples; SMARTer ultra low RNA kit for RIP samples RNA Seq RIP and ssRNA seq Ribo Ziro		tissue:Whole embryo lysate\|cell type:8 cell stage\|genotype:tgactb2:3xflag sfGFP eIF4E1b	GSM7430665	GSM7430665: eIF4E1b input biol rep 3; Danio rerio; RIP Seq	GSM7430665 r1	GSM7430665	1	RNA Clean & Concentrator kit Zymo Research of RIP and input samples SMARTerStrandedRNA library Ribo Zero for input samples; SMARTer ultra low RNA kit for RIP samples RNA Seq RIP and ssRNA seq Ribo Ziro		RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP439774	loader:fastq load.py	e1b-RIP_input_3_1.fastq.gz e1b-RIP_input_3_2.fastq.gz	fastq fastq	3660782976.0	18122688.0	GSM7430665 r1	0:101 1:101	A:876719214;C:899453202;G:975602464;T:908960466;N:47630	101	101	876719214	899453202	975602464	908960466	47630	SRX20523360	SRS17832944	SRA1645065	IMP	IMP	2	0.89893	0.89289	0.06445	0.06826	0.77114	0.77106	0.5217	0.5193	101	101	B	B	biological fallback assumption	illumina	novaseq_era	full_length	rrna_depletion	ribozero	bulk	unknown	unknown	Austria	2023-05-26	Cleavage	Embryo	Whole Organism	All anatomical structures
75637	75637	SRR24746220	SRX20523359	SRS17832948	SRP439774	PRJNA976671	RNA seq of RNAs immunoprecipitated with eIF4E1c and eiF4E1c in early zebrafish embryos	GSE233570	Other	To investigate the mRNAs that are bound by eIF4E1b and eIF4E1c we performed RNA immunoprecipitation RIP experiments using anti GFP beads and transgenic embryos expressing GFP eIF4E1b or GFP eIF4E1c at the 8 cell stage. Overall design: We performed differential expression gene analyses of eIF4E1b n = 3 biological replicates versus eIF4E1c n = 2 biological replciates RIP and input samples.		pubmed:38177902	eIF4E1b input biol rep 2	GSM7430664	source name:Whole embryo lysate\|tissue:Whole embryo lysate\|cell type:8 cell stage\|genotype:tgactb2:3xflag sfGFP eIF4E1b\|geo loc name:missing\|collection date:missing	eIF4E1b input biol rep 2	RNA seq reads were trimmed using trim galore v0.5.0 and reads mapping to abundant sequences Dr mitochondrial chromosome SILVA Dr ribosomal RNA phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts with parameter s 0 for unstranded analysis subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts	Whole embryo lysate	RNA Clean & Concentrator kit Zymo Research of RIP and input samples SMARTerStrandedRNA library Ribo Zero for input samples; SMARTer ultra low RNA kit for RIP samples RNA Seq RIP and ssRNA seq Ribo Ziro		tissue:Whole embryo lysate\|cell type:8 cell stage\|genotype:tgactb2:3xflag sfGFP eIF4E1b	GSM7430664	GSM7430664: eIF4E1b input biol rep 2; Danio rerio; RIP Seq	GSM7430664 r1	GSM7430664	1	RNA Clean & Concentrator kit Zymo Research of RIP and input samples SMARTerStrandedRNA library Ribo Zero for input samples; SMARTer ultra low RNA kit for RIP samples RNA Seq RIP and ssRNA seq Ribo Ziro		RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP439774	loader:fastq load.py	e1b-RIP_input_2_1.fastq.gz e1b-RIP_input_2_2.fastq.gz	fastq fastq	3693089644.0	18282622.0	GSM7430664 r1	0:101 1:101	A:870145891;C:921396875;G:999553442;T:901944778;N:48658	101	101	870145891	921396875	999553442	901944778	48658	SRX20523359	SRS17832948	SRA1645065	IMP	IMP	2	0.90101	0.89457	0.06635	0.06977	0.76873	0.77007	0.54396	0.53678	101	101	B	B	biological fallback assumption	illumina	novaseq_era	full_length	rrna_depletion	ribozero	bulk	unknown	unknown	Austria	2023-05-26	Cleavage	Embryo	Whole Organism	All anatomical structures
75638	75638	SRR24746221	SRX20523358	SRS17832946	SRP439774	PRJNA976671	RNA seq of RNAs immunoprecipitated with eIF4E1c and eiF4E1c in early zebrafish embryos	GSE233570	Other	To investigate the mRNAs that are bound by eIF4E1b and eIF4E1c we performed RNA immunoprecipitation RIP experiments using anti GFP beads and transgenic embryos expressing GFP eIF4E1b or GFP eIF4E1c at the 8 cell stage. Overall design: We performed differential expression gene analyses of eIF4E1b n = 3 biological replicates versus eIF4E1c n = 2 biological replciates RIP and input samples.		pubmed:38177902	eIF4E1b input biol rep 1	GSM7430663	source name:Whole embryo lysate\|tissue:Whole embryo lysate\|cell type:8 cell stage\|genotype:tgactb2:3xflag sfGFP eIF4E1b\|geo loc name:missing\|collection date:missing	eIF4E1b input biol rep 1	RNA seq reads were trimmed using trim galore v0.5.0 and reads mapping to abundant sequences Dr mitochondrial chromosome SILVA Dr ribosomal RNA phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts with parameter s 0 for unstranded analysis subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts	Whole embryo lysate	RNA Clean & Concentrator kit Zymo Research of RIP and input samples SMARTerStrandedRNA library Ribo Zero for input samples; SMARTer ultra low RNA kit for RIP samples RNA Seq RIP and ssRNA seq Ribo Ziro		tissue:Whole embryo lysate\|cell type:8 cell stage\|genotype:tgactb2:3xflag sfGFP eIF4E1b	GSM7430663	GSM7430663: eIF4E1b input biol rep 1; Danio rerio; RIP Seq	GSM7430663 r1	GSM7430663	1	RNA Clean & Concentrator kit Zymo Research of RIP and input samples SMARTerStrandedRNA library Ribo Zero for input samples; SMARTer ultra low RNA kit for RIP samples RNA Seq RIP and ssRNA seq Ribo Ziro		RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP439774	loader:fastq load.py	e1b-RIP_input_1_1.fastq.gz e1b-RIP_input_1_2.fastq.gz	fastq fastq	3651955778.0	18078989.0	GSM7430663 r1	0:101 1:101	A:867085618;C:901659067;G:977824622;T:905338212;N:48259	101	101	867085618	901659067	977824622	905338212	48259	SRX20523358	SRS17832946	SRA1645065	IMP	IMP	2	0.90365	0.89737	0.05502	0.05755	0.76972	0.77047	0.56957	0.56902	101	101	B	B	biological fallback assumption	illumina	novaseq_era	full_length	rrna_depletion	ribozero	bulk	unknown	unknown	Austria	2023-05-26	Cleavage	Embryo	Whole Organism	All anatomical structures
75639	75639	SRR24746222	SRX20523357	SRS17832947	SRP439774	PRJNA976671	RNA seq of RNAs immunoprecipitated with eIF4E1c and eiF4E1c in early zebrafish embryos	GSE233570	Other	To investigate the mRNAs that are bound by eIF4E1b and eIF4E1c we performed RNA immunoprecipitation RIP experiments using anti GFP beads and transgenic embryos expressing GFP eIF4E1b or GFP eIF4E1c at the 8 cell stage. Overall design: We performed differential expression gene analyses of eIF4E1b n = 3 biological replicates versus eIF4E1c n = 2 biological replciates RIP and input samples.		pubmed:38177902	eIF4E1c RIP biol rep 2	GSM7430662	source name:Embryo lysate RIP\|tissue:Embryo lysate RIP\|cell type:8 cell stage\|genotype:tgactb2:3xflag sfGFP eIF4E1c\|geo loc name:missing\|collection date:missing	eIF4E1c RIP biol rep 2	RNA seq reads were trimmed using trim galore v0.5.0 and reads mapping to abundant sequences Dr mitochondrial chromosome SILVA Dr ribosomal RNA phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts with parameter s 0 for unstranded analysis subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts	Embryo lysate RIP	RNA Clean & Concentrator kit Zymo Research of RIP and input samples SMARTerStrandedRNA library Ribo Zero for input samples; SMARTer ultra low RNA kit for RIP samples RNA Seq RIP and ssRNA seq Ribo Ziro		tissue:Embryo lysate RIP\|cell type:8 cell stage\|genotype:tgactb2:3xflag sfGFP eIF4E1c	GSM7430662	GSM7430662: eIF4E1c RIP biol rep 2; Danio rerio; RIP Seq	GSM7430662 r1	GSM7430662	1	RNA Clean & Concentrator kit Zymo Research of RIP and input samples SMARTerStrandedRNA library Ribo Zero for input samples; SMARTer ultra low RNA kit for RIP samples RNA Seq RIP and ssRNA seq Ribo Ziro		RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP439774	loader:fastq load.py	e1c-RIP_3_1.fastq.gz e1c-RIP_3_2.fastq.gz	fastq fastq	3658509264.0	18111432.0	GSM7430662 r1	0:101 1:101	A:1021449118;C:787165883;G:803394137;T:1046320964;N:179162	101	101	1021449118	787165883	803394137	1046320964	179162	SRX20523357	SRS17832947	SRA1645065	IMP	IMP	2	0.89621	0.89533	0.04125	0.04128	0.7722	0.77244	0.5895	0.5976	101	101	B	B	biological fallback assumption	illumina	novaseq_era	full_length	rrna_depletion	ribozero	bulk	unknown	unknown	Austria	2023-05-26	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
75640	75640	SRR24746223	SRX20523356	SRS17832945	SRP439774	PRJNA976671	RNA seq of RNAs immunoprecipitated with eIF4E1c and eiF4E1c in early zebrafish embryos	GSE233570	Other	To investigate the mRNAs that are bound by eIF4E1b and eIF4E1c we performed RNA immunoprecipitation RIP experiments using anti GFP beads and transgenic embryos expressing GFP eIF4E1b or GFP eIF4E1c at the 8 cell stage. Overall design: We performed differential expression gene analyses of eIF4E1b n = 3 biological replicates versus eIF4E1c n = 2 biological replciates RIP and input samples.		pubmed:38177902	eIF4E1c RIP biol rep 1	GSM7430661	source name:Embryo lysate RIP\|tissue:Embryo lysate RIP\|cell type:8 cell stage\|genotype:tgactb2:3xflag sfGFP eIF4E1c\|geo loc name:missing\|collection date:missing	eIF4E1c RIP biol rep 1	RNA seq reads were trimmed using trim galore v0.5.0 and reads mapping to abundant sequences Dr mitochondrial chromosome SILVA Dr ribosomal RNA phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts with parameter s 0 for unstranded analysis subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts	Embryo lysate RIP	RNA Clean & Concentrator kit Zymo Research of RIP and input samples SMARTerStrandedRNA library Ribo Zero for input samples; SMARTer ultra low RNA kit for RIP samples RNA Seq RIP and ssRNA seq Ribo Ziro		tissue:Embryo lysate RIP\|cell type:8 cell stage\|genotype:tgactb2:3xflag sfGFP eIF4E1c	GSM7430661	GSM7430661: eIF4E1c RIP biol rep 1; Danio rerio; RIP Seq	GSM7430661 r1	GSM7430661	1	RNA Clean & Concentrator kit Zymo Research of RIP and input samples SMARTerStrandedRNA library Ribo Zero for input samples; SMARTer ultra low RNA kit for RIP samples RNA Seq RIP and ssRNA seq Ribo Ziro		RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP439774	loader:fastq load.py	e1c-RIP_1_1.fastq.gz e1c-RIP_1_2.fastq.gz	fastq fastq	3661517448.0	18126324.0	GSM7430661 r1	0:101 1:101	A:1033737040;C:769143038;G:789231169;T:1069383557;N:22644	101	101	1033737040	769143038	789231169	1069383557	22644	SRX20523356	SRS17832945	SRA1645065	IMP	IMP	2	0.63898	0.63654	0.0292	0.02977	0.8202	0.8216	0.63773	0.65353	101	101	B	B	biological fallback assumption	illumina	novaseq_era	full_length	rrna_depletion	ribozero	bulk	unknown	unknown	Austria	2023-05-26	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
75641	75641	SRR24746224	SRX20523355	SRS17832943	SRP439774	PRJNA976671	RNA seq of RNAs immunoprecipitated with eIF4E1c and eiF4E1c in early zebrafish embryos	GSE233570	Other	To investigate the mRNAs that are bound by eIF4E1b and eIF4E1c we performed RNA immunoprecipitation RIP experiments using anti GFP beads and transgenic embryos expressing GFP eIF4E1b or GFP eIF4E1c at the 8 cell stage. Overall design: We performed differential expression gene analyses of eIF4E1b n = 3 biological replicates versus eIF4E1c n = 2 biological replciates RIP and input samples.		pubmed:38177902	eIF4E1b RIP biol rep 3	GSM7430660	source name:Embryo lysate RIP\|tissue:Embryo lysate RIP\|cell type:8 cell stage\|genotype:tgactb2:3xflag sfGFP eIF4E1b\|geo loc name:missing\|collection date:missing	eIF4E1b RIP biol rep 3	RNA seq reads were trimmed using trim galore v0.5.0 and reads mapping to abundant sequences Dr mitochondrial chromosome SILVA Dr ribosomal RNA phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts with parameter s 0 for unstranded analysis subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts	Embryo lysate RIP	RNA Clean & Concentrator kit Zymo Research of RIP and input samples SMARTerStrandedRNA library Ribo Zero for input samples; SMARTer ultra low RNA kit for RIP samples RNA Seq RIP and ssRNA seq Ribo Ziro		tissue:Embryo lysate RIP\|cell type:8 cell stage\|genotype:tgactb2:3xflag sfGFP eIF4E1b	GSM7430660	GSM7430660: eIF4E1b RIP biol rep 3; Danio rerio; RIP Seq	GSM7430660 r1	GSM7430660	1	RNA Clean & Concentrator kit Zymo Research of RIP and input samples SMARTerStrandedRNA library Ribo Zero for input samples; SMARTer ultra low RNA kit for RIP samples RNA Seq RIP and ssRNA seq Ribo Ziro		RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP439774	loader:fastq load.py	e1b-RIP_3_1.fastq.gz e1b-RIP_3_2.fastq.gz	fastq fastq	3668401608.0	18160404.0	GSM7430660 r1	0:101 1:101	A:994142435;C:809751406;G:823521552;T:1040962762;N:23453	101	101	994142435	809751406	823521552	1040962762	23453	SRX20523355	SRS17832943	SRA1645065	IMP	IMP	2	0.89614	0.8938	0.02204	0.02191	0.77968	0.77938	0.46572	0.46433	101	101	B	B	biological fallback assumption	illumina	novaseq_era	full_length	rrna_depletion	ribozero	bulk	unknown	unknown	Austria	2023-05-26	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
75642	75642	SRR24746225	SRX20523354	SRS17832942	SRP439774	PRJNA976671	RNA seq of RNAs immunoprecipitated with eIF4E1c and eiF4E1c in early zebrafish embryos	GSE233570	Other	To investigate the mRNAs that are bound by eIF4E1b and eIF4E1c we performed RNA immunoprecipitation RIP experiments using anti GFP beads and transgenic embryos expressing GFP eIF4E1b or GFP eIF4E1c at the 8 cell stage. Overall design: We performed differential expression gene analyses of eIF4E1b n = 3 biological replicates versus eIF4E1c n = 2 biological replciates RIP and input samples.		pubmed:38177902	eIF4E1b RIP biol rep 2	GSM7430659	source name:Embryo lysate RIP\|tissue:Embryo lysate RIP\|cell type:8 cell stage\|genotype:tgactb2:3xflag sfGFP eIF4E1b\|geo loc name:missing\|collection date:missing	eIF4E1b RIP biol rep 2	RNA seq reads were trimmed using trim galore v0.5.0 and reads mapping to abundant sequences Dr mitochondrial chromosome SILVA Dr ribosomal RNA phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts with parameter s 0 for unstranded analysis subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts	Embryo lysate RIP	RNA Clean & Concentrator kit Zymo Research of RIP and input samples SMARTerStrandedRNA library Ribo Zero for input samples; SMARTer ultra low RNA kit for RIP samples RNA Seq RIP and ssRNA seq Ribo Ziro		tissue:Embryo lysate RIP\|cell type:8 cell stage\|genotype:tgactb2:3xflag sfGFP eIF4E1b	GSM7430659	GSM7430659: eIF4E1b RIP biol rep 2; Danio rerio; RIP Seq	GSM7430659 r1	GSM7430659	1	RNA Clean & Concentrator kit Zymo Research of RIP and input samples SMARTerStrandedRNA library Ribo Zero for input samples; SMARTer ultra low RNA kit for RIP samples RNA Seq RIP and ssRNA seq Ribo Ziro		RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP439774	loader:fastq load.py	e1b-RIP_2_1.fastq.gz e1b-RIP_2_2.fastq.gz	fastq fastq	3659386752.0	18115776.0	GSM7430659 r1	0:101 1:101	A:989766620;C:801915789;G:824369857;T:1043313396;N:21090	101	101	989766620	801915789	824369857	1043313396	21090	SRX20523354	SRS17832942	SRA1645065	IMP	IMP	2	0.89181	0.89107	0.0234	0.02432	0.77254	0.77341	0.4984	0.49917	101	101	B	B	biological fallback assumption	illumina	novaseq_era	full_length	rrna_depletion	ribozero	bulk	unknown	unknown	Austria	2023-05-26	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
75643	75643	SRR24746226	SRX20523353	SRS17832941	SRP439774	PRJNA976671	RNA seq of RNAs immunoprecipitated with eIF4E1c and eiF4E1c in early zebrafish embryos	GSE233570	Other	To investigate the mRNAs that are bound by eIF4E1b and eIF4E1c we performed RNA immunoprecipitation RIP experiments using anti GFP beads and transgenic embryos expressing GFP eIF4E1b or GFP eIF4E1c at the 8 cell stage. Overall design: We performed differential expression gene analyses of eIF4E1b n = 3 biological replicates versus eIF4E1c n = 2 biological replciates RIP and input samples.		pubmed:38177902	eIF4E1b RIP biol rep 1	GSM7430658	source name:Embryo lysate RIP\|tissue:Embryo lysate RIP\|cell type:8 cell stage\|genotype:tgactb2:3xflag sfGFP eIF4E1b\|geo loc name:missing\|collection date:missing	eIF4E1b RIP biol rep 1	RNA seq reads were trimmed using trim galore v0.5.0 and reads mapping to abundant sequences Dr mitochondrial chromosome SILVA Dr ribosomal RNA phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts with parameter s 0 for unstranded analysis subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts	Embryo lysate RIP	RNA Clean & Concentrator kit Zymo Research of RIP and input samples SMARTerStrandedRNA library Ribo Zero for input samples; SMARTer ultra low RNA kit for RIP samples RNA Seq RIP and ssRNA seq Ribo Ziro		tissue:Embryo lysate RIP\|cell type:8 cell stage\|genotype:tgactb2:3xflag sfGFP eIF4E1b	GSM7430658	GSM7430658: eIF4E1b RIP biol rep 1; Danio rerio; RIP Seq	GSM7430658 r1	GSM7430658	1	RNA Clean & Concentrator kit Zymo Research of RIP and input samples SMARTerStrandedRNA library Ribo Zero for input samples; SMARTer ultra low RNA kit for RIP samples RNA Seq RIP and ssRNA seq Ribo Ziro		RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP439774	loader:fastq load.py	e1b-RIP_1_1.fastq.gz e1b-RIP_1_2.fastq.gz	fastq fastq	3664341206.0	18140303.0	GSM7430658 r1	0:101 1:101	A:1002079901;C:797505762;G:819102400;T:1045629643;N:23500	101	101	1002079901	797505762	819102400	1045629643	23500	SRX20523353	SRS17832941	SRA1645065	IMP	IMP	2	0.89693	0.89111	0.03355	0.03395	0.77009	0.77157	0.48797	0.48637	101	101	B	B	biological fallback assumption	illumina	novaseq_era	full_length	rrna_depletion	ribozero	bulk	unknown	unknown	Austria	2023-05-26	Cleavage	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");;