metadata: run_metadata: 75 rows where experiment.library_source = "TRANSCRIPTOMIC", experiment.library_strategy = "RIP-Seq" and tissue

75 rows where experiment.library_source = "TRANSCRIPTOMIC", experiment.library_strategy = "RIP-Seq" and tissue_curation = "Whole Organism"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.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
34614	34614	SRR32137213	SRX27483377	SRS23906281	SRP560121	PRJNA1216205	rbm24a is an organizer component of germ plasm to determine germ cell fate 202409 validation	GSE288109	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 comprehensively characterize the RNA binding landscape of Rbm24a in zebrafish we performed RIP seq analysis using rbm24a GFP knock in samples with IgG serving as the control.			Zebrafish RIP seq Rbm24a Knock in2 IP2	GSM8759069	source name:whole embryo\|tissue:whole embryo\|cell line:4 cell stage\|cell type:embryonic cell\|genotype:knock in\|geo loc name:missing\|collection date:missing	Zebrafish RIP seq Rbm24a Knock in2 IP2	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 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 of immunoprecipitated RNA was utilized for library construction. Ribosomal RNA depletion was performed using RNase H based probes followed by magnetic bead purification. RNA fragmentation was achieved through magnesium catalyzed hydrolysis under elevated temperature 94°C for 6 min. First strand cDNA synthesis was initiated with random hexamer primers and reverse transcriptase followed by second strand synthesis using DNA polymerase I with dUTP incorporation for strand marking. Double stranded cDNA fragments underwent end repair and three prime adenylation using a single tube enzymatic reaction system. Illumina compatible adaptors with unique dual indexes were ligated to both ends of the DNA fragments. Size selection of adaptor ligated products 180 250 bp was performed using double sided SPRI bead purification. PCR amplification was conducted with P5/P7 primers for 12 cycles followed by AMPure XP bead purification to remove primer dimers. Library quality was verified by Agilent 2100 Bioanalyzer DNA High Sensitivity chip analysis. Indexed libraries were pooled in equimolar ratios and subjected to paired end sequencing 2×150 bp on an Illumina NovaSeq 6000 platform following the manufacturer's standardized workflow.	Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C	tissue:whole embryo\|cell line:4 cell stage\|cell type:embryonic cell\|genotype:knock in	GSM8759069	GSM8759069: Zebrafish RIP seq Rbm24a Knock in2 IP2; Danio rerio; RIP Seq	GSM8759069 r1	GSM8759069	1	Total RNAs were extracted from 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 of immunoprecipitated RNA was utilized for library construction. Ribosomal RNA depletion was performed using RNase H based probes followed by magnetic bead purification. RNA fragmentation was achieved through magnesium catalyzed hydrolysis under elevated temperature 94°C for 6 min. First strand cDNA synthesis was initiated with random hexamer primers and reverse transcriptase followed by second strand synthesis using DNA polymerase I with dUTP incorporation for strand marking. Double stranded cDNA fragments underwent end repair and three prime adenylation using a single tube enzymatic reaction system. Illumina compatible adaptors with unique dual indexes were ligated to both ends of the DNA fragments. Size selection of adaptor ligated products 180 250 bp was performed using double sided SPRI bead purification. PCR amplification was conducted with P5/P7 primers for 12 cycles followed by AMPure XP bead purification to remove primer dimers. Library quality was verified by Agilent 2100 Bioanalyzer DNA High Sensitivity chip analysis. Indexed libraries were pooled in equimolar ratios and subjected to paired end sequencing 2×150 bp on an Illumina NovaSeq 6000 platform following the manufacturer's standardized workflow.		RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP560121		RIP_IP2.R1.fq.gz RIP_IP2.R2.fq.gz	fastq fastq	18215080774.0	60314837.0	GSM8759069 r1	0:151 1:151	A:3824315591;C:5035112770;G:5644328190;T:3707941000;N:3383223	151	151	3824315591	5035112770	5644328190	3707941000	3383223	SRX27483377	SRS23906281	SRA2061743	Ang Li, College of Life Sciences, shandong university	Ang Li, College of Life Sciences, shandong university												B	B	mate2-mate1 similar by mapping diff	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2025-01-27	Multi-stage	Embryo	Whole Organism	All anatomical structures
34615	34615	SRR32137214	SRX27483376	SRS23906280	SRP560121	PRJNA1216205	rbm24a is an organizer component of germ plasm to determine germ cell fate 202409 validation	GSE288109	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 comprehensively characterize the RNA binding landscape of Rbm24a in zebrafish we performed RIP seq analysis using rbm24a GFP knock in samples with IgG serving as the control.			Zebrafish RIP seq Rbm24a Knock in1 IP1	GSM8759068	source name:whole embryo\|tissue:whole embryo\|cell line:4 cell stage\|cell type:embryonic cell\|genotype:knock in\|geo loc name:missing\|collection date:missing	Zebrafish RIP seq Rbm24a Knock in1 IP1	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 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 of immunoprecipitated RNA was utilized for library construction. Ribosomal RNA depletion was performed using RNase H based probes followed by magnetic bead purification. RNA fragmentation was achieved through magnesium catalyzed hydrolysis under elevated temperature 94°C for 6 min. First strand cDNA synthesis was initiated with random hexamer primers and reverse transcriptase followed by second strand synthesis using DNA polymerase I with dUTP incorporation for strand marking. Double stranded cDNA fragments underwent end repair and three prime adenylation using a single tube enzymatic reaction system. Illumina compatible adaptors with unique dual indexes were ligated to both ends of the DNA fragments. Size selection of adaptor ligated products 180 250 bp was performed using double sided SPRI bead purification. PCR amplification was conducted with P5/P7 primers for 12 cycles followed by AMPure XP bead purification to remove primer dimers. Library quality was verified by Agilent 2100 Bioanalyzer DNA High Sensitivity chip analysis. Indexed libraries were pooled in equimolar ratios and subjected to paired end sequencing 2×150 bp on an Illumina NovaSeq 6000 platform following the manufacturer's standardized workflow.	Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C	tissue:whole embryo\|cell line:4 cell stage\|cell type:embryonic cell\|genotype:knock in	GSM8759068	GSM8759068: Zebrafish RIP seq Rbm24a Knock in1 IP1; Danio rerio; RIP Seq	GSM8759068 r1	GSM8759068	1	Total RNAs were extracted from 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 of immunoprecipitated RNA was utilized for library construction. Ribosomal RNA depletion was performed using RNase H based probes followed by magnetic bead purification. RNA fragmentation was achieved through magnesium catalyzed hydrolysis under elevated temperature 94°C for 6 min. First strand cDNA synthesis was initiated with random hexamer primers and reverse transcriptase followed by second strand synthesis using DNA polymerase I with dUTP incorporation for strand marking. Double stranded cDNA fragments underwent end repair and three prime adenylation using a single tube enzymatic reaction system. Illumina compatible adaptors with unique dual indexes were ligated to both ends of the DNA fragments. Size selection of adaptor ligated products 180 250 bp was performed using double sided SPRI bead purification. PCR amplification was conducted with P5/P7 primers for 12 cycles followed by AMPure XP bead purification to remove primer dimers. Library quality was verified by Agilent 2100 Bioanalyzer DNA High Sensitivity chip analysis. Indexed libraries were pooled in equimolar ratios and subjected to paired end sequencing 2×150 bp on an Illumina NovaSeq 6000 platform following the manufacturer's standardized workflow.		RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP560121		RIP_IP1.R1.fq.gz RIP_IP1.R2.fq.gz	fastq fastq	22190472874.0	73478387.0	GSM8759068 r1	0:151 1:151	A:4585155428;C:6233832602;G:6882198251;T:4484977909;N:4308684	151	151	4585155428	6233832602	6882198251	4484977909	4308684	SRX27483376	SRS23906280	SRA2061743	Ang Li, College of Life Sciences, shandong university	Ang Li, College of Life Sciences, shandong university												B	B	mate2-mate1 similar by mapping diff	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2025-01-27	Multi-stage	Embryo	Whole Organism	All anatomical structures
34616	34616	SRR32137215	SRX27483375	SRS23906279	SRP560121	PRJNA1216205	rbm24a is an organizer component of germ plasm to determine germ cell fate 202409 validation	GSE288109	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 comprehensively characterize the RNA binding landscape of Rbm24a in zebrafish we performed RIP seq analysis using rbm24a GFP knock in samples with IgG serving as the control.			Zebrafish RIP seq Rbm24a Knock in2 IgG2	GSM8759067	source name:whole embryo\|tissue:whole embryo\|cell line:4 cell stage\|cell type:embryonic cell\|genotype:knock in\|geo loc name:missing\|collection date:missing	Zebrafish RIP seq Rbm24a Knock in2 IgG2	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 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 of immunoprecipitated RNA was utilized for library construction. Ribosomal RNA depletion was performed using RNase H based probes followed by magnetic bead purification. RNA fragmentation was achieved through magnesium catalyzed hydrolysis under elevated temperature 94°C for 6 min. First strand cDNA synthesis was initiated with random hexamer primers and reverse transcriptase followed by second strand synthesis using DNA polymerase I with dUTP incorporation for strand marking. Double stranded cDNA fragments underwent end repair and three prime adenylation using a single tube enzymatic reaction system. Illumina compatible adaptors with unique dual indexes were ligated to both ends of the DNA fragments. Size selection of adaptor ligated products 180 250 bp was performed using double sided SPRI bead purification. PCR amplification was conducted with P5/P7 primers for 12 cycles followed by AMPure XP bead purification to remove primer dimers. Library quality was verified by Agilent 2100 Bioanalyzer DNA High Sensitivity chip analysis. Indexed libraries were pooled in equimolar ratios and subjected to paired end sequencing 2×150 bp on an Illumina NovaSeq 6000 platform following the manufacturer's standardized workflow.	Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C	tissue:whole embryo\|cell line:4 cell stage\|cell type:embryonic cell\|genotype:knock in	GSM8759067	GSM8759067: Zebrafish RIP seq Rbm24a Knock in2 IgG2; Danio rerio; RIP Seq	GSM8759067 r1	GSM8759067	1	Total RNAs were extracted from 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 of immunoprecipitated RNA was utilized for library construction. Ribosomal RNA depletion was performed using RNase H based probes followed by magnetic bead purification. RNA fragmentation was achieved through magnesium catalyzed hydrolysis under elevated temperature 94°C for 6 min. First strand cDNA synthesis was initiated with random hexamer primers and reverse transcriptase followed by second strand synthesis using DNA polymerase I with dUTP incorporation for strand marking. Double stranded cDNA fragments underwent end repair and three prime adenylation using a single tube enzymatic reaction system. Illumina compatible adaptors with unique dual indexes were ligated to both ends of the DNA fragments. Size selection of adaptor ligated products 180 250 bp was performed using double sided SPRI bead purification. PCR amplification was conducted with P5/P7 primers for 12 cycles followed by AMPure XP bead purification to remove primer dimers. Library quality was verified by Agilent 2100 Bioanalyzer DNA High Sensitivity chip analysis. Indexed libraries were pooled in equimolar ratios and subjected to paired end sequencing 2×150 bp on an Illumina NovaSeq 6000 platform following the manufacturer's standardized workflow.		RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP560121		RIP_IgG2.R1.fq.gz RIP_IgG2.R2.fq.gz	fastq fastq	18588838088.0	61552444.0	GSM8759067 r1	0:151 1:151	A:3864885070;C:5250483318;G:5713729791;T:3756127723;N:3612186	151	151	3864885070	5250483318	5713729791	3756127723	3612186	SRX27483375	SRS23906279	SRA2061743	Ang Li, College of Life Sciences, shandong university	Ang Li, College of Life Sciences, shandong university												B	T	mate2 technical by mapping diff	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2025-01-27	Multi-stage	Embryo	Whole Organism	All anatomical structures
34617	34617	SRR32137216	SRX27483374	SRS23906278	SRP560121	PRJNA1216205	rbm24a is an organizer component of germ plasm to determine germ cell fate 202409 validation	GSE288109	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 comprehensively characterize the RNA binding landscape of Rbm24a in zebrafish we performed RIP seq analysis using rbm24a GFP knock in samples with IgG serving as the control.			Zebrafish RIP seq Rbm24a Knock in1 IgG1	GSM8759066	source name:whole embryo\|tissue:whole embryo\|cell line:4 cell stage\|cell type:embryonic cell\|genotype:knock in\|geo loc name:missing\|collection date:missing	Zebrafish RIP seq Rbm24a Knock in1 IgG1	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 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 of immunoprecipitated RNA was utilized for library construction. Ribosomal RNA depletion was performed using RNase H based probes followed by magnetic bead purification. RNA fragmentation was achieved through magnesium catalyzed hydrolysis under elevated temperature 94°C for 6 min. First strand cDNA synthesis was initiated with random hexamer primers and reverse transcriptase followed by second strand synthesis using DNA polymerase I with dUTP incorporation for strand marking. Double stranded cDNA fragments underwent end repair and three prime adenylation using a single tube enzymatic reaction system. Illumina compatible adaptors with unique dual indexes were ligated to both ends of the DNA fragments. Size selection of adaptor ligated products 180 250 bp was performed using double sided SPRI bead purification. PCR amplification was conducted with P5/P7 primers for 12 cycles followed by AMPure XP bead purification to remove primer dimers. Library quality was verified by Agilent 2100 Bioanalyzer DNA High Sensitivity chip analysis. Indexed libraries were pooled in equimolar ratios and subjected to paired end sequencing 2×150 bp on an Illumina NovaSeq 6000 platform following the manufacturer's standardized workflow.	Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C	tissue:whole embryo\|cell line:4 cell stage\|cell type:embryonic cell\|genotype:knock in	GSM8759066	GSM8759066: Zebrafish RIP seq Rbm24a Knock in1 IgG1; Danio rerio; RIP Seq	GSM8759066 r1	GSM8759066	1	Total RNAs were extracted from 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 of immunoprecipitated RNA was utilized for library construction. Ribosomal RNA depletion was performed using RNase H based probes followed by magnetic bead purification. RNA fragmentation was achieved through magnesium catalyzed hydrolysis under elevated temperature 94°C for 6 min. First strand cDNA synthesis was initiated with random hexamer primers and reverse transcriptase followed by second strand synthesis using DNA polymerase I with dUTP incorporation for strand marking. Double stranded cDNA fragments underwent end repair and three prime adenylation using a single tube enzymatic reaction system. Illumina compatible adaptors with unique dual indexes were ligated to both ends of the DNA fragments. Size selection of adaptor ligated products 180 250 bp was performed using double sided SPRI bead purification. PCR amplification was conducted with P5/P7 primers for 12 cycles followed by AMPure XP bead purification to remove primer dimers. Library quality was verified by Agilent 2100 Bioanalyzer DNA High Sensitivity chip analysis. Indexed libraries were pooled in equimolar ratios and subjected to paired end sequencing 2×150 bp on an Illumina NovaSeq 6000 platform following the manufacturer's standardized workflow.		RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP560121		RIP_IgG1.R1.fq.gz RIP_IgG1.R2.fq.gz	fastq fastq	18008086350.0	59629425.0	GSM8759066 r1	0:151 1:151	A:3736851298;C:5091099145;G:5529269310;T:3647429389;N:3437208	151	151	3736851298	5091099145	5529269310	3647429389	3437208	SRX27483374	SRS23906278	SRA2061743	Ang Li, College of Life Sciences, shandong university	Ang Li, College of Life Sciences, shandong university												B	T	mate2 technical by mapping diff	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2025-01-27	Multi-stage	Embryo	Whole Organism	All anatomical structures
40576	40576	SRR3228716	SRX1634616	SRS1345843	SRP071818	PRJNA315314	The functions of m6A and Ythdf2 during zebrafish early development	GSE79213	Other	We report the m6A methylation maps of zebrafish embryos during early development and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish MZT highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0 2 4 6 8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0 2 4 6 8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6 8 12 24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx 36 48 h.p.f. Replicate of each seq is also included.		pubmed:28192787	m6A CLIP 8	GSM2088181	tissue:whole zebrafish embryo\|genotype:WT\|treatment:n1	m6A CLIP 8	Data analysis for each experiment: 1 for m6A seq reads were aligned to the reference genome danRer10 using Tophat v2.0.14 ref with parameter g 1 library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a median reads count of the IP sample in all 100 bp windows on the current mRNA b reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a×d/b×c. 2 for m6A CLIP seq post removing the adapter sequence the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation wer…	whole zebrafish embryo		total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	embryos were collected and cultured in medium at 28.5 °C and then harvested at each time point into TRIzol.	development time h.p.f.:8\|genotype:WT\|treatment:n1	GSM2088181	GSM2088181: m6A CLIP 8; Danio rerio; RIP Seq	GSM2088181		1	total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	GEO Accession:GSM2088181	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP071818		CLIP_8h-IP.fastq.gz	fastq	921977050.0	18439541.0	GSM2088181 r1	0:50	A:233396466;C:263744643;G:252737160;T:172064890;N:33891	50		233396466	263744643	252737160	172064890	33891	SRX1634616	SRS1345843	SRA385720	GEO	Chuan He Lab, Chemistry, University of Chicago	1	0.61408		0.1783		0.88032		0.72361		50		B		usable mapping rate	illumina	hiseq_era	unknown	other	trueseq	bulk	unknown	unknown	United States	2016-03-14	Undetermined	Embryo	Whole Organism	All anatomical structures
40577	40577	SRR3228715	SRX1634615	SRS1345844	SRP071818	PRJNA315314	The functions of m6A and Ythdf2 during zebrafish early development	GSE79213	Other	We report the m6A methylation maps of zebrafish embryos during early development and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish MZT highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0 2 4 6 8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0 2 4 6 8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6 8 12 24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx 36 48 h.p.f. Replicate of each seq is also included.		pubmed:28192787	m6A CLIP 6	GSM2088180	tissue:whole zebrafish embryo\|genotype:WT\|treatment:n1	m6A CLIP 6	Data analysis for each experiment: 1 for m6A seq reads were aligned to the reference genome danRer10 using Tophat v2.0.14 ref with parameter g 1 library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a median reads count of the IP sample in all 100 bp windows on the current mRNA b reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a×d/b×c. 2 for m6A CLIP seq post removing the adapter sequence the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation wer…	whole zebrafish embryo		total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	embryos were collected and cultured in medium at 28.5 °C and then harvested at each time point into TRIzol.	development time h.p.f.:6\|genotype:WT\|treatment:n1	GSM2088180	GSM2088180: m6A CLIP 6; Danio rerio; RIP Seq	GSM2088180		1	total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	GEO Accession:GSM2088180	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP071818		CLIP_6h-IP.fastq.gz	fastq	811777600.0	16235552.0	GSM2088180 r1	0:50	A:214241727;C:241830821;G:208608337;T:147066789;N:29926	50		214241727	241830821	208608337	147066789	29926	SRX1634615	SRS1345844	SRA385720	GEO	Chuan He Lab, Chemistry, University of Chicago	1	0.68946		0.17622		0.9194		0.62968		50		B		usable mapping rate	illumina	hiseq_era	unknown	other	trueseq	bulk	unknown	unknown	United States	2016-03-14	Undetermined	Embryo	Whole Organism	All anatomical structures
40578	40578	SRR3228714	SRX1634614	SRS1345845	SRP071818	PRJNA315314	The functions of m6A and Ythdf2 during zebrafish early development	GSE79213	Other	We report the m6A methylation maps of zebrafish embryos during early development and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish MZT highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0 2 4 6 8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0 2 4 6 8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6 8 12 24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx 36 48 h.p.f. Replicate of each seq is also included.		pubmed:28192787	m6A CLIP 4	GSM2088179	tissue:whole zebrafish embryo\|genotype:WT\|treatment:n1	m6A CLIP 4	Data analysis for each experiment: 1 for m6A seq reads were aligned to the reference genome danRer10 using Tophat v2.0.14 ref with parameter g 1 library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a median reads count of the IP sample in all 100 bp windows on the current mRNA b reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a×d/b×c. 2 for m6A CLIP seq post removing the adapter sequence the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation wer…	whole zebrafish embryo		total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	embryos were collected and cultured in medium at 28.5 °C and then harvested at each time point into TRIzol.	development time h.p.f.:4\|genotype:WT\|treatment:n1	GSM2088179	GSM2088179: m6A CLIP 4; Danio rerio; RIP Seq	GSM2088179		1	total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	GEO Accession:GSM2088179	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP071818		CLIP_4h-IP.fastq.gz	fastq	746223800.0	14924476.0	GSM2088179 r1	0:50	A:185147085;C:236139555;G:187875436;T:137034934;N:26790	50		185147085	236139555	187875436	137034934	26790	SRX1634614	SRS1345845	SRA385720	GEO	Chuan He Lab, Chemistry, University of Chicago	1	0.80174		0.17015		0.86164		0.77262		50		B		usable mapping rate	illumina	hiseq_era	unknown	other	trueseq	bulk	unknown	unknown	United States	2016-03-14	Undetermined	Embryo	Whole Organism	All anatomical structures
40579	40579	SRR3228713	SRX1634613	SRS1345846	SRP071818	PRJNA315314	The functions of m6A and Ythdf2 during zebrafish early development	GSE79213	Other	We report the m6A methylation maps of zebrafish embryos during early development and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish MZT highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0 2 4 6 8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0 2 4 6 8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6 8 12 24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx 36 48 h.p.f. Replicate of each seq is also included.		pubmed:28192787	m6A CLIP 2	GSM2088178	tissue:whole zebrafish embryo\|genotype:WT\|treatment:n1	m6A CLIP 2	Data analysis for each experiment: 1 for m6A seq reads were aligned to the reference genome danRer10 using Tophat v2.0.14 ref with parameter g 1 library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a median reads count of the IP sample in all 100 bp windows on the current mRNA b reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a×d/b×c. 2 for m6A CLIP seq post removing the adapter sequence the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation wer…	whole zebrafish embryo		total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	embryos were collected and cultured in medium at 28.5 °C and then harvested at each time point into TRIzol.	development time h.p.f.:2\|genotype:WT\|treatment:n1	GSM2088178	GSM2088178: m6A CLIP 2; Danio rerio; RIP Seq	GSM2088178		1	total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	GEO Accession:GSM2088178	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP071818		CLIP_2h-IP.fastq.gz	fastq	937426800.0	18748536.0	GSM2088178 r1	0:50	A:263526034;C:262864870;G:241415141;T:169586820;N:33935	50		263526034	262864870	241415141	169586820	33935	SRX1634613	SRS1345846	SRA385720	GEO	Chuan He Lab, Chemistry, University of Chicago	1	0.75612		0.2242		0.87823		0.61308		50		B		usable mapping rate	illumina	hiseq_era	unknown	other	trueseq	bulk	unknown	unknown	United States	2016-03-14	Undetermined	Embryo	Whole Organism	All anatomical structures
40580	40580	SRR3228712	SRX1634612	SRS1345847	SRP071818	PRJNA315314	The functions of m6A and Ythdf2 during zebrafish early development	GSE79213	Other	We report the m6A methylation maps of zebrafish embryos during early development and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish MZT highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0 2 4 6 8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0 2 4 6 8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6 8 12 24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx 36 48 h.p.f. Replicate of each seq is also included.		pubmed:28192787	m6A CLIP 0	GSM2088177	tissue:whole zebrafish embryo\|genotype:WT\|treatment:n1	m6A CLIP 0	Data analysis for each experiment: 1 for m6A seq reads were aligned to the reference genome danRer10 using Tophat v2.0.14 ref with parameter g 1 library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a median reads count of the IP sample in all 100 bp windows on the current mRNA b reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a×d/b×c. 2 for m6A CLIP seq post removing the adapter sequence the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation wer…	whole zebrafish embryo		total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	embryos were collected and cultured in medium at 28.5 °C and then harvested at each time point into TRIzol.	development time h.p.f.:0\|genotype:WT\|treatment:n1	GSM2088177	GSM2088177: m6A CLIP 0; Danio rerio; RIP Seq	GSM2088177		1	total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	GEO Accession:GSM2088177	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP071818		CLIP_0h-IP.fastq.gz	fastq	1320186200.0	26403724.0	GSM2088177 r1	0:50	A:362282258;C:387362464;G:326692598;T:243799324;N:49556	50		362282258	387362464	326692598	243799324	49556	SRX1634612	SRS1345847	SRA385720	GEO	Chuan He Lab, Chemistry, University of Chicago	1	0.50689		0.10395		0.89755		0.72663		50		B		usable mapping rate	illumina	hiseq_era	unknown	other	trueseq	bulk	unknown	unknown	United States	2016-03-14	Undetermined	Embryo	Whole Organism	All anatomical structures
40581	40581	SRR3228711	SRX1634611	SRS1345848	SRP071818	PRJNA315314	The functions of m6A and Ythdf2 during zebrafish early development	GSE79213	Other	We report the m6A methylation maps of zebrafish embryos during early development and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish MZT highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0 2 4 6 8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0 2 4 6 8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6 8 12 24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx 36 48 h.p.f. Replicate of each seq is also included.		pubmed:28192787	input CLIP 8	GSM2088176	tissue:whole zebrafish embryo\|genotype:WT\|treatment:n1	input CLIP 8	Data analysis for each experiment: 1 for m6A seq reads were aligned to the reference genome danRer10 using Tophat v2.0.14 ref with parameter g 1 library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a median reads count of the IP sample in all 100 bp windows on the current mRNA b reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a×d/b×c. 2 for m6A CLIP seq post removing the adapter sequence the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation wer…	whole zebrafish embryo		total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	embryos were collected and cultured in medium at 28.5 °C and then harvested at each time point into TRIzol.	development time h.p.f.:8\|genotype:WT\|treatment:n1	GSM2088176	GSM2088176: input CLIP 8; Danio rerio; RIP Seq	GSM2088176		1	total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	GEO Accession:GSM2088176	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP071818		CLIP_8h-input.fastq.gz	fastq	1971263900.0	39425278.0	GSM2088176 r1	0:50	A:530986171;C:559974651;G:547087685;T:333110850;N:104543	50		530986171	559974651	547087685	333110850	104543	SRX1634611	SRS1345848	SRA385720	GEO	Chuan He Lab, Chemistry, University of Chicago	1	0.64576		0.23563		0.91618		0.71461		50		B		usable mapping rate	illumina	hiseq_era	unknown	other	trueseq	bulk	unknown	unknown	United States	2016-03-14	Undetermined	Embryo	Whole Organism	All anatomical structures
40582	40582	SRR3228710	SRX1634610	SRS1345849	SRP071818	PRJNA315314	The functions of m6A and Ythdf2 during zebrafish early development	GSE79213	Other	We report the m6A methylation maps of zebrafish embryos during early development and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish MZT highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0 2 4 6 8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0 2 4 6 8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6 8 12 24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx 36 48 h.p.f. Replicate of each seq is also included.		pubmed:28192787	input CLIP 6	GSM2088175	tissue:whole zebrafish embryo\|genotype:WT\|treatment:n1	input CLIP 6	Data analysis for each experiment: 1 for m6A seq reads were aligned to the reference genome danRer10 using Tophat v2.0.14 ref with parameter g 1 library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a median reads count of the IP sample in all 100 bp windows on the current mRNA b reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a×d/b×c. 2 for m6A CLIP seq post removing the adapter sequence the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation wer…	whole zebrafish embryo		total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	embryos were collected and cultured in medium at 28.5 °C and then harvested at each time point into TRIzol.	development time h.p.f.:6\|genotype:WT\|treatment:n1	GSM2088175	GSM2088175: input CLIP 6; Danio rerio; RIP Seq	GSM2088175		1	total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	GEO Accession:GSM2088175	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP071818		CLIP_6h-input.fastq.gz	fastq	2424925650.0	48498513.0	GSM2088175 r1	0:50	A:622469966;C:699224547;G:701719139;T:401382845;N:129153	50		622469966	699224547	701719139	401382845	129153	SRX1634610	SRS1345849	SRA385720	GEO	Chuan He Lab, Chemistry, University of Chicago	1	0.68121		0.23857		0.93123		0.73919		50		B		usable mapping rate	illumina	hiseq_era	unknown	other	trueseq	bulk	unknown	unknown	United States	2016-03-14	Undetermined	Embryo	Whole Organism	All anatomical structures
40583	40583	SRR3228709	SRX1634609	SRS1345850	SRP071818	PRJNA315314	The functions of m6A and Ythdf2 during zebrafish early development	GSE79213	Other	We report the m6A methylation maps of zebrafish embryos during early development and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish MZT highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0 2 4 6 8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0 2 4 6 8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6 8 12 24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx 36 48 h.p.f. Replicate of each seq is also included.		pubmed:28192787	input CLIP 4	GSM2088174	tissue:whole zebrafish embryo\|genotype:WT\|treatment:n1	input CLIP 4	Data analysis for each experiment: 1 for m6A seq reads were aligned to the reference genome danRer10 using Tophat v2.0.14 ref with parameter g 1 library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a median reads count of the IP sample in all 100 bp windows on the current mRNA b reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a×d/b×c. 2 for m6A CLIP seq post removing the adapter sequence the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation wer…	whole zebrafish embryo		total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	embryos were collected and cultured in medium at 28.5 °C and then harvested at each time point into TRIzol.	development time h.p.f.:4\|genotype:WT\|treatment:n1	GSM2088174	GSM2088174: input CLIP 4; Danio rerio; RIP Seq	GSM2088174		1	total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	GEO Accession:GSM2088174	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP071818		CLIP_4h-input.fastq.gz	fastq	1996829250.0	39936585.0	GSM2088174 r1	0:50	A:527211013;C:600800804;G:528828160;T:339883128;N:106145	50		527211013	600800804	528828160	339883128	106145	SRX1634609	SRS1345850	SRA385720	GEO	Chuan He Lab, Chemistry, University of Chicago	1	0.60745		0.19305		0.92537		0.74508		50		B		usable mapping rate	illumina	hiseq_era	unknown	other	trueseq	bulk	unknown	unknown	United States	2016-03-14	Undetermined	Embryo	Whole Organism	All anatomical structures
40584	40584	SRR3228708	SRX1634608	SRS1345851	SRP071818	PRJNA315314	The functions of m6A and Ythdf2 during zebrafish early development	GSE79213	Other	We report the m6A methylation maps of zebrafish embryos during early development and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish MZT highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0 2 4 6 8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0 2 4 6 8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6 8 12 24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx 36 48 h.p.f. Replicate of each seq is also included.		pubmed:28192787	input CLIP 2	GSM2088173	tissue:whole zebrafish embryo\|genotype:WT\|treatment:n1	input CLIP 2	Data analysis for each experiment: 1 for m6A seq reads were aligned to the reference genome danRer10 using Tophat v2.0.14 ref with parameter g 1 library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a median reads count of the IP sample in all 100 bp windows on the current mRNA b reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a×d/b×c. 2 for m6A CLIP seq post removing the adapter sequence the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation wer…	whole zebrafish embryo		total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	embryos were collected and cultured in medium at 28.5 °C and then harvested at each time point into TRIzol.	development time h.p.f.:2\|genotype:WT\|treatment:n1	GSM2088173	GSM2088173: input CLIP 2; Danio rerio; RIP Seq	GSM2088173		1	total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	GEO Accession:GSM2088173	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP071818		CLIP_2h-input.fastq.gz	fastq	2119606350.0	42392127.0	GSM2088173 r1	0:50	A:555894042;C:598667411;G:609233481;T:355698501;N:112915	50		555894042	598667411	609233481	355698501	112915	SRX1634608	SRS1345851	SRA385720	GEO	Chuan He Lab, Chemistry, University of Chicago	1	0.65392		0.2263		0.9049		0.72736		50		B		usable mapping rate	illumina	hiseq_era	unknown	other	trueseq	bulk	unknown	unknown	United States	2016-03-14	Undetermined	Embryo	Whole Organism	All anatomical structures
40585	40585	SRR3228707	SRX1634607	SRS1345852	SRP071818	PRJNA315314	The functions of m6A and Ythdf2 during zebrafish early development	GSE79213	Other	We report the m6A methylation maps of zebrafish embryos during early development and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish MZT highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0 2 4 6 8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0 2 4 6 8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6 8 12 24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx 36 48 h.p.f. Replicate of each seq is also included.		pubmed:28192787	input CLIP 0	GSM2088172	tissue:whole zebrafish embryo\|genotype:WT\|treatment:n1	input CLIP 0	Data analysis for each experiment: 1 for m6A seq reads were aligned to the reference genome danRer10 using Tophat v2.0.14 ref with parameter g 1 library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a median reads count of the IP sample in all 100 bp windows on the current mRNA b reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a×d/b×c. 2 for m6A CLIP seq post removing the adapter sequence the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation wer…	whole zebrafish embryo		total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	embryos were collected and cultured in medium at 28.5 °C and then harvested at each time point into TRIzol.	development time h.p.f.:0\|genotype:WT\|treatment:n1	GSM2088172	GSM2088172: input CLIP 0; Danio rerio; RIP Seq	GSM2088172		1	total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	GEO Accession:GSM2088172	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP071818		CLIP_0h-input.fastq.gz	fastq	2150269400.0	43005388.0	GSM2088172 r1										SRX1634607	SRS1345852	SRA385720	GEO	Chuan He Lab, Chemistry, University of Chicago	1	0.57233		0.18947		0.91323		0.75741		50		B		usable mapping rate	illumina	hiseq_era	unknown	other	trueseq	bulk	unknown	unknown	United States	2016-03-14	Undetermined	Embryo	Whole Organism	All anatomical structures
40586	40586	SRR3228706	SRX1634606	SRS1345853	SRP071818	PRJNA315314	The functions of m6A and Ythdf2 during zebrafish early development	GSE79213	Other	We report the m6A methylation maps of zebrafish embryos during early development and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish MZT highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0 2 4 6 8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0 2 4 6 8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6 8 12 24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx 36 48 h.p.f. Replicate of each seq is also included.		pubmed:28192787	m6A IP 8	GSM2088171	tissue:whole zebrafish embryo\|genotype:WT\|treatment:n1	m6A IP 8	Data analysis for each experiment: 1 for m6A seq reads were aligned to the reference genome danRer10 using Tophat v2.0.14 ref with parameter g 1 library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a median reads count of the IP sample in all 100 bp windows on the current mRNA b reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a×d/b×c. 2 for m6A CLIP seq post removing the adapter sequence the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation wer…	whole zebrafish embryo		total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	embryos were collected and cultured in medium at 28.5 °C and then harvested at each time point into TRIzol.	development time h.p.f.:8\|genotype:WT\|treatment:n1	GSM2088171	GSM2088171: m6A IP 8; Danio rerio; RIP Seq	GSM2088171		1	total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	GEO Accession:GSM2088171	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP071818		m6A_8h.IP.fastq.gz	fastq	527347000.0	10546940.0	GSM2088171 r1	0:50	A:90387238;C:157767772;G:129133581;T:150048442;N:9967	50		90387238	157767772	129133581	150048442	9967	SRX1634606	SRS1345853	SRA385720	GEO	Chuan He Lab, Chemistry, University of Chicago	1	0.90207		0.11796		0.80208		0.51587		50		B		usable mapping rate	illumina	hiseq_era	unknown	other	trueseq	bulk	unknown	unknown	United States	2016-03-14	Undetermined	Embryo	Whole Organism	All anatomical structures
40587	40587	SRR3228705	SRX1634605	SRS1345854	SRP071818	PRJNA315314	The functions of m6A and Ythdf2 during zebrafish early development	GSE79213	Other	We report the m6A methylation maps of zebrafish embryos during early development and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish MZT highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0 2 4 6 8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0 2 4 6 8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6 8 12 24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx 36 48 h.p.f. Replicate of each seq is also included.		pubmed:28192787	m6A IP 6	GSM2088170	tissue:whole zebrafish embryo\|genotype:WT\|treatment:n1	m6A IP 6	Data analysis for each experiment: 1 for m6A seq reads were aligned to the reference genome danRer10 using Tophat v2.0.14 ref with parameter g 1 library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a median reads count of the IP sample in all 100 bp windows on the current mRNA b reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a×d/b×c. 2 for m6A CLIP seq post removing the adapter sequence the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation wer…	whole zebrafish embryo		total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	embryos were collected and cultured in medium at 28.5 °C and then harvested at each time point into TRIzol.	development time h.p.f.:6\|genotype:WT\|treatment:n1	GSM2088170	GSM2088170: m6A IP 6; Danio rerio; RIP Seq	GSM2088170		1	total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	GEO Accession:GSM2088170	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP071818		m6A_6h.IP.fastq.gz	fastq	606551300.0	12131026.0	GSM2088170 r1	0:50	A:100429722;C:200919401;G:156361859;T:148828837;N:11481	50		100429722	200919401	156361859	148828837	11481	SRX1634605	SRS1345854	SRA385720	GEO	Chuan He Lab, Chemistry, University of Chicago	1	0.94517		0.23269		0.84571		0.73203		50		B		usable mapping rate	illumina	hiseq_era	unknown	other	trueseq	bulk	unknown	unknown	United States	2016-03-14	Undetermined	Embryo	Whole Organism	All anatomical structures
40588	40588	SRR3228704	SRX1634604	SRS1345855	SRP071818	PRJNA315314	The functions of m6A and Ythdf2 during zebrafish early development	GSE79213	Other	We report the m6A methylation maps of zebrafish embryos during early development and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish MZT highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0 2 4 6 8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0 2 4 6 8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6 8 12 24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx 36 48 h.p.f. Replicate of each seq is also included.		pubmed:28192787	m6A IP 4	GSM2088169	tissue:whole zebrafish embryo\|genotype:WT\|treatment:n1	m6A IP 4	Data analysis for each experiment: 1 for m6A seq reads were aligned to the reference genome danRer10 using Tophat v2.0.14 ref with parameter g 1 library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a median reads count of the IP sample in all 100 bp windows on the current mRNA b reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a×d/b×c. 2 for m6A CLIP seq post removing the adapter sequence the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation wer…	whole zebrafish embryo		total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	embryos were collected and cultured in medium at 28.5 °C and then harvested at each time point into TRIzol.	development time h.p.f.:4\|genotype:WT\|treatment:n1	GSM2088169	GSM2088169: m6A IP 4; Danio rerio; RIP Seq	GSM2088169		1	total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	GEO Accession:GSM2088169	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP071818		m6A_4h.IP.fastq.gz	fastq	616373350.0	12327467.0	GSM2088169 r1	0:50	A:103511937;C:199101152;G:159952372;T:153796186;N:11703	50		103511937	199101152	159952372	153796186	11703	SRX1634604	SRS1345855	SRA385720	GEO	Chuan He Lab, Chemistry, University of Chicago	1	0.9484		0.20806		0.81349		0.68893		50		B		usable mapping rate	illumina	hiseq_era	unknown	other	trueseq	bulk	unknown	unknown	United States	2016-03-14	Undetermined	Embryo	Whole Organism	All anatomical structures
40589	40589	SRR3228703	SRX1634603	SRS1345856	SRP071818	PRJNA315314	The functions of m6A and Ythdf2 during zebrafish early development	GSE79213	Other	We report the m6A methylation maps of zebrafish embryos during early development and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish MZT highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0 2 4 6 8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0 2 4 6 8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6 8 12 24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx 36 48 h.p.f. Replicate of each seq is also included.		pubmed:28192787	m6A IP 2	GSM2088168	tissue:whole zebrafish embryo\|genotype:WT\|treatment:n1	m6A IP 2	Data analysis for each experiment: 1 for m6A seq reads were aligned to the reference genome danRer10 using Tophat v2.0.14 ref with parameter g 1 library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a median reads count of the IP sample in all 100 bp windows on the current mRNA b reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a×d/b×c. 2 for m6A CLIP seq post removing the adapter sequence the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation wer…	whole zebrafish embryo		total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	embryos were collected and cultured in medium at 28.5 °C and then harvested at each time point into TRIzol.	development time h.p.f.:2\|genotype:WT\|treatment:n1	GSM2088168	GSM2088168: m6A IP 2; Danio rerio; RIP Seq	GSM2088168		1	total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	GEO Accession:GSM2088168	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP071818		m6A_2h.IP.fastq.gz	fastq	560037350.0	11200747.0	GSM2088168 r1	0:50	A:90079119;C:192220024;G:154098019;T:123629702;N:10486	50		90079119	192220024	154098019	123629702	10486	SRX1634603	SRS1345856	SRA385720	GEO	Chuan He Lab, Chemistry, University of Chicago	1	0.95056		0.25053		0.87322		0.82008		50		B		usable mapping rate	illumina	hiseq_era	unknown	other	trueseq	bulk	unknown	unknown	United States	2016-03-14	Undetermined	Embryo	Whole Organism	All anatomical structures
40590	40590	SRR3228702	SRX1634602	SRS1345857	SRP071818	PRJNA315314	The functions of m6A and Ythdf2 during zebrafish early development	GSE79213	Other	We report the m6A methylation maps of zebrafish embryos during early development and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish MZT highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0 2 4 6 8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0 2 4 6 8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6 8 12 24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx 36 48 h.p.f. Replicate of each seq is also included.		pubmed:28192787	m6A IP 0	GSM2088167	tissue:whole zebrafish embryo\|genotype:WT\|treatment:n1	m6A IP 0	Data analysis for each experiment: 1 for m6A seq reads were aligned to the reference genome danRer10 using Tophat v2.0.14 ref with parameter g 1 library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a median reads count of the IP sample in all 100 bp windows on the current mRNA b reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a×d/b×c. 2 for m6A CLIP seq post removing the adapter sequence the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation wer…	whole zebrafish embryo		total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	embryos were collected and cultured in medium at 28.5 °C and then harvested at each time point into TRIzol.	development time h.p.f.:0\|genotype:WT\|treatment:n1	GSM2088167	GSM2088167: m6A IP 0; Danio rerio; RIP Seq	GSM2088167		1	total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	GEO Accession:GSM2088167	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP071818		m6A_0h.IP.fastq.gz	fastq	458827450.0	9176549.0	GSM2088167 r1	0:50	A:74889651;C:150121353;G:121032505;T:112775237;N:8704	50		74889651	150121353	121032505	112775237	8704	SRX1634602	SRS1345857	SRA385720	GEO	Chuan He Lab, Chemistry, University of Chicago	1	0.96567		0.22221		0.84471		0.70341		50		B		usable mapping rate	illumina	hiseq_era	unknown	other	trueseq	bulk	unknown	unknown	United States	2016-03-14	Undetermined	Embryo	Whole Organism	All anatomical structures
40591	40591	SRR3228701	SRX1634601	SRS1345858	SRP071818	PRJNA315314	The functions of m6A and Ythdf2 during zebrafish early development	GSE79213	Other	We report the m6A methylation maps of zebrafish embryos during early development and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish MZT highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0 2 4 6 8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0 2 4 6 8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6 8 12 24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx 36 48 h.p.f. Replicate of each seq is also included.		pubmed:28192787	input 8	GSM2088166	tissue:whole zebrafish embryo\|genotype:WT\|treatment:n1	input 8	Data analysis for each experiment: 1 for m6A seq reads were aligned to the reference genome danRer10 using Tophat v2.0.14 ref with parameter g 1 library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a median reads count of the IP sample in all 100 bp windows on the current mRNA b reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a×d/b×c. 2 for m6A CLIP seq post removing the adapter sequence the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation wer…	whole zebrafish embryo		total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	embryos were collected and cultured in medium at 28.5 °C and then harvested at each time point into TRIzol.	development time h.p.f.:8\|genotype:WT\|treatment:n1	GSM2088166	GSM2088166: input 8; Danio rerio; RIP Seq	GSM2088166		1	total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	GEO Accession:GSM2088166	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP071818		m6A_8h.input.fastq.gz	fastq	575536100.0	11510722.0	GSM2088166 r1	0:50	A:111158012;C:168916114;G:151564939;T:143886262;N:10773	50		111158012	168916114	151564939	143886262	10773	SRX1634601	SRS1345858	SRA385720	GEO	Chuan He Lab, Chemistry, University of Chicago	1	0.95515		0.19883		0.79245		0.6247		50		B		usable mapping rate	illumina	hiseq_era	unknown	other	trueseq	bulk	unknown	unknown	United States	2016-03-14	Undetermined	Embryo	Whole Organism	All anatomical structures
40592	40592	SRR3228700	SRX1634600	SRS1345859	SRP071818	PRJNA315314	The functions of m6A and Ythdf2 during zebrafish early development	GSE79213	Other	We report the m6A methylation maps of zebrafish embryos during early development and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish MZT highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0 2 4 6 8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0 2 4 6 8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6 8 12 24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx 36 48 h.p.f. Replicate of each seq is also included.		pubmed:28192787	input 6	GSM2088165	tissue:whole zebrafish embryo\|genotype:WT\|treatment:n1	input 6	Data analysis for each experiment: 1 for m6A seq reads were aligned to the reference genome danRer10 using Tophat v2.0.14 ref with parameter g 1 library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a median reads count of the IP sample in all 100 bp windows on the current mRNA b reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a×d/b×c. 2 for m6A CLIP seq post removing the adapter sequence the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation wer…	whole zebrafish embryo		total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	embryos were collected and cultured in medium at 28.5 °C and then harvested at each time point into TRIzol.	development time h.p.f.:6\|genotype:WT\|treatment:n1	GSM2088165	GSM2088165: input 6; Danio rerio; RIP Seq	GSM2088165		1	total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	GEO Accession:GSM2088165	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP071818		m6A_6h.input.fastq.gz	fastq	613333150.0	12266663.0	GSM2088165 r1	0:50	A:113451661;C:194144306;G:164598114;T:141127589;N:11480	50		113451661	194144306	164598114	141127589	11480	SRX1634600	SRS1345859	SRA385720	GEO	Chuan He Lab, Chemistry, University of Chicago	1	0.97989		0.33526		0.84798		0.72512		50		B		usable mapping rate	illumina	hiseq_era	unknown	other	trueseq	bulk	unknown	unknown	United States	2016-03-14	Undetermined	Embryo	Whole Organism	All anatomical structures
40593	40593	SRR3228699	SRX1634599	SRS1345860	SRP071818	PRJNA315314	The functions of m6A and Ythdf2 during zebrafish early development	GSE79213	Other	We report the m6A methylation maps of zebrafish embryos during early development and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish MZT highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0 2 4 6 8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0 2 4 6 8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6 8 12 24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx 36 48 h.p.f. Replicate of each seq is also included.		pubmed:28192787	input 4	GSM2088164	tissue:whole zebrafish embryo\|genotype:WT\|treatment:n1	input 4	Data analysis for each experiment: 1 for m6A seq reads were aligned to the reference genome danRer10 using Tophat v2.0.14 ref with parameter g 1 library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a median reads count of the IP sample in all 100 bp windows on the current mRNA b reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a×d/b×c. 2 for m6A CLIP seq post removing the adapter sequence the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation wer…	whole zebrafish embryo		total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	embryos were collected and cultured in medium at 28.5 °C and then harvested at each time point into TRIzol.	development time h.p.f.:4\|genotype:WT\|treatment:n1	GSM2088164	GSM2088164: input 4; Danio rerio; RIP Seq	GSM2088164		1	total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	GEO Accession:GSM2088164	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP071818		m6A_4h.input.fastq.gz	fastq	576058200.0	11521164.0	GSM2088164 r1	0:50	A:108062480;C:178888385;G:153976688;T:135119699;N:10948	50		108062480	178888385	153976688	135119699	10948	SRX1634599	SRS1345860	SRA385720	GEO	Chuan He Lab, Chemistry, University of Chicago	1	0.97495		0.29544		0.81162		0.71268		50		B		usable mapping rate	illumina	hiseq_era	unknown	other	trueseq	bulk	unknown	unknown	United States	2016-03-14	Undetermined	Embryo	Whole Organism	All anatomical structures
40594	40594	SRR3228698	SRX1634598	SRS1345861	SRP071818	PRJNA315314	The functions of m6A and Ythdf2 during zebrafish early development	GSE79213	Other	We report the m6A methylation maps of zebrafish embryos during early development and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish MZT highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0 2 4 6 8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0 2 4 6 8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6 8 12 24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx 36 48 h.p.f. Replicate of each seq is also included.		pubmed:28192787	input 2	GSM2088163	tissue:whole zebrafish embryo\|genotype:WT\|treatment:n1	input 2	Data analysis for each experiment: 1 for m6A seq reads were aligned to the reference genome danRer10 using Tophat v2.0.14 ref with parameter g 1 library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a median reads count of the IP sample in all 100 bp windows on the current mRNA b reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a×d/b×c. 2 for m6A CLIP seq post removing the adapter sequence the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation wer…	whole zebrafish embryo		total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	embryos were collected and cultured in medium at 28.5 °C and then harvested at each time point into TRIzol.	development time h.p.f.:2\|genotype:WT\|treatment:n1	GSM2088163	GSM2088163: input 2; Danio rerio; RIP Seq	GSM2088163		1	total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	GEO Accession:GSM2088163	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP071818		m6A_2h.input.fastq.gz	fastq	703375200.0	14067504.0	GSM2088163 r1	0:50	A:125686246;C:228251341;G:193846290;T:155577830;N:13493	50		125686246	228251341	193846290	155577830	13493	SRX1634598	SRS1345861	SRA385720	GEO	Chuan He Lab, Chemistry, University of Chicago	1	0.98596		0.35619		0.88521		0.80927		50		B		usable mapping rate	illumina	hiseq_era	unknown	other	trueseq	bulk	unknown	unknown	United States	2016-03-14	Undetermined	Embryo	Whole Organism	All anatomical structures
40595	40595	SRR3228697	SRX1634597	SRS1345862	SRP071818	PRJNA315314	The functions of m6A and Ythdf2 during zebrafish early development	GSE79213	Other	We report the m6A methylation maps of zebrafish embryos during early development and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish MZT highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0 2 4 6 8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0 2 4 6 8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6 8 12 24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx 36 48 h.p.f. Replicate of each seq is also included.		pubmed:28192787	input 0	GSM2088162	tissue:whole zebrafish embryo\|genotype:WT\|treatment:n1	input 0	Data analysis for each experiment: 1 for m6A seq reads were aligned to the reference genome danRer10 using Tophat v2.0.14 ref with parameter g 1 library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a median reads count of the IP sample in all 100 bp windows on the current mRNA b reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a×d/b×c. 2 for m6A CLIP seq post removing the adapter sequence the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation wer…	whole zebrafish embryo		total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	embryos were collected and cultured in medium at 28.5 °C and then harvested at each time point into TRIzol.	development time h.p.f.:0\|genotype:WT\|treatment:n1	GSM2088162	GSM2088162: input 0; Danio rerio; RIP Seq	GSM2088162		1	total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.	GEO Accession:GSM2088162	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP071818		m6A_0h.input.fastq.gz	fastq	650787500.0	13015750.0	GSM2088162 r1	0:50	A:117902403;C:207274717;G:177773347;T:147824646;N:12387	50		117902403	207274717	177773347	147824646	12387	SRX1634597	SRS1345862	SRA385720	GEO	Chuan He Lab, Chemistry, University of Chicago	1	0.98268		0.32108		0.85669		0.76239		50		B		usable mapping rate	illumina	hiseq_era	unknown	other	trueseq	bulk	unknown	unknown	United States	2016-03-14	Undetermined	Embryo	Whole Organism	All anatomical structures
43454	43454	SRR7169686	SRX4087616	SRS3304345	SRP115900	PRJNA399133	RNA seq profiling of the Tgmyo6b:GFP 2A rpl10a 3xHA zebrafish hair cell IP vs. whole fish IN	GSE102861	Transcriptome Analysis	We have developed and tested the efficiency of the Tgmyo6b:GFP 2A rpl10a 3xHA zebrafish to specifically enrich for and evaluate the translatome of inner ear and lateral line sensory hair cells IP compared to the whole fish transcriptome IN. We show through RNA seq that HA tagged ribosome immunoprecipitation significantly enriches for RNA transcripts of known zebrafish hair cell expressed transcripts. Overall design: Tgmyo6b:GFP 2A rpl10a 3xHA were homogenized at 5dpf and the hair cell translatome was enriched for by HA tagged ribosome immunoprecipitation followed by RNA extraction. IP samples were compared to input RNA controls IN in independent biological triplicates.		pubmed:29765956	IN wholefishtranscriptome RNAseq rep4	GSM3143177	source name:Tgmyo6b:GFP 2A rpl10a 3xHA\|developmental stage:5dpf\|tissue:whole fish\|antibody:n1	IN wholefishtranscriptome RNAseq rep4	Base calls were performed using the built in Illumina basecaller Sequenced reads were trimmed for adaptor sequence and then mapped to Mouse GRCm38 reference using the TopHat splice aware aligner Reads Per Kilobase of gene per Million mapped reads RPKM were calculated for each sample. Differential expression of genes were computed between infected and uninfected samples Genome build: Danio rerioGRCz10 Supplementary files format and content: tab delimited text files include RPKM values for each sample	Tgmyo6b:GFP 2A rpl10a 3xHA	Untreated	RNA was isolated from the immunoprecipitated and input samples using the Qiagen RNeasy Plus Micro kit Cat#74034.HC translatome was enriched for by ribosome immunoprecipitation using an HA antibody see manuscript for full protocol Libraries were prepared from 25ng of RNA using the TruSeq RNA Sample Prep kit Illumina per manufacturer’s instructions with an additional PCR cycle.RNA libraries were prepared for sequencing using standard Illumina protocols	embryos were grown at 28 degrees C in E3 media until 5dpf	developmental stage:5dpf\|tissue:whole fish\|antibody:n1	GSM3143177	GSM3143177: IN wholefishtranscriptome RNAseq rep4; Danio rerio; RIP Seq	GSM3143177		1	RNA was isolated from the immunoprecipitated and input samples using the Qiagen RNeasy Plus Micro kit Cat#74034.HC translatome was enriched for by ribosome immunoprecipitation using an HA antibody see manuscript for full protocol Libraries were prepared from 25ng of RNA using the TruSeq RNA Sample Prep kit Illumina per manufacturer's instructions with an additional PCR cycle.RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM3143177	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP115900		RiboZF_IN3_R1.fastq.gz RiboZF_IN3_R2.fastq.gz	fastq fastq	9065897639.0	60495321.0	GSM3143177 r1	0:74.96 1:74.90	A:2375136682;C:2190164060;G:2113095817;T:2385734886;N:1766194	74	74	2375136682	2190164060	2113095817	2385734886	1766194	SRX4087616	SRS3304345	SRA601675	GEO	Department: Institute for Genome Sciences, University of Maryland in Baltimore	2	0.92807	0.92373	0.0842	0.08335	0.71754	0.72305	0.45254	0.46074	75	75	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	trueseq	bulk	unknown	unknown	United States	2018-05-16	Larval	Larval	Whole Organism	All anatomical structures
43455	43455	SRR5952030	SRX3110524	SRS2445617	SRP115900	PRJNA399133	RNA seq profiling of the Tgmyo6b:GFP 2A rpl10a 3xHA zebrafish hair cell IP vs. whole fish IN	GSE102861	Transcriptome Analysis	We have developed and tested the efficiency of the Tgmyo6b:GFP 2A rpl10a 3xHA zebrafish to specifically enrich for and evaluate the translatome of inner ear and lateral line sensory hair cells IP compared to the whole fish transcriptome IN. We show through RNA seq that HA tagged ribosome immunoprecipitation significantly enriches for RNA transcripts of known zebrafish hair cell expressed transcripts. Overall design: Tgmyo6b:GFP 2A rpl10a 3xHA were homogenized at 5dpf and the hair cell translatome was enriched for by HA tagged ribosome immunoprecipitation followed by RNA extraction. IP samples were compared to input RNA controls IN in independent biological triplicates.		pubmed:29765956	IN wholefishtranscriptome RNAseq rep3	GSM2747297	source name:Tgmyo6b:GFP 2A rpl10a 3xHA\|developmental stage:5dpf\|tissue:whole fish\|antibody:n1	IN wholefishtranscriptome RNAseq rep3	Base calls were performed using the built in Illumina basecaller Sequenced reads were trimmed for adaptor sequence and then mapped to Mouse GRCm38 reference using the TopHat splice aware aligner Reads Per Kilobase of gene per Million mapped reads RPKM were calculated for each sample. Differential expression of genes were computed between infected and uninfected samples Genome build: Danio rerioGRCz10 Supplementary files format and content: tab delimited text files include RPKM values for each sample	Tgmyo6b:GFP 2A rpl10a 3xHA	Untreated	RNA was isolated from the infected mouse tissues using the Qiagen Rneasy mini kit Cat#74104.HC translatome was enriched for by ribosome immunoprecipitation using an HA antibody see manuscript for full protocol Libraries were prepared from 25ng of RNA using the TruSeq RNA Sample Prep kit Illumina per manufacturer’s instructions with an additional PCR cycle.RNA libraries were prepared for sequencing using standard Illumina protocols	embryos were grown at 28 degrees C in E3 media until 5dpf	developmental stage:5dpf\|tissue:whole fish\|antibody:n1	GSM2747297	GSM2747297: IN wholefishtranscriptome RNAseq rep3; Danio rerio; RIP Seq	GSM2747297		1	RNA was isolated from the infected mouse tissues using the Qiagen Rneasy mini kit Cat#74104.HC translatome was enriched for by ribosome immunoprecipitation using an HA antibody see manuscript for full protocol Libraries were prepared from 25ng of RNA using the TruSeq RNA Sample Prep kit Illumina per manufacturer’s instructions with an additional PCR cycle.RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2747297	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP115900		RiboZF_IN4_R1.fastq.gz RiboZF_IN4_R2.fastq.gz	fastq fastq	8796307376.0	58697576.0	GSM2747297 r1	0:74.96 1:74.90	A:2326140676;C:2104630190;G:2033251376;T:2330582425;N:1702709	74	74	2326140676	2104630190	2033251376	2330582425	1702709	SRX3110524	SRS2445617	SRA601675	GEO	Department: Institute for Genome Sciences, University of Maryland in Baltimore	2	0.94186	0.93847	0.08006	0.08004	0.70169	0.70778	0.46714	0.45678	75	75	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	trueseq	bulk	unknown	unknown	United States	2017-08-21	Larval	Larval	Whole Organism	All anatomical structures
43456	43456	SRR5952029	SRX3110523	SRS2445616	SRP115900	PRJNA399133	RNA seq profiling of the Tgmyo6b:GFP 2A rpl10a 3xHA zebrafish hair cell IP vs. whole fish IN	GSE102861	Transcriptome Analysis	We have developed and tested the efficiency of the Tgmyo6b:GFP 2A rpl10a 3xHA zebrafish to specifically enrich for and evaluate the translatome of inner ear and lateral line sensory hair cells IP compared to the whole fish transcriptome IN. We show through RNA seq that HA tagged ribosome immunoprecipitation significantly enriches for RNA transcripts of known zebrafish hair cell expressed transcripts. Overall design: Tgmyo6b:GFP 2A rpl10a 3xHA were homogenized at 5dpf and the hair cell translatome was enriched for by HA tagged ribosome immunoprecipitation followed by RNA extraction. IP samples were compared to input RNA controls IN in independent biological triplicates.		pubmed:29765956	IN wholefishtranscriptome RNAseq rep2	GSM2747296	source name:Tgmyo6b:GFP 2A rpl10a 3xHA\|developmental stage:5dpf\|tissue:whole fish\|antibody:n1	IN wholefishtranscriptome RNAseq rep2	Base calls were performed using the built in Illumina basecaller Sequenced reads were trimmed for adaptor sequence and then mapped to Mouse GRCm38 reference using the TopHat splice aware aligner Reads Per Kilobase of gene per Million mapped reads RPKM were calculated for each sample. Differential expression of genes were computed between infected and uninfected samples Genome build: Danio rerioGRCz10 Supplementary files format and content: tab delimited text files include RPKM values for each sample	Tgmyo6b:GFP 2A rpl10a 3xHA	Untreated	RNA was isolated from the infected mouse tissues using the Qiagen Rneasy mini kit Cat#74104.HC translatome was enriched for by ribosome immunoprecipitation using an HA antibody see manuscript for full protocol Libraries were prepared from 25ng of RNA using the TruSeq RNA Sample Prep kit Illumina per manufacturer’s instructions with an additional PCR cycle.RNA libraries were prepared for sequencing using standard Illumina protocols	embryos were grown at 28 degrees C in E3 media until 5dpf	developmental stage:5dpf\|tissue:whole fish\|antibody:n1	GSM2747296	GSM2747296: IN wholefishtranscriptome RNAseq rep2; Danio rerio; RIP Seq	GSM2747296		1	RNA was isolated from the infected mouse tissues using the Qiagen Rneasy mini kit Cat#74104.HC translatome was enriched for by ribosome immunoprecipitation using an HA antibody see manuscript for full protocol Libraries were prepared from 25ng of RNA using the TruSeq RNA Sample Prep kit Illumina per manufacturer’s instructions with an additional PCR cycle.RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2747296	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP115900		RiboZF_IN2_R1.fastq.gz RiboZF_IN2_R2.fastq.gz	fastq fastq	7407816750.0	49385445.0	GSM2747296 r1	0:75 1:75	A:1965588922;C:1772589081;G:1716538525;T:1951670484;N:1429738	75	75	1965588922	1772589081	1716538525	1951670484	1429738	SRX3110523	SRS2445616	SRA601675	GEO	Department: Institute for Genome Sciences, University of Maryland in Baltimore	2	0.93743	0.9347	0.07981	0.07938	0.69721	0.70246	0.46381	0.46767	75	75	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	trueseq	bulk	unknown	unknown	United States	2017-08-21	Larval	Larval	Whole Organism	All anatomical structures
43457	43457	SRR5952028	SRX3110522	SRS2445615	SRP115900	PRJNA399133	RNA seq profiling of the Tgmyo6b:GFP 2A rpl10a 3xHA zebrafish hair cell IP vs. whole fish IN	GSE102861	Transcriptome Analysis	We have developed and tested the efficiency of the Tgmyo6b:GFP 2A rpl10a 3xHA zebrafish to specifically enrich for and evaluate the translatome of inner ear and lateral line sensory hair cells IP compared to the whole fish transcriptome IN. We show through RNA seq that HA tagged ribosome immunoprecipitation significantly enriches for RNA transcripts of known zebrafish hair cell expressed transcripts. Overall design: Tgmyo6b:GFP 2A rpl10a 3xHA were homogenized at 5dpf and the hair cell translatome was enriched for by HA tagged ribosome immunoprecipitation followed by RNA extraction. IP samples were compared to input RNA controls IN in independent biological triplicates.		pubmed:29765956	IN wholefishtranscriptome RNAseq rep1	GSM2747295	source name:Tgmyo6b:GFP 2A rpl10a 3xHA\|developmental stage:5dpf\|tissue:whole fish\|antibody:n1	IN wholefishtranscriptome RNAseq rep1	Base calls were performed using the built in Illumina basecaller Sequenced reads were trimmed for adaptor sequence and then mapped to Mouse GRCm38 reference using the TopHat splice aware aligner Reads Per Kilobase of gene per Million mapped reads RPKM were calculated for each sample. Differential expression of genes were computed between infected and uninfected samples Genome build: Danio rerioGRCz10 Supplementary files format and content: tab delimited text files include RPKM values for each sample	Tgmyo6b:GFP 2A rpl10a 3xHA	Untreated	RNA was isolated from the infected mouse tissues using the Qiagen Rneasy mini kit Cat#74104.HC translatome was enriched for by ribosome immunoprecipitation using an HA antibody see manuscript for full protocol Libraries were prepared from 25ng of RNA using the TruSeq RNA Sample Prep kit Illumina per manufacturer’s instructions with an additional PCR cycle.RNA libraries were prepared for sequencing using standard Illumina protocols	embryos were grown at 28 degrees C in E3 media until 5dpf	developmental stage:5dpf\|tissue:whole fish\|antibody:n1	GSM2747295	GSM2747295: IN wholefishtranscriptome RNAseq rep1; Danio rerio; RIP Seq	GSM2747295		1	RNA was isolated from the infected mouse tissues using the Qiagen Rneasy mini kit Cat#74104.HC translatome was enriched for by ribosome immunoprecipitation using an HA antibody see manuscript for full protocol Libraries were prepared from 25ng of RNA using the TruSeq RNA Sample Prep kit Illumina per manufacturer’s instructions with an additional PCR cycle.RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2747295	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP115900		RiboZF_IN1_R1.fastq.gz RiboZF_IN1_R2.fastq.gz	fastq fastq	4971869342.0	33177517.0	GSM2747295 r1	0:74.96 1:74.90	A:1277896624;C:1224383725;G:1184225816;T:1284401610;N:961567	74	74	1277896624	1224383725	1184225816	1284401610	961567	SRX3110522	SRS2445615	SRA601675	GEO	Department: Institute for Genome Sciences, University of Maryland in Baltimore	2	0.94557	0.94195	0.09264	0.0931	0.69785	0.70337	0.48067	0.48526	75	74	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	trueseq	bulk	unknown	unknown	United States	2017-08-21	Larval	Larval	Whole Organism	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
49541	49541	SRR8937003	SRX5717516	SRS4655936	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 0hpf rep2	GSM3732423	source name:RIP INPUT 0hpf\|strain:AB strain\|age:0 hpf\|tissue:whole embryo	RIP INPUT 0hpf 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 0hpf		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:0 hpf\|tissue:whole embryo	GSM3732423	GSM3732423: RIP INPUT 0hpf rep2; Danio rerio; RIP Seq	GSM3732423		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:GSM3732423	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP162876		RIP-INPUT_0hpf_rep2_R1.fastq.gz RIP-INPUT_0hpf_rep2_R2.fastq.gz	fastq fastq	17402218800.0	58007396.0	GSM3732423 r1	0:150 1:150	A:3416144403;C:5315174821;G:5345201218;T:3320906221;N:4792137	150	150	3416144403	5315174821	5345201218	3320906221	4792137	SRX5717516	SRS4655936	SRA786939	GEO	Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)	2	0.9819	0.9814	0.33605	0.34016	0.93458	0.93963	0.90172	0.91272	150	150	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	smarter	bulk	clip	iclip	China	2019-04-22	Zygote	Embryo	Whole Organism	All anatomical structures
49542	49542	SRR8937002	SRX5717515	SRS4655935	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 0hpf rep1	GSM3732422	source name:RIP INPUT 0hpf\|strain:AB strain\|age:0 hpf\|tissue:whole embryo	RIP INPUT 0hpf 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 0hpf		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:0 hpf\|tissue:whole embryo	GSM3732422	GSM3732422: RIP INPUT 0hpf rep1; Danio rerio; RIP Seq	GSM3732422		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:GSM3732422	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP162876		RIP-INPUT_0hpf_rep1_R1.fastq.gz RIP-INPUT_0hpf_rep1_R2.fastq.gz	fastq fastq	16615204800.0	55384016.0	GSM3732422 r1	0:150 1:150	A:2869477028;C:5392959051;G:5575878422;T:2776252538;N:637761	150	150	2869477028	5392959051	5575878422	2776252538	637761	SRX5717515	SRS4655935	SRA786939	GEO	Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)	2	0.97584	0.96561	0.04007	0.03832	0.9262	0.933	0.94642	0.94376	150	150	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	smarter	bulk	clip	iclip	China	2019-04-22	Zygote	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
49545	49545	SRR8936999	SRX5717512	SRS4655932	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 0hpf rep2	GSM3732419	source name:RIP 0hpf\|strain:AB strain\|age:0 hpf\|tissue:whole embryo\|rip antibody:rabbit polyclonal anti Ybx1 antibody	RIP 0hpf 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 0hpf		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:0 hpf\|tissue:whole embryo\|rip antibody:rabbit polyclonal anti Ybx1 antibody	GSM3732419	GSM3732419: RIP 0hpf rep2; Danio rerio; RIP Seq	GSM3732419		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:GSM3732419	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP162876		RIP_0hpf_rep2_R1.fastq.gz RIP_0hpf_rep2_R2.fastq.gz	fastq fastq	14319153300.0	47730511.0	GSM3732419 r1	0:150 1:150	A:3633266473;C:3581763715;G:3602109377;T:3500497801;N:1515934	150	150	3633266473	3581763715	3602109377	3500497801	1515934	SRX5717512	SRS4655932	SRA786939	GEO	Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)	2	0.96309	0.96299	0.09978	0.09922	0.80012	0.80635	0.7641	0.76535	150	150	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	smarter	bulk	clip	iclip	China	2019-04-22	Zygote	Embryo	Whole Organism	All anatomical structures
49546	49546	SRR8936998	SRX5717511	SRS4655931	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 0hpf rep1	GSM3732418	source name:RIP 0hpf\|strain:AB strain\|age:0 hpf\|tissue:whole embryo\|rip antibody:rabbit polyclonal anti Ybx1 antibody	RIP 0hpf 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 0hpf		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:0 hpf\|tissue:whole embryo\|rip antibody:rabbit polyclonal anti Ybx1 antibody	GSM3732418	GSM3732418: RIP 0hpf rep1; Danio rerio; RIP Seq	GSM3732418		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:GSM3732418	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP162876		RIP_0hpf_rep1_R1.fastq.gz RIP_0hpf_rep1_R2.fastq.gz	fastq fastq	7807878000.0	26026260.0	GSM3732418 r1	0:150 1:150	A:1698013251;C:2200605244;G:2305251364;T:1602824248;N:1183893	150	150	1698013251	2200605244	2305251364	1602824248	1183893	SRX5717511	SRS4655931	SRA786939	GEO	Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)	2	0.89154	0.89105	0.26373	0.26886	0.82477	0.827	0.79125	0.77711	150	150	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	smarter	bulk	clip	iclip	China	2019-04-22	Zygote	Embryo	Whole Organism	All anatomical structures
49549	49549	SRR7942636	SRX4776901	SRS3857441	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 4hpf rep2	GSM3406902	source name:Zebrafish embryo\|strain:AB strain\|cell type:Zebrafish embryo\|age:4 hpf\|tissue:whole embryo	RIP 4hpf rep2	RIP seq and iCLIP seq reads were aligned to the zv9 genome assembly using TopHat v2.1.1 and BWA v0.7.10 respectively. RIP seq: MACS2 v2.1.1 were used for the peak calling and peaks were annotated by applying BEDTools’ intersectBed. iCLIP: To identify the Ybx1 targets’ locus the mode of truncation calling was performed. For each truncation position the coverages of unique tag k and truncations m were determined by CIMS.pl program CLIP Tool Kit CTK. The sites were annotated by applying BEDTools’ intersectBed. Genome build: zv9 Supplementary files format and content: Ybx1 binding sites in two biological replicates.	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/μl RNasin by rotating at 4°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 4°C for 1 h. 50 μl 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 μl Protein A Dynabeads for 4 h at 4°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/µl RNasin for eight times and once with 1ml ice cold 1× PK buffer 100 mM Tris HCl pH 7.4 50 mM NaCl 10 mM EDTA 0.2% SDS the beads was treated in 200 ul PK buffer containing 20 ul proteinase K Roche 0311582001 for 1 h at 55°C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 pH4.34.7 and ethanol precipitation. The Input RNA was extracted by using TRIzol reagent. Both the Input and IP RNA were treated by TURBO™ DNase Invitrogen AM2238. iCLIP seq: 1000 zebrafish embryos at 4 hpf were irradiated twice with 0.8 J/cm2 Stratalinker 2400 Stratagene lysed and subjected to mild fragmentation. Crosslinked RNA protein complexes were immunoprecipated using polyclonal Ybx1 antibody Abmax and protein A dynabeads. 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\|cell type:Zebrafish embryo\|age:4 hpf\|tissue:whole embryo	GSM3406902	GSM3406902: RIP 4hpf rep2; Danio rerio; RIP Seq	GSM3406902		1	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/μl RNasin by rotating at 4°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 4°C for 1 h. 50 μl 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 μl Protein A Dynabeads for 4 h at 4°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/µl RNasin for eight times and once with 1ml ice cold 1× PK buffer 100 mM Tris HCl pH 7.4 50 mM NaCl 10 mM EDTA 0.2% SDS the beads was treated in 200 ul PK buffer containing 20 ul proteinase K Roche 0311582001 for 1 h at 55°C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 pH4.34.7 and ethanol precipitation. The Input RNA was extracted by using TRIzol reagent. Both the Input and IP RNA were treated by TURBO™ DNase Invitrogen AM2238. iCLIP seq: 1000 zebrafish embryos at 4 hpf were irradiated twice with 0.8 J/cm2 Stratalinker 2400 Stratagene lysed and subjected to mild fragmentation. Crosslinked RNA protein complexes were immunoprecipated using polyclonal Ybx1 antibody Abmax and protein A dynabeads. 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:GSM3406902	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP162876		RIP_4hpf_rep2_R1.fastq.gz RIP_4hpf_rep2_R2.fastq.gz	fastq fastq	22888305600.0	76294352.0	GSM3406902 r1	0:150 1:150	A:5927520807;C:4846894836;G:4996844576;T:7111789925;N:5255456	150	150	5927520807	4846894836	4996844576	7111789925	5255456	SRX4776901	SRS3857441	SRA786939	GEO	Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)	2	0.2704	0.17205	0.06114	0.06961	0.95879	0.9698	0.94515	0.83252	150	150	B	B	mate2-mate1 similar by mapping diff	illumina	hiseq_era	full_length	random_priming	smarter	bulk	clip	iclip	China	2018-09-28	Blastula	Embryo	Whole Organism	All anatomical structures
49550	49550	SRR7942635	SRX4776900	SRS3857440	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 4hpf rep1	GSM3406901	source name:Zebrafish embryo\|strain:AB strain\|cell type:Zebrafish embryo\|age:4 hpf\|tissue:whole embryo	RIP 4hpf rep1	RIP seq and iCLIP seq reads were aligned to the zv9 genome assembly using TopHat v2.1.1 and BWA v0.7.10 respectively. RIP seq: MACS2 v2.1.1 were used for the peak calling and peaks were annotated by applying BEDTools’ intersectBed. iCLIP: To identify the Ybx1 targets’ locus the mode of truncation calling was performed. For each truncation position the coverages of unique tag k and truncations m were determined by CIMS.pl program CLIP Tool Kit CTK. The sites were annotated by applying BEDTools’ intersectBed. Genome build: zv9 Supplementary files format and content: Ybx1 binding sites in two biological replicates.	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/μl RNasin by rotating at 4°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 4°C for 1 h. 50 μl 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 μl Protein A Dynabeads for 4 h at 4°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/µl RNasin for eight times and once with 1ml ice cold 1× PK buffer 100 mM Tris HCl pH 7.4 50 mM NaCl 10 mM EDTA 0.2% SDS the beads was treated in 200 ul PK buffer containing 20 ul proteinase K Roche 0311582001 for 1 h at 55°C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 pH4.34.7 and ethanol precipitation. The Input RNA was extracted by using TRIzol reagent. Both the Input and IP RNA were treated by TURBO™ DNase Invitrogen AM2238. iCLIP seq: 1000 zebrafish embryos at 4 hpf were irradiated twice with 0.8 J/cm2 Stratalinker 2400 Stratagene lysed and subjected to mild fragmentation. Crosslinked RNA protein complexes were immunoprecipated using polyclonal Ybx1 antibody Abmax and protein A dynabeads. 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\|cell type:Zebrafish embryo\|age:4 hpf\|tissue:whole embryo	GSM3406901	GSM3406901: RIP 4hpf rep1; Danio rerio; RIP Seq	GSM3406901		1	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/μl RNasin by rotating at 4°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 4°C for 1 h. 50 μl 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 μl Protein A Dynabeads for 4 h at 4°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/µl RNasin for eight times and once with 1ml ice cold 1× PK buffer 100 mM Tris HCl pH 7.4 50 mM NaCl 10 mM EDTA 0.2% SDS the beads was treated in 200 ul PK buffer containing 20 ul proteinase K Roche 0311582001 for 1 h at 55°C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 pH4.34.7 and ethanol precipitation. The Input RNA was extracted by using TRIzol reagent. Both the Input and IP RNA were treated by TURBO™ DNase Invitrogen AM2238. iCLIP seq: 1000 zebrafish embryos at 4 hpf were irradiated twice with 0.8 J/cm2 Stratalinker 2400 Stratagene lysed and subjected to mild fragmentation. Crosslinked RNA protein complexes were immunoprecipated using polyclonal Ybx1 antibody Abmax and protein A dynabeads. 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:GSM3406901	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP162876		RIP_4hpf_rep1_R1.fastq.gz RIP_4hpf_rep1_R2.fastq.gz	fastq fastq	19929300600.0	66431002.0	GSM3406901 r1	0:150 1:150	A:5076575451;C:4235012507;G:4442151234;T:6170975339;N:4586069	150	150	5076575451	4235012507	4442151234	6170975339	4586069	SRX4776900	SRS3857440	SRA786939	GEO	Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)	2	0.27932	0.16557	0.06585	0.06178	0.95692	0.96844	0.94238	0.84334	150	150	B	B	mate2-mate1 similar by mapping diff	illumina	hiseq_era	full_length	random_priming	smarter	bulk	clip	iclip	China	2018-09-28	Blastula	Embryo	Whole Organism	All anatomical structures
53427	53427	SRR9854014	SRX6608456	SRS5172704	SRP216689	PRJNA557179	Role of the Exon Junction Complex in Danio rerio	GSE135019	Transcriptome Analysis	The exon junction complex EJC is composed of three core proteins Rbm8a Magoh and Eif4a3 and is thought to play a role in several post transcriptional processes. In this study we focus on understanding the role of EJC in zebrafish development. We identified transcriptome wide binding sites of EJC in zebrafish via RNA:protein immunoprecipitation followed by deep sequencing RIP Seq. We find that as in human cells zebrafish EJC is deposited about 24 nts upstream of exon exon junctions. We also identify transcripts regulated by Rbm8a and Magoh in zebrafish embryos using whole embryo RNA seq from rbm8a mutant magoh mutant and wild type sibling embryos. This study shows that nonsense mediated mRNA decay is dysregulated in zebrafish EJC mutants. Overall design: Analysis of exon junction complex EJC footprints in Danio rerio and analysis of gene expression in Danio rerio EJC mutants			RBM8A RIPSEQ Rep3	GSM3983830	tissue:Whole embryo\|developmental stage:24 hpf\|rip antibody:Human Y14 Sigma cat# Y1253\|genotype/variation:RBM8A	RBM8A RIPSEQ Rep3	Base calling was performed automatically in Illumina BaseSpace post sequencing Sequenced reads were trimmed for adaptor sequence and random barcodes using cutadapt v1.16 with parameters m 20 discard untrimmed then mapped to hg38 whole genome using tophat v2.0.14 with default parameters p 12 Multi mapped reads were removed based on tophat alignment score < 50 and PCR duplicates were removed only for the RIP seq data based on random barcodes RIP Seq coverage data was generated using bedtools intersect v 2.25.0 with parameters s c F 0.51 sorted Genome build: GRCz10 Supplementary files format and content: RNA Seq: FPKM as caculated by DESeq2 for each gene in the samples Supplementary files format and content: RIP seq: RPKM each transcript in the samples	Whole embryo	None NA	RIP Seq samples were extracted from the IP eluate by Phenol Chloroform Isoamyl alcohol extraction. RNA seq samples were obatined by harvesting whole embryos in TRIZOL. Libraries were prepared using a custom protocol described in detail in Gangras et al. Methods Mol Biol. 2018;1680:1 28. Briefly a DNA adapter ligated to RNA fragments was used to obtain a reverse transcription RT product which was circularized and used for PCR amplification with primers for Illumina HiSeq sequencing.	All embryos were raised at 28.5C upto the required developmental timepoint.	developmental stage:24 hpf\|rip antibody:Human Y14 Sigma cat# Y1253\|genotype/variation:RBM8A	GSM3983830	GSM3983830: RBM8A RIPSEQ Rep3; Danio rerio; RIP Seq	GSM3983830		1	RIP Seq samples were extracted from the IP eluate by Phenol Chloroform Isoamyl alcohol extraction. RNA seq samples were obatined by harvesting whole embryos in TRIZOL. Libraries were prepared using a custom protocol described in detail in Gangras et al. Methods Mol Biol. 2018;1680:1 28. Briefly a DNA adapter ligated to RNA fragments was used to obtain a reverse transcription RT product which was circularized and used for PCR amplification with primers for Illumina HiSeq sequencing.	GEO Accession:GSM3983830	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP216689	loader:fastq load.py	ripseqB3.fastq.gz	fastq	1174462616.0	32753220.0	GSM3983830 r1	0:35.86	A:277856243;C:303697175;G:340240303;T:252574884;N:94011	35		277856243	303697175	340240303	252574884	94011	SRX6608456	SRS5172704	SRA928193	GEO	Guramrit Singh, Molecular Genetics, The Ohio State University	1	0.90426		0.1746		0.77341		0.57553		35		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2019-07-29	Pharyngula	Embryo	Whole Organism	All anatomical structures
53428	53428	SRR9854013	SRX6608455	SRS5172702	SRP216689	PRJNA557179	Role of the Exon Junction Complex in Danio rerio	GSE135019	Transcriptome Analysis	The exon junction complex EJC is composed of three core proteins Rbm8a Magoh and Eif4a3 and is thought to play a role in several post transcriptional processes. In this study we focus on understanding the role of EJC in zebrafish development. We identified transcriptome wide binding sites of EJC in zebrafish via RNA:protein immunoprecipitation followed by deep sequencing RIP Seq. We find that as in human cells zebrafish EJC is deposited about 24 nts upstream of exon exon junctions. We also identify transcripts regulated by Rbm8a and Magoh in zebrafish embryos using whole embryo RNA seq from rbm8a mutant magoh mutant and wild type sibling embryos. This study shows that nonsense mediated mRNA decay is dysregulated in zebrafish EJC mutants. Overall design: Analysis of exon junction complex EJC footprints in Danio rerio and analysis of gene expression in Danio rerio EJC mutants			RBM8A RIPSEQ Rep2	GSM3983829	tissue:Whole embryo\|developmental stage:24 hpf\|rip antibody:Human Y14 Sigma cat# Y1253\|genotype/variation:RBM8A	RBM8A RIPSEQ Rep2	Base calling was performed automatically in Illumina BaseSpace post sequencing Sequenced reads were trimmed for adaptor sequence and random barcodes using cutadapt v1.16 with parameters m 20 discard untrimmed then mapped to hg38 whole genome using tophat v2.0.14 with default parameters p 12 Multi mapped reads were removed based on tophat alignment score < 50 and PCR duplicates were removed only for the RIP seq data based on random barcodes RIP Seq coverage data was generated using bedtools intersect v 2.25.0 with parameters s c F 0.51 sorted Genome build: GRCz10 Supplementary files format and content: RNA Seq: FPKM as caculated by DESeq2 for each gene in the samples Supplementary files format and content: RIP seq: RPKM each transcript in the samples	Whole embryo	None NA	RIP Seq samples were extracted from the IP eluate by Phenol Chloroform Isoamyl alcohol extraction. RNA seq samples were obatined by harvesting whole embryos in TRIZOL. Libraries were prepared using a custom protocol described in detail in Gangras et al. Methods Mol Biol. 2018;1680:1 28. Briefly a DNA adapter ligated to RNA fragments was used to obtain a reverse transcription RT product which was circularized and used for PCR amplification with primers for Illumina HiSeq sequencing.	All embryos were raised at 28.5C upto the required developmental timepoint.	developmental stage:24 hpf\|rip antibody:Human Y14 Sigma cat# Y1253\|genotype/variation:RBM8A	GSM3983829	GSM3983829: RBM8A RIPSEQ Rep2; Danio rerio; RIP Seq	GSM3983829		1	RIP Seq samples were extracted from the IP eluate by Phenol Chloroform Isoamyl alcohol extraction. RNA seq samples were obatined by harvesting whole embryos in TRIZOL. Libraries were prepared using a custom protocol described in detail in Gangras et al. Methods Mol Biol. 2018;1680:1 28. Briefly a DNA adapter ligated to RNA fragments was used to obtain a reverse transcription RT product which was circularized and used for PCR amplification with primers for Illumina HiSeq sequencing.	GEO Accession:GSM3983829	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP216689	loader:fastq load.py	ripseqB2.fastq.gz	fastq	65641776.0	2466295.0	GSM3983829 r1	0:26.62	A:18933213;C:16060113;G:13492679;T:17151951;N:3820	26		18933213	16060113	13492679	17151951	3820	SRX6608455	SRS5172702	SRA928193	GEO	Guramrit Singh, Molecular Genetics, The Ohio State University	1	0.17621		0.02351		0.88069		0.60622		15		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2019-07-29	Pharyngula	Embryo	Whole Organism	All anatomical structures
53429	53429	SRR9854012	SRX6608454	SRS5172701	SRP216689	PRJNA557179	Role of the Exon Junction Complex in Danio rerio	GSE135019	Transcriptome Analysis	The exon junction complex EJC is composed of three core proteins Rbm8a Magoh and Eif4a3 and is thought to play a role in several post transcriptional processes. In this study we focus on understanding the role of EJC in zebrafish development. We identified transcriptome wide binding sites of EJC in zebrafish via RNA:protein immunoprecipitation followed by deep sequencing RIP Seq. We find that as in human cells zebrafish EJC is deposited about 24 nts upstream of exon exon junctions. We also identify transcripts regulated by Rbm8a and Magoh in zebrafish embryos using whole embryo RNA seq from rbm8a mutant magoh mutant and wild type sibling embryos. This study shows that nonsense mediated mRNA decay is dysregulated in zebrafish EJC mutants. Overall design: Analysis of exon junction complex EJC footprints in Danio rerio and analysis of gene expression in Danio rerio EJC mutants			RBM8A RIPSEQ Rep1	GSM3983828	tissue:Whole embryo\|developmental stage:24 hpf\|rip antibody:Human Y14 Sigma cat# Y1253\|genotype/variation:RBM8A	RBM8A RIPSEQ Rep1	Base calling was performed automatically in Illumina BaseSpace post sequencing Sequenced reads were trimmed for adaptor sequence and random barcodes using cutadapt v1.16 with parameters m 20 discard untrimmed then mapped to hg38 whole genome using tophat v2.0.14 with default parameters p 12 Multi mapped reads were removed based on tophat alignment score < 50 and PCR duplicates were removed only for the RIP seq data based on random barcodes RIP Seq coverage data was generated using bedtools intersect v 2.25.0 with parameters s c F 0.51 sorted Genome build: GRCz10 Supplementary files format and content: RNA Seq: FPKM as caculated by DESeq2 for each gene in the samples Supplementary files format and content: RIP seq: RPKM each transcript in the samples	Whole embryo	None NA	RIP Seq samples were extracted from the IP eluate by Phenol Chloroform Isoamyl alcohol extraction. RNA seq samples were obatined by harvesting whole embryos in TRIZOL. Libraries were prepared using a custom protocol described in detail in Gangras et al. Methods Mol Biol. 2018;1680:1 28. Briefly a DNA adapter ligated to RNA fragments was used to obtain a reverse transcription RT product which was circularized and used for PCR amplification with primers for Illumina HiSeq sequencing.	All embryos were raised at 28.5C upto the required developmental timepoint.	developmental stage:24 hpf\|rip antibody:Human Y14 Sigma cat# Y1253\|genotype/variation:RBM8A	GSM3983828	GSM3983828: RBM8A RIPSEQ Rep1; Danio rerio; RIP Seq	GSM3983828		1	RIP Seq samples were extracted from the IP eluate by Phenol Chloroform Isoamyl alcohol extraction. RNA seq samples were obatined by harvesting whole embryos in TRIZOL. Libraries were prepared using a custom protocol described in detail in Gangras et al. Methods Mol Biol. 2018;1680:1 28. Briefly a DNA adapter ligated to RNA fragments was used to obtain a reverse transcription RT product which was circularized and used for PCR amplification with primers for Illumina HiSeq sequencing.	GEO Accession:GSM3983828	RIP-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP216689	loader:fastq load.py	ripseqB1.fastq.gz	fastq	403183413.0	11908151.0	GSM3983828 r1	0:33.86	A:80085450;C:111343041;G:140916198;T:70619085;N:219639	33		80085450	111343041	140916198	70619085	219639	SRX6608454	SRS5172701	SRA928193	GEO	Guramrit Singh, Molecular Genetics, The Ohio State University	1	0.862		0.1026		0.95359		0.79372		33		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2019-07-29	Pharyngula	Embryo	Whole Organism	All anatomical structures
71624	71624	SRR21849078	SRX17837652	SRS15359804	SRP401744	PRJNA888821	The RNA binding protein CSDE1 promotes hematopoietic stem and progenitor cell generation via translational control of Wnt signaling	PRJNA888821	Other	We identified RBP as an important post transcriptional regulator of HSPC generation and elucidated the underlying molecular mechanisms. The study also provides helpful insights into designing novel strategies for HSPC generation in vitro.			33 hpf Zebrafish Bulk RIP seq.Flag hCsde1 2	Zebrafish 33 hpf.Bulk RIP seq.Flag hCsde1 2	breed:Zebrafish\|age:33 hpf\|dev stage:HSPC generation\|sex:pooled male and female\|tissue:whole embryos\|treatment:8\|BioSampleModel:Model organism or animal									33 hpf Zebrafish Bulk RIP seq.Flag hCsde1 2	Flag hCsde1 2	Flag hCsde1 2	RIP Seq			RIP-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP401744		Flag-hCsde1-2_1.fq.gz Flag-hCsde1-2_2.fq.gz	fastq fastq	7253178600.0	24177262.0	Flag hCsde1 2 1.fq.gz	0:150 1:150	A:1490001899;C:2113749179;G:2152941566;T:1496406491;N:79465	150	150	1490001899	2113749179	2152941566	1496406491	79465	SRX17837652	SRS15359804	SRA1516844	Institute of Hematology & Blood Diseases Hospital\|State Key Laboratory of Experimental Hematology	Institute of Hematology & Blood Diseases Hospital	2	0.9907	0.98973	0.51575	0.5119	0.9459	0.94631	0.80609	0.80353	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2022-10-09	Pharyngula	Embryo	Whole Organism	All anatomical structures
71625	71625	SRR21849079	SRX17837651	SRS15359803	SRP401744	PRJNA888821	The RNA binding protein CSDE1 promotes hematopoietic stem and progenitor cell generation via translational control of Wnt signaling	PRJNA888821	Other	We identified RBP as an important post transcriptional regulator of HSPC generation and elucidated the underlying molecular mechanisms. The study also provides helpful insights into designing novel strategies for HSPC generation in vitro.			33 hpf Zebrafish Bulk RIP seq.Flag hCsde1 1	Zebrafish 33 hpf.Bulk RIP seq.Flag hCsde1 1	breed:Zebrafish\|age:33 hpf\|dev stage:HSPC generation\|sex:pooled male and female\|tissue:whole embryos\|treatment:7\|BioSampleModel:Model organism or animal									33 hpf Zebrafish Bulk RIP seq.Flag hCsde1 1	Flag hCsde1 1	Flag hCsde1 1	RIP Seq			RIP-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP401744		Flag-hCsde1-1_1.fq.gz Flag-hCsde1-1_2.fq.gz	fastq fastq	5032252500.0	16774175.0	Flag hCsde1 1 1.fq.gz	0:150 1:150	A:1150344713;C:1135461821;G:1687878347;T:1058543429;N:24190	150	150	1150344713	1135461821	1687878347	1058543429	24190	SRX17837651	SRS15359803	SRA1516844	Institute of Hematology & Blood Diseases Hospital\|State Key Laboratory of Experimental Hematology	Institute of Hematology & Blood Diseases Hospital	2	0.22813	0.23161	0.06226	0.06317	0.92801	0.92719	0.73744	0.71685	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2022-10-09	Pharyngula	Embryo	Whole Organism	All anatomical structures
71626	71626	SRR21849080	SRX17837650	SRS15359801	SRP401744	PRJNA888821	The RNA binding protein CSDE1 promotes hematopoietic stem and progenitor cell generation via translational control of Wnt signaling	PRJNA888821	Other	We identified RBP as an important post transcriptional regulator of HSPC generation and elucidated the underlying molecular mechanisms. The study also provides helpful insights into designing novel strategies for HSPC generation in vitro.			33 hpf Zebrafish Bulk RIP seq.Control2	Zebrafish 33 hpf.Bulk RIP seq.Control2	breed:Zebrafish\|age:33 hpf\|dev stage:HSPC generation\|sex:pooled male and female\|tissue:whole embryos\|treatment:6\|BioSampleModel:Model organism or animal									33 hpf Zebrafish Bulk RIP seq.Control2	Control2	Control2	RIP Seq			RIP-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP401744		Control2_1.fq.gz Control2_2.fq.gz	fastq fastq	7884108600.0	26280362.0	Control2 1.fq.gz	0:150 1:150	A:1586894082;C:2334065454;G:2372509011;T:1590552802;N:87251	150	150	1586894082	2334065454	2372509011	1590552802	87251	SRX17837650	SRS15359801	SRA1516844	Institute of Hematology & Blood Diseases Hospital\|State Key Laboratory of Experimental Hematology	Institute of Hematology & Blood Diseases Hospital	2	0.98745	0.98691	0.48401	0.48011	0.94095	0.94113	0.74796	0.74138	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2022-10-09	Pharyngula	Embryo	Whole Organism	All anatomical structures
71627	71627	SRR21849081	SRX17837649	SRS15359800	SRP401744	PRJNA888821	The RNA binding protein CSDE1 promotes hematopoietic stem and progenitor cell generation via translational control of Wnt signaling	PRJNA888821	Other	We identified RBP as an important post transcriptional regulator of HSPC generation and elucidated the underlying molecular mechanisms. The study also provides helpful insights into designing novel strategies for HSPC generation in vitro.			33 hpf Zebrafish Bulk RIP seq.Control1	Zebrafish 33 hpf.Bulk RIP seq.Control1	breed:Zebrafish\|age:33 hpf\|dev stage:HSPC generation\|sex:pooled male and female\|tissue:whole embryos\|treatment:5\|BioSampleModel:Model organism or animal									33 hpf Zebrafish Bulk RIP seq.Control1	Control1	Control1	RIP Seq			RIP-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP401744		Control1_1.fq.gz Control1_2.fq.gz	fastq fastq	6838591200.0	22795304.0	Control1 1.fq.gz	0:150 1:150	A:1483754703;C:1578056923;G:2412990846;T:1363739708;N:49020	150	150	1483754703	1578056923	2412990846	1363739708	49020	SRX17837649	SRS15359800	SRA1516844	Institute of Hematology & Blood Diseases Hospital\|State Key Laboratory of Experimental Hematology	Institute of Hematology & Blood Diseases Hospital	2	0.34381	0.34082	0.09181	0.09135	0.95144	0.95148	0.81928	0.81462	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2022-10-09	Pharyngula	Embryo	Whole Organism	All anatomical structures
72384	72384	SRR22805230	SRX18764963	SRS16199859	SRP413700	PRJNA906294	Danio rerio Raw sequence reads	PRJNA906294	Other	Investigating BPA substitute BHbisPhenolF for zebrafish cardiac and vascular toxicity			28	28.ythdf2 MO m6A meRIP replicate 2	strain:AB\|isolate:28\|dev stage:34hpf\|sex:not determined\|tissue:whole embryos\|BioSampleModel:Model organism or animal									28.ythdf2 MO m6A meRIP replicate 2	28	28	28			RIP-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP413700		ythdf2_MO_m6A_meRIP_replicate_2_R1.fastq.gz ythdf2_MO_m6A_meRIP_replicate_2_R2.fastq.gz	fastq fastq	7361721649.0	26446542.0	ythdf2 MO m6A meRIP replicate 2 R1.fastq.gz	0:139.19 1:139.17	A:1963471349;C:1716978769;G:1713549467;T:1967688429;N:33635	139	139	1963471349	1716978769	1713549467	1967688429	33635	SRX18764963	SRS16199859	SRA1560952	Zhejiang University\|Institute of Genetics	Zhejiang University	2	0.95246	0.9547	0.1386	0.13796	0.69757	0.69593	0.44772	0.44911	138	138	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-12-19	Pharyngula	Embryo	Whole Organism	All anatomical structures
72385	72385	SRR22805231	SRX18764962	SRS16199858	SRP413700	PRJNA906294	Danio rerio Raw sequence reads	PRJNA906294	Other	Investigating BPA substitute BHbisPhenolF for zebrafish cardiac and vascular toxicity			27	27.ythdf2 MO m6A meRIP replicate 1	strain:AB\|isolate:27\|dev stage:34hpf\|sex:not determined\|tissue:whole embryos\|BioSampleModel:Model organism or animal									27.ythdf2 MO m6A meRIP replicate 1	27	27	27			RIP-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP413700		ythdf2_MO_m6A_meRIP_replicate_1_R1.fastq.gz ythdf2_MO_m6A_meRIP_replicate_1_R2.fastq.gz	fastq fastq	7064658336.0	25169165.0	ythdf2 MO m6A meRIP replicate 1 R1.fastq.gz	0:140.35 1:140.33	A:1889792523;C:1642179006;G:1639348147;T:1893307582;N:31078	140	140	1889792523	1642179006	1639348147	1893307582	31078	SRX18764962	SRS16199858	SRA1560952	Zhejiang University\|Institute of Genetics	Zhejiang University	2	0.95312	0.95495	0.14782	0.14808	0.69856	0.69656	0.46053	0.45683	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-12-19	Pharyngula	Embryo	Whole Organism	All anatomical structures
72386	72386	SRR22805232	SRX18764961	SRS16199857	SRP413700	PRJNA906294	Danio rerio Raw sequence reads	PRJNA906294	Other	Investigating BPA substitute BHbisPhenolF for zebrafish cardiac and vascular toxicity			26	26.Control knockdown m6A meRIP replicate 2	strain:AB\|isolate:26\|dev stage:34hpf\|sex:not determined\|tissue:whole embryos\|BioSampleModel:Model organism or animal									26.Control knockdown m6A meRIP replicate 2	26	26	26			RIP-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP413700		Control_knockdown_m6A_meRIP_replicate_2_R1.fastq.gz Control_knockdown_m6A_meRIP_replicate_2_R2.fastq.gz	fastq fastq	6960835520.0	25210812.0	Control knockdown m6A meRIP replicate 2 R1.fastq.gz	0:138.06 1:138.04	A:1851748550;C:1628253635;G:1624430306;T:1856371475;N:31554	138	138	1851748550	1628253635	1624430306	1856371475	31554	SRX18764961	SRS16199857	SRA1560952	Zhejiang University\|Institute of Genetics	Zhejiang University	2	0.95077	0.95337	0.12974	0.13019	0.69846	0.69737	0.45561	0.45724	134	134	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-12-19	Pharyngula	Embryo	Whole Organism	All anatomical structures
72387	72387	SRR22805233	SRX18764960	SRS16199856	SRP413700	PRJNA906294	Danio rerio Raw sequence reads	PRJNA906294	Other	Investigating BPA substitute BHbisPhenolF for zebrafish cardiac and vascular toxicity			25	25.Control knockdown m6A meRIP replicate 1	strain:AB\|isolate:25\|dev stage:34hpf\|sex:not determined\|tissue:whole embryos\|BioSampleModel:Model organism or animal									25.Control knockdown m6A meRIP replicate 1	25	25	25			RIP-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP413700		Control_knockdown_m6A_meRIP_replicate_1_R1.fastq.gz Control_knockdown_m6A_meRIP_replicate_1_R2.fastq.gz	fastq fastq	7116588450.0	25626978.0	Control knockdown m6A meRIP replicate 1 R1.fastq.gz	0:138.86 1:138.84	A:1872021500;C:1685125220;G:1683152373;T:1876257768;N:31589	138	138	1872021500	1685125220	1683152373	1876257768	31589	SRX18764960	SRS16199856	SRA1560952	Zhejiang University\|Institute of Genetics	Zhejiang University	2	0.95363	0.95468	0.05483	0.05373	0.76777	0.76648	0.4523	0.45215	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-12-19	Pharyngula	Embryo	Whole Organism	All anatomical structures
72393	72393	SRR22805239	SRX18764954	SRS16199850	SRP413700	PRJNA906294	Danio rerio Raw sequence reads	PRJNA906294	Other	Investigating BPA substitute BHbisPhenolF for zebrafish cardiac and vascular toxicity			20	20.BHbisPhenolF 10uM m6A meRIP replicate 2	strain:AB\|isolate:20\|dev stage:34hpf\|sex:not determined\|tissue:whole embryos\|BioSampleModel:Model organism or animal									20.BHbisPhenolF 10uM m6A meRIP replicate 2	20	20	20			RIP-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP413700		BHPF_10uM_m6A_meRIP_replicate_2_R1.fastq.gz BHPF_10uM_m6A_meRIP_replicate_2_R2.fastq.gz	fastq fastq	7491317369.0	26658666.0	BHbisPhenolF 10uM m6A meRIP replicate 2 R1.fastq.gz	0:140.51 1:140.49	A:1978702731;C:1766538897;G:1763052208;T:1982989954;N:33579	140	140	1978702731	1766538897	1763052208	1982989954	33579	SRX18764954	SRS16199850	SRA1560952	Zhejiang University\|Institute of Genetics	Zhejiang University	2	0.9529	0.95443	0.08298	0.08205	0.68891	0.68846	0.47278	0.47013	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-12-19	Pharyngula	Embryo	Whole Organism	All anatomical structures
72394	72394	SRR22805240	SRX18764953	SRS16199849	SRP413700	PRJNA906294	Danio rerio Raw sequence reads	PRJNA906294	Other	Investigating BPA substitute BHbisPhenolF for zebrafish cardiac and vascular toxicity			19	19.BHbisPhenolF 10uM m6A meRIP replicate 1	strain:AB\|isolate:19\|dev stage:34hpf\|sex:not determined\|tissue:whole embryos\|BioSampleModel:Model organism or animal									19.BHbisPhenolF 10uM m6A meRIP replicate 1	19	19	19			RIP-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP413700		BHPF_10uM_m6A_meRIP_replicate_1_R1.fastq.gz BHPF_10uM_m6A_meRIP_replicate_1_R2.fastq.gz	fastq fastq	7103220388.0	25558854.0	BHbisPhenolF 10uM m6A meRIP replicate 1 R1.fastq.gz	0:138.97 1:138.95	A:1882505135;C:1667796740;G:1665421739;T:1887465071;N:31703	138	138	1882505135	1667796740	1665421739	1887465071	31703	SRX18764953	SRS16199849	SRA1560952	Zhejiang University\|Institute of Genetics	Zhejiang University	2	0.95261	0.95474	0.09233	0.09094	0.69794	0.6966	0.46269	0.46455	111	111	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-12-19	Pharyngula	Embryo	Whole Organism	All anatomical structures
72395	72395	SRR22805241	SRX18764952	SRS16199848	SRP413700	PRJNA906294	Danio rerio Raw sequence reads	PRJNA906294	Other	Investigating BPA substitute BHbisPhenolF for zebrafish cardiac and vascular toxicity			18	18.DMSO control m6A meRIP replicate 2	strain:AB\|isolate:18\|dev stage:34hpf\|sex:not determined\|tissue:whole embryos\|BioSampleModel:Model organism or animal									18.DMSO control m6A meRIP replicate 2	18	18	18			RIP-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP413700		DMSO_control_m6A_meRIP_replicate_2_R1.fastq.gz DMSO_control_m6A_meRIP_replicate_2_R2.fastq.gz	fastq fastq	7608584716.0	27081562.0	DMSO control m6A meRIP replicate 2 R1.fastq.gz	0:140.48 1:140.47	A:2016159583;C:1788089257;G:1783486901;T:2020815087;N:33888	140	140	2016159583	1788089257	1783486901	2020815087	33888	SRX18764952	SRS16199848	SRA1560952	Zhejiang University\|Institute of Genetics	Zhejiang University	2	0.9526	0.95462	0.08497	0.08367	0.69822	0.69755	0.46646	0.4688	114	114	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-12-19	Pharyngula	Embryo	Whole Organism	All anatomical structures
72396	72396	SRR22805242	SRX18764951	SRS16199847	SRP413700	PRJNA906294	Danio rerio Raw sequence reads	PRJNA906294	Other	Investigating BPA substitute BHbisPhenolF for zebrafish cardiac and vascular toxicity			17	17.DMSO control m6A meRIP replicate 1	strain:AB\|isolate:17\|dev stage:34hpf\|sex:not determined\|tissue:whole embryos\|BioSampleModel:Model organism or animal									17.DMSO control m6A meRIP replicate 1	17	17	17			RIP-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP413700		DMSO_control_m6A_meRIP_replicate_1_R1.fastq.gz DMSO_control_m6A_meRIP_replicate_1_R2.fastq.gz	fastq fastq	7394836277.0	26199072.0	DMSO control m6A meRIP replicate 1 R1.fastq.gz	0:141.14 1:141.12	A:1964011730;C:1732461692;G:1728237059;T:1970092128;N:33668	141	141	1964011730	1732461692	1728237059	1970092128	33668	SRX18764951	SRS16199847	SRA1560952	Zhejiang University\|Institute of Genetics	Zhejiang University	2	0.95315	0.95536	0.1083	0.1071	0.70694	0.70587	0.47144	0.47082	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-12-19	Pharyngula	Embryo	Whole Organism	All anatomical structures
72695	72695	SRR23071963	SRX19025119	SRS16444168	SRP417272	PRJNA923391	MBD5 a m5C RNA reader regulates histone ubiquitylation in development and function	GSE222803	Other	Methyl CpG binding domain MBD containing proteins are readers of epigenetic information. The founding member MeCP2 mutated in the Rett Syndrome binds to methylated CpG DNAs. MBD5 is an evolutionarily conserved MBD family member associated with epilepsy autism spectrum disorders ASD and early onset dementia. The mechanism of action of MBD5 remains unclear. Here we report that mbd5 regulates embryonic development erythrocyte differentiation iron metabolism and behavior in zebrafish. MBD5 is essential to activate the expression of erythrocyte differentiation genes e.g. hbae3 iron regulated genes e.g. fth1 and ASD related genes e.g. gabbr2 by binding to 5 methylcytosine m5C modified mRNAs interacting with and stabilizing Additional Sex Combs Like 1 ASXL1 a component of the Polycomb Repressive Deubiquinase PR DUB complex to facilitate removal of the repressive monoubiquitin mark at histone H2A H2A K119Ub thereby facilitating gene activation. Together these findings reveal MBD5 as a m5C RNA reader that links RNA methylation to histone modification in vivo. Overall design: [Dataset 1] 6 samples. Triplicates for ribo minus RNA Seq from 78 hpf zebrafish embryos treated with control or mbd5 morpholino [Dataset 2] 16 samples. Duplicates for CLIP seq experiments from 48 hpf 78 hpf zebrafish embryos treated with 0.5 mM DFO or 1 mM FAC		pubmed:38366571	fac input rep2	GSM6932553	source name:whole embryo\|tissue:whole embryo\|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]\|treatment:1 mM FAC from 48 hpf to 78 hpf\|geo loc name:missing\|collection date:missing	fac input rep2	Adapter trimming by Cutadapt Reads mapping by STAR to the transcriptome peak calling with pureCLIP or differential gene expression with DESeq2 Assembly: dr10 Supplementary files format and content: For [Dataset 1] excel xlsx files with differential expression by DESeq2. For [Dataset 2] excel xlsx files with CLIP seq peaks identified by pureCLIP algorithm	whole embryo	For [Dataset 1] morpholino oligonucleotides are applied by microinjection. For [Dataset 2] FAC F5879 Sigma Aldrich was dissolved in E3 medium at 50 mM and stored at 4°C. zebrafish were treated with 1 mM fresh FAC from 3 dpf 6 dpf every day prior to behavior analysis. DFO D9533 Sigma Aldrich was dissolved in E3 medium at 150 mM and stored at 20°C. Zebrafish were treated with 0.5 mM DFO from 3 dpf 6 dpf replenished every day prior to behavior analysis.	For [Dataset 1] total RNAs were extracted with standard TRIzol protocol. For [Dataset 2] 76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5 150 mM KCl 2 mM EDTA 0.5% v/v NP 40 0.5 mM DTT 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5 300 mM KCl 0.05% v/v NP 40 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1] RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa 634417 with ribo minus RNA as input. For [Dataset 2] RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.	Zebrafish embryos were treated with 0.003% 1 phenyl 2 thiourea PTU in E3 medium to prevent pigment formation. 3 month 9 month aged wild type or mbd5 mutant lines generated in this study were used for breeding or adult behavior analyses. Developmental stages were determined according to their morphology.	tissue:whole embryo\|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]\|treatment:1 mM FAC from 48 hpf to 78 hpf	GSM6932553	GSM6932553: fac input rep2; Danio rerio; RIP Seq	GSM6932553 r1	GSM6932553	1	For [Dataset 1] total RNAs were extracted with standard TRIzol protocol. For [Dataset 2] 76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5 150 mM KCl 2 mM EDTA 0.5% v/v NP 40 0.5 mM DTT 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5 300 mM KCl 0.05% v/v NP 40 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1] RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa 634417 with ribo minus RNA as input. For [Dataset 2] RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.		RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP417272	loader:fastq load.py	fac_input_rep2.r1.fastq.gz fac_input_rep2.r2.fastq.gz	fastq fastq	2715443520.0	22628696.0	GSM6932553 r1	0:60 1:60	A:568252635;C:811004878;G:879629678;T:456548654;N:7675	60	60	568252635	811004878	879629678	456548654	7675	SRX19025119	SRS16444168	SRA1573941	University of Chicago	University of Chicago	2	0.76709	0.75848	0.06636	0.06594	0.96465	0.96617	0.79957	0.75254	60	60	B	B	biological fallback assumption	illumina	novaseq_era	full_length	small_rna	smarter	bulk	unknown	unknown	United States	2023-01-12	Multi-stage	Multi-stage	Whole Organism	All anatomical structures
72696	72696	SRR23071964	SRX19025118	SRS16444167	SRP417272	PRJNA923391	MBD5 a m5C RNA reader regulates histone ubiquitylation in development and function	GSE222803	Other	Methyl CpG binding domain MBD containing proteins are readers of epigenetic information. The founding member MeCP2 mutated in the Rett Syndrome binds to methylated CpG DNAs. MBD5 is an evolutionarily conserved MBD family member associated with epilepsy autism spectrum disorders ASD and early onset dementia. The mechanism of action of MBD5 remains unclear. Here we report that mbd5 regulates embryonic development erythrocyte differentiation iron metabolism and behavior in zebrafish. MBD5 is essential to activate the expression of erythrocyte differentiation genes e.g. hbae3 iron regulated genes e.g. fth1 and ASD related genes e.g. gabbr2 by binding to 5 methylcytosine m5C modified mRNAs interacting with and stabilizing Additional Sex Combs Like 1 ASXL1 a component of the Polycomb Repressive Deubiquinase PR DUB complex to facilitate removal of the repressive monoubiquitin mark at histone H2A H2A K119Ub thereby facilitating gene activation. Together these findings reveal MBD5 as a m5C RNA reader that links RNA methylation to histone modification in vivo. Overall design: [Dataset 1] 6 samples. Triplicates for ribo minus RNA Seq from 78 hpf zebrafish embryos treated with control or mbd5 morpholino [Dataset 2] 16 samples. Duplicates for CLIP seq experiments from 48 hpf 78 hpf zebrafish embryos treated with 0.5 mM DFO or 1 mM FAC		pubmed:38366571	fac input rep1	GSM6932552	source name:whole embryo\|tissue:whole embryo\|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]\|treatment:1 mM FAC from 48 hpf to 78 hpf\|geo loc name:missing\|collection date:missing	fac input rep1	Adapter trimming by Cutadapt Reads mapping by STAR to the transcriptome peak calling with pureCLIP or differential gene expression with DESeq2 Assembly: dr10 Supplementary files format and content: For [Dataset 1] excel xlsx files with differential expression by DESeq2. For [Dataset 2] excel xlsx files with CLIP seq peaks identified by pureCLIP algorithm	whole embryo	For [Dataset 1] morpholino oligonucleotides are applied by microinjection. For [Dataset 2] FAC F5879 Sigma Aldrich was dissolved in E3 medium at 50 mM and stored at 4°C. zebrafish were treated with 1 mM fresh FAC from 3 dpf 6 dpf every day prior to behavior analysis. DFO D9533 Sigma Aldrich was dissolved in E3 medium at 150 mM and stored at 20°C. Zebrafish were treated with 0.5 mM DFO from 3 dpf 6 dpf replenished every day prior to behavior analysis.	For [Dataset 1] total RNAs were extracted with standard TRIzol protocol. For [Dataset 2] 76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5 150 mM KCl 2 mM EDTA 0.5% v/v NP 40 0.5 mM DTT 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5 300 mM KCl 0.05% v/v NP 40 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1] RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa 634417 with ribo minus RNA as input. For [Dataset 2] RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.	Zebrafish embryos were treated with 0.003% 1 phenyl 2 thiourea PTU in E3 medium to prevent pigment formation. 3 month 9 month aged wild type or mbd5 mutant lines generated in this study were used for breeding or adult behavior analyses. Developmental stages were determined according to their morphology.	tissue:whole embryo\|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]\|treatment:1 mM FAC from 48 hpf to 78 hpf	GSM6932552	GSM6932552: fac input rep1; Danio rerio; RIP Seq	GSM6932552 r1	GSM6932552	1	For [Dataset 1] total RNAs were extracted with standard TRIzol protocol. For [Dataset 2] 76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5 150 mM KCl 2 mM EDTA 0.5% v/v NP 40 0.5 mM DTT 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5 300 mM KCl 0.05% v/v NP 40 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1] RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa 634417 with ribo minus RNA as input. For [Dataset 2] RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.		RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP417272	loader:fastq load.py	fac_input_rep1.r1.fastq.gz fac_input_rep1.r2.fastq.gz	fastq fastq	2788666560.0	23238888.0	GSM6932552 r1	0:60 1:60	A:597611112;C:824776004;G:894293861;T:471977509;N:8074	60	60	597611112	824776004	894293861	471977509	8074	SRX19025118	SRS16444167	SRA1573941	University of Chicago	University of Chicago	2	0.75557	0.74928	0.06802	0.06744	0.96364	0.96508	0.80265	0.73963	60	60	B	B	biological fallback assumption	illumina	novaseq_era	full_length	small_rna	smarter	bulk	unknown	unknown	United States	2023-01-12	Multi-stage	Multi-stage	Whole Organism	All anatomical structures
72697	72697	SRR23071965	SRX19025117	SRS16444166	SRP417272	PRJNA923391	MBD5 a m5C RNA reader regulates histone ubiquitylation in development and function	GSE222803	Other	Methyl CpG binding domain MBD containing proteins are readers of epigenetic information. The founding member MeCP2 mutated in the Rett Syndrome binds to methylated CpG DNAs. MBD5 is an evolutionarily conserved MBD family member associated with epilepsy autism spectrum disorders ASD and early onset dementia. The mechanism of action of MBD5 remains unclear. Here we report that mbd5 regulates embryonic development erythrocyte differentiation iron metabolism and behavior in zebrafish. MBD5 is essential to activate the expression of erythrocyte differentiation genes e.g. hbae3 iron regulated genes e.g. fth1 and ASD related genes e.g. gabbr2 by binding to 5 methylcytosine m5C modified mRNAs interacting with and stabilizing Additional Sex Combs Like 1 ASXL1 a component of the Polycomb Repressive Deubiquinase PR DUB complex to facilitate removal of the repressive monoubiquitin mark at histone H2A H2A K119Ub thereby facilitating gene activation. Together these findings reveal MBD5 as a m5C RNA reader that links RNA methylation to histone modification in vivo. Overall design: [Dataset 1] 6 samples. Triplicates for ribo minus RNA Seq from 78 hpf zebrafish embryos treated with control or mbd5 morpholino [Dataset 2] 16 samples. Duplicates for CLIP seq experiments from 48 hpf 78 hpf zebrafish embryos treated with 0.5 mM DFO or 1 mM FAC		pubmed:38366571	fac clip rep2	GSM6932551	source name:whole embryo\|tissue:whole embryo\|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]\|treatment:1 mM FAC from 48 hpf to 78 hpf\|geo loc name:missing\|collection date:missing	fac clip rep2	Adapter trimming by Cutadapt Reads mapping by STAR to the transcriptome peak calling with pureCLIP or differential gene expression with DESeq2 Assembly: dr10 Supplementary files format and content: For [Dataset 1] excel xlsx files with differential expression by DESeq2. For [Dataset 2] excel xlsx files with CLIP seq peaks identified by pureCLIP algorithm	whole embryo	For [Dataset 1] morpholino oligonucleotides are applied by microinjection. For [Dataset 2] FAC F5879 Sigma Aldrich was dissolved in E3 medium at 50 mM and stored at 4°C. zebrafish were treated with 1 mM fresh FAC from 3 dpf 6 dpf every day prior to behavior analysis. DFO D9533 Sigma Aldrich was dissolved in E3 medium at 150 mM and stored at 20°C. Zebrafish were treated with 0.5 mM DFO from 3 dpf 6 dpf replenished every day prior to behavior analysis.	For [Dataset 1] total RNAs were extracted with standard TRIzol protocol. For [Dataset 2] 76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5 150 mM KCl 2 mM EDTA 0.5% v/v NP 40 0.5 mM DTT 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5 300 mM KCl 0.05% v/v NP 40 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1] RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa 634417 with ribo minus RNA as input. For [Dataset 2] RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.	Zebrafish embryos were treated with 0.003% 1 phenyl 2 thiourea PTU in E3 medium to prevent pigment formation. 3 month 9 month aged wild type or mbd5 mutant lines generated in this study were used for breeding or adult behavior analyses. Developmental stages were determined according to their morphology.	tissue:whole embryo\|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]\|treatment:1 mM FAC from 48 hpf to 78 hpf	GSM6932551	GSM6932551: fac clip rep2; Danio rerio; RIP Seq	GSM6932551 r1	GSM6932551	1	For [Dataset 1] total RNAs were extracted with standard TRIzol protocol. For [Dataset 2] 76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5 150 mM KCl 2 mM EDTA 0.5% v/v NP 40 0.5 mM DTT 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5 300 mM KCl 0.05% v/v NP 40 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1] RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa 634417 with ribo minus RNA as input. For [Dataset 2] RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.		RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP417272	loader:fastq load.py	fac_clip_rep2.r1.fastq.gz fac_clip_rep2.r2.fastq.gz	fastq fastq	3636207480.0	30301729.0	GSM6932551 r1	0:60 1:60	A:856114407;C:984704325;G:1019721588;T:775657296;N:9864	60	60	856114407	984704325	1019721588	775657296	9864	SRX19025117	SRS16444166	SRA1573941	University of Chicago	University of Chicago	2	0.95337	0.93978	0.20127	0.22016	0.90295	0.90893	0.69108	0.66666	60	60	B	B	biological fallback assumption	illumina	novaseq_era	full_length	small_rna	smarter	bulk	unknown	unknown	United States	2023-01-12	Multi-stage	Multi-stage	Whole Organism	All anatomical structures
72698	72698	SRR23071966	SRX19025116	SRS16444165	SRP417272	PRJNA923391	MBD5 a m5C RNA reader regulates histone ubiquitylation in development and function	GSE222803	Other	Methyl CpG binding domain MBD containing proteins are readers of epigenetic information. The founding member MeCP2 mutated in the Rett Syndrome binds to methylated CpG DNAs. MBD5 is an evolutionarily conserved MBD family member associated with epilepsy autism spectrum disorders ASD and early onset dementia. The mechanism of action of MBD5 remains unclear. Here we report that mbd5 regulates embryonic development erythrocyte differentiation iron metabolism and behavior in zebrafish. MBD5 is essential to activate the expression of erythrocyte differentiation genes e.g. hbae3 iron regulated genes e.g. fth1 and ASD related genes e.g. gabbr2 by binding to 5 methylcytosine m5C modified mRNAs interacting with and stabilizing Additional Sex Combs Like 1 ASXL1 a component of the Polycomb Repressive Deubiquinase PR DUB complex to facilitate removal of the repressive monoubiquitin mark at histone H2A H2A K119Ub thereby facilitating gene activation. Together these findings reveal MBD5 as a m5C RNA reader that links RNA methylation to histone modification in vivo. Overall design: [Dataset 1] 6 samples. Triplicates for ribo minus RNA Seq from 78 hpf zebrafish embryos treated with control or mbd5 morpholino [Dataset 2] 16 samples. Duplicates for CLIP seq experiments from 48 hpf 78 hpf zebrafish embryos treated with 0.5 mM DFO or 1 mM FAC		pubmed:38366571	fac clip rep1	GSM6932550	source name:whole embryo\|tissue:whole embryo\|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]\|treatment:1 mM FAC from 48 hpf to 78 hpf\|geo loc name:missing\|collection date:missing	fac clip rep1	Adapter trimming by Cutadapt Reads mapping by STAR to the transcriptome peak calling with pureCLIP or differential gene expression with DESeq2 Assembly: dr10 Supplementary files format and content: For [Dataset 1] excel xlsx files with differential expression by DESeq2. For [Dataset 2] excel xlsx files with CLIP seq peaks identified by pureCLIP algorithm	whole embryo	For [Dataset 1] morpholino oligonucleotides are applied by microinjection. For [Dataset 2] FAC F5879 Sigma Aldrich was dissolved in E3 medium at 50 mM and stored at 4°C. zebrafish were treated with 1 mM fresh FAC from 3 dpf 6 dpf every day prior to behavior analysis. DFO D9533 Sigma Aldrich was dissolved in E3 medium at 150 mM and stored at 20°C. Zebrafish were treated with 0.5 mM DFO from 3 dpf 6 dpf replenished every day prior to behavior analysis.	For [Dataset 1] total RNAs were extracted with standard TRIzol protocol. For [Dataset 2] 76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5 150 mM KCl 2 mM EDTA 0.5% v/v NP 40 0.5 mM DTT 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5 300 mM KCl 0.05% v/v NP 40 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1] RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa 634417 with ribo minus RNA as input. For [Dataset 2] RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.	Zebrafish embryos were treated with 0.003% 1 phenyl 2 thiourea PTU in E3 medium to prevent pigment formation. 3 month 9 month aged wild type or mbd5 mutant lines generated in this study were used for breeding or adult behavior analyses. Developmental stages were determined according to their morphology.	tissue:whole embryo\|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]\|treatment:1 mM FAC from 48 hpf to 78 hpf	GSM6932550	GSM6932550: fac clip rep1; Danio rerio; RIP Seq	GSM6932550 r1	GSM6932550	1	For [Dataset 1] total RNAs were extracted with standard TRIzol protocol. For [Dataset 2] 76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5 150 mM KCl 2 mM EDTA 0.5% v/v NP 40 0.5 mM DTT 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5 300 mM KCl 0.05% v/v NP 40 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1] RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa 634417 with ribo minus RNA as input. For [Dataset 2] RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.		RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP417272	loader:fastq load.py	fac_clip_rep1.r1.fastq.gz fac_clip_rep1.r2.fastq.gz	fastq fastq	4241534520.0	35346121.0	GSM6932550 r1	0:60 1:60	A:1001822053;C:1148816744;G:1187189848;T:903693863;N:12012	60	60	1001822053	1148816744	1187189848	903693863	12012	SRX19025116	SRS16444165	SRA1573941	University of Chicago	University of Chicago	2	0.9489	0.9407	0.19979	0.22138	0.90161	0.90741	0.67794	0.66231	60	60	B	B	biological fallback assumption	illumina	novaseq_era	full_length	small_rna	smarter	bulk	unknown	unknown	United States	2023-01-12	Multi-stage	Multi-stage	Whole Organism	All anatomical structures
72699	72699	SRR23071967	SRX19025115	SRS16444164	SRP417272	PRJNA923391	MBD5 a m5C RNA reader regulates histone ubiquitylation in development and function	GSE222803	Other	Methyl CpG binding domain MBD containing proteins are readers of epigenetic information. The founding member MeCP2 mutated in the Rett Syndrome binds to methylated CpG DNAs. MBD5 is an evolutionarily conserved MBD family member associated with epilepsy autism spectrum disorders ASD and early onset dementia. The mechanism of action of MBD5 remains unclear. Here we report that mbd5 regulates embryonic development erythrocyte differentiation iron metabolism and behavior in zebrafish. MBD5 is essential to activate the expression of erythrocyte differentiation genes e.g. hbae3 iron regulated genes e.g. fth1 and ASD related genes e.g. gabbr2 by binding to 5 methylcytosine m5C modified mRNAs interacting with and stabilizing Additional Sex Combs Like 1 ASXL1 a component of the Polycomb Repressive Deubiquinase PR DUB complex to facilitate removal of the repressive monoubiquitin mark at histone H2A H2A K119Ub thereby facilitating gene activation. Together these findings reveal MBD5 as a m5C RNA reader that links RNA methylation to histone modification in vivo. Overall design: [Dataset 1] 6 samples. Triplicates for ribo minus RNA Seq from 78 hpf zebrafish embryos treated with control or mbd5 morpholino [Dataset 2] 16 samples. Duplicates for CLIP seq experiments from 48 hpf 78 hpf zebrafish embryos treated with 0.5 mM DFO or 1 mM FAC		pubmed:38366571	dfo input rep2	GSM6932549	source name:whole embryo\|tissue:whole embryo\|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]\|treatment:0.5 mM DFO from 48 hpf to 78 hpf\|geo loc name:missing\|collection date:missing	dfo input rep2	Adapter trimming by Cutadapt Reads mapping by STAR to the transcriptome peak calling with pureCLIP or differential gene expression with DESeq2 Assembly: dr10 Supplementary files format and content: For [Dataset 1] excel xlsx files with differential expression by DESeq2. For [Dataset 2] excel xlsx files with CLIP seq peaks identified by pureCLIP algorithm	whole embryo	For [Dataset 1] morpholino oligonucleotides are applied by microinjection. For [Dataset 2] FAC F5879 Sigma Aldrich was dissolved in E3 medium at 50 mM and stored at 4°C. zebrafish were treated with 1 mM fresh FAC from 3 dpf 6 dpf every day prior to behavior analysis. DFO D9533 Sigma Aldrich was dissolved in E3 medium at 150 mM and stored at 20°C. Zebrafish were treated with 0.5 mM DFO from 3 dpf 6 dpf replenished every day prior to behavior analysis.	For [Dataset 1] total RNAs were extracted with standard TRIzol protocol. For [Dataset 2] 76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5 150 mM KCl 2 mM EDTA 0.5% v/v NP 40 0.5 mM DTT 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5 300 mM KCl 0.05% v/v NP 40 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1] RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa 634417 with ribo minus RNA as input. For [Dataset 2] RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.	Zebrafish embryos were treated with 0.003% 1 phenyl 2 thiourea PTU in E3 medium to prevent pigment formation. 3 month 9 month aged wild type or mbd5 mutant lines generated in this study were used for breeding or adult behavior analyses. Developmental stages were determined according to their morphology.	tissue:whole embryo\|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]\|treatment:0.5 mM DFO from 48 hpf to 78 hpf	GSM6932549	GSM6932549: dfo input rep2; Danio rerio; RIP Seq	GSM6932549 r1	GSM6932549	1	For [Dataset 1] total RNAs were extracted with standard TRIzol protocol. For [Dataset 2] 76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5 150 mM KCl 2 mM EDTA 0.5% v/v NP 40 0.5 mM DTT 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5 300 mM KCl 0.05% v/v NP 40 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1] RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa 634417 with ribo minus RNA as input. For [Dataset 2] RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.		RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP417272	loader:fastq load.py	dfo_input_rep2.r1.fastq.gz dfo_input_rep2.r2.fastq.gz	fastq fastq	2472387240.0	20603227.0	GSM6932549 r1	0:60 1:60	A:522247513;C:735343841;G:798068271;T:416720603;N:7012	60	60	522247513	735343841	798068271	416720603	7012	SRX19025115	SRS16444164	SRA1573941	University of Chicago	University of Chicago	2	0.7577	0.75837	0.06797	0.06744	0.96437	0.96627	0.80292	0.74592	60	60	B	B	biological fallback assumption	illumina	novaseq_era	full_length	small_rna	smarter	bulk	unknown	unknown	United States	2023-01-12	Multi-stage	Multi-stage	Whole Organism	All anatomical structures
72700	72700	SRR23071968	SRX19025114	SRS16444163	SRP417272	PRJNA923391	MBD5 a m5C RNA reader regulates histone ubiquitylation in development and function	GSE222803	Other	Methyl CpG binding domain MBD containing proteins are readers of epigenetic information. The founding member MeCP2 mutated in the Rett Syndrome binds to methylated CpG DNAs. MBD5 is an evolutionarily conserved MBD family member associated with epilepsy autism spectrum disorders ASD and early onset dementia. The mechanism of action of MBD5 remains unclear. Here we report that mbd5 regulates embryonic development erythrocyte differentiation iron metabolism and behavior in zebrafish. MBD5 is essential to activate the expression of erythrocyte differentiation genes e.g. hbae3 iron regulated genes e.g. fth1 and ASD related genes e.g. gabbr2 by binding to 5 methylcytosine m5C modified mRNAs interacting with and stabilizing Additional Sex Combs Like 1 ASXL1 a component of the Polycomb Repressive Deubiquinase PR DUB complex to facilitate removal of the repressive monoubiquitin mark at histone H2A H2A K119Ub thereby facilitating gene activation. Together these findings reveal MBD5 as a m5C RNA reader that links RNA methylation to histone modification in vivo. Overall design: [Dataset 1] 6 samples. Triplicates for ribo minus RNA Seq from 78 hpf zebrafish embryos treated with control or mbd5 morpholino [Dataset 2] 16 samples. Duplicates for CLIP seq experiments from 48 hpf 78 hpf zebrafish embryos treated with 0.5 mM DFO or 1 mM FAC		pubmed:38366571	dfo input rep1	GSM6932548	source name:whole embryo\|tissue:whole embryo\|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]\|treatment:0.5 mM DFO from 48 hpf to 78 hpf\|geo loc name:missing\|collection date:missing	dfo input rep1	Adapter trimming by Cutadapt Reads mapping by STAR to the transcriptome peak calling with pureCLIP or differential gene expression with DESeq2 Assembly: dr10 Supplementary files format and content: For [Dataset 1] excel xlsx files with differential expression by DESeq2. For [Dataset 2] excel xlsx files with CLIP seq peaks identified by pureCLIP algorithm	whole embryo	For [Dataset 1] morpholino oligonucleotides are applied by microinjection. For [Dataset 2] FAC F5879 Sigma Aldrich was dissolved in E3 medium at 50 mM and stored at 4°C. zebrafish were treated with 1 mM fresh FAC from 3 dpf 6 dpf every day prior to behavior analysis. DFO D9533 Sigma Aldrich was dissolved in E3 medium at 150 mM and stored at 20°C. Zebrafish were treated with 0.5 mM DFO from 3 dpf 6 dpf replenished every day prior to behavior analysis.	For [Dataset 1] total RNAs were extracted with standard TRIzol protocol. For [Dataset 2] 76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5 150 mM KCl 2 mM EDTA 0.5% v/v NP 40 0.5 mM DTT 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5 300 mM KCl 0.05% v/v NP 40 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1] RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa 634417 with ribo minus RNA as input. For [Dataset 2] RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.	Zebrafish embryos were treated with 0.003% 1 phenyl 2 thiourea PTU in E3 medium to prevent pigment formation. 3 month 9 month aged wild type or mbd5 mutant lines generated in this study were used for breeding or adult behavior analyses. Developmental stages were determined according to their morphology.	tissue:whole embryo\|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]\|treatment:0.5 mM DFO from 48 hpf to 78 hpf	GSM6932548	GSM6932548: dfo input rep1; Danio rerio; RIP Seq	GSM6932548 r1	GSM6932548	1	For [Dataset 1] total RNAs were extracted with standard TRIzol protocol. For [Dataset 2] 76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5 150 mM KCl 2 mM EDTA 0.5% v/v NP 40 0.5 mM DTT 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5 300 mM KCl 0.05% v/v NP 40 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1] RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa 634417 with ribo minus RNA as input. For [Dataset 2] RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.		RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP417272	loader:fastq load.py	dfo_input_rep1.fastq.gz dfo_input_rep1.r2.fastq.gz	fastq fastq	2546588760.0	21221573.0	GSM6932548 r1	0:60 1:60	A:536450815;C:753080253;G:819027741;T:438022880;N:7071	60	60	536450815	753080253	819027741	438022880	7071	SRX19025114	SRS16444163	SRA1573941	University of Chicago	University of Chicago	2	0.75957	0.75514	0.06963	0.06896	0.96345	0.96526	0.80322	0.73584	60	60	B	B	biological fallback assumption	illumina	novaseq_era	full_length	small_rna	smarter	bulk	unknown	unknown	United States	2023-01-12	Multi-stage	Multi-stage	Whole Organism	All anatomical structures
72701	72701	SRR23071969	SRX19025113	SRS16444162	SRP417272	PRJNA923391	MBD5 a m5C RNA reader regulates histone ubiquitylation in development and function	GSE222803	Other	Methyl CpG binding domain MBD containing proteins are readers of epigenetic information. The founding member MeCP2 mutated in the Rett Syndrome binds to methylated CpG DNAs. MBD5 is an evolutionarily conserved MBD family member associated with epilepsy autism spectrum disorders ASD and early onset dementia. The mechanism of action of MBD5 remains unclear. Here we report that mbd5 regulates embryonic development erythrocyte differentiation iron metabolism and behavior in zebrafish. MBD5 is essential to activate the expression of erythrocyte differentiation genes e.g. hbae3 iron regulated genes e.g. fth1 and ASD related genes e.g. gabbr2 by binding to 5 methylcytosine m5C modified mRNAs interacting with and stabilizing Additional Sex Combs Like 1 ASXL1 a component of the Polycomb Repressive Deubiquinase PR DUB complex to facilitate removal of the repressive monoubiquitin mark at histone H2A H2A K119Ub thereby facilitating gene activation. Together these findings reveal MBD5 as a m5C RNA reader that links RNA methylation to histone modification in vivo. Overall design: [Dataset 1] 6 samples. Triplicates for ribo minus RNA Seq from 78 hpf zebrafish embryos treated with control or mbd5 morpholino [Dataset 2] 16 samples. Duplicates for CLIP seq experiments from 48 hpf 78 hpf zebrafish embryos treated with 0.5 mM DFO or 1 mM FAC		pubmed:38366571	dfo clip rep2	GSM6932547	source name:whole embryo\|tissue:whole embryo\|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]\|treatment:0.5 mM DFO from 48 hpf to 78 hpf\|geo loc name:missing\|collection date:missing	dfo clip rep2	Adapter trimming by Cutadapt Reads mapping by STAR to the transcriptome peak calling with pureCLIP or differential gene expression with DESeq2 Assembly: dr10 Supplementary files format and content: For [Dataset 1] excel xlsx files with differential expression by DESeq2. For [Dataset 2] excel xlsx files with CLIP seq peaks identified by pureCLIP algorithm	whole embryo	For [Dataset 1] morpholino oligonucleotides are applied by microinjection. For [Dataset 2] FAC F5879 Sigma Aldrich was dissolved in E3 medium at 50 mM and stored at 4°C. zebrafish were treated with 1 mM fresh FAC from 3 dpf 6 dpf every day prior to behavior analysis. DFO D9533 Sigma Aldrich was dissolved in E3 medium at 150 mM and stored at 20°C. Zebrafish were treated with 0.5 mM DFO from 3 dpf 6 dpf replenished every day prior to behavior analysis.	For [Dataset 1] total RNAs were extracted with standard TRIzol protocol. For [Dataset 2] 76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5 150 mM KCl 2 mM EDTA 0.5% v/v NP 40 0.5 mM DTT 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5 300 mM KCl 0.05% v/v NP 40 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1] RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa 634417 with ribo minus RNA as input. For [Dataset 2] RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.	Zebrafish embryos were treated with 0.003% 1 phenyl 2 thiourea PTU in E3 medium to prevent pigment formation. 3 month 9 month aged wild type or mbd5 mutant lines generated in this study were used for breeding or adult behavior analyses. Developmental stages were determined according to their morphology.	tissue:whole embryo\|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]\|treatment:0.5 mM DFO from 48 hpf to 78 hpf	GSM6932547	GSM6932547: dfo clip rep2; Danio rerio; RIP Seq	GSM6932547 r1	GSM6932547	1	For [Dataset 1] total RNAs were extracted with standard TRIzol protocol. For [Dataset 2] 76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5 150 mM KCl 2 mM EDTA 0.5% v/v NP 40 0.5 mM DTT 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5 300 mM KCl 0.05% v/v NP 40 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1] RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa 634417 with ribo minus RNA as input. For [Dataset 2] RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.		RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP417272	loader:fastq load.py	dfo_clip_rep2.r1.fastq.gz dfo_clip_rep2.r2.fastq.gz	fastq fastq	4151061480.0	34592179.0	GSM6932547 r1	0:60 1:60	A:968004394;C:1130874104;G:1164829960;T:887341478;N:11544	60	60	968004394	1130874104	1164829960	887341478	11544	SRX19025113	SRS16444162	SRA1573941	University of Chicago	University of Chicago	2	0.92425	0.93056	0.20043	0.2242	0.8966	0.901	0.68964	0.62588	60	60	B	B	biological fallback assumption	illumina	novaseq_era	full_length	small_rna	smarter	bulk	unknown	unknown	United States	2023-01-12	Multi-stage	Multi-stage	Whole Organism	All anatomical structures
72702	72702	SRR23071970	SRX19025112	SRS16444161	SRP417272	PRJNA923391	MBD5 a m5C RNA reader regulates histone ubiquitylation in development and function	GSE222803	Other	Methyl CpG binding domain MBD containing proteins are readers of epigenetic information. The founding member MeCP2 mutated in the Rett Syndrome binds to methylated CpG DNAs. MBD5 is an evolutionarily conserved MBD family member associated with epilepsy autism spectrum disorders ASD and early onset dementia. The mechanism of action of MBD5 remains unclear. Here we report that mbd5 regulates embryonic development erythrocyte differentiation iron metabolism and behavior in zebrafish. MBD5 is essential to activate the expression of erythrocyte differentiation genes e.g. hbae3 iron regulated genes e.g. fth1 and ASD related genes e.g. gabbr2 by binding to 5 methylcytosine m5C modified mRNAs interacting with and stabilizing Additional Sex Combs Like 1 ASXL1 a component of the Polycomb Repressive Deubiquinase PR DUB complex to facilitate removal of the repressive monoubiquitin mark at histone H2A H2A K119Ub thereby facilitating gene activation. Together these findings reveal MBD5 as a m5C RNA reader that links RNA methylation to histone modification in vivo. Overall design: [Dataset 1] 6 samples. Triplicates for ribo minus RNA Seq from 78 hpf zebrafish embryos treated with control or mbd5 morpholino [Dataset 2] 16 samples. Duplicates for CLIP seq experiments from 48 hpf 78 hpf zebrafish embryos treated with 0.5 mM DFO or 1 mM FAC		pubmed:38366571	dfo clip rep1	GSM6932546	source name:whole embryo\|tissue:whole embryo\|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]\|treatment:0.5 mM DFO from 48 hpf to 78 hpf\|geo loc name:missing\|collection date:missing	dfo clip rep1	Adapter trimming by Cutadapt Reads mapping by STAR to the transcriptome peak calling with pureCLIP or differential gene expression with DESeq2 Assembly: dr10 Supplementary files format and content: For [Dataset 1] excel xlsx files with differential expression by DESeq2. For [Dataset 2] excel xlsx files with CLIP seq peaks identified by pureCLIP algorithm	whole embryo	For [Dataset 1] morpholino oligonucleotides are applied by microinjection. For [Dataset 2] FAC F5879 Sigma Aldrich was dissolved in E3 medium at 50 mM and stored at 4°C. zebrafish were treated with 1 mM fresh FAC from 3 dpf 6 dpf every day prior to behavior analysis. DFO D9533 Sigma Aldrich was dissolved in E3 medium at 150 mM and stored at 20°C. Zebrafish were treated with 0.5 mM DFO from 3 dpf 6 dpf replenished every day prior to behavior analysis.	For [Dataset 1] total RNAs were extracted with standard TRIzol protocol. For [Dataset 2] 76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5 150 mM KCl 2 mM EDTA 0.5% v/v NP 40 0.5 mM DTT 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5 300 mM KCl 0.05% v/v NP 40 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1] RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa 634417 with ribo minus RNA as input. For [Dataset 2] RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.	Zebrafish embryos were treated with 0.003% 1 phenyl 2 thiourea PTU in E3 medium to prevent pigment formation. 3 month 9 month aged wild type or mbd5 mutant lines generated in this study were used for breeding or adult behavior analyses. Developmental stages were determined according to their morphology.	tissue:whole embryo\|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]\|treatment:0.5 mM DFO from 48 hpf to 78 hpf	GSM6932546	GSM6932546: dfo clip rep1; Danio rerio; RIP Seq	GSM6932546 r1	GSM6932546	1	For [Dataset 1] total RNAs were extracted with standard TRIzol protocol. For [Dataset 2] 76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5 150 mM KCl 2 mM EDTA 0.5% v/v NP 40 0.5 mM DTT 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5 300 mM KCl 0.05% v/v NP 40 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1] RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa 634417 with ribo minus RNA as input. For [Dataset 2] RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.		RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP417272	loader:fastq load.py	dfo_clip_rep1.r1.fastq.gz dfo_clip_rep1.r2.fastq.gz	fastq fastq	3549376560.0	29578138.0	GSM6932546 r1	0:60 1:60	A:829453498;C:966398146;G:998787767;T:754727094;N:10055	60	60	829453498	966398146	998787767	754727094	10055	SRX19025112	SRS16444161	SRA1573941	University of Chicago	University of Chicago	2	0.94985	0.93128	0.20616	0.22409	0.89548	0.90055	0.67094	0.65117	60	60	B	B	biological fallback assumption	illumina	novaseq_era	full_length	small_rna	smarter	bulk	unknown	unknown	United States	2023-01-12	Multi-stage	Multi-stage	Whole Organism	All anatomical structures
72703	72703	SRR23071971	SRX19025111	SRS16444160	SRP417272	PRJNA923391	MBD5 a m5C RNA reader regulates histone ubiquitylation in development and function	GSE222803	Other	Methyl CpG binding domain MBD containing proteins are readers of epigenetic information. The founding member MeCP2 mutated in the Rett Syndrome binds to methylated CpG DNAs. MBD5 is an evolutionarily conserved MBD family member associated with epilepsy autism spectrum disorders ASD and early onset dementia. The mechanism of action of MBD5 remains unclear. Here we report that mbd5 regulates embryonic development erythrocyte differentiation iron metabolism and behavior in zebrafish. MBD5 is essential to activate the expression of erythrocyte differentiation genes e.g. hbae3 iron regulated genes e.g. fth1 and ASD related genes e.g. gabbr2 by binding to 5 methylcytosine m5C modified mRNAs interacting with and stabilizing Additional Sex Combs Like 1 ASXL1 a component of the Polycomb Repressive Deubiquinase PR DUB complex to facilitate removal of the repressive monoubiquitin mark at histone H2A H2A K119Ub thereby facilitating gene activation. Together these findings reveal MBD5 as a m5C RNA reader that links RNA methylation to histone modification in vivo. Overall design: [Dataset 1] 6 samples. Triplicates for ribo minus RNA Seq from 78 hpf zebrafish embryos treated with control or mbd5 morpholino [Dataset 2] 16 samples. Duplicates for CLIP seq experiments from 48 hpf 78 hpf zebrafish embryos treated with 0.5 mM DFO or 1 mM FAC		pubmed:38366571	ctrl input rep2	GSM6932545	source name:whole embryo\|tissue:whole embryo\|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]\|treatment:No treatment\|geo loc name:missing\|collection date:missing	ctrl input rep2	Adapter trimming by Cutadapt Reads mapping by STAR to the transcriptome peak calling with pureCLIP or differential gene expression with DESeq2 Assembly: dr10 Supplementary files format and content: For [Dataset 1] excel xlsx files with differential expression by DESeq2. For [Dataset 2] excel xlsx files with CLIP seq peaks identified by pureCLIP algorithm	whole embryo	For [Dataset 1] morpholino oligonucleotides are applied by microinjection. For [Dataset 2] FAC F5879 Sigma Aldrich was dissolved in E3 medium at 50 mM and stored at 4°C. zebrafish were treated with 1 mM fresh FAC from 3 dpf 6 dpf every day prior to behavior analysis. DFO D9533 Sigma Aldrich was dissolved in E3 medium at 150 mM and stored at 20°C. Zebrafish were treated with 0.5 mM DFO from 3 dpf 6 dpf replenished every day prior to behavior analysis.	For [Dataset 1] total RNAs were extracted with standard TRIzol protocol. For [Dataset 2] 76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5 150 mM KCl 2 mM EDTA 0.5% v/v NP 40 0.5 mM DTT 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5 300 mM KCl 0.05% v/v NP 40 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1] RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa 634417 with ribo minus RNA as input. For [Dataset 2] RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.	Zebrafish embryos were treated with 0.003% 1 phenyl 2 thiourea PTU in E3 medium to prevent pigment formation. 3 month 9 month aged wild type or mbd5 mutant lines generated in this study were used for breeding or adult behavior analyses. Developmental stages were determined according to their morphology.	tissue:whole embryo\|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]\|treatment:No treatment	GSM6932545	GSM6932545: ctrl input rep2; Danio rerio; RIP Seq	GSM6932545 r1	GSM6932545	1	For [Dataset 1] total RNAs were extracted with standard TRIzol protocol. For [Dataset 2] 76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5 150 mM KCl 2 mM EDTA 0.5% v/v NP 40 0.5 mM DTT 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5 300 mM KCl 0.05% v/v NP 40 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1] RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa 634417 with ribo minus RNA as input. For [Dataset 2] RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.		RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP417272	loader:fastq load.py	ctrl_input_rep2.r1.fastq.gz ctrl_input_rep2.r2.fastq.gz	fastq fastq	2305351440.0	19211262.0	GSM6932545 r1	0:60 1:60	A:494731676;C:683635423;G:735706555;T:391271420;N:6366	60	60	494731676	683635423	735706555	391271420	6366	SRX19025111	SRS16444160	SRA1573941	University of Chicago	University of Chicago	2	0.75012	0.76494	0.06496	0.06503	0.9696	0.97023	0.80848	0.76006	60	60	B	B	biological fallback assumption	illumina	novaseq_era	full_length	small_rna	smarter	bulk	unknown	unknown	United States	2023-01-12	Multi-stage	Multi-stage	Whole Organism	All anatomical structures
72704	72704	SRR23071972	SRX19025110	SRS16444159	SRP417272	PRJNA923391	MBD5 a m5C RNA reader regulates histone ubiquitylation in development and function	GSE222803	Other	Methyl CpG binding domain MBD containing proteins are readers of epigenetic information. The founding member MeCP2 mutated in the Rett Syndrome binds to methylated CpG DNAs. MBD5 is an evolutionarily conserved MBD family member associated with epilepsy autism spectrum disorders ASD and early onset dementia. The mechanism of action of MBD5 remains unclear. Here we report that mbd5 regulates embryonic development erythrocyte differentiation iron metabolism and behavior in zebrafish. MBD5 is essential to activate the expression of erythrocyte differentiation genes e.g. hbae3 iron regulated genes e.g. fth1 and ASD related genes e.g. gabbr2 by binding to 5 methylcytosine m5C modified mRNAs interacting with and stabilizing Additional Sex Combs Like 1 ASXL1 a component of the Polycomb Repressive Deubiquinase PR DUB complex to facilitate removal of the repressive monoubiquitin mark at histone H2A H2A K119Ub thereby facilitating gene activation. Together these findings reveal MBD5 as a m5C RNA reader that links RNA methylation to histone modification in vivo. Overall design: [Dataset 1] 6 samples. Triplicates for ribo minus RNA Seq from 78 hpf zebrafish embryos treated with control or mbd5 morpholino [Dataset 2] 16 samples. Duplicates for CLIP seq experiments from 48 hpf 78 hpf zebrafish embryos treated with 0.5 mM DFO or 1 mM FAC		pubmed:38366571	ctrl input rep1	GSM6932544	source name:whole embryo\|tissue:whole embryo\|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]\|treatment:No treatment\|geo loc name:missing\|collection date:missing	ctrl input rep1	Adapter trimming by Cutadapt Reads mapping by STAR to the transcriptome peak calling with pureCLIP or differential gene expression with DESeq2 Assembly: dr10 Supplementary files format and content: For [Dataset 1] excel xlsx files with differential expression by DESeq2. For [Dataset 2] excel xlsx files with CLIP seq peaks identified by pureCLIP algorithm	whole embryo	For [Dataset 1] morpholino oligonucleotides are applied by microinjection. For [Dataset 2] FAC F5879 Sigma Aldrich was dissolved in E3 medium at 50 mM and stored at 4°C. zebrafish were treated with 1 mM fresh FAC from 3 dpf 6 dpf every day prior to behavior analysis. DFO D9533 Sigma Aldrich was dissolved in E3 medium at 150 mM and stored at 20°C. Zebrafish were treated with 0.5 mM DFO from 3 dpf 6 dpf replenished every day prior to behavior analysis.	For [Dataset 1] total RNAs were extracted with standard TRIzol protocol. For [Dataset 2] 76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5 150 mM KCl 2 mM EDTA 0.5% v/v NP 40 0.5 mM DTT 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5 300 mM KCl 0.05% v/v NP 40 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1] RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa 634417 with ribo minus RNA as input. For [Dataset 2] RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.	Zebrafish embryos were treated with 0.003% 1 phenyl 2 thiourea PTU in E3 medium to prevent pigment formation. 3 month 9 month aged wild type or mbd5 mutant lines generated in this study were used for breeding or adult behavior analyses. Developmental stages were determined according to their morphology.	tissue:whole embryo\|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]\|treatment:No treatment	GSM6932544	GSM6932544: ctrl input rep1; Danio rerio; RIP Seq	GSM6932544 r1	GSM6932544	1	For [Dataset 1] total RNAs were extracted with standard TRIzol protocol. For [Dataset 2] 76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5 150 mM KCl 2 mM EDTA 0.5% v/v NP 40 0.5 mM DTT 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5 300 mM KCl 0.05% v/v NP 40 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1] RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa 634417 with ribo minus RNA as input. For [Dataset 2] RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.		RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP417272	loader:fastq load.py	ctrl_input_rep1.r1.fastq.gz ctrl_input_rep1.r2.fastq.gz	fastq fastq	2870115000.0	23917625.0	GSM6932544 r1	0:60 1:60	A:616586993;C:849261640;G:916690149;T:487568187;N:8031	60	60	616586993	849261640	916690149	487568187	8031	SRX19025110	SRS16444159	SRA1573941	University of Chicago	University of Chicago	2	0.76321	0.76237	0.06602	0.06566	0.97064	0.96903	0.68553	0.75314	60	60	B	B	biological fallback assumption	illumina	novaseq_era	full_length	small_rna	smarter	bulk	unknown	unknown	United States	2023-01-12	Multi-stage	Multi-stage	Whole Organism	All anatomical structures
72705	72705	SRR23071973	SRX19025109	SRS16444158	SRP417272	PRJNA923391	MBD5 a m5C RNA reader regulates histone ubiquitylation in development and function	GSE222803	Other	Methyl CpG binding domain MBD containing proteins are readers of epigenetic information. The founding member MeCP2 mutated in the Rett Syndrome binds to methylated CpG DNAs. MBD5 is an evolutionarily conserved MBD family member associated with epilepsy autism spectrum disorders ASD and early onset dementia. The mechanism of action of MBD5 remains unclear. Here we report that mbd5 regulates embryonic development erythrocyte differentiation iron metabolism and behavior in zebrafish. MBD5 is essential to activate the expression of erythrocyte differentiation genes e.g. hbae3 iron regulated genes e.g. fth1 and ASD related genes e.g. gabbr2 by binding to 5 methylcytosine m5C modified mRNAs interacting with and stabilizing Additional Sex Combs Like 1 ASXL1 a component of the Polycomb Repressive Deubiquinase PR DUB complex to facilitate removal of the repressive monoubiquitin mark at histone H2A H2A K119Ub thereby facilitating gene activation. Together these findings reveal MBD5 as a m5C RNA reader that links RNA methylation to histone modification in vivo. Overall design: [Dataset 1] 6 samples. Triplicates for ribo minus RNA Seq from 78 hpf zebrafish embryos treated with control or mbd5 morpholino [Dataset 2] 16 samples. Duplicates for CLIP seq experiments from 48 hpf 78 hpf zebrafish embryos treated with 0.5 mM DFO or 1 mM FAC		pubmed:38366571	ctrl clip rep2	GSM6932543	source name:whole embryo\|tissue:whole embryo\|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]\|treatment:No treatment\|geo loc name:missing\|collection date:missing	ctrl clip rep2	Adapter trimming by Cutadapt Reads mapping by STAR to the transcriptome peak calling with pureCLIP or differential gene expression with DESeq2 Assembly: dr10 Supplementary files format and content: For [Dataset 1] excel xlsx files with differential expression by DESeq2. For [Dataset 2] excel xlsx files with CLIP seq peaks identified by pureCLIP algorithm	whole embryo	For [Dataset 1] morpholino oligonucleotides are applied by microinjection. For [Dataset 2] FAC F5879 Sigma Aldrich was dissolved in E3 medium at 50 mM and stored at 4°C. zebrafish were treated with 1 mM fresh FAC from 3 dpf 6 dpf every day prior to behavior analysis. DFO D9533 Sigma Aldrich was dissolved in E3 medium at 150 mM and stored at 20°C. Zebrafish were treated with 0.5 mM DFO from 3 dpf 6 dpf replenished every day prior to behavior analysis.	For [Dataset 1] total RNAs were extracted with standard TRIzol protocol. For [Dataset 2] 76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5 150 mM KCl 2 mM EDTA 0.5% v/v NP 40 0.5 mM DTT 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5 300 mM KCl 0.05% v/v NP 40 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1] RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa 634417 with ribo minus RNA as input. For [Dataset 2] RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.	Zebrafish embryos were treated with 0.003% 1 phenyl 2 thiourea PTU in E3 medium to prevent pigment formation. 3 month 9 month aged wild type or mbd5 mutant lines generated in this study were used for breeding or adult behavior analyses. Developmental stages were determined according to their morphology.	tissue:whole embryo\|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]\|treatment:No treatment	GSM6932543	GSM6932543: ctrl clip rep2; Danio rerio; RIP Seq	GSM6932543 r1	GSM6932543	1	For [Dataset 1] total RNAs were extracted with standard TRIzol protocol. For [Dataset 2] 76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5 150 mM KCl 2 mM EDTA 0.5% v/v NP 40 0.5 mM DTT 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5 300 mM KCl 0.05% v/v NP 40 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1] RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa 634417 with ribo minus RNA as input. For [Dataset 2] RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.		RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP417272	loader:fastq load.py	ctrl_clip_rep2.r1.fastq.gz ctrl_clip_rep2.r2.fastq.gz	fastq fastq	3309978960.0	27583158.0	GSM6932543 r1	0:60 1:60	A:774105538;C:895792317;G:931799487;T:708272623;N:8995	60	60	774105538	895792317	931799487	708272623	8995	SRX19025109	SRS16444158	SRA1573941	University of Chicago	University of Chicago	2	0.94553	0.92262	0.21092	0.22735	0.90985	0.91407	0.67372	0.67171	60	60	B	B	biological fallback assumption	illumina	novaseq_era	full_length	small_rna	smarter	bulk	unknown	unknown	United States	2023-01-12	Multi-stage	Multi-stage	Whole Organism	All anatomical structures
72706	72706	SRR23071974	SRX19025108	SRS16444157	SRP417272	PRJNA923391	MBD5 a m5C RNA reader regulates histone ubiquitylation in development and function	GSE222803	Other	Methyl CpG binding domain MBD containing proteins are readers of epigenetic information. The founding member MeCP2 mutated in the Rett Syndrome binds to methylated CpG DNAs. MBD5 is an evolutionarily conserved MBD family member associated with epilepsy autism spectrum disorders ASD and early onset dementia. The mechanism of action of MBD5 remains unclear. Here we report that mbd5 regulates embryonic development erythrocyte differentiation iron metabolism and behavior in zebrafish. MBD5 is essential to activate the expression of erythrocyte differentiation genes e.g. hbae3 iron regulated genes e.g. fth1 and ASD related genes e.g. gabbr2 by binding to 5 methylcytosine m5C modified mRNAs interacting with and stabilizing Additional Sex Combs Like 1 ASXL1 a component of the Polycomb Repressive Deubiquinase PR DUB complex to facilitate removal of the repressive monoubiquitin mark at histone H2A H2A K119Ub thereby facilitating gene activation. Together these findings reveal MBD5 as a m5C RNA reader that links RNA methylation to histone modification in vivo. Overall design: [Dataset 1] 6 samples. Triplicates for ribo minus RNA Seq from 78 hpf zebrafish embryos treated with control or mbd5 morpholino [Dataset 2] 16 samples. Duplicates for CLIP seq experiments from 48 hpf 78 hpf zebrafish embryos treated with 0.5 mM DFO or 1 mM FAC		pubmed:38366571	ctrl clip rep1	GSM6932542	source name:whole embryo\|tissue:whole embryo\|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]\|treatment:No treatment\|geo loc name:missing\|collection date:missing	ctrl clip rep1	Adapter trimming by Cutadapt Reads mapping by STAR to the transcriptome peak calling with pureCLIP or differential gene expression with DESeq2 Assembly: dr10 Supplementary files format and content: For [Dataset 1] excel xlsx files with differential expression by DESeq2. For [Dataset 2] excel xlsx files with CLIP seq peaks identified by pureCLIP algorithm	whole embryo	For [Dataset 1] morpholino oligonucleotides are applied by microinjection. For [Dataset 2] FAC F5879 Sigma Aldrich was dissolved in E3 medium at 50 mM and stored at 4°C. zebrafish were treated with 1 mM fresh FAC from 3 dpf 6 dpf every day prior to behavior analysis. DFO D9533 Sigma Aldrich was dissolved in E3 medium at 150 mM and stored at 20°C. Zebrafish were treated with 0.5 mM DFO from 3 dpf 6 dpf replenished every day prior to behavior analysis.	For [Dataset 1] total RNAs were extracted with standard TRIzol protocol. For [Dataset 2] 76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5 150 mM KCl 2 mM EDTA 0.5% v/v NP 40 0.5 mM DTT 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5 300 mM KCl 0.05% v/v NP 40 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1] RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa 634417 with ribo minus RNA as input. For [Dataset 2] RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.	Zebrafish embryos were treated with 0.003% 1 phenyl 2 thiourea PTU in E3 medium to prevent pigment formation. 3 month 9 month aged wild type or mbd5 mutant lines generated in this study were used for breeding or adult behavior analyses. Developmental stages were determined according to their morphology.	tissue:whole embryo\|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]\|treatment:No treatment	GSM6932542	GSM6932542: ctrl clip rep1; Danio rerio; RIP Seq	GSM6932542 r1	GSM6932542	1	For [Dataset 1] total RNAs were extracted with standard TRIzol protocol. For [Dataset 2] 76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5 150 mM KCl 2 mM EDTA 0.5% v/v NP 40 0.5 mM DTT 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5 300 mM KCl 0.05% v/v NP 40 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail 1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1] RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa 634417 with ribo minus RNA as input. For [Dataset 2] RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.		RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP417272	loader:fastq load.py	ctrl_clip_rep1.r1.fastq.gz ctrl_clip_rep1.r2.fastq.gz	fastq fastq	3392768880.0	28273074.0	GSM6932542 r1	0:60 1:60	A:795387316;C:918606802;G:949982957;T:728782720;N:9085	60	60	795387316	918606802	949982957	728782720	9085	SRX19025108	SRS16444157	SRA1573941	University of Chicago	University of Chicago	2	0.92844	0.92193	0.20693	0.22683	0.90826	0.91297	0.68754	0.67062	60	60	B	B	biological fallback assumption	illumina	novaseq_era	full_length	small_rna	smarter	bulk	unknown	unknown	United States	2023-01-12	Multi-stage	Multi-stage	Whole Organism	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

Advanced export

JSON shape: default, array, newline-delimited

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