metadata: run_metadata: 110 rows where experiment.library_layout = "PAIRED", experiment.library_source = "TRANSCRIPTOMIC" and experiment.library

110 rows where experiment.library_layout = "PAIRED", experiment.library_source = "TRANSCRIPTOMIC" and experiment.library_strategy = "RIP-Seq"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.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
33123	33123	SRR29672615	SRX25176099	SRS21866000	SRP517393	PRJNA1130538	ac4C transcriptomes of Zebrafish and Worm	GSE271258	Other	ac4C modification appears in mutilple model organisms including Zebrafish and Worm Overall design: To investigate whether ac4C modification is involved in evolution we performed ac4C RIP seq on Zebrafish and Worm.			Zebrafish ac4C	GSM8372406	tissue:Animal organ cells\|cell type:Animal organ cells\|genotype:Wild type\|rip antibody:anti ac4C Abcam catalog No. ab252215\|geo loc name:missing\|collection date:missing	Zebrafish ac4C	The raw ac4C RIP seq data were aligned to genome reference sequences by Hisat2. The aligned reads were used for ac4C modification peak calling and the significant methylation was identified by exomepeak2 and the ac4C peak calling can be visualized by IGV software. The MetaTX was used to examine the distribution pattern of epitranscriptome profiles. The STREME was used to determine if the ac4C peaks contained the consensus of ac4C motif sequences. For mRNA seq the mRNA expression level was analyzed by StringTie and differentially expressed mRNAs were calculated by DEseq. The substrates of ac4C regulators were obtained from starBase v2.0. The statistical enrichment analysis of Gene Ontology GO and Kyoto Encyclopedia of Genes and Genomes KEGG pathway for differentially expressed genes DEGs and differentially methylated mRNAs were applied by DAVID. Assembly: danRer10 or WBcel235 Supplementary files format and content: The processed data files is in CSV format containing the expression levels and ac4C status changes for each gene.	Animal organ cells		Total RNA was extracted according to manufacturer’s instruction. The stranded RNA sequencing library was constructed by KC DigitalTM Stranded mRNA Library Prep Kit for Illumina® Catalog NO. DR08502 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction. The kit eliminates duplication bias in PCR and sequencing steps by using unique molecular identifier UMI of 8 random bases to label the pre amplified cDNA molecules. The library products corresponding to 200 500 bps were enriched		cell type:Animal organ cells\|genotype:Wild type\|rip antibody:anti ac4C Abcam catalog No. ab252215	GSM8372406	GSM8372406: Zebrafish ac4C; Danio rerio; RIP Seq	GSM8372406 r1	GSM8372406	1	Total RNA was extracted according to manufacturer's instruction. The stranded RNA sequencing library was constructed by KC DigitalTM Stranded mRNA Library Prep Kit for Illumina® Catalog NO. DR08502 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction. The kit eliminates duplication bias in PCR and sequencing steps by using unique molecular identifier UMI of 8 random bases to label the pre amplified cDNA molecules. The library products corresponding to 200 500 bps were enriched		RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP517393		Fish_IP.clean.R2.fastq.gz Fish_IP.clean.R1.fastq.gz	fastq fastq	816231517.0	3830403.0	GSM8372406 r1	0:102.34 1:110.76	A:199381841;C:207571478;G:205740791;T:203535549;N:1858	102	110	199381841	207571478	205740791	203535549	1858	SRX25176099	SRS21866000	SRA1914369	Fujian Medical University	Fujian Medical University	2	0.60415	0.60545	0.08824	0.08794	0.78796	0.78733	0.43432	0.43842	126	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-07-01	Undetermined	Undetermined	Undetermined	Undetermined
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
41511	41511	SRR5004963	SRX2336797	SRS1790193	SRP092907	PRJNA352850	Transcriptomics analysis of gene expressions m6A enrichment levels and ythdf2 binding targets in control and mettl3 or ythdf2 morphants zebrafish embryos	GSE89655	Other	RNA was isolated from control and mettl3 or ythdf2 morphants zebrafish cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2500 or HiSeq 3000 Illumina in paired read mode creating reads with a length of 101 or 151 bp. Sequencing chemistry v2 Illumina was used. Overall design: Examination of gene expressive levels m6A enrichment levels m6A single uncleotide sites and ythdf2 binding targets in normal and mettl3 or ythdf2 morphants zebrafish cells		pubmed:28869969	zebrafish embryos ythdf2 RIP rep2	GSM2386192	source name:zebrafish embryos\|genotype/variation:normal\|cell type:embryos cells\|age:28hpf\|tissue:trunk	zebrafish embryos ythdf2 RIP rep2	Reads were aligned to the zv9 genome assembly using TopHat v2.0.9 For each sample reads counts of all genes were computed using HTSeq v0.5.3p9 Genome build: zv9 Supplementary files format and content: reads count HTSeq.xls: Reads count for each gene of all samples Supplementary files format and content: ythdf2 binding target.xls: ythdf2 binding targets identified by macs2 software	zebrafish embryos		For RIP seq RNA was isolate from ythdf2 Flag mRNA injected zebrafish embryos and the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode creating reads with a length of 101 bp.		genotype/variation:normal\|cell type:embryos cells\|age:28hpf\|tissue:trunk	GSM2386192	GSM2386192: zebrafish embryos ythdf2 RIP rep2; Danio rerio; RIP Seq	GSM2386192		1	For RIP seq RNA was isolate from ythdf2 Flag mRNA injected zebrafish embryos and the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode creating reads with a length of 101 bp.	GEO Accession:GSM2386192	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 3000	SRP092907		ythdf2_RIP_rep2_1.fastq.gz ythdf2_RIP_rep2_2.fastq.gz	fastq fastq	4007024510.0	19836755.0	GSM2386192 r1	0:101 1:101	A:769487104;C:1245093129;G:1251328145;T:740377823;N:738309	101	101	769487104	1245093129	1251328145	740377823	738309	SRX2336797	SRS1790193	SRA491654	GEO	Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)	2	0.97768	0.97802	0.22786	0.21743	0.89885	0.89968	0.77584	0.83808	101	101	B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	trueseq	bulk	bulk	bulk	China	2016-11-08	Pharyngula	Embryo	Trunk	Surface Structure
41512	41512	SRR5004962	SRX2336796	SRS1790194	SRP092907	PRJNA352850	Transcriptomics analysis of gene expressions m6A enrichment levels and ythdf2 binding targets in control and mettl3 or ythdf2 morphants zebrafish embryos	GSE89655	Other	RNA was isolated from control and mettl3 or ythdf2 morphants zebrafish cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2500 or HiSeq 3000 Illumina in paired read mode creating reads with a length of 101 or 151 bp. Sequencing chemistry v2 Illumina was used. Overall design: Examination of gene expressive levels m6A enrichment levels m6A single uncleotide sites and ythdf2 binding targets in normal and mettl3 or ythdf2 morphants zebrafish cells		pubmed:28869969	zebrafish embryos ythdf2 RIP rep1	GSM2386191	source name:zebrafish embryos\|genotype/variation:normal\|cell type:embryos cells\|age:28hpf\|tissue:trunk	zebrafish embryos ythdf2 RIP rep1	Reads were aligned to the zv9 genome assembly using TopHat v2.0.9 For each sample reads counts of all genes were computed using HTSeq v0.5.3p9 Genome build: zv9 Supplementary files format and content: reads count HTSeq.xls: Reads count for each gene of all samples Supplementary files format and content: ythdf2 binding target.xls: ythdf2 binding targets identified by macs2 software	zebrafish embryos		For RIP seq RNA was isolate from ythdf2 Flag mRNA injected zebrafish embryos and the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode creating reads with a length of 101 bp.		genotype/variation:normal\|cell type:embryos cells\|age:28hpf\|tissue:trunk	GSM2386191	GSM2386191: zebrafish embryos ythdf2 RIP rep1; Danio rerio; RIP Seq	GSM2386191		1	For RIP seq RNA was isolate from ythdf2 Flag mRNA injected zebrafish embryos and the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode creating reads with a length of 101 bp.	GEO Accession:GSM2386191	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP092907		ythdf2_RIP_rep1_1.fastq.gz ythdf2_RIP_rep1_2.fastq.gz	fastq fastq	6144583662.0	30418731.0	GSM2386191 r1	0:101 1:101	A:1227614258;C:1869131844;G:1825793436;T:1220118819;N:1925305	101	101	1227614258	1869131844	1825793436	1220118819	1925305	SRX2336796	SRS1790194	SRA491654	GEO	Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)	2	0.96857	0.96917	0.23397	0.22377	0.89832	0.90147	0.78619	0.8258	101	101	B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	trueseq	bulk	bulk	bulk	China	2016-11-08	Pharyngula	Embryo	Trunk	Surface Structure
42000	42000	SRR5379364	SRX2674572	SRS2073700	SRP102513	PRJNA380609	Transcriptome analysis on wild type and ddx39a mutant zebrafish embryos by Next Generation Sequencing	GSE97067	Other	DEAD box RNA helicase DDX39A has been shown to regulate RNA metabolism; however its role in vertebrate development has not previously been examined. To determine the impact of loss of ddx39a on transcriptome during vertebrate early development we pursued transcriptome analysis RNA Seq on wild type and ddx39a mutant zebrafish embryos at 24 hpf And by using RIP seq to identify targeted RNA which were DDX39A binded. Overall design: Using RNA seq to identify the changes in the transcriptomic landscape in ddx39a mutants. Using RIP seq to identify DDX39A binding RNAs.		pubmed:29636379	ddx39a 24hpf RIPseq	GSM2550918	source name:embryos\|genotype:ddx39a mutant\|tissue:embryo\|developmental stage:24hpf	ddx39a 24hpf RIPseq	Illumina bcl2fastq2 v 2.16.0.10 software was used for base calling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.5. High quality reads were alligned to GRCz10 whole genome using tophat V2.2.1 and bowtie2 v2.2.3 with parameters q p 8 no novel juncs G o. Raw counts of sequencing reads were generated by using HTSeq v 0.6.1p1. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample	embryos		Microinjection ddx39a Flag mRNA in ddx39a mutant embryos at one cell stage. Lysates were clarified from 24hpf embryos were isolated with anti Flag beads. RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. Magnetic beads with oligodT were used to enrich the mRNAs and then Frag/Prime buffer was added to fragment the mRNAs. The short mRNA fragments were used as templates and random hexamers were used to synthesize first strand cDNA. Then double stranded cDNA was synthesized by adding buffer solution dNTPs and DNA polymeraseΙ. The double stranded cDNAs were purified by DNA clean beads according to the manufacturer’s instructions then repaired at the tail ends polyA added and enriched by PCR amplification. Finally we tested the inserts sizes in the cDNA libraries on an Agilent 2100 Bioanalyzer.		genotype:ddx39a mutant\|tissue:embryo\|developmental stage:24hpf	GSM2550918	GSM2550918: ddx39a 24hpf RIPseq; Danio rerio; RIP Seq	GSM2550918		1	Microinjection ddx39a Flag mRNA in ddx39a mutant embryos at one cell stage. Lysates were clarified from 24hpf embryos were isolated with anti Flag beads. RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. Magnetic beads with oligodT were used to enrich the mRNAs and then Frag/Prime buffer was added to fragment the mRNAs. The short mRNA fragments were used as templates and random hexamers were used to synthesize first strand cDNA. Then double stranded cDNA was synthesized by adding buffer solution dNTPs and DNA polymeraseΙ. The double stranded cDNAs were purified by DNA clean beads according to the manufacturer’s instructions then repaired at the tail ends polyA added and enriched by PCR amplification. Finally we tested the inserts sizes in the cDNA libraries on an Agilent 2100 Bioanalyzer.	GEO Accession:GSM2550918	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP102513		RDWHDANwwwCAABRAAPEI-206_1.fq.gz RDWHDANwwwCAABRAAPEI-206_2.fq.gz	fastq fastq	3819239400.0	19096197.0	GSM2550918 r1	0:100 1:100	A:751858949;C:1169790479;G:1139713624;T:756987876;N:888472	100	100	751858949	1169790479	1139713624	756987876	888472	SRX2674572	SRS2073700	SRA549449	GEO	Xin Lou Lab, Medical School, Nanjing University	2	0.98659	0.98572	0.28836	0.28975	0.89422	0.89558	0.75396	0.78553	100	100	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	China	2017-03-27	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
42001	42001	SRR5379363	SRX2674571	SRS2073697	SRP102513	PRJNA380609	Transcriptome analysis on wild type and ddx39a mutant zebrafish embryos by Next Generation Sequencing	GSE97067	Other	DEAD box RNA helicase DDX39A has been shown to regulate RNA metabolism; however its role in vertebrate development has not previously been examined. To determine the impact of loss of ddx39a on transcriptome during vertebrate early development we pursued transcriptome analysis RNA Seq on wild type and ddx39a mutant zebrafish embryos at 24 hpf And by using RIP seq to identify targeted RNA which were DDX39A binded. Overall design: Using RNA seq to identify the changes in the transcriptomic landscape in ddx39a mutants. Using RIP seq to identify DDX39A binding RNAs.		pubmed:29636379	WT 24hpf RIPseq	GSM2550917	source name:embryos\|genotype:wild type\|tissue:embryo\|developmental stage:24hpf	WT 24hpf RIPseq	Illumina bcl2fastq2 v 2.16.0.10 software was used for base calling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.5. High quality reads were alligned to GRCz10 whole genome using tophat V2.2.1 and bowtie2 v2.2.3 with parameters q p 8 no novel juncs G o. Raw counts of sequencing reads were generated by using HTSeq v 0.6.1p1. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample	embryos		Microinjection ddx39a Flag mRNA in ddx39a mutant embryos at one cell stage. Lysates were clarified from 24hpf embryos were isolated with anti Flag beads. RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. Magnetic beads with oligodT were used to enrich the mRNAs and then Frag/Prime buffer was added to fragment the mRNAs. The short mRNA fragments were used as templates and random hexamers were used to synthesize first strand cDNA. Then double stranded cDNA was synthesized by adding buffer solution dNTPs and DNA polymeraseΙ. The double stranded cDNAs were purified by DNA clean beads according to the manufacturer’s instructions then repaired at the tail ends polyA added and enriched by PCR amplification. Finally we tested the inserts sizes in the cDNA libraries on an Agilent 2100 Bioanalyzer.		genotype:wild type\|tissue:embryo\|developmental stage:24hpf	GSM2550917	GSM2550917: WT 24hpf RIPseq; Danio rerio; RIP Seq	GSM2550917		1	Microinjection ddx39a Flag mRNA in ddx39a mutant embryos at one cell stage. Lysates were clarified from 24hpf embryos were isolated with anti Flag beads. RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. Magnetic beads with oligodT were used to enrich the mRNAs and then Frag/Prime buffer was added to fragment the mRNAs. The short mRNA fragments were used as templates and random hexamers were used to synthesize first strand cDNA. Then double stranded cDNA was synthesized by adding buffer solution dNTPs and DNA polymeraseΙ. The double stranded cDNAs were purified by DNA clean beads according to the manufacturer’s instructions then repaired at the tail ends polyA added and enriched by PCR amplification. Finally we tested the inserts sizes in the cDNA libraries on an Agilent 2100 Bioanalyzer.	GEO Accession:GSM2550917	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP102513		RDWHDANwwwCAAARAAPEI-205_2.fq.gz RDWHDANwwwCAAARAAPEI-205_1.fq.gz	fastq fastq	3802882200.0	19014411.0	GSM2550917 r1	0:100 1:100	A:733911232;C:1178365174;G:1154031422;T:735690235;N:884137	100	100	733911232	1178365174	1154031422	735690235	884137	SRX2674571	SRS2073697	SRA549449	GEO	Xin Lou Lab, Medical School, Nanjing University	2	0.9866	0.98469	0.30567	0.30486	0.90796	0.90928	0.82926	0.83029	100	100	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	China	2017-03-27	Pharyngula	Embryo	Embryo Imprecise	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
43458	43458	SRR5952027	SRX3110521	SRS2445614	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	IP HCtranslatome RNAseq rep3	GSM2747294	source name:Tgmyo6b:GFP 2A rpl10a 3xHA\|developmental stage:5dpf\|tissue:hair cells enriched\|antibody:HA	IP HCtranslatome 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:hair cells enriched\|antibody:HA	GSM2747294	GSM2747294: IP HCtranslatome RNAseq rep3; Danio rerio; RIP Seq	GSM2747294		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:GSM2747294	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP115900		RiboZF_IP4_R1.fastq.gz RiboZF_IP4_R2.fastq.gz	fastq fastq	4994833580.0	33330363.0	GSM2747294 r1	0:74.96 1:74.90	A:1202677579;C:1288784412;G:1278463604;T:1223941397;N:966588	74	74	1202677579	1288784412	1278463604	1223941397	966588	SRX3110521	SRS2445614	SRA601675	GEO	Department: Institute for Genome Sciences, University of Maryland in Baltimore	2	0.61854	0.6151	0.20328	0.19651	0.83599	0.84104	0.60632	0.59954	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	Embryo Imprecise	All anatomical structures
43459	43459	SRR5952026	SRX3110520	SRS2445613	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	IP HCtranslatome RNAseq rep2	GSM2747293	source name:Tgmyo6b:GFP 2A rpl10a 3xHA\|developmental stage:5dpf\|tissue:hair cells enriched\|antibody:HA	IP HCtranslatome 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:hair cells enriched\|antibody:HA	GSM2747293	GSM2747293: IP HCtranslatome RNAseq rep2; Danio rerio; RIP Seq	GSM2747293		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:GSM2747293	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP115900		RiboZF_IP2_R1.fastq.gz RiboZF_IP2_R2.fastq.gz	fastq fastq	4530855300.0	30205702.0	GSM2747293 r1	0:75 1:75	A:1112381418;C:1153277132;G:1147183468;T:1117133915;N:879367	75	75	1112381418	1153277132	1147183468	1117133915	879367	SRX3110520	SRS2445613	SRA601675	GEO	Department: Institute for Genome Sciences, University of Maryland in Baltimore	2	0.64948	0.64878	0.15967	0.15683	0.80756	0.81288	0.56438	0.56275	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	Embryo Imprecise	All anatomical structures
43460	43460	SRR5952025	SRX3110519	SRS2445612	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	IP HCtranslatome RNAseq rep1	GSM2747292	source name:Tgmyo6b:GFP 2A rpl10a 3xHA\|developmental stage:5dpf\|tissue:hair cells enriched\|antibody:HA	IP HCtranslatome 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:hair cells enriched\|antibody:HA	GSM2747292	GSM2747292: IP HCtranslatome RNAseq rep1; Danio rerio; RIP Seq	GSM2747292		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:GSM2747292	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP115900		RiboZF_IP1_R1.fastq.gz RiboZF_IP1_R2.fastq.gz	fastq fastq	5261113350.0	35074089.0	GSM2747292 r1	0:75 1:75	A:1356848229;C:1276483567;G:1260001700;T:1366757927;N:1021927	75	75	1356848229	1276483567	1260001700	1366757927	1021927	SRX3110519	SRS2445612	SRA601675	GEO	Department: Institute for Genome Sciences, University of Maryland in Baltimore	2	0.66363	0.6599	0.15644	0.15316	0.76808	0.7725	0.48538	0.48933	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	Embryo Imprecise	All anatomical structures
49539	49539	SRR8937005	SRX5717518	SRS4655938	SRP162876	PRJNA493828	Ybx1 binding sites and Ybx1 binding m5C sites in zebrafish embryo sample.	GSE120646	Other	The maternal to zygotic transition MZT is a conserved and fundamental process during which the embryo undergoes dramatic reprogramming to convert maternal environment to embryonic driven programing. However how the maternally supplied transcripts are dynamically regulated during MZT remains largely unknown. Herein through genome wide profiling of RNA 5 methylcytosine m5C in zebrafish early embryos we show that m5C methylated maternal mRNAs display higher stability during MZT. We identify that the Y box binding protein 1 Ybx1 prefers to recognizing m5C modified mRNAs through p p interaction with a key residue Trp45 in its cold shock domain CSD which plays essential roles in maternal mRNA stability and early embryogenesis of zebrafish. Cooperated with an mRNA stabilizer Pabpc1a Ybx1 promotes the stability of its target mRNAs in an m5C dependent manner. Our study demonstrates a novel mechanism of RNA m5C methylation regulated maternal mRNA stability during zebrafish MZT highlighting the critical role of m5C mRNA methylation in early development. Overall design: Examination of Ybx1 binding sites and Ybx1 binding m5C sites in zebrafish embryo. RIP seq: Briefly 500 zebrafish embryos at shield stage 4 hpf were resuspended with 2 ml lysis buffer 150 mM KCl 10 mM HEPES pH 7.6 2 mM EDTA 0.5% NP 40 0.5 mM DTT 1:100 protease inhibitor cocktail 0.4 U/Î¼l RNasin by rotating at 4Â°C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4Â°C for 1 h. 50 Î¼l pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax China and 30 Î¼l Protein A Dynabeads for 4 h at 4Â°C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl 50 mM HEPES pH 7.6 2 mM EDTA 0.05% NP 40 0.5 mM DTT 0.4U/Âµl RNasin for eight times and once with 1ml ice cold 1Ã— PK buffer 100 mM Tris HCl pH 7.4 50 mM NaCl 10 mM EDTA 0.2% SDS the beads was treated i…	parent bioproject:PRJNA534030		RIP INPUT 2hpf rep2	GSM3732425	source name:RIP INPUT 2hpf\|strain:AB strain\|age:2 hpf\|tissue:whole embryo	RIP INPUT 2hpf rep2	Reads were aligned to the zv9 genome assembly using TopHat v2.1.1. MACS2 v2.1.1 were used for the peak calling and peaks were annotated by applying BEDTools’ intersectBed. Genome build: zv9 Supplementary files format and content: Ybx1 binding sites in two biological replicates.	RIP INPUT 2hpf		Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA BisSeq library construction. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode creating reads with a length of 150 bp.		strain:AB strain\|age:2 hpf\|tissue:whole embryo	GSM3732425	GSM3732425: RIP INPUT 2hpf rep2; Danio rerio; RIP Seq	GSM3732425		1	Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA BisSeq library construction. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode creating reads with a length of 150 bp.	GEO Accession:GSM3732425	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP162876		RIP-INPUT_2hpf_rep2_R1.fastq.gz RIP-INPUT_2hpf_rep2_R2.fastq.gz	fastq fastq	16388119500.0	54627065.0	GSM3732425 r1	0:150 1:150	A:3232127065;C:4976385987;G:5052844082;T:3122288663;N:4473703	150	150	3232127065	4976385987	5052844082	3122288663	4473703	SRX5717518	SRS4655938	SRA786939	GEO	Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)	2	0.98209	0.9812	0.33332	0.33565	0.93811	0.94186	0.95153	0.95984	150	150	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	smarter	bulk	clip	iclip	China	2019-04-22	Cleavage	Embryo	Whole Organism	All anatomical structures
49540	49540	SRR8937004	SRX5717517	SRS4655937	SRP162876	PRJNA493828	Ybx1 binding sites and Ybx1 binding m5C sites in zebrafish embryo sample.	GSE120646	Other	The maternal to zygotic transition MZT is a conserved and fundamental process during which the embryo undergoes dramatic reprogramming to convert maternal environment to embryonic driven programing. However how the maternally supplied transcripts are dynamically regulated during MZT remains largely unknown. Herein through genome wide profiling of RNA 5 methylcytosine m5C in zebrafish early embryos we show that m5C methylated maternal mRNAs display higher stability during MZT. We identify that the Y box binding protein 1 Ybx1 prefers to recognizing m5C modified mRNAs through p p interaction with a key residue Trp45 in its cold shock domain CSD which plays essential roles in maternal mRNA stability and early embryogenesis of zebrafish. Cooperated with an mRNA stabilizer Pabpc1a Ybx1 promotes the stability of its target mRNAs in an m5C dependent manner. Our study demonstrates a novel mechanism of RNA m5C methylation regulated maternal mRNA stability during zebrafish MZT highlighting the critical role of m5C mRNA methylation in early development. Overall design: Examination of Ybx1 binding sites and Ybx1 binding m5C sites in zebrafish embryo. RIP seq: Briefly 500 zebrafish embryos at shield stage 4 hpf were resuspended with 2 ml lysis buffer 150 mM KCl 10 mM HEPES pH 7.6 2 mM EDTA 0.5% NP 40 0.5 mM DTT 1:100 protease inhibitor cocktail 0.4 U/Î¼l RNasin by rotating at 4Â°C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4Â°C for 1 h. 50 Î¼l pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax China and 30 Î¼l Protein A Dynabeads for 4 h at 4Â°C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl 50 mM HEPES pH 7.6 2 mM EDTA 0.05% NP 40 0.5 mM DTT 0.4U/Âµl RNasin for eight times and once with 1ml ice cold 1Ã— PK buffer 100 mM Tris HCl pH 7.4 50 mM NaCl 10 mM EDTA 0.2% SDS the beads was treated i…	parent bioproject:PRJNA534030		RIP INPUT 2hpf rep1	GSM3732424	source name:RIP INPUT 2hpf\|strain:AB strain\|age:2 hpf\|tissue:whole embryo	RIP INPUT 2hpf rep1	Reads were aligned to the zv9 genome assembly using TopHat v2.1.1. MACS2 v2.1.1 were used for the peak calling and peaks were annotated by applying BEDTools’ intersectBed. Genome build: zv9 Supplementary files format and content: Ybx1 binding sites in two biological replicates.	RIP INPUT 2hpf		Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA BisSeq library construction. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode creating reads with a length of 150 bp.		strain:AB strain\|age:2 hpf\|tissue:whole embryo	GSM3732424	GSM3732424: RIP INPUT 2hpf rep1; Danio rerio; RIP Seq	GSM3732424		1	Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA BisSeq library construction. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode creating reads with a length of 150 bp.	GEO Accession:GSM3732424	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP162876		RIP-INPUT_2hpf_rep1_R1.fastq.gz RIP-INPUT_2hpf_rep1_R2.fastq.gz	fastq fastq	18857336400.0	62857788.0	GSM3732424 r1	0:150 1:150	A:3116761123;C:6239715125;G:6450542871;T:3049605751;N:711530	150	150	3116761123	6239715125	6450542871	3049605751	711530	SRX5717517	SRS4655937	SRA786939	GEO	Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)	2	0.97874	0.96891	0.03494	0.03355	0.92693	0.93456	0.9502	0.94986	150	150	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	smarter	bulk	clip	iclip	China	2019-04-22	Cleavage	Embryo	Whole Organism	All anatomical structures
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
54307	54307	SRR10129555	SRX6857975	SRS5395856	SRP221863	PRJNA565584	The functions of igf2bp3 during zebrafish early development	PRJNA565584	Whole Genome Sequencing	RNA seq and RIP seq data of wild type and maternal igf2bp3 mutant embryos at different stages.			Model organism or animal sample from Danio rerio	RIP seq zebrafish embryo HA rabbit	strain:AB\|dev stage:embryo\|sex:not applicable\|tissue:embryo\|BioSampleModel:Model organism or animal									RIP seq zebrafish embryo sphere HA	HA sphere	HA sphere	RIP seq			RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP221863		IP2_R1.fq.gz IP2_R2.fq.gz	fastq fastq	7528561800.0	25095206.0	IP2 R1.fq.gz	0:150 1:150	A:1638987252;C:1830922014;G:2628590112;T:1430016657;N:45765	150	150	1638987252	1830922014	2628590112	1430016657	45765	SRX6857975	SRS5395856	SRA962995	Huazhong Agricultural University\|College of Fisheries	Huazhong Agricultural University	2	0.92316	0.96332	0.32571	0.34771	0.89173	0.88962	0.89557	0.89793	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2019-09-17	Blastula	Embryo	Embryo Imprecise	All anatomical structures
54308	54308	SRR10129346	SRX6857766	SRS5395649	SRP221863	PRJNA565584	The functions of igf2bp3 during zebrafish early development	PRJNA565584	Whole Genome Sequencing	RNA seq and RIP seq data of wild type and maternal igf2bp3 mutant embryos at different stages.			Model organism or animal sample from Danio rerio	RIP seq zebrafish embryo IgG rabbit	strain:AB\|dev stage:embryo\|sex:not applicable\|tissue:embryo\|BioSampleModel:Model organism or animal									RIP seq zebrafish embryo sphere IgG	IgG sphere	IgG sphere	RIP seq			RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP221863		IgG1_R1.fq.gz IgG1_R2.fq.gz	fastq fastq	2647374600.0	8824582.0	IgG1 R1.fq.gz	0:150 1:150	A:565620765;C:650153559;G:936592543;T:494992101;N:15632	150	150	565620765	650153559	936592543	494992101	15632	SRX6857766	SRS5395649	SRA962944	Huazhong Agricultural University\|College of Fisheries	Huazhong Agricultural University	2	0.95349	0.96423	0.33504	0.34458	0.93748	0.93726	0.85176	0.91118	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2019-09-17	Blastula	Embryo	Embryo Imprecise	All anatomical structures
60021	60021	SRR12103084	SRX8627422	SRS6915731	SRP269070	PRJNA642405	Changes of m6A RNA methylation following spinal cord injury	PRJNA642405	Other	Results of methylation profiling by MeRIP Seq in both control and larvae with spinal cord injury				SCI IP	strain:not applicable\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:not applicable\|sex:pooled male and female\|tissue:trunk\|sample type:SCI IP\|BioSampleModel:Model organism or animal									IP library sequencing data of treated sample	SCIIP BKDL192540807 1a	SCIIP BKDL192540807 1a	IP library sequencing data of treated sample			RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	HiSeq X Ten	SRP269070		SCIIP_BKDL192540807-1a_1.fq.gz SCIIP_BKDL192540807-1a_2.fq.gz	fastq fastq	7110503700.0	23701679.0	SCIIP BKDL192540807 1a 1.fq.gz	0:150 1:150	A:1520693228;C:1953670419;G:2215620460;T:1420407690;N:111903	150	150	1520693228	1953670419	2215620460	1420407690	111903	SRX8627422	SRS6915731	SRA1091926	Nantong University\|Key Laboratory of Neuroregeneration of Jiangsu and	Nantong University	2	0.9115	0.9147	0.19936	0.2033	0.81864	0.81919	0.66838	0.6677	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2020-06-28	Undetermined	Larval	Trunk	Surface Structure
60022	60022	SRR12103085	SRX8627421	SRS6915730	SRP269070	PRJNA642405	Changes of m6A RNA methylation following spinal cord injury	PRJNA642405	Other	Results of methylation profiling by MeRIP Seq in both control and larvae with spinal cord injury				SCI Input	strain:not applicable\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:not applicable\|sex:pooled male and female\|tissue:trunk\|sample type:SCI Input\|BioSampleModel:Model organism or animal									Input library sequencing data of treated sample	SCIIN BKDL192540809 1a	SCIIN BKDL192540809 1a	Input library sequencing data of treated sample			RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	HiSeq X Ten	SRP269070		SCIIN_BKDL192540809-1a_2.fq.gz SCIIN_BKDL192540809-1a_1.fq.gz	fastq fastq	7774587300.0	25915291.0	SCIIN BKDL192540809 1a 1.fq.gz	0:150 1:150	A:1595151855;C:2243828590;G:2397611978;T:1537918306;N:76571	150	150	1595151855	2243828590	2397611978	1537918306	76571	SRX8627421	SRS6915730	SRA1091926	Nantong University\|Key Laboratory of Neuroregeneration of Jiangsu and	Nantong University	2	0.96018	0.96291	0.23754	0.23744	0.84904	0.85245	0.74661	0.74738	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2020-06-28	Undetermined	Larval	Trunk	Surface Structure
60023	60023	SRR12103086	SRX8627420	SRS6915729	SRP269070	PRJNA642405	Changes of m6A RNA methylation following spinal cord injury	PRJNA642405	Other	Results of methylation profiling by MeRIP Seq in both control and larvae with spinal cord injury				Control IP	strain:not applicable\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:not applicable\|sex:pooled male and female\|tissue:trunk\|sample type:Control IP\|BioSampleModel:Model organism or animal									IP library sequencing data of control sample	controlIP BKDL192540808 1a	controlIP BKDL192540808 1a	IP library sequencing data of control sample			RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	HiSeq X Ten	SRP269070		controlIP_BKDL192540808-1a_2.fq.gz controlIP_BKDL192540808-1a_1.fq.gz	fastq fastq	7359972600.0	24533242.0	controlIP BKDL192540808 1a 1.fq.gz	0:150 1:150	A:1569051886;C:2002692591;G:2333418000;T:1454676484;N:133639	150	150	1569051886	2002692591	2333418000	1454676484	133639	SRX8627420	SRS6915729	SRA1091926	Nantong University\|Key Laboratory of Neuroregeneration of Jiangsu and	Nantong University	2	0.92004	0.92293	0.20272	0.20739	0.83254	0.83291	0.68471	0.65224	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2020-06-28	Undetermined	Larval	Trunk	Surface Structure
60024	60024	SRR12103087	SRX8627419	SRS6915728	SRP269070	PRJNA642405	Changes of m6A RNA methylation following spinal cord injury	PRJNA642405	Other	Results of methylation profiling by MeRIP Seq in both control and larvae with spinal cord injury				Control Input	strain:not applicable\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:not applicable\|sex:pooled male and female\|tissue:trunk\|sample type:Control Input\|BioSampleModel:Model organism or animal									Input library sequencing data of control sample	controlIN BKDL192540810 1a	controlIN BKDL192540810 1a	Input library sequencing data of control sample			RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	HiSeq X Ten	SRP269070		controlIN_BKDL192540810-1a_1.fq.gz controlIN_BKDL192540810-1a_2.fq.gz	fastq fastq	7830123600.0	26100412.0	controlIN BKDL192540810 1a 1.fq.gz	0:150 1:150	A:1589371287;C:2296547915;G:2409439612;T:1534684151;N:80635	150	150	1589371287	2296547915	2409439612	1534684151	80635	SRX8627419	SRS6915728	SRA1091926	Nantong University\|Key Laboratory of Neuroregeneration of Jiangsu and	Nantong University	2	0.97501	0.97626	0.23177	0.23578	0.89497	0.8971	0.78501	0.77674	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2020-06-28	Undetermined	Larval	Trunk	Surface Structure
60025	60025	SRR12103783	SRX8627954	SRS6916259	SRP269097	PRJNA642647	PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos	GSE153436	Other	Chemical modifications of proteins DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs m6A sites are preferentially enriched near stop codons in three prime UTRs and within exons suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes it is important to understand the effects of exposure on this important layer of gene regulation. Hence the objective of this study was to characterize the acute effects of developmental exposure to PCB126 an environmentally relevant dioxin like PCB on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK Hedgehog Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly none of the AHR target genes overlapped with …		pubmed:33064826	PCB4 IP	GSM4644253	tissue:78 hpf embryos\|agent:PCB126\|strain:AB\|fraction:m6A immunoprecipitated sample\|antibody:m6A antibody Synaptic Systems catalog#202 003; RRID: AB 2279217	PCB4 IP	Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf	78 hpf embryos		AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.		agent:PCB126\|strain:AB\|fraction:m6A immunoprecipitated sample\|antibody:m6A antibody Synaptic Systems catalog#202 003; RRID: AB 2279217	GSM4644253	GSM4644253: PCB4 IP; Danio rerio; RIP Seq	GSM4644253		1	AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.	GEO Accession:GSM4644253	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP269097		P4_m6A-IP_S16_R1_001.fastq.gz P4_m6A-IP_S16_R2_001.fastq.gz	fastq fastq	2309150560.0	15191780.0	GSM4644253 r1	0:76 1:76	A:490672579;C:656568819;G:666651729;T:495020365;N:237068	76	76	490672579	656568819	666651729	495020365	237068	SRX8627954	SRS6916259	SRA1091999	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	2	0.94474	0.944	0.18094	0.18203	0.7515	0.75554	0.60771	0.6152	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	United States	2020-06-28	Larval	Larval	Embryo Imprecise	All anatomical structures
60026	60026	SRR12103782	SRX8627953	SRS6916258	SRP269097	PRJNA642647	PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos	GSE153436	Other	Chemical modifications of proteins DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs m6A sites are preferentially enriched near stop codons in three prime UTRs and within exons suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes it is important to understand the effects of exposure on this important layer of gene regulation. Hence the objective of this study was to characterize the acute effects of developmental exposure to PCB126 an environmentally relevant dioxin like PCB on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK Hedgehog Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly none of the AHR target genes overlapped with …		pubmed:33064826	PCB3 IP	GSM4644252	tissue:78 hpf embryos\|agent:PCB126\|strain:AB\|fraction:m6A immunoprecipitated sample\|antibody:m6A antibody Synaptic Systems catalog#202 003; RRID: AB 2279216	PCB3 IP	Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf	78 hpf embryos		AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.		agent:PCB126\|strain:AB\|fraction:m6A immunoprecipitated sample\|antibody:m6A antibody Synaptic Systems catalog#202 003; RRID: AB 2279216	GSM4644252	GSM4644252: PCB3 IP; Danio rerio; RIP Seq	GSM4644252		1	AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.	GEO Accession:GSM4644252	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP269097		P3_m6A-IP_S15_R2_001.fastq.gz P3_m6A-IP_S15_R1_001.fastq.gz	fastq fastq	2965972504.0	19512977.0	GSM4644252 r1	0:76 1:76	A:620624207;C:853765538;G:874990332;T:616281897;N:310530	76	76	620624207	853765538	874990332	616281897	310530	SRX8627953	SRS6916258	SRA1091999	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	2	0.93433	0.93213	0.16543	0.16208	0.75043	0.753	0.62186	0.64359	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	United States	2020-06-28	Larval	Larval	Embryo Imprecise	All anatomical structures
60027	60027	SRR12103781	SRX8627952	SRS6916257	SRP269097	PRJNA642647	PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos	GSE153436	Other	Chemical modifications of proteins DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs m6A sites are preferentially enriched near stop codons in three prime UTRs and within exons suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes it is important to understand the effects of exposure on this important layer of gene regulation. Hence the objective of this study was to characterize the acute effects of developmental exposure to PCB126 an environmentally relevant dioxin like PCB on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK Hedgehog Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly none of the AHR target genes overlapped with …		pubmed:33064826	PCB2 IP	GSM4644251	tissue:78 hpf embryos\|agent:PCB126\|strain:AB\|fraction:m6A immunoprecipitated sample\|antibody:m6A antibody Synaptic Systems catalog#202 003; RRID: AB 2279215	PCB2 IP	Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf	78 hpf embryos		AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.		agent:PCB126\|strain:AB\|fraction:m6A immunoprecipitated sample\|antibody:m6A antibody Synaptic Systems catalog#202 003; RRID: AB 2279215	GSM4644251	GSM4644251: PCB2 IP; Danio rerio; RIP Seq	GSM4644251		1	AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.	GEO Accession:GSM4644251	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP269097		P2_m6A-IP_S14_R2_001.fastq.gz P2_m6A-IP_S14_R1_001.fastq.gz	fastq fastq	2687973472.0	17684036.0	GSM4644251 r1	0:76 1:76	A:585901626;C:744255122;G:756993274;T:600539454;N:283996	76	76	585901626	744255122	756993274	600539454	283996	SRX8627952	SRS6916257	SRA1091999	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	2	0.9445	0.94466	0.16876	0.17035	0.74728	0.75022	0.57878	0.57933	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	United States	2020-06-28	Larval	Larval	Embryo Imprecise	All anatomical structures
60028	60028	SRR12103780	SRX8627951	SRS6916256	SRP269097	PRJNA642647	PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos	GSE153436	Other	Chemical modifications of proteins DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs m6A sites are preferentially enriched near stop codons in three prime UTRs and within exons suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes it is important to understand the effects of exposure on this important layer of gene regulation. Hence the objective of this study was to characterize the acute effects of developmental exposure to PCB126 an environmentally relevant dioxin like PCB on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK Hedgehog Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly none of the AHR target genes overlapped with …		pubmed:33064826	PCB1 IP	GSM4644250	tissue:78 hpf embryos\|agent:PCB126\|strain:AB\|fraction:m6A immunoprecipitated sample\|antibody:m6A antibody Synaptic Systems catalog#202 003; RRID: AB 2279214	PCB1 IP	Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf	78 hpf embryos		AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.		agent:PCB126\|strain:AB\|fraction:m6A immunoprecipitated sample\|antibody:m6A antibody Synaptic Systems catalog#202 003; RRID: AB 2279214	GSM4644250	GSM4644250: PCB1 IP; Danio rerio; RIP Seq	GSM4644250		1	AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.	GEO Accession:GSM4644250	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP269097		P1_m6A-IP_S13_R1_001.fastq.gz P1_m6A-IP_S13_R2_001.fastq.gz	fastq fastq	2596174288.0	17080094.0	GSM4644250 r1	0:76 1:76	A:564523297;C:723443207;G:735894528;T:572044392;N:268864	76	76	564523297	723443207	735894528	572044392	268864	SRX8627951	SRS6916256	SRA1091999	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	2	0.93494	0.93528	0.17469	0.17518	0.746	0.74803	0.60114	0.60005	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	United States	2020-06-28	Larval	Larval	Embryo Imprecise	All anatomical structures
60029	60029	SRR12103779	SRX8627950	SRS6916255	SRP269097	PRJNA642647	PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos	GSE153436	Other	Chemical modifications of proteins DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs m6A sites are preferentially enriched near stop codons in three prime UTRs and within exons suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes it is important to understand the effects of exposure on this important layer of gene regulation. Hence the objective of this study was to characterize the acute effects of developmental exposure to PCB126 an environmentally relevant dioxin like PCB on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK Hedgehog Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly none of the AHR target genes overlapped with …		pubmed:33064826	PCB4 Input	GSM4644249	tissue:78 hpf embryos\|agent:PCB126\|strain:AB\|fraction:input control\|antibody:n1	PCB4 Input	Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf	78 hpf embryos		AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.		agent:PCB126\|strain:AB\|fraction:input control\|antibody:n1	GSM4644249	GSM4644249: PCB4 Input; Danio rerio; RIP Seq	GSM4644249		1	AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.	GEO Accession:GSM4644249	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP269097		P4_INPUT_S8_R1_001.fastq.gz P4_INPUT_S8_R2_001.fastq.gz	fastq fastq	3655473384.0	24049167.0	GSM4644249 r1	0:76 1:76	A:680110064;C:1145409769;G:1179103219;T:650470372;N:379960	76	76	680110064	1145409769	1179103219	650470372	379960	SRX8627950	SRS6916255	SRA1091999	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	2	0.93037	0.96319	0.21668	0.22563	0.86338	0.86385	0.77257	0.70059	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	United States	2020-06-28	Larval	Larval	Embryo Imprecise	All anatomical structures
60030	60030	SRR12103778	SRX8627949	SRS6916254	SRP269097	PRJNA642647	PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos	GSE153436	Other	Chemical modifications of proteins DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs m6A sites are preferentially enriched near stop codons in three prime UTRs and within exons suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes it is important to understand the effects of exposure on this important layer of gene regulation. Hence the objective of this study was to characterize the acute effects of developmental exposure to PCB126 an environmentally relevant dioxin like PCB on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK Hedgehog Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly none of the AHR target genes overlapped with …		pubmed:33064826	PCB3 Input	GSM4644248	tissue:78 hpf embryos\|agent:PCB126\|strain:AB\|fraction:input control\|antibody:n1	PCB3 Input	Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf	78 hpf embryos		AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.		agent:PCB126\|strain:AB\|fraction:input control\|antibody:n1	GSM4644248	GSM4644248: PCB3 Input; Danio rerio; RIP Seq	GSM4644248		1	AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.	GEO Accession:GSM4644248	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP269097		P3_INPUT_S7_R1_001.fastq.gz P3_INPUT_S7_R2_001.fastq.gz	fastq fastq	4926238376.0	32409463.0	GSM4644248 r1	0:76 1:76	A:929043061;C:1530175131;G:1577898210;T:888604850;N:517124	76	76	929043061	1530175131	1577898210	888604850	517124	SRX8627949	SRS6916254	SRA1091999	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	2	0.92875	0.95698	0.21539	0.22073	0.85253	0.85431	0.76235	0.68659	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	United States	2020-06-28	Larval	Larval	Embryo Imprecise	All anatomical structures
60031	60031	SRR12103777	SRX8627948	SRS6916253	SRP269097	PRJNA642647	PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos	GSE153436	Other	Chemical modifications of proteins DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs m6A sites are preferentially enriched near stop codons in three prime UTRs and within exons suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes it is important to understand the effects of exposure on this important layer of gene regulation. Hence the objective of this study was to characterize the acute effects of developmental exposure to PCB126 an environmentally relevant dioxin like PCB on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK Hedgehog Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly none of the AHR target genes overlapped with …		pubmed:33064826	PCB2 Input	GSM4644247	tissue:78 hpf embryos\|agent:PCB126\|strain:AB\|fraction:input control\|antibody:n1	PCB2 Input	Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf	78 hpf embryos		AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.		agent:PCB126\|strain:AB\|fraction:input control\|antibody:n1	GSM4644247	GSM4644247: PCB2 Input; Danio rerio; RIP Seq	GSM4644247		1	AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.	GEO Accession:GSM4644247	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP269097		P2_INPUT_S6_R1_001.fastq.gz P2_INPUT_S6_R2_001.fastq.gz	fastq fastq	5669611400.0	37300075.0	GSM4644247 r1	0:76 1:76	A:1050955836;C:1780355588;G:1829450728;T:1008257255;N:591993	76	76	1050955836	1780355588	1829450728	1008257255	591993	SRX8627948	SRS6916253	SRA1091999	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	2	0.93297	0.93791	0.21298	0.21667	0.85902	0.86302	0.7387	0.69759	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	United States	2020-06-28	Larval	Larval	Embryo Imprecise	All anatomical structures
60032	60032	SRR12103776	SRX8627947	SRS6916252	SRP269097	PRJNA642647	PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos	GSE153436	Other	Chemical modifications of proteins DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs m6A sites are preferentially enriched near stop codons in three prime UTRs and within exons suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes it is important to understand the effects of exposure on this important layer of gene regulation. Hence the objective of this study was to characterize the acute effects of developmental exposure to PCB126 an environmentally relevant dioxin like PCB on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK Hedgehog Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly none of the AHR target genes overlapped with …		pubmed:33064826	PCB1 Input	GSM4644246	tissue:78 hpf embryos\|agent:PCB126\|strain:AB\|fraction:input control\|antibody:n1	PCB1 Input	Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf	78 hpf embryos		AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.		agent:PCB126\|strain:AB\|fraction:input control\|antibody:n1	GSM4644246	GSM4644246: PCB1 Input; Danio rerio; RIP Seq	GSM4644246		1	AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.	GEO Accession:GSM4644246	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP269097		P1_INPUT_S5_R1_001.fastq.gz P1_INPUT_S5_R2_001.fastq.gz	fastq fastq	4154972744.0	27335347.0	GSM4644246 r1	0:76 1:76	A:764769282;C:1310937656;G:1344287240;T:734545457;N:433109	76	76	764769282	1310937656	1344287240	734545457	433109	SRX8627947	SRS6916252	SRA1091999	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	2	0.92033	0.95428	0.21666	0.2245	0.86571	0.8678	0.74089	0.68247	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	United States	2020-06-28	Larval	Larval	Embryo Imprecise	All anatomical structures
60033	60033	SRR12103775	SRX8627946	SRS6916251	SRP269097	PRJNA642647	PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos	GSE153436	Other	Chemical modifications of proteins DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs m6A sites are preferentially enriched near stop codons in three prime UTRs and within exons suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes it is important to understand the effects of exposure on this important layer of gene regulation. Hence the objective of this study was to characterize the acute effects of developmental exposure to PCB126 an environmentally relevant dioxin like PCB on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK Hedgehog Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly none of the AHR target genes overlapped with …		pubmed:33064826	DMSO4 IP	GSM4644245	tissue:78 hpf embryos\|agent:DMSO control\|strain:AB\|fraction:m6A immunoprecipitated sample\|antibody:m6A antibody Synaptic Systems catalog#202 003; RRID: AB 2279217	DMSO4 IP	Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf	78 hpf embryos		AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.		agent:DMSO control\|strain:AB\|fraction:m6A immunoprecipitated sample\|antibody:m6A antibody Synaptic Systems catalog#202 003; RRID: AB 2279217	GSM4644245	GSM4644245: DMSO4 IP; Danio rerio; RIP Seq	GSM4644245		1	AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.	GEO Accession:GSM4644245	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP269097		D4_m6A-IP_S12_R1_001.fastq.gz D4_m6A-IP_S12_R2_001.fastq.gz	fastq fastq	2415539920.0	15891710.0	GSM4644245 r1	0:76 1:76	A:519904759;C:674887600;G:688106098;T:532387711;N:253752	76	76	519904759	674887600	688106098	532387711	253752	SRX8627946	SRS6916251	SRA1091999	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	2	0.94931	0.94824	0.16515	0.16656	0.74858	0.7497	0.57724	0.58102	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	United States	2020-06-28	Larval	Larval	Embryo Imprecise	All anatomical structures
60034	60034	SRR12103774	SRX8627945	SRS6916250	SRP269097	PRJNA642647	PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos	GSE153436	Other	Chemical modifications of proteins DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs m6A sites are preferentially enriched near stop codons in three prime UTRs and within exons suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes it is important to understand the effects of exposure on this important layer of gene regulation. Hence the objective of this study was to characterize the acute effects of developmental exposure to PCB126 an environmentally relevant dioxin like PCB on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK Hedgehog Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly none of the AHR target genes overlapped with …		pubmed:33064826	DMSO3 IP	GSM4644244	tissue:78 hpf embryos\|agent:DMSO control\|strain:AB\|fraction:m6A immunoprecipitated sample\|antibody:m6A antibody Synaptic Systems catalog#202 003; RRID: AB 2279216	DMSO3 IP	Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf	78 hpf embryos		AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.		agent:DMSO control\|strain:AB\|fraction:m6A immunoprecipitated sample\|antibody:m6A antibody Synaptic Systems catalog#202 003; RRID: AB 2279216	GSM4644244	GSM4644244: DMSO3 IP; Danio rerio; RIP Seq	GSM4644244		1	AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.	GEO Accession:GSM4644244	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP269097		D3_m6A-IP_S11_R1_001.fastq.gz D3_m6A-IP_S11_R2_001.fastq.gz	fastq fastq	2419255408.0	15916154.0	GSM4644244 r1	0:76 1:76	A:524637988;C:675158080;G:687344217;T:531861650;N:253473	76	76	524637988	675158080	687344217	531861650	253473	SRX8627945	SRS6916250	SRA1091999	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	2	0.93623	0.93621	0.18212	0.18165	0.74308	0.74426	0.60527	0.60757	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	United States	2020-06-28	Larval	Larval	Embryo Imprecise	All anatomical structures
60035	60035	SRR12103773	SRX8627944	SRS6916249	SRP269097	PRJNA642647	PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos	GSE153436	Other	Chemical modifications of proteins DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs m6A sites are preferentially enriched near stop codons in three prime UTRs and within exons suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes it is important to understand the effects of exposure on this important layer of gene regulation. Hence the objective of this study was to characterize the acute effects of developmental exposure to PCB126 an environmentally relevant dioxin like PCB on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK Hedgehog Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly none of the AHR target genes overlapped with …		pubmed:33064826	DMSO2 IP	GSM4644243	tissue:78 hpf embryos\|agent:DMSO control\|strain:AB\|fraction:m6A immunoprecipitated sample\|antibody:m6A antibody Synaptic Systems catalog#202 003; RRID: AB 2279215	DMSO2 IP	Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf	78 hpf embryos		AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.		agent:DMSO control\|strain:AB\|fraction:m6A immunoprecipitated sample\|antibody:m6A antibody Synaptic Systems catalog#202 003; RRID: AB 2279215	GSM4644243	GSM4644243: DMSO2 IP; Danio rerio; RIP Seq	GSM4644243		1	AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.	GEO Accession:GSM4644243	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP269097		D2_m6A-IP_S10_R1_001.fastq.gz D2_m6A-IP_S10_R2_001.fastq.gz	fastq fastq	2698406448.0	17752674.0	GSM4644243 r1	0:76 1:76	A:578126060;C:760791571;G:775423382;T:583783650;N:281785	76	76	578126060	760791571	775423382	583783650	281785	SRX8627944	SRS6916249	SRA1091999	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	2	0.9433	0.94318	0.17976	0.1816	0.74992	0.75215	0.58844	0.61497	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	United States	2020-06-28	Larval	Larval	Embryo Imprecise	All anatomical structures
60036	60036	SRR12103772	SRX8627943	SRS6916248	SRP269097	PRJNA642647	PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos	GSE153436	Other	Chemical modifications of proteins DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs m6A sites are preferentially enriched near stop codons in three prime UTRs and within exons suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes it is important to understand the effects of exposure on this important layer of gene regulation. Hence the objective of this study was to characterize the acute effects of developmental exposure to PCB126 an environmentally relevant dioxin like PCB on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK Hedgehog Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly none of the AHR target genes overlapped with …		pubmed:33064826	DMSO1 IP	GSM4644242	tissue:78 hpf embryos\|agent:DMSO control\|strain:AB\|fraction:m6A immunoprecipitated sample\|antibody:m6A antibody Synaptic Systems catalog#202 003; RRID: AB 2279214	DMSO1 IP	Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf	78 hpf embryos		AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.		agent:DMSO control\|strain:AB\|fraction:m6A immunoprecipitated sample\|antibody:m6A antibody Synaptic Systems catalog#202 003; RRID: AB 2279214	GSM4644242	GSM4644242: DMSO1 IP; Danio rerio; RIP Seq	GSM4644242		1	AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.	GEO Accession:GSM4644242	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP269097		D1_m6A-IP_S9_R1_001.fastq.gz D1_m6A-IP_S9_R2_001.fastq.gz	fastq fastq	2588221344.0	17027772.0	GSM4644242 r1	0:76 1:76	A:552076254;C:730948542;G:744135059;T:560788856;N:272633	76	76	552076254	730948542	744135059	560788856	272633	SRX8627943	SRS6916248	SRA1091999	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	2	0.93871	0.9398	0.17681	0.17588	0.74688	0.74915	0.59376	0.61045	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	United States	2020-06-28	Larval	Larval	Embryo Imprecise	All anatomical structures
60037	60037	SRR12103771	SRX8627942	SRS6916247	SRP269097	PRJNA642647	PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos	GSE153436	Other	Chemical modifications of proteins DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs m6A sites are preferentially enriched near stop codons in three prime UTRs and within exons suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes it is important to understand the effects of exposure on this important layer of gene regulation. Hence the objective of this study was to characterize the acute effects of developmental exposure to PCB126 an environmentally relevant dioxin like PCB on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK Hedgehog Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly none of the AHR target genes overlapped with …		pubmed:33064826	DMSO4 Input	GSM4644241	tissue:78 hpf embryos\|agent:DMSO control\|strain:AB\|fraction:input control\|antibody:n1	DMSO4 Input	Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf	78 hpf embryos		AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.		agent:DMSO control\|strain:AB\|fraction:input control\|antibody:n1	GSM4644241	GSM4644241: DMSO4 Input; Danio rerio; RIP Seq	GSM4644241		1	AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.	GEO Accession:GSM4644241	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP269097		D4_INPUT_S4_R1_001.fastq.gz D4_INPUT_S4_R2_001.fastq.gz	fastq fastq	4085824752.0	26880426.0	GSM4644241 r1	0:76 1:76	A:734095239;C:1307425224;G:1339970208;T:703907493;N:426588	76	76	734095239	1307425224	1339970208	703907493	426588	SRX8627942	SRS6916247	SRA1091999	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	2	0.94341	0.94693	0.21035	0.21294	0.86306	0.86571	0.66228	0.69648	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	United States	2020-06-28	Larval	Larval	Embryo Imprecise	All anatomical structures
60038	60038	SRR12103770	SRX8627941	SRS6916246	SRP269097	PRJNA642647	PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos	GSE153436	Other	Chemical modifications of proteins DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs m6A sites are preferentially enriched near stop codons in three prime UTRs and within exons suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes it is important to understand the effects of exposure on this important layer of gene regulation. Hence the objective of this study was to characterize the acute effects of developmental exposure to PCB126 an environmentally relevant dioxin like PCB on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK Hedgehog Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly none of the AHR target genes overlapped with …		pubmed:33064826	DMSO3 Input	GSM4644240	tissue:78 hpf embryos\|agent:DMSO control\|strain:AB\|fraction:input control\|antibody:n1	DMSO3 Input	Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf	78 hpf embryos		AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.		agent:DMSO control\|strain:AB\|fraction:input control\|antibody:n1	GSM4644240	GSM4644240: DMSO3 Input; Danio rerio; RIP Seq	GSM4644240		1	AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.	GEO Accession:GSM4644240	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP269097		D3_INPUT_S3_R1_001.fastq.gz D3_INPUT_S3_R2_001.fastq.gz	fastq fastq	3627749800.0	23866775.0	GSM4644240 r1	0:76 1:76	A:677883991;C:1133504965;G:1166401920;T:649582074;N:376850	76	76	677883991	1133504965	1166401920	649582074	376850	SRX8627941	SRS6916246	SRA1091999	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	2	0.92028	0.96282	0.2164	0.22913	0.86517	0.8661	0.73802	0.70578	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	United States	2020-06-28	Larval	Larval	Embryo Imprecise	All anatomical structures
60039	60039	SRR12103769	SRX8627940	SRS6916245	SRP269097	PRJNA642647	PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos	GSE153436	Other	Chemical modifications of proteins DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs m6A sites are preferentially enriched near stop codons in three prime UTRs and within exons suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes it is important to understand the effects of exposure on this important layer of gene regulation. Hence the objective of this study was to characterize the acute effects of developmental exposure to PCB126 an environmentally relevant dioxin like PCB on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK Hedgehog Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly none of the AHR target genes overlapped with …		pubmed:33064826	DMSO2 Input	GSM4644239	tissue:78 hpf embryos\|agent:DMSO control\|strain:AB\|fraction:input control\|antibody:n1	DMSO2 Input	Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf	78 hpf embryos		AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.		agent:DMSO control\|strain:AB\|fraction:input control\|antibody:n1	GSM4644239	GSM4644239: DMSO2 Input; Danio rerio; RIP Seq	GSM4644239		1	AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.	GEO Accession:GSM4644239	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP269097		D2_INPUT_S2_R2_001.fastq.gz D2_INPUT_S2_R1_001.fastq.gz	fastq fastq	2991355592.0	19679971.0	GSM4644239 r1	0:76 1:76	A:555548434;C:937287598;G:965607991;T:532600162;N:311407	76	76	555548434	937287598	965607991	532600162	311407	SRX8627940	SRS6916245	SRA1091999	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	2	0.92966	0.96538	0.21752	0.22835	0.86137	0.86701	0.71065	0.70316	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	United States	2020-06-28	Larval	Larval	Embryo Imprecise	All anatomical structures
60040	60040	SRR12103768	SRX8627939	SRS6916244	SRP269097	PRJNA642647	PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos	GSE153436	Other	Chemical modifications of proteins DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs m6A sites are preferentially enriched near stop codons in three prime UTRs and within exons suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes it is important to understand the effects of exposure on this important layer of gene regulation. Hence the objective of this study was to characterize the acute effects of developmental exposure to PCB126 an environmentally relevant dioxin like PCB on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK Hedgehog Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly none of the AHR target genes overlapped with …		pubmed:33064826	DMSO1 Input	GSM4644238	tissue:78 hpf embryos\|agent:DMSO control\|strain:AB\|fraction:input control\|antibody:n1	DMSO1 Input	Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf	78 hpf embryos		AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.		agent:DMSO control\|strain:AB\|fraction:input control\|antibody:n1	GSM4644238	GSM4644238: DMSO1 Input; Danio rerio; RIP Seq	GSM4644238		1	AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl 99.2% purity; UltraScientific RI USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing. Four biological replicates per treatment condition.	GEO Accession:GSM4644238	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP269097		D1_INPUT_S1_R1_001.fastq.gz D1_INPUT_S1_R2_001.fastq.gz	fastq fastq	3551567552.0	23365576.0	GSM4644238 r1	0:76 1:76	A:659305531;C:1112775748;G:1146213503;T:632894453;N:378317	76	76	659305531	1112775748	1146213503	632894453	378317	SRX8627939	SRS6916244	SRA1091999	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	2	0.92942	0.96366	0.21295	0.2231	0.8574	0.85934	0.75989	0.75855	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	United States	2020-06-28	Larval	Larval	Embryo Imprecise	All anatomical structures
66194	66194	SRR16096233	SRX12382357	SRS10353019	SRP339082	PRJNA766854	RNA m6A methylome from zebrafish zygotes mouse liver polyA selected RNAs mouse embryonic stem cells spike in RNA controls and single mouse oocytes and embryos	GSE184893	Other	N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes including meiosis and early embryo development. Despite advances in methodology for m6A mapping the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA mouse embryonic stem cells and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes 3 biological replicates for 5 zygotes and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng 1 ng and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line from ATCC SCRC 1011 samples: 1000 cells 100 cells and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula S. et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula S. et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages and embryos at zygote 2 cell 8 cell and…		pubmed:37349523	ZF zygote IP 1cell Rep5	GSM5599725	tissue:ZF zygote IP 1cell\|developmental stage:Zygote\|molecule subtype:rRNA free RNA	ZF zygote IP 1cell Rep5	Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713 GSM5599714 GSM5599715 GSM5599716 GSM5599717 GSM5599718 GSM5599719 GSM5599720 GSM5599721 GSM5599722 GSM5599723 GSM5599724 GSM5599725 mouse polyA selected RNA samples GSM5599726 GSM5599727 GSM5599728 GSM5599729 GSM5599730 GSM5599731 GSM5599732 GSM5599733 and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter “ 5 8 no mixed no discordant”. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter “ bs 10 normalizeUsing RPKM”. Genome build: mm10 for mouse danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.	ZF zygote IP 1cell	For mouse GV oocyte collection 8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida followed by three washes in M2 medium. For mouse MII oocyte collection 4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium. For mouse early embryo collection 8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28 hours zygote 39 43 hours 2 cell 68 70 hours 8 cell and 92 94 hours blastocyst post hCG administration the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium.	For zebrafish bulk zygote samples total RNA was extracted from 100 zebrafish zygotes using TRIzol™ Reagent and eluated in 100 μl of RNase free water. Then 10 μl and 5 μl samples were taken for 10 zygote and 5 zygote samples respectively and volumes were adjusted to 12 μl with nuclease free water. For zebrafish single zygote samples single zygote was manually picked and distributed into 12 μl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples the cells were sorted into 12 μl 1X Lysis buffer using BD FACSMelody™ Cell Sorter BD Biosciences. For mouse oocyte and embryo samples post three washes in M2 medium oocytes and embryos were manually picked and put into 12 μl 1X Lysis buffer. For picoMeRIP seq experiment NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.		developmental stage:Zygote\|molecule subtype:rRNA free RNA	GSM5599725	GSM5599725: ZF zygote IP 1cell Rep5; Danio rerio; RIP Seq	GSM5599725		1	For mouse liver total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote mouse MII oocyte and mouse blastocyst samples the single cells were manually picked and sorted into 12 μl 1X lysis buffer Takara; NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2 × 30 seconds incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.	GEO Accession:GSM5599725	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP339082	loader:fastq load.py	ZF_zygote_IP_1cell_Rep5_R1.fastq.gz ZF_zygote_IP_1cell_Rep5_R2.fastq.gz	fastq fastq	3660517860.0	35887430.0	GSM5599725 r1	0:51 1:51	A:858138600;C:924733544;G:1002150083;T:875349961;N:145672	51	51	858138600	924733544	1002150083	875349961	145672	SRX12382357	SRS10353019	SRA1301707	GEO	Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan	2	0.83384	0.82667	0.09687	0.11892	0.79076	0.79326	0.63739	0.60941	51	51	B	B	biological fallback assumption	illumina	novaseq_era	3prime	poly_a	nebnext	bulk	bulk	bulk	United States	2021-09-28	Zygote	Embryo	Oocyte	Reproductive System
66195	66195	SRR16096232	SRX12382356	SRS10353018	SRP339082	PRJNA766854	RNA m6A methylome from zebrafish zygotes mouse liver polyA selected RNAs mouse embryonic stem cells spike in RNA controls and single mouse oocytes and embryos	GSE184893	Other	N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes including meiosis and early embryo development. Despite advances in methodology for m6A mapping the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA mouse embryonic stem cells and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes 3 biological replicates for 5 zygotes and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng 1 ng and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line from ATCC SCRC 1011 samples: 1000 cells 100 cells and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula S. et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula S. et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages and embryos at zygote 2 cell 8 cell and…		pubmed:37349523	ZF zygote IP 1cell Rep4	GSM5599724	tissue:ZF zygote IP 1cell\|developmental stage:Zygote\|molecule subtype:rRNA free RNA	ZF zygote IP 1cell Rep4	Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713 GSM5599714 GSM5599715 GSM5599716 GSM5599717 GSM5599718 GSM5599719 GSM5599720 GSM5599721 GSM5599722 GSM5599723 GSM5599724 GSM5599725 mouse polyA selected RNA samples GSM5599726 GSM5599727 GSM5599728 GSM5599729 GSM5599730 GSM5599731 GSM5599732 GSM5599733 and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter “ 5 8 no mixed no discordant”. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter “ bs 10 normalizeUsing RPKM”. Genome build: mm10 for mouse danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.	ZF zygote IP 1cell	For mouse GV oocyte collection 8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida followed by three washes in M2 medium. For mouse MII oocyte collection 4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium. For mouse early embryo collection 8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28 hours zygote 39 43 hours 2 cell 68 70 hours 8 cell and 92 94 hours blastocyst post hCG administration the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium.	For zebrafish bulk zygote samples total RNA was extracted from 100 zebrafish zygotes using TRIzol™ Reagent and eluated in 100 μl of RNase free water. Then 10 μl and 5 μl samples were taken for 10 zygote and 5 zygote samples respectively and volumes were adjusted to 12 μl with nuclease free water. For zebrafish single zygote samples single zygote was manually picked and distributed into 12 μl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples the cells were sorted into 12 μl 1X Lysis buffer using BD FACSMelody™ Cell Sorter BD Biosciences. For mouse oocyte and embryo samples post three washes in M2 medium oocytes and embryos were manually picked and put into 12 μl 1X Lysis buffer. For picoMeRIP seq experiment NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.		developmental stage:Zygote\|molecule subtype:rRNA free RNA	GSM5599724	GSM5599724: ZF zygote IP 1cell Rep4; Danio rerio; RIP Seq	GSM5599724		1	For mouse liver total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote mouse MII oocyte and mouse blastocyst samples the single cells were manually picked and sorted into 12 μl 1X lysis buffer Takara; NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2 × 30 seconds incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.	GEO Accession:GSM5599724	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP339082	loader:fastq load.py	ZF_zygote_IP_1cell_Rep4_R1.fastq.gz ZF_zygote_IP_1cell_Rep4_R2.fastq.gz	fastq fastq	3660205842.0	35884371.0	GSM5599724 r1	0:51 1:51	A:895738659;C:880838836;G:971118499;T:912364119;N:145729	51	51	895738659	880838836	971118499	912364119	145729	SRX12382356	SRS10353018	SRA1301707	GEO	Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan	2	0.87258	0.86932	0.06573	0.07958	0.78044	0.78374	0.55531	0.5462	51	51	B	B	biological fallback assumption	illumina	novaseq_era	3prime	poly_a	nebnext	bulk	bulk	bulk	United States	2021-09-28	Zygote	Embryo	Oocyte	Reproductive System
66196	66196	SRR16096231	SRX12382355	SRS10353016	SRP339082	PRJNA766854	RNA m6A methylome from zebrafish zygotes mouse liver polyA selected RNAs mouse embryonic stem cells spike in RNA controls and single mouse oocytes and embryos	GSE184893	Other	N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes including meiosis and early embryo development. Despite advances in methodology for m6A mapping the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA mouse embryonic stem cells and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes 3 biological replicates for 5 zygotes and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng 1 ng and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line from ATCC SCRC 1011 samples: 1000 cells 100 cells and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula S. et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula S. et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages and embryos at zygote 2 cell 8 cell and…		pubmed:37349523	ZF zygote IP 1cell Rep3	GSM5599723	tissue:ZF zygote IP 1cell\|developmental stage:Zygote\|molecule subtype:rRNA free RNA	ZF zygote IP 1cell Rep3	Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713 GSM5599714 GSM5599715 GSM5599716 GSM5599717 GSM5599718 GSM5599719 GSM5599720 GSM5599721 GSM5599722 GSM5599723 GSM5599724 GSM5599725 mouse polyA selected RNA samples GSM5599726 GSM5599727 GSM5599728 GSM5599729 GSM5599730 GSM5599731 GSM5599732 GSM5599733 and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter “ 5 8 no mixed no discordant”. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter “ bs 10 normalizeUsing RPKM”. Genome build: mm10 for mouse danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.	ZF zygote IP 1cell	For mouse GV oocyte collection 8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida followed by three washes in M2 medium. For mouse MII oocyte collection 4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium. For mouse early embryo collection 8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28 hours zygote 39 43 hours 2 cell 68 70 hours 8 cell and 92 94 hours blastocyst post hCG administration the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium.	For zebrafish bulk zygote samples total RNA was extracted from 100 zebrafish zygotes using TRIzol™ Reagent and eluated in 100 μl of RNase free water. Then 10 μl and 5 μl samples were taken for 10 zygote and 5 zygote samples respectively and volumes were adjusted to 12 μl with nuclease free water. For zebrafish single zygote samples single zygote was manually picked and distributed into 12 μl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples the cells were sorted into 12 μl 1X Lysis buffer using BD FACSMelody™ Cell Sorter BD Biosciences. For mouse oocyte and embryo samples post three washes in M2 medium oocytes and embryos were manually picked and put into 12 μl 1X Lysis buffer. For picoMeRIP seq experiment NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.		developmental stage:Zygote\|molecule subtype:rRNA free RNA	GSM5599723	GSM5599723: ZF zygote IP 1cell Rep3; Danio rerio; RIP Seq	GSM5599723		1	For mouse liver total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote mouse MII oocyte and mouse blastocyst samples the single cells were manually picked and sorted into 12 μl 1X lysis buffer Takara; NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2 × 30 seconds incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.	GEO Accession:GSM5599723	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP339082	loader:fastq load.py	ZF_zygote_IP_1cell_Rep3_R1.fastq.gz ZF_zygote_IP_1cell_Rep3_R2.fastq.gz	fastq fastq	2732409048.0	26788324.0	GSM5599723 r1	0:51 1:51	A:669345195;C:656715671;G:724415204;T:681825149;N:107829	51	51	669345195	656715671	724415204	681825149	107829	SRX12382355	SRS10353016	SRA1301707	GEO	Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan	2	0.85204	0.83607	0.06526	0.08046	0.78535	0.78748	0.60467	0.50165	51	51	B	B	biological fallback assumption	illumina	novaseq_era	3prime	poly_a	nebnext	bulk	bulk	bulk	United States	2021-09-28	Zygote	Embryo	Oocyte	Reproductive System
66197	66197	SRR16096230	SRX12382354	SRS10353017	SRP339082	PRJNA766854	RNA m6A methylome from zebrafish zygotes mouse liver polyA selected RNAs mouse embryonic stem cells spike in RNA controls and single mouse oocytes and embryos	GSE184893	Other	N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes including meiosis and early embryo development. Despite advances in methodology for m6A mapping the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA mouse embryonic stem cells and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes 3 biological replicates for 5 zygotes and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng 1 ng and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line from ATCC SCRC 1011 samples: 1000 cells 100 cells and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula S. et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula S. et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages and embryos at zygote 2 cell 8 cell and…		pubmed:37349523	ZF zygote IP 1cell Rep2	GSM5599722	tissue:ZF zygote IP 1cell\|developmental stage:Zygote\|molecule subtype:rRNA free RNA	ZF zygote IP 1cell Rep2	Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713 GSM5599714 GSM5599715 GSM5599716 GSM5599717 GSM5599718 GSM5599719 GSM5599720 GSM5599721 GSM5599722 GSM5599723 GSM5599724 GSM5599725 mouse polyA selected RNA samples GSM5599726 GSM5599727 GSM5599728 GSM5599729 GSM5599730 GSM5599731 GSM5599732 GSM5599733 and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter “ 5 8 no mixed no discordant”. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter “ bs 10 normalizeUsing RPKM”. Genome build: mm10 for mouse danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.	ZF zygote IP 1cell	For mouse GV oocyte collection 8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida followed by three washes in M2 medium. For mouse MII oocyte collection 4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium. For mouse early embryo collection 8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28 hours zygote 39 43 hours 2 cell 68 70 hours 8 cell and 92 94 hours blastocyst post hCG administration the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium.	For zebrafish bulk zygote samples total RNA was extracted from 100 zebrafish zygotes using TRIzol™ Reagent and eluated in 100 μl of RNase free water. Then 10 μl and 5 μl samples were taken for 10 zygote and 5 zygote samples respectively and volumes were adjusted to 12 μl with nuclease free water. For zebrafish single zygote samples single zygote was manually picked and distributed into 12 μl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples the cells were sorted into 12 μl 1X Lysis buffer using BD FACSMelody™ Cell Sorter BD Biosciences. For mouse oocyte and embryo samples post three washes in M2 medium oocytes and embryos were manually picked and put into 12 μl 1X Lysis buffer. For picoMeRIP seq experiment NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.		developmental stage:Zygote\|molecule subtype:rRNA free RNA	GSM5599722	GSM5599722: ZF zygote IP 1cell Rep2; Danio rerio; RIP Seq	GSM5599722		1	For mouse liver total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote mouse MII oocyte and mouse blastocyst samples the single cells were manually picked and sorted into 12 μl 1X lysis buffer Takara; NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2 × 30 seconds incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.	GEO Accession:GSM5599722	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP339082	loader:fastq load.py	ZF_zygote_IP_1cell_Rep2_R1.fastq.gz ZF_zygote_IP_1cell_Rep2_R2.fastq.gz	fastq fastq	2235668028.0	21918314.0	GSM5599722 r1	0:51 1:51	A:552522700;C:535947981;G:588168855;T:558939713;N:88779	51	51	552522700	535947981	588168855	558939713	88779	SRX12382354	SRS10353017	SRA1301707	GEO	Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan	2	0.85597	0.85298	0.06663	0.07927	0.79058	0.79237	0.57626	0.56525	51	51	B	B	biological fallback assumption	illumina	novaseq_era	3prime	poly_a	nebnext	bulk	bulk	bulk	United States	2021-09-28	Zygote	Embryo	Oocyte	Reproductive System
66198	66198	SRR16096229	SRX12382353	SRS10353015	SRP339082	PRJNA766854	RNA m6A methylome from zebrafish zygotes mouse liver polyA selected RNAs mouse embryonic stem cells spike in RNA controls and single mouse oocytes and embryos	GSE184893	Other	N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes including meiosis and early embryo development. Despite advances in methodology for m6A mapping the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA mouse embryonic stem cells and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes 3 biological replicates for 5 zygotes and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng 1 ng and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line from ATCC SCRC 1011 samples: 1000 cells 100 cells and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula S. et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula S. et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages and embryos at zygote 2 cell 8 cell and…		pubmed:37349523	ZF zygote IP 1cell Rep1	GSM5599721	tissue:ZF zygote IP 1cell\|developmental stage:Zygote\|molecule subtype:rRNA free RNA	ZF zygote IP 1cell Rep1	Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713 GSM5599714 GSM5599715 GSM5599716 GSM5599717 GSM5599718 GSM5599719 GSM5599720 GSM5599721 GSM5599722 GSM5599723 GSM5599724 GSM5599725 mouse polyA selected RNA samples GSM5599726 GSM5599727 GSM5599728 GSM5599729 GSM5599730 GSM5599731 GSM5599732 GSM5599733 and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter “ 5 8 no mixed no discordant”. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter “ bs 10 normalizeUsing RPKM”. Genome build: mm10 for mouse danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.	ZF zygote IP 1cell	For mouse GV oocyte collection 8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida followed by three washes in M2 medium. For mouse MII oocyte collection 4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium. For mouse early embryo collection 8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28 hours zygote 39 43 hours 2 cell 68 70 hours 8 cell and 92 94 hours blastocyst post hCG administration the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium.	For zebrafish bulk zygote samples total RNA was extracted from 100 zebrafish zygotes using TRIzol™ Reagent and eluated in 100 μl of RNase free water. Then 10 μl and 5 μl samples were taken for 10 zygote and 5 zygote samples respectively and volumes were adjusted to 12 μl with nuclease free water. For zebrafish single zygote samples single zygote was manually picked and distributed into 12 μl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples the cells were sorted into 12 μl 1X Lysis buffer using BD FACSMelody™ Cell Sorter BD Biosciences. For mouse oocyte and embryo samples post three washes in M2 medium oocytes and embryos were manually picked and put into 12 μl 1X Lysis buffer. For picoMeRIP seq experiment NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.		developmental stage:Zygote\|molecule subtype:rRNA free RNA	GSM5599721	GSM5599721: ZF zygote IP 1cell Rep1; Danio rerio; RIP Seq	GSM5599721		1	For mouse liver total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote mouse MII oocyte and mouse blastocyst samples the single cells were manually picked and sorted into 12 μl 1X lysis buffer Takara; NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2 × 30 seconds incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.	GEO Accession:GSM5599721	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP339082	loader:fastq load.py	ZF_zygote_IP_1cell_Rep1_R1.fastq.gz ZF_zygote_IP_1cell_Rep1_R2.fastq.gz	fastq fastq	1785761736.0	17507468.0	GSM5599721 r1	0:51 1:51	A:429081683;C:435813601;G:481376346;T:439419714;N:70392	51	51	429081683	435813601	481376346	439419714	70392	SRX12382353	SRS10353015	SRA1301707	GEO	Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan	2	0.75314	0.75693	0.0543	0.06639	0.79482	0.79594	0.57979	0.56522	51	51	B	B	biological fallback assumption	illumina	novaseq_era	3prime	poly_a	nebnext	bulk	bulk	bulk	United States	2021-09-28	Zygote	Embryo	Oocyte	Reproductive System
66199	66199	SRR16096228	SRX12382352	SRS10353014	SRP339082	PRJNA766854	RNA m6A methylome from zebrafish zygotes mouse liver polyA selected RNAs mouse embryonic stem cells spike in RNA controls and single mouse oocytes and embryos	GSE184893	Other	N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes including meiosis and early embryo development. Despite advances in methodology for m6A mapping the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA mouse embryonic stem cells and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes 3 biological replicates for 5 zygotes and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng 1 ng and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line from ATCC SCRC 1011 samples: 1000 cells 100 cells and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula S. et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula S. et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages and embryos at zygote 2 cell 8 cell and…		pubmed:37349523	ZF zygote IP 5cell Rep3	GSM5599720	tissue:ZF zygote IP 5cell\|developmental stage:Zygote\|molecule subtype:rRNA free RNA	ZF zygote IP 5cell Rep3	Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713 GSM5599714 GSM5599715 GSM5599716 GSM5599717 GSM5599718 GSM5599719 GSM5599720 GSM5599721 GSM5599722 GSM5599723 GSM5599724 GSM5599725 mouse polyA selected RNA samples GSM5599726 GSM5599727 GSM5599728 GSM5599729 GSM5599730 GSM5599731 GSM5599732 GSM5599733 and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter “ 5 8 no mixed no discordant”. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter “ bs 10 normalizeUsing RPKM”. Genome build: mm10 for mouse danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.	ZF zygote IP 5cell	For mouse GV oocyte collection 8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida followed by three washes in M2 medium. For mouse MII oocyte collection 4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium. For mouse early embryo collection 8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28 hours zygote 39 43 hours 2 cell 68 70 hours 8 cell and 92 94 hours blastocyst post hCG administration the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium.	For zebrafish bulk zygote samples total RNA was extracted from 100 zebrafish zygotes using TRIzol™ Reagent and eluated in 100 μl of RNase free water. Then 10 μl and 5 μl samples were taken for 10 zygote and 5 zygote samples respectively and volumes were adjusted to 12 μl with nuclease free water. For zebrafish single zygote samples single zygote was manually picked and distributed into 12 μl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples the cells were sorted into 12 μl 1X Lysis buffer using BD FACSMelody™ Cell Sorter BD Biosciences. For mouse oocyte and embryo samples post three washes in M2 medium oocytes and embryos were manually picked and put into 12 μl 1X Lysis buffer. For picoMeRIP seq experiment NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.		developmental stage:Zygote\|molecule subtype:rRNA free RNA	GSM5599720	GSM5599720: ZF zygote IP 5cell Rep3; Danio rerio; RIP Seq	GSM5599720		1	For mouse liver total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote mouse MII oocyte and mouse blastocyst samples the single cells were manually picked and sorted into 12 μl 1X lysis buffer Takara; NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2 × 30 seconds incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.	GEO Accession:GSM5599720	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP339082	loader:fastq load.py	ZF_zygote_IP_5cell_Rep3_R1.fastq.gz ZF_zygote_IP_5cell_Rep3_R2.fastq.gz	fastq fastq	2179659420.0	21369210.0	GSM5599720 r1	0:51 1:51	A:539092949;C:513857324;G:569620218;T:556940661;N:148268	51	51	539092949	513857324	569620218	556940661	148268	SRX12382352	SRS10353014	SRA1301707	GEO	Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan	2	0.92028	0.90706	0.03967	0.05572	0.78431	0.78886	0.49727	0.48541	51	51	B	B	biological fallback assumption	illumina	novaseq_era	3prime	poly_a	nebnext	bulk	bulk	bulk	United States	2021-09-28	Zygote	Embryo	Oocyte	Reproductive System
66200	66200	SRR16096227	SRX12382351	SRS10353012	SRP339082	PRJNA766854	RNA m6A methylome from zebrafish zygotes mouse liver polyA selected RNAs mouse embryonic stem cells spike in RNA controls and single mouse oocytes and embryos	GSE184893	Other	N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes including meiosis and early embryo development. Despite advances in methodology for m6A mapping the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA mouse embryonic stem cells and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes 3 biological replicates for 5 zygotes and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng 1 ng and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line from ATCC SCRC 1011 samples: 1000 cells 100 cells and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula S. et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula S. et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages and embryos at zygote 2 cell 8 cell and…		pubmed:37349523	ZF zygote IP 5cell Rep2	GSM5599719	tissue:ZF zygote IP 5cell\|developmental stage:Zygote\|molecule subtype:rRNA free RNA	ZF zygote IP 5cell Rep2	Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713 GSM5599714 GSM5599715 GSM5599716 GSM5599717 GSM5599718 GSM5599719 GSM5599720 GSM5599721 GSM5599722 GSM5599723 GSM5599724 GSM5599725 mouse polyA selected RNA samples GSM5599726 GSM5599727 GSM5599728 GSM5599729 GSM5599730 GSM5599731 GSM5599732 GSM5599733 and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter “ 5 8 no mixed no discordant”. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter “ bs 10 normalizeUsing RPKM”. Genome build: mm10 for mouse danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.	ZF zygote IP 5cell	For mouse GV oocyte collection 8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida followed by three washes in M2 medium. For mouse MII oocyte collection 4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium. For mouse early embryo collection 8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28 hours zygote 39 43 hours 2 cell 68 70 hours 8 cell and 92 94 hours blastocyst post hCG administration the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium.	For zebrafish bulk zygote samples total RNA was extracted from 100 zebrafish zygotes using TRIzol™ Reagent and eluated in 100 μl of RNase free water. Then 10 μl and 5 μl samples were taken for 10 zygote and 5 zygote samples respectively and volumes were adjusted to 12 μl with nuclease free water. For zebrafish single zygote samples single zygote was manually picked and distributed into 12 μl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples the cells were sorted into 12 μl 1X Lysis buffer using BD FACSMelody™ Cell Sorter BD Biosciences. For mouse oocyte and embryo samples post three washes in M2 medium oocytes and embryos were manually picked and put into 12 μl 1X Lysis buffer. For picoMeRIP seq experiment NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.		developmental stage:Zygote\|molecule subtype:rRNA free RNA	GSM5599719	GSM5599719: ZF zygote IP 5cell Rep2; Danio rerio; RIP Seq	GSM5599719		1	For mouse liver total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote mouse MII oocyte and mouse blastocyst samples the single cells were manually picked and sorted into 12 μl 1X lysis buffer Takara; NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2 × 30 seconds incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.	GEO Accession:GSM5599719	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP339082	loader:fastq load.py	ZF_zygote_IP_5cell_Rep2_R1.fastq.gz ZF_zygote_IP_5cell_Rep2_R2.fastq.gz	fastq fastq	2527184538.0	24776319.0	GSM5599719 r1	0:51 1:51	A:628307375;C:594702688;G:657847712;T:646151885;N:174878	51	51	628307375	594702688	657847712	646151885	174878	SRX12382351	SRS10353012	SRA1301707	GEO	Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan	2	0.91811	0.90487	0.03919	0.05376	0.78315	0.78729	0.49414	0.48564	51	51	B	B	biological fallback assumption	illumina	novaseq_era	3prime	poly_a	nebnext	bulk	bulk	bulk	United States	2021-09-28	Zygote	Embryo	Oocyte	Reproductive System
66201	66201	SRR16096226	SRX12382350	SRS10353011	SRP339082	PRJNA766854	RNA m6A methylome from zebrafish zygotes mouse liver polyA selected RNAs mouse embryonic stem cells spike in RNA controls and single mouse oocytes and embryos	GSE184893	Other	N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes including meiosis and early embryo development. Despite advances in methodology for m6A mapping the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA mouse embryonic stem cells and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes 3 biological replicates for 5 zygotes and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng 1 ng and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line from ATCC SCRC 1011 samples: 1000 cells 100 cells and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula S. et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula S. et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages and embryos at zygote 2 cell 8 cell and…		pubmed:37349523	ZF zygote IP 5cell Rep1	GSM5599718	tissue:ZF zygote IP 5cell\|developmental stage:Zygote\|molecule subtype:rRNA free RNA	ZF zygote IP 5cell Rep1	Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713 GSM5599714 GSM5599715 GSM5599716 GSM5599717 GSM5599718 GSM5599719 GSM5599720 GSM5599721 GSM5599722 GSM5599723 GSM5599724 GSM5599725 mouse polyA selected RNA samples GSM5599726 GSM5599727 GSM5599728 GSM5599729 GSM5599730 GSM5599731 GSM5599732 GSM5599733 and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter “ 5 8 no mixed no discordant”. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter “ bs 10 normalizeUsing RPKM”. Genome build: mm10 for mouse danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.	ZF zygote IP 5cell	For mouse GV oocyte collection 8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida followed by three washes in M2 medium. For mouse MII oocyte collection 4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium. For mouse early embryo collection 8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28 hours zygote 39 43 hours 2 cell 68 70 hours 8 cell and 92 94 hours blastocyst post hCG administration the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium.	For zebrafish bulk zygote samples total RNA was extracted from 100 zebrafish zygotes using TRIzol™ Reagent and eluated in 100 μl of RNase free water. Then 10 μl and 5 μl samples were taken for 10 zygote and 5 zygote samples respectively and volumes were adjusted to 12 μl with nuclease free water. For zebrafish single zygote samples single zygote was manually picked and distributed into 12 μl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples the cells were sorted into 12 μl 1X Lysis buffer using BD FACSMelody™ Cell Sorter BD Biosciences. For mouse oocyte and embryo samples post three washes in M2 medium oocytes and embryos were manually picked and put into 12 μl 1X Lysis buffer. For picoMeRIP seq experiment NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.		developmental stage:Zygote\|molecule subtype:rRNA free RNA	GSM5599718	GSM5599718: ZF zygote IP 5cell Rep1; Danio rerio; RIP Seq	GSM5599718		1	For mouse liver total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote mouse MII oocyte and mouse blastocyst samples the single cells were manually picked and sorted into 12 μl 1X lysis buffer Takara; NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2 × 30 seconds incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.	GEO Accession:GSM5599718	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP339082	loader:fastq load.py	ZF_zygote_IP_5cell_Rep1_R1.fastq.gz ZF_zygote_IP_5cell_Rep1_R2.fastq.gz	fastq fastq	3481342518.0	34130809.0	GSM5599718 r1	0:51 1:51	A:865680250;C:823420389;G:907146965;T:884854199;N:240715	51	51	865680250	823420389	907146965	884854199	240715	SRX12382350	SRS10353011	SRA1301707	GEO	Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan	2	0.91893	0.90939	0.04544	0.06005	0.78025	0.78348	0.50569	0.49155	51	51	B	B	biological fallback assumption	illumina	novaseq_era	3prime	poly_a	nebnext	bulk	bulk	bulk	United States	2021-09-28	Zygote	Embryo	Oocyte	Reproductive System
66202	66202	SRR16096225	SRX12382349	SRS10353013	SRP339082	PRJNA766854	RNA m6A methylome from zebrafish zygotes mouse liver polyA selected RNAs mouse embryonic stem cells spike in RNA controls and single mouse oocytes and embryos	GSE184893	Other	N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes including meiosis and early embryo development. Despite advances in methodology for m6A mapping the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA mouse embryonic stem cells and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes 3 biological replicates for 5 zygotes and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng 1 ng and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line from ATCC SCRC 1011 samples: 1000 cells 100 cells and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula S. et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula S. et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages and embryos at zygote 2 cell 8 cell and…		pubmed:37349523	ZF zygote IP 10cell Rep3	GSM5599717	tissue:ZF zygote IP 10cell\|developmental stage:Zygote\|molecule subtype:rRNA free RNA	ZF zygote IP 10cell Rep3	Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713 GSM5599714 GSM5599715 GSM5599716 GSM5599717 GSM5599718 GSM5599719 GSM5599720 GSM5599721 GSM5599722 GSM5599723 GSM5599724 GSM5599725 mouse polyA selected RNA samples GSM5599726 GSM5599727 GSM5599728 GSM5599729 GSM5599730 GSM5599731 GSM5599732 GSM5599733 and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter “ 5 8 no mixed no discordant”. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter “ bs 10 normalizeUsing RPKM”. Genome build: mm10 for mouse danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.	ZF zygote IP 10cell	For mouse GV oocyte collection 8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida followed by three washes in M2 medium. For mouse MII oocyte collection 4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium. For mouse early embryo collection 8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28 hours zygote 39 43 hours 2 cell 68 70 hours 8 cell and 92 94 hours blastocyst post hCG administration the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium.	For zebrafish bulk zygote samples total RNA was extracted from 100 zebrafish zygotes using TRIzol™ Reagent and eluated in 100 μl of RNase free water. Then 10 μl and 5 μl samples were taken for 10 zygote and 5 zygote samples respectively and volumes were adjusted to 12 μl with nuclease free water. For zebrafish single zygote samples single zygote was manually picked and distributed into 12 μl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples the cells were sorted into 12 μl 1X Lysis buffer using BD FACSMelody™ Cell Sorter BD Biosciences. For mouse oocyte and embryo samples post three washes in M2 medium oocytes and embryos were manually picked and put into 12 μl 1X Lysis buffer. For picoMeRIP seq experiment NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.		developmental stage:Zygote\|molecule subtype:rRNA free RNA	GSM5599717	GSM5599717: ZF zygote IP 10cell Rep3; Danio rerio; RIP Seq	GSM5599717		1	For mouse liver total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote mouse MII oocyte and mouse blastocyst samples the single cells were manually picked and sorted into 12 μl 1X lysis buffer Takara; NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2 × 30 seconds incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.	GEO Accession:GSM5599717	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP339082	loader:fastq load.py	ZF_zygote_IP_10cell_Rep3_R1.fastq.gz ZF_zygote_IP_10cell_Rep3_R2.fastq.gz	fastq fastq	2172362850.0	21297675.0	GSM5599717 r1	0:51 1:51	A:536043605;C:513512883;G:568368414;T:554284996;N:152952	51	51	536043605	513512883	568368414	554284996	152952	SRX12382349	SRS10353013	SRA1301707	GEO	Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan	2	0.91859	0.90522	0.03736	0.05214	0.78715	0.79129	0.49736	0.48681	51	51	B	B	biological fallback assumption	illumina	novaseq_era	3prime	poly_a	nebnext	bulk	bulk	bulk	United States	2021-09-28	Zygote	Embryo	Oocyte	Reproductive System
66203	66203	SRR16096224	SRX12382348	SRS10353010	SRP339082	PRJNA766854	RNA m6A methylome from zebrafish zygotes mouse liver polyA selected RNAs mouse embryonic stem cells spike in RNA controls and single mouse oocytes and embryos	GSE184893	Other	N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes including meiosis and early embryo development. Despite advances in methodology for m6A mapping the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA mouse embryonic stem cells and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes 3 biological replicates for 5 zygotes and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng 1 ng and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line from ATCC SCRC 1011 samples: 1000 cells 100 cells and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula S. et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula S. et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages and embryos at zygote 2 cell 8 cell and…		pubmed:37349523	ZF zygote IP 10cell Rep2	GSM5599716	tissue:ZF zygote IP 10cell\|developmental stage:Zygote\|molecule subtype:rRNA free RNA	ZF zygote IP 10cell Rep2	Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713 GSM5599714 GSM5599715 GSM5599716 GSM5599717 GSM5599718 GSM5599719 GSM5599720 GSM5599721 GSM5599722 GSM5599723 GSM5599724 GSM5599725 mouse polyA selected RNA samples GSM5599726 GSM5599727 GSM5599728 GSM5599729 GSM5599730 GSM5599731 GSM5599732 GSM5599733 and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter “ 5 8 no mixed no discordant”. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter “ bs 10 normalizeUsing RPKM”. Genome build: mm10 for mouse danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.	ZF zygote IP 10cell	For mouse GV oocyte collection 8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida followed by three washes in M2 medium. For mouse MII oocyte collection 4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium. For mouse early embryo collection 8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28 hours zygote 39 43 hours 2 cell 68 70 hours 8 cell and 92 94 hours blastocyst post hCG administration the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium.	For zebrafish bulk zygote samples total RNA was extracted from 100 zebrafish zygotes using TRIzol™ Reagent and eluated in 100 μl of RNase free water. Then 10 μl and 5 μl samples were taken for 10 zygote and 5 zygote samples respectively and volumes were adjusted to 12 μl with nuclease free water. For zebrafish single zygote samples single zygote was manually picked and distributed into 12 μl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples the cells were sorted into 12 μl 1X Lysis buffer using BD FACSMelody™ Cell Sorter BD Biosciences. For mouse oocyte and embryo samples post three washes in M2 medium oocytes and embryos were manually picked and put into 12 μl 1X Lysis buffer. For picoMeRIP seq experiment NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.		developmental stage:Zygote\|molecule subtype:rRNA free RNA	GSM5599716	GSM5599716: ZF zygote IP 10cell Rep2; Danio rerio; RIP Seq	GSM5599716		1	For mouse liver total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote mouse MII oocyte and mouse blastocyst samples the single cells were manually picked and sorted into 12 μl 1X lysis buffer Takara; NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2 × 30 seconds incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.	GEO Accession:GSM5599716	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP339082	loader:fastq load.py	ZF_zygote_IP_10cell_Rep2_R1.fastq.gz ZF_zygote_IP_10cell_Rep2_R2.fastq.gz	fastq fastq	1840839492.0	18047446.0	GSM5599716 r1	0:51 1:51	A:454385290;C:437082102;G:482351138;T:466893642;N:127320	51	51	454385290	437082102	482351138	466893642	127320	SRX12382348	SRS10353010	SRA1301707	GEO	Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan	2	0.92217	0.90956	0.04012	0.05483	0.78819	0.79318	0.49756	0.48256	51	51	B	B	biological fallback assumption	illumina	novaseq_era	3prime	poly_a	nebnext	bulk	bulk	bulk	United States	2021-09-28	Zygote	Embryo	Oocyte	Reproductive System
66204	66204	SRR16096223	SRX12382347	SRS10353009	SRP339082	PRJNA766854	RNA m6A methylome from zebrafish zygotes mouse liver polyA selected RNAs mouse embryonic stem cells spike in RNA controls and single mouse oocytes and embryos	GSE184893	Other	N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes including meiosis and early embryo development. Despite advances in methodology for m6A mapping the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA mouse embryonic stem cells and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes 3 biological replicates for 5 zygotes and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng 1 ng and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line from ATCC SCRC 1011 samples: 1000 cells 100 cells and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula S. et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula S. et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages and embryos at zygote 2 cell 8 cell and…		pubmed:37349523	ZF zygote IP 10cell Rep1	GSM5599715	tissue:ZF zygote IP 10cell\|developmental stage:Zygote\|molecule subtype:rRNA free RNA	ZF zygote IP 10cell Rep1	Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713 GSM5599714 GSM5599715 GSM5599716 GSM5599717 GSM5599718 GSM5599719 GSM5599720 GSM5599721 GSM5599722 GSM5599723 GSM5599724 GSM5599725 mouse polyA selected RNA samples GSM5599726 GSM5599727 GSM5599728 GSM5599729 GSM5599730 GSM5599731 GSM5599732 GSM5599733 and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter “ 5 8 no mixed no discordant”. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter “ bs 10 normalizeUsing RPKM”. Genome build: mm10 for mouse danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.	ZF zygote IP 10cell	For mouse GV oocyte collection 8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida followed by three washes in M2 medium. For mouse MII oocyte collection 4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium. For mouse early embryo collection 8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28 hours zygote 39 43 hours 2 cell 68 70 hours 8 cell and 92 94 hours blastocyst post hCG administration the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium.	For zebrafish bulk zygote samples total RNA was extracted from 100 zebrafish zygotes using TRIzol™ Reagent and eluated in 100 μl of RNase free water. Then 10 μl and 5 μl samples were taken for 10 zygote and 5 zygote samples respectively and volumes were adjusted to 12 μl with nuclease free water. For zebrafish single zygote samples single zygote was manually picked and distributed into 12 μl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples the cells were sorted into 12 μl 1X Lysis buffer using BD FACSMelody™ Cell Sorter BD Biosciences. For mouse oocyte and embryo samples post three washes in M2 medium oocytes and embryos were manually picked and put into 12 μl 1X Lysis buffer. For picoMeRIP seq experiment NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.		developmental stage:Zygote\|molecule subtype:rRNA free RNA	GSM5599715	GSM5599715: ZF zygote IP 10cell Rep1; Danio rerio; RIP Seq	GSM5599715		1	For mouse liver total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote mouse MII oocyte and mouse blastocyst samples the single cells were manually picked and sorted into 12 μl 1X lysis buffer Takara; NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2 × 30 seconds incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.	GEO Accession:GSM5599715	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP339082	loader:fastq load.py	ZF_zygote_IP_10cell_Rep1_R1.fastq.gz ZF_zygote_IP_10cell_Rep1_R2.fastq.gz	fastq fastq	2400553680.0	23534840.0	GSM5599715 r1	0:51 1:51	A:594878203;C:567573525;G:625488388;T:612448386;N:165178	51	51	594878203	567573525	625488388	612448386	165178	SRX12382347	SRS10353009	SRA1301707	GEO	Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan	2	0.91641	0.908	0.03979	0.05394	0.78455	0.7892	0.48862	0.47478	51	51	B	B	biological fallback assumption	illumina	novaseq_era	3prime	poly_a	nebnext	bulk	bulk	bulk	United States	2021-09-28	Zygote	Embryo	Oocyte	Reproductive System
66205	66205	SRR16096222	SRX12382346	SRS10353008	SRP339082	PRJNA766854	RNA m6A methylome from zebrafish zygotes mouse liver polyA selected RNAs mouse embryonic stem cells spike in RNA controls and single mouse oocytes and embryos	GSE184893	Other	N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes including meiosis and early embryo development. Despite advances in methodology for m6A mapping the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA mouse embryonic stem cells and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes 3 biological replicates for 5 zygotes and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng 1 ng and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line from ATCC SCRC 1011 samples: 1000 cells 100 cells and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula S. et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula S. et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages and embryos at zygote 2 cell 8 cell and…		pubmed:37349523	ZF zygote Input 10cell Rep2	GSM5599714	tissue:ZF zygote Input 10cell\|developmental stage:Zygote\|molecule subtype:rRNA free RNA	ZF zygote Input 10cell Rep2	Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713 GSM5599714 GSM5599715 GSM5599716 GSM5599717 GSM5599718 GSM5599719 GSM5599720 GSM5599721 GSM5599722 GSM5599723 GSM5599724 GSM5599725 mouse polyA selected RNA samples GSM5599726 GSM5599727 GSM5599728 GSM5599729 GSM5599730 GSM5599731 GSM5599732 GSM5599733 and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter “ 5 8 no mixed no discordant”. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter “ bs 10 normalizeUsing RPKM”. Genome build: mm10 for mouse danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.	ZF zygote Input 10cell	For mouse GV oocyte collection 8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida followed by three washes in M2 medium. For mouse MII oocyte collection 4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium. For mouse early embryo collection 8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28 hours zygote 39 43 hours 2 cell 68 70 hours 8 cell and 92 94 hours blastocyst post hCG administration the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium.	For zebrafish bulk zygote samples total RNA was extracted from 100 zebrafish zygotes using TRIzol™ Reagent and eluated in 100 μl of RNase free water. Then 10 μl and 5 μl samples were taken for 10 zygote and 5 zygote samples respectively and volumes were adjusted to 12 μl with nuclease free water. For zebrafish single zygote samples single zygote was manually picked and distributed into 12 μl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples the cells were sorted into 12 μl 1X Lysis buffer using BD FACSMelody™ Cell Sorter BD Biosciences. For mouse oocyte and embryo samples post three washes in M2 medium oocytes and embryos were manually picked and put into 12 μl 1X Lysis buffer. For picoMeRIP seq experiment NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.		developmental stage:Zygote\|molecule subtype:rRNA free RNA	GSM5599714	GSM5599714: ZF zygote Input 10cell Rep2; Danio rerio; RIP Seq	GSM5599714		1	For mouse liver total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote mouse MII oocyte and mouse blastocyst samples the single cells were manually picked and sorted into 12 μl 1X lysis buffer Takara; NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2 × 30 seconds incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.	GEO Accession:GSM5599714	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP339082	loader:fastq load.py	ZF_zygote_Input_10cell_Rep2_R1.fastq.gz ZF_zygote_Input_10cell_Rep2_R2.fastq.gz	fastq fastq	3842772582.0	37674241.0	GSM5599714 r1	0:51 1:51	A:843564828;C:1054412690;G:1130769812;T:813758353;N:266899	51	51	843564828	1054412690	1130769812	813758353	266899	SRX12382346	SRS10353008	SRA1301707	GEO	Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan	2	0.91511	0.90868	0.32791	0.38048	0.89457	0.89441	0.81532	0.75274	51	51	B	B	biological fallback assumption	illumina	novaseq_era	3prime	poly_a	nebnext	bulk	bulk	bulk	United States	2021-09-28	Zygote	Embryo	Oocyte	Reproductive System
66206	66206	SRR16096221	SRX12382345	SRS10353007	SRP339082	PRJNA766854	RNA m6A methylome from zebrafish zygotes mouse liver polyA selected RNAs mouse embryonic stem cells spike in RNA controls and single mouse oocytes and embryos	GSE184893	Other	N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes including meiosis and early embryo development. Despite advances in methodology for m6A mapping the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA mouse embryonic stem cells and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes 3 biological replicates for 5 zygotes and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng 1 ng and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line from ATCC SCRC 1011 samples: 1000 cells 100 cells and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula S. et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula S. et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages and embryos at zygote 2 cell 8 cell and…		pubmed:37349523	ZF zygote Input 10cell Rep1	GSM5599713	tissue:ZF zygote Input 10cell\|developmental stage:Zygote\|molecule subtype:rRNA free RNA	ZF zygote Input 10cell Rep1	Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713 GSM5599714 GSM5599715 GSM5599716 GSM5599717 GSM5599718 GSM5599719 GSM5599720 GSM5599721 GSM5599722 GSM5599723 GSM5599724 GSM5599725 mouse polyA selected RNA samples GSM5599726 GSM5599727 GSM5599728 GSM5599729 GSM5599730 GSM5599731 GSM5599732 GSM5599733 and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter “ 5 8 no mixed no discordant”. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter “ bs 10 normalizeUsing RPKM”. Genome build: mm10 for mouse danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.	ZF zygote Input 10cell	For mouse GV oocyte collection 8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida followed by three washes in M2 medium. For mouse MII oocyte collection 4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium. For mouse early embryo collection 8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28 hours zygote 39 43 hours 2 cell 68 70 hours 8 cell and 92 94 hours blastocyst post hCG administration the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium.	For zebrafish bulk zygote samples total RNA was extracted from 100 zebrafish zygotes using TRIzol™ Reagent and eluated in 100 μl of RNase free water. Then 10 μl and 5 μl samples were taken for 10 zygote and 5 zygote samples respectively and volumes were adjusted to 12 μl with nuclease free water. For zebrafish single zygote samples single zygote was manually picked and distributed into 12 μl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples the cells were sorted into 12 μl 1X Lysis buffer using BD FACSMelody™ Cell Sorter BD Biosciences. For mouse oocyte and embryo samples post three washes in M2 medium oocytes and embryos were manually picked and put into 12 μl 1X Lysis buffer. For picoMeRIP seq experiment NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.		developmental stage:Zygote\|molecule subtype:rRNA free RNA	GSM5599713	GSM5599713: ZF zygote Input 10cell Rep1; Danio rerio; RIP Seq	GSM5599713		1	For mouse liver total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote mouse MII oocyte and mouse blastocyst samples the single cells were manually picked and sorted into 12 μl 1X lysis buffer Takara; NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2 × 30 seconds incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.	GEO Accession:GSM5599713	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP339082	loader:fastq load.py	ZF_zygote_Input_10cell_Rep1_R1.fastq.gz ZF_zygote_Input_10cell_Rep1_R2.fastq.gz	fastq fastq	4029368016.0	39503608.0	GSM5599713 r1	0:51 1:51	A:893562237;C:1096986475;G:1180690796;T:857849967;N:278541	51	51	893562237	1096986475	1180690796	857849967	278541	SRX12382345	SRS10353007	SRA1301707	GEO	Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan	2	0.91491	0.90807	0.32799	0.37836	0.89292	0.89282	0.81006	0.73354	51	51	B	B	biological fallback assumption	illumina	novaseq_era	3prime	poly_a	nebnext	bulk	bulk	bulk	United States	2021-09-28	Zygote	Embryo	Oocyte	Reproductive System
70712	70712	SRR20077343	SRX16115141	SRS13777745	SRP385866	PRJNA857663	RIP seq for Cpeb1b in zebrafish embryos	GSE207904	Transcriptome Analysis	Cpeb1b mediated cytoplasmic polyadenylation modulates hematopoietic stem and progenitor cell development via translational control Overall design: RIP seq of 2 samples from Flag cpeb1b mRNA injected zebrafish embryos at xxx hpf including two biological replicates	parent bioproject:PRJNA857656		Flag Cpeb1b replicate 2	GSM6322839	source name:Flag Cpeb1b replicate 2\|tissue:zebrafish embryos\|genotype:wild type\|age:16 hpf	Flag Cpeb1b replicate 2	The quality of raw sequencing reads was processed using FastQC and low quality bases were trimmed and filtered by cutadapt V 1.13 11 and Trimmomatic V 0.36 12. Processed reads were mapped to the zebrafish genome Zv9 using TopHat v2.1.1 18 with ‘‘–bowtie1’’. The target binding regions of Cpeb1b were identified using MACS2 software version 2.0.10. The target genes were annotated based on Ensembl release 79 gene annotation information by applying BEDTools’ intersectBed version 2.16.2. Assembly: Zv9 Supplementary files format and content: rpkm for samples	Flag Cpeb1b replicate 2		Flag cpeb1b mRNA injected embryos were collected at xxx hpf and lysed in NETN lysis buffer 150 mM NaCl 0.5% NP 40 50 mM Tris HCl pH 7.4 RNase inhibitor Roche cocktail protease inhibitor. The lysate was incubated with anti FLAG M2 Magnetic Beads Merck for 4 h at 4 °C. Then the beads were washed five times with the lysis buffer and five times with TBS buffer. For RIP seq assay the bead bound RNA was extracted and then fragmented by RNA Fragmentation Reagent Ambion. The fragmented RNA was subjected to library construction using the SMARTer smRNA Seq kit Clontech.		tissue:zebrafish embryos\|genotype:wild type\|age:16 hpf	GSM6322839	GSM6322839: Flag Cpeb1b replicate 2; Danio rerio; RIP Seq	GSM6322839 r1	GSM6322839	1	Flag cpeb1b mRNA injected embryos were collected at xxx hpf and lysed in NETN lysis buffer 150 mM NaCl 0.5% NP 40 50 mM Tris HCl pH 7.4 RNase inhibitor Roche cocktail protease inhibitor. The lysate was incubated with anti FLAG M2 Magnetic Beads Merck for 4 h at 4 °C. Then the beads were washed five times with the lysis buffer and five times with TBS buffer. For RIP seq assay the bead bound RNA was extracted and then fragmented by RNA Fragmentation Reagent Ambion. The fragmented RNA was subjected to library construction using the SMARTer smRNA Seq kit Clontech.		RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP385866	loader:fastq load.py	Flag_Cpeb1b_replicate_2.R1.fq.gz Flag_Cpeb1b_replicate_2.R2.fq.gz	fastq fastq	14733801000.0	49112670.0	GSM6322839 r1	0:150 1:150	A:4141614412;C:3363207101;G:3881752054;T:3344596903;N:2630530	150	150	4141614412	3363207101	3881752054	3344596903	2630530	SRX16115141	SRS13777745	SRA1452503	Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)	Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)	2	0.05175	0.02071	0.01394	0.00703	0.99383	0.99758	0.80854	0.85616	150	150	T	T	mates < 9% mapping rate	illumina	novaseq_era	full_length	other	smarter	bulk	unknown	unknown	China	2022-07-11	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
70713	70713	SRR20077344	SRX16115140	SRS13777744	SRP385866	PRJNA857663	RIP seq for Cpeb1b in zebrafish embryos	GSE207904	Transcriptome Analysis	Cpeb1b mediated cytoplasmic polyadenylation modulates hematopoietic stem and progenitor cell development via translational control Overall design: RIP seq of 2 samples from Flag cpeb1b mRNA injected zebrafish embryos at xxx hpf including two biological replicates	parent bioproject:PRJNA857656		Flag Cpeb1b replicate 1	GSM6322838	source name:Flag Cpeb1b replicate 1\|tissue:zebrafish embryos\|genotype:wild type\|age:16 hpf	Flag Cpeb1b replicate 1	The quality of raw sequencing reads was processed using FastQC and low quality bases were trimmed and filtered by cutadapt V 1.13 11 and Trimmomatic V 0.36 12. Processed reads were mapped to the zebrafish genome Zv9 using TopHat v2.1.1 18 with ‘‘–bowtie1’’. The target binding regions of Cpeb1b were identified using MACS2 software version 2.0.10. The target genes were annotated based on Ensembl release 79 gene annotation information by applying BEDTools’ intersectBed version 2.16.2. Assembly: Zv9 Supplementary files format and content: rpkm for samples	Flag Cpeb1b replicate 1		Flag cpeb1b mRNA injected embryos were collected at xxx hpf and lysed in NETN lysis buffer 150 mM NaCl 0.5% NP 40 50 mM Tris HCl pH 7.4 RNase inhibitor Roche cocktail protease inhibitor. The lysate was incubated with anti FLAG M2 Magnetic Beads Merck for 4 h at 4 °C. Then the beads were washed five times with the lysis buffer and five times with TBS buffer. For RIP seq assay the bead bound RNA was extracted and then fragmented by RNA Fragmentation Reagent Ambion. The fragmented RNA was subjected to library construction using the SMARTer smRNA Seq kit Clontech.		tissue:zebrafish embryos\|genotype:wild type\|age:16 hpf	GSM6322838	GSM6322838: Flag Cpeb1b replicate 1; Danio rerio; RIP Seq	GSM6322838 r1	GSM6322838	1	Flag cpeb1b mRNA injected embryos were collected at xxx hpf and lysed in NETN lysis buffer 150 mM NaCl 0.5% NP 40 50 mM Tris HCl pH 7.4 RNase inhibitor Roche cocktail protease inhibitor. The lysate was incubated with anti FLAG M2 Magnetic Beads Merck for 4 h at 4 °C. Then the beads were washed five times with the lysis buffer and five times with TBS buffer. For RIP seq assay the bead bound RNA was extracted and then fragmented by RNA Fragmentation Reagent Ambion. The fragmented RNA was subjected to library construction using the SMARTer smRNA Seq kit Clontech.		RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP385866	loader:fastq load.py	Flag_Cpeb1b_replicate_1.R1.fq.gz Flag_Cpeb1b_replicate_1.R2.fq.gz	fastq fastq	15482669700.0	51608899.0	GSM6322838 r1	0:150 1:150	A:4303443264;C:3570990345;G:4030059369;T:3575508224;N:2668498	150	150	4303443264	3570990345	4030059369	3575508224	2668498	SRX16115140	SRS13777744	SRA1452503	Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)	Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)	2	0.03751	0.01773	0.01056	0.00621	0.99346	0.99736	0.89693	0.8036	150	150	T	T	mates < 9% mapping rate	illumina	novaseq_era	full_length	other	smarter	bulk	unknown	unknown	China	2022-07-11	Segmentation	Embryo	Embryo Imprecise	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
74097	74097	SRR23433707	SRX19347585	SRS16745103	SRP422577	PRJNA934472	Mettl16 promotes hematopoietic stem and progenitor cell expansion in embryonic hematopoiesis [m6A Seq]	GSE225136	Other	The RNA N6 methyladenosine m6A modification has emerged as an essential regulator of vertebrate embryogenesis and malignancies. However its functions and underlying molecular mechanisms in the expansion of hematopoietic stem and progenitor cells HSPCs during early embryonic development remain elusive. Here we show that Mettl16 an RNA methyltransferase identified recently is specifically required for HSPC expansion during zebrafish early embryonic development in an m6A dependent manner. In mettl16 deficient embryos HSPCs exhibit defective proliferation capacity due to G0/G1 arrest. Mechanistically HSPC proliferation is blocked by impaired methyltransferase function of Mettl16 in vivo. We identify cell cycle gene mybl2b as a novel direct m6A target of Mettl16 and Mettl16 deficiency destabilizes mybl2b mRNA which is mediated by m6A reader Igf2bp1. Moreover we revealed that the METTL16 m6A MYBL2 IGF2BP1 signaling axis in G1/S progression is conserved in humans. Collectively our findings demonstrate the critical function of m6A modification deposited by Mettl16 in HSPC expansion during early embryonic development. Overall design: m6A seq profiles of sibling and mettl16 / zebrafish embryos at 3 dpf for triplicates	parent bioproject:PRJNA934075	pubmed:38605226	mt input rep2	GSM7039976	source name:trunk region of zebrafish embryos\|tissue:trunk region of zebrafish embryos\|genotype:mettl16 / \|treatment:gene knockout\|rip antibody:n1\|geo loc name:missing\|collection date:missing	mt input rep2	Illumina Casava 1.8 software used for basecalling. fastp software were used to remove the reads that contained adaptor contamination low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp. HISAT2 was used to map reads to zebrafish reference genome Ensembl GRCz11. Mapped reads of IP and input libraries were provided for R package exomePeak which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software. StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM total exon fragments /mapped reads millions × exon length kB. The differentially expressed mRNAs were selected by R package edgeR. Assembly: GRCz11 Supplementary files format and content: BW files include peak files with quantitative data for each gene and each sample	trunk region of zebrafish embryos		Total RNA was isolated from the trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003 Synaptic Systems was applied for m6A immunoprecipitation. Then the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq		tissue:trunk region of zebrafish embryos\|genotype:mettl16 / \|treatment:gene knockout\|rip antibody:n1	GSM7039976	GSM7039976: mt input rep2; Danio rerio; RIP Seq	GSM7039976 r1	GSM7039976	1	Total RNA was isolated from the trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003 Synaptic Systems was applied for m6A immunoprecipitation. Then the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq		RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP422577	loader:fastq load.py	mt2_input_R1.fastq.gz mt2_input_R2.fastq.gz	fastq fastq	11987520719.0	46102921.0	GSM7039976 r1	0:129.98 1:130.04	A:2818961833;C:3185310727;G:3125514774;T:2857679978;N:53407	129	130	2818961833	3185310727	3125514774	2857679978	53407	SRX19347585	SRS16745103	SRA1590470	Huazhong University of Science and Technology	Huazhong University of Science and Technology	2	0.92498	0.92723	0.26901	0.26318	0.72691	0.72646	0.55297	0.56674	103	103	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2023-02-12	Undetermined	Embryo	Trunk	Surface Structure
74098	74098	SRR23433708	SRX19347584	SRS16745102	SRP422577	PRJNA934472	Mettl16 promotes hematopoietic stem and progenitor cell expansion in embryonic hematopoiesis [m6A Seq]	GSE225136	Other	The RNA N6 methyladenosine m6A modification has emerged as an essential regulator of vertebrate embryogenesis and malignancies. However its functions and underlying molecular mechanisms in the expansion of hematopoietic stem and progenitor cells HSPCs during early embryonic development remain elusive. Here we show that Mettl16 an RNA methyltransferase identified recently is specifically required for HSPC expansion during zebrafish early embryonic development in an m6A dependent manner. In mettl16 deficient embryos HSPCs exhibit defective proliferation capacity due to G0/G1 arrest. Mechanistically HSPC proliferation is blocked by impaired methyltransferase function of Mettl16 in vivo. We identify cell cycle gene mybl2b as a novel direct m6A target of Mettl16 and Mettl16 deficiency destabilizes mybl2b mRNA which is mediated by m6A reader Igf2bp1. Moreover we revealed that the METTL16 m6A MYBL2 IGF2BP1 signaling axis in G1/S progression is conserved in humans. Collectively our findings demonstrate the critical function of m6A modification deposited by Mettl16 in HSPC expansion during early embryonic development. Overall design: m6A seq profiles of sibling and mettl16 / zebrafish embryos at 3 dpf for triplicates	parent bioproject:PRJNA934075	pubmed:38605226	mt IP rep2	GSM7039975	source name:trunk region of zebrafish embryos\|tissue:trunk region of zebrafish embryos\|genotype:mettl16 / \|treatment:gene knockout\|rip antibody:anti m6A\|geo loc name:missing\|collection date:missing	mt IP rep2	Illumina Casava 1.8 software used for basecalling. fastp software were used to remove the reads that contained adaptor contamination low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp. HISAT2 was used to map reads to zebrafish reference genome Ensembl GRCz11. Mapped reads of IP and input libraries were provided for R package exomePeak which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software. StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM total exon fragments /mapped reads millions × exon length kB. The differentially expressed mRNAs were selected by R package edgeR. Assembly: GRCz11 Supplementary files format and content: BW files include peak files with quantitative data for each gene and each sample	trunk region of zebrafish embryos		Total RNA was isolated from the trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003 Synaptic Systems was applied for m6A immunoprecipitation. Then the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq		tissue:trunk region of zebrafish embryos\|genotype:mettl16 / \|treatment:gene knockout\|rip antibody:anti m6A	GSM7039975	GSM7039975: mt IP rep2; Danio rerio; RIP Seq	GSM7039975 r1	GSM7039975	1	Total RNA was isolated from the trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003 Synaptic Systems was applied for m6A immunoprecipitation. Then the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq		RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP422577	loader:fastq load.py	mt2_IP_R1.fastq.gz mt2_IP_R2.fastq.gz	fastq fastq	10153956215.0	38248544.0	GSM7039975 r1	0:132.74 1:132.73	A:2745473943;C:2337991849;G:2337827470;T:2732618213;N:44740	132	132	2745473943	2337991849	2337827470	2732618213	44740	SRX19347584	SRS16745102	SRA1590470	Huazhong University of Science and Technology	Huazhong University of Science and Technology	2	0.91716	0.92124	0.17169	0.17213	0.69057	0.69092	0.45478	0.4582	133	133	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2023-02-12	Undetermined	Embryo	Trunk	Surface Structure
74099	74099	SRR23433709	SRX19347583	SRS16745101	SRP422577	PRJNA934472	Mettl16 promotes hematopoietic stem and progenitor cell expansion in embryonic hematopoiesis [m6A Seq]	GSE225136	Other	The RNA N6 methyladenosine m6A modification has emerged as an essential regulator of vertebrate embryogenesis and malignancies. However its functions and underlying molecular mechanisms in the expansion of hematopoietic stem and progenitor cells HSPCs during early embryonic development remain elusive. Here we show that Mettl16 an RNA methyltransferase identified recently is specifically required for HSPC expansion during zebrafish early embryonic development in an m6A dependent manner. In mettl16 deficient embryos HSPCs exhibit defective proliferation capacity due to G0/G1 arrest. Mechanistically HSPC proliferation is blocked by impaired methyltransferase function of Mettl16 in vivo. We identify cell cycle gene mybl2b as a novel direct m6A target of Mettl16 and Mettl16 deficiency destabilizes mybl2b mRNA which is mediated by m6A reader Igf2bp1. Moreover we revealed that the METTL16 m6A MYBL2 IGF2BP1 signaling axis in G1/S progression is conserved in humans. Collectively our findings demonstrate the critical function of m6A modification deposited by Mettl16 in HSPC expansion during early embryonic development. Overall design: m6A seq profiles of sibling and mettl16 / zebrafish embryos at 3 dpf for triplicates	parent bioproject:PRJNA934075	pubmed:38605226	mt input rep1	GSM7039974	source name:trunk region of zebrafish embryos\|tissue:trunk region of zebrafish embryos\|genotype:mettl16 / \|treatment:gene knockout\|rip antibody:n1\|geo loc name:missing\|collection date:missing	mt input rep1	Illumina Casava 1.8 software used for basecalling. fastp software were used to remove the reads that contained adaptor contamination low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp. HISAT2 was used to map reads to zebrafish reference genome Ensembl GRCz11. Mapped reads of IP and input libraries were provided for R package exomePeak which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software. StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM total exon fragments /mapped reads millions × exon length kB. The differentially expressed mRNAs were selected by R package edgeR. Assembly: GRCz11 Supplementary files format and content: BW files include peak files with quantitative data for each gene and each sample	trunk region of zebrafish embryos		Total RNA was isolated from the trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003 Synaptic Systems was applied for m6A immunoprecipitation. Then the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq		tissue:trunk region of zebrafish embryos\|genotype:mettl16 / \|treatment:gene knockout\|rip antibody:n1	GSM7039974	GSM7039974: mt input rep1; Danio rerio; RIP Seq	GSM7039974 r1	GSM7039974	1	Total RNA was isolated from the trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003 Synaptic Systems was applied for m6A immunoprecipitation. Then the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq		RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP422577	loader:fastq load.py	mt1_input_R1.fastq.gz mt1_input_R2.fastq.gz	fastq fastq	11979139891.0	42665152.0	GSM7039974 r1	0:140.37 1:140.40	A:3143624979;C:2854874515;G:2775482425;T:3204809556;N:348416	140	140	3143624979	2854874515	2775482425	3204809556	348416	SRX19347583	SRS16745101	SRA1590470	Huazhong University of Science and Technology	Huazhong University of Science and Technology	2	0.89189	0.90001	0.35263	0.34917	0.71058	0.70907	0.54777	0.55293	125	125	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2023-02-12	Undetermined	Embryo	Trunk	Surface Structure
74100	74100	SRR23433710	SRX19347582	SRS16745100	SRP422577	PRJNA934472	Mettl16 promotes hematopoietic stem and progenitor cell expansion in embryonic hematopoiesis [m6A Seq]	GSE225136	Other	The RNA N6 methyladenosine m6A modification has emerged as an essential regulator of vertebrate embryogenesis and malignancies. However its functions and underlying molecular mechanisms in the expansion of hematopoietic stem and progenitor cells HSPCs during early embryonic development remain elusive. Here we show that Mettl16 an RNA methyltransferase identified recently is specifically required for HSPC expansion during zebrafish early embryonic development in an m6A dependent manner. In mettl16 deficient embryos HSPCs exhibit defective proliferation capacity due to G0/G1 arrest. Mechanistically HSPC proliferation is blocked by impaired methyltransferase function of Mettl16 in vivo. We identify cell cycle gene mybl2b as a novel direct m6A target of Mettl16 and Mettl16 deficiency destabilizes mybl2b mRNA which is mediated by m6A reader Igf2bp1. Moreover we revealed that the METTL16 m6A MYBL2 IGF2BP1 signaling axis in G1/S progression is conserved in humans. Collectively our findings demonstrate the critical function of m6A modification deposited by Mettl16 in HSPC expansion during early embryonic development. Overall design: m6A seq profiles of sibling and mettl16 / zebrafish embryos at 3 dpf for triplicates	parent bioproject:PRJNA934075	pubmed:38605226	mt IP rep1	GSM7039973	source name:trunk region of zebrafish embryos\|tissue:trunk region of zebrafish embryos\|genotype:mettl16 / \|treatment:gene knockout\|rip antibody:anti m6A\|geo loc name:missing\|collection date:missing	mt IP rep1	Illumina Casava 1.8 software used for basecalling. fastp software were used to remove the reads that contained adaptor contamination low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp. HISAT2 was used to map reads to zebrafish reference genome Ensembl GRCz11. Mapped reads of IP and input libraries were provided for R package exomePeak which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software. StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM total exon fragments /mapped reads millions × exon length kB. The differentially expressed mRNAs were selected by R package edgeR. Assembly: GRCz11 Supplementary files format and content: BW files include peak files with quantitative data for each gene and each sample	trunk region of zebrafish embryos		Total RNA was isolated from the trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003 Synaptic Systems was applied for m6A immunoprecipitation. Then the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq		tissue:trunk region of zebrafish embryos\|genotype:mettl16 / \|treatment:gene knockout\|rip antibody:anti m6A	GSM7039973	GSM7039973: mt IP rep1; Danio rerio; RIP Seq	GSM7039973 r1	GSM7039973	1	Total RNA was isolated from the trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003 Synaptic Systems was applied for m6A immunoprecipitation. Then the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq		RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP422577	loader:fastq load.py	mt1_IP_R1.fastq.gz mt1_IP_R2.fastq.gz	fastq fastq	12145897814.0	43352862.0	GSM7039973 r1	0:140.09 1:140.07	A:3459248498;C:2615706052;G:2628261332;T:3442334843;N:347089	140	140	3459248498	2615706052	2628261332	3442334843	347089	SRX19347582	SRS16745100	SRA1590470	Huazhong University of Science and Technology	Huazhong University of Science and Technology	2	0.86681	0.87664	0.304	0.305	0.68012	0.67831	0.44055	0.4418	142	142	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2023-02-12	Undetermined	Embryo	Trunk	Surface Structure
74101	74101	SRR23433711	SRX19347581	SRS16745099	SRP422577	PRJNA934472	Mettl16 promotes hematopoietic stem and progenitor cell expansion in embryonic hematopoiesis [m6A Seq]	GSE225136	Other	The RNA N6 methyladenosine m6A modification has emerged as an essential regulator of vertebrate embryogenesis and malignancies. However its functions and underlying molecular mechanisms in the expansion of hematopoietic stem and progenitor cells HSPCs during early embryonic development remain elusive. Here we show that Mettl16 an RNA methyltransferase identified recently is specifically required for HSPC expansion during zebrafish early embryonic development in an m6A dependent manner. In mettl16 deficient embryos HSPCs exhibit defective proliferation capacity due to G0/G1 arrest. Mechanistically HSPC proliferation is blocked by impaired methyltransferase function of Mettl16 in vivo. We identify cell cycle gene mybl2b as a novel direct m6A target of Mettl16 and Mettl16 deficiency destabilizes mybl2b mRNA which is mediated by m6A reader Igf2bp1. Moreover we revealed that the METTL16 m6A MYBL2 IGF2BP1 signaling axis in G1/S progression is conserved in humans. Collectively our findings demonstrate the critical function of m6A modification deposited by Mettl16 in HSPC expansion during early embryonic development. Overall design: m6A seq profiles of sibling and mettl16 / zebrafish embryos at 3 dpf for triplicates	parent bioproject:PRJNA934075	pubmed:38605226	sibling input rep2	GSM7039972	source name:trunk region of zebrafish embryos\|tissue:trunk region of zebrafish embryos\|genotype:mettl16+/+\|treatment:no treatment\|rip antibody:n1\|geo loc name:missing\|collection date:missing	sibling input rep2	Illumina Casava 1.8 software used for basecalling. fastp software were used to remove the reads that contained adaptor contamination low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp. HISAT2 was used to map reads to zebrafish reference genome Ensembl GRCz11. Mapped reads of IP and input libraries were provided for R package exomePeak which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software. StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM total exon fragments /mapped reads millions × exon length kB. The differentially expressed mRNAs were selected by R package edgeR. Assembly: GRCz11 Supplementary files format and content: BW files include peak files with quantitative data for each gene and each sample	trunk region of zebrafish embryos		Total RNA was isolated from the trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003 Synaptic Systems was applied for m6A immunoprecipitation. Then the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq		tissue:trunk region of zebrafish embryos\|genotype:mettl16+/+\|treatment:no treatment\|rip antibody:n1	GSM7039972	GSM7039972: sibling input rep2; Danio rerio; RIP Seq	GSM7039972 r1	GSM7039972	1	Total RNA was isolated from the trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003 Synaptic Systems was applied for m6A immunoprecipitation. Then the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq		RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP422577	loader:fastq load.py	sibling2_input_R1.fastq.gz sibling2_input_R2.fastq.gz	fastq fastq	12272791017.0	47579480.0	GSM7039972 r1	0:128.94 1:129.00	A:2905993856;C:3237323144;G:3186607999;T:2942811604;N:54414	128	129	2905993856	3237323144	3186607999	2942811604	54414	SRX19347581	SRS16745099	SRA1590470	Huazhong University of Science and Technology	Huazhong University of Science and Technology	2	0.92733	0.92947	0.27234	0.26711	0.72391	0.72409	0.52625	0.55052	126	126	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2023-02-12	Undetermined	Embryo	Trunk	Surface Structure
74102	74102	SRR23433712	SRX19347580	SRS16745098	SRP422577	PRJNA934472	Mettl16 promotes hematopoietic stem and progenitor cell expansion in embryonic hematopoiesis [m6A Seq]	GSE225136	Other	The RNA N6 methyladenosine m6A modification has emerged as an essential regulator of vertebrate embryogenesis and malignancies. However its functions and underlying molecular mechanisms in the expansion of hematopoietic stem and progenitor cells HSPCs during early embryonic development remain elusive. Here we show that Mettl16 an RNA methyltransferase identified recently is specifically required for HSPC expansion during zebrafish early embryonic development in an m6A dependent manner. In mettl16 deficient embryos HSPCs exhibit defective proliferation capacity due to G0/G1 arrest. Mechanistically HSPC proliferation is blocked by impaired methyltransferase function of Mettl16 in vivo. We identify cell cycle gene mybl2b as a novel direct m6A target of Mettl16 and Mettl16 deficiency destabilizes mybl2b mRNA which is mediated by m6A reader Igf2bp1. Moreover we revealed that the METTL16 m6A MYBL2 IGF2BP1 signaling axis in G1/S progression is conserved in humans. Collectively our findings demonstrate the critical function of m6A modification deposited by Mettl16 in HSPC expansion during early embryonic development. Overall design: m6A seq profiles of sibling and mettl16 / zebrafish embryos at 3 dpf for triplicates	parent bioproject:PRJNA934075	pubmed:38605226	sibling IP rep2	GSM7039971	source name:trunk region of zebrafish embryos\|tissue:trunk region of zebrafish embryos\|genotype:mettl16+/+\|treatment:no treatment\|rip antibody:anti m6A\|geo loc name:missing\|collection date:missing	sibling IP rep2	Illumina Casava 1.8 software used for basecalling. fastp software were used to remove the reads that contained adaptor contamination low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp. HISAT2 was used to map reads to zebrafish reference genome Ensembl GRCz11. Mapped reads of IP and input libraries were provided for R package exomePeak which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software. StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM total exon fragments /mapped reads millions × exon length kB. The differentially expressed mRNAs were selected by R package edgeR. Assembly: GRCz11 Supplementary files format and content: BW files include peak files with quantitative data for each gene and each sample	trunk region of zebrafish embryos		Total RNA was isolated from the trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003 Synaptic Systems was applied for m6A immunoprecipitation. Then the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq		tissue:trunk region of zebrafish embryos\|genotype:mettl16+/+\|treatment:no treatment\|rip antibody:anti m6A	GSM7039971	GSM7039971: sibling IP rep2; Danio rerio; RIP Seq	GSM7039971 r1	GSM7039971	1	Total RNA was isolated from the trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003 Synaptic Systems was applied for m6A immunoprecipitation. Then the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq		RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP422577	loader:fastq load.py	sibling2_IP_R1.fastq.gz sibling2_IP_R2.fastq.gz	fastq fastq	10402768351.0	39113148.0	GSM7039971 r1	0:132.99 1:132.98	A:2806053427;C:2400476074;G:2403977422;T:2792214821;N:46607	132	132	2806053427	2400476074	2403977422	2792214821	46607	SRX19347580	SRS16745098	SRA1590470	Huazhong University of Science and Technology	Huazhong University of Science and Technology	2	0.90198	0.9063	0.18008	0.18091	0.69428	0.69396	0.44811	0.42925	147	147	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2023-02-12	Undetermined	Embryo	Trunk	Surface Structure
74103	74103	SRR23433713	SRX19347579	SRS16745097	SRP422577	PRJNA934472	Mettl16 promotes hematopoietic stem and progenitor cell expansion in embryonic hematopoiesis [m6A Seq]	GSE225136	Other	The RNA N6 methyladenosine m6A modification has emerged as an essential regulator of vertebrate embryogenesis and malignancies. However its functions and underlying molecular mechanisms in the expansion of hematopoietic stem and progenitor cells HSPCs during early embryonic development remain elusive. Here we show that Mettl16 an RNA methyltransferase identified recently is specifically required for HSPC expansion during zebrafish early embryonic development in an m6A dependent manner. In mettl16 deficient embryos HSPCs exhibit defective proliferation capacity due to G0/G1 arrest. Mechanistically HSPC proliferation is blocked by impaired methyltransferase function of Mettl16 in vivo. We identify cell cycle gene mybl2b as a novel direct m6A target of Mettl16 and Mettl16 deficiency destabilizes mybl2b mRNA which is mediated by m6A reader Igf2bp1. Moreover we revealed that the METTL16 m6A MYBL2 IGF2BP1 signaling axis in G1/S progression is conserved in humans. Collectively our findings demonstrate the critical function of m6A modification deposited by Mettl16 in HSPC expansion during early embryonic development. Overall design: m6A seq profiles of sibling and mettl16 / zebrafish embryos at 3 dpf for triplicates	parent bioproject:PRJNA934075	pubmed:38605226	sibling input rep1	GSM7039970	source name:trunk region of zebrafish embryos\|tissue:trunk region of zebrafish embryos\|genotype:mettl16+/+\|treatment:no treatment\|rip antibody:n1\|geo loc name:missing\|collection date:missing	sibling input rep1	Illumina Casava 1.8 software used for basecalling. fastp software were used to remove the reads that contained adaptor contamination low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp. HISAT2 was used to map reads to zebrafish reference genome Ensembl GRCz11. Mapped reads of IP and input libraries were provided for R package exomePeak which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software. StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM total exon fragments /mapped reads millions × exon length kB. The differentially expressed mRNAs were selected by R package edgeR. Assembly: GRCz11 Supplementary files format and content: BW files include peak files with quantitative data for each gene and each sample	trunk region of zebrafish embryos		Total RNA was isolated from the trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003 Synaptic Systems was applied for m6A immunoprecipitation. Then the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq		tissue:trunk region of zebrafish embryos\|genotype:mettl16+/+\|treatment:no treatment\|rip antibody:n1	GSM7039970	GSM7039970: sibling input rep1; Danio rerio; RIP Seq	GSM7039970 r1	GSM7039970	1	Total RNA was isolated from the trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003 Synaptic Systems was applied for m6A immunoprecipitation. Then the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq		RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP422577	loader:fastq load.py	sibling1_input_R1.fastq.gz sibling1_input_R2.fastq.gz	fastq fastq	13094981449.0	46647417.0	GSM7039970 r1	0:140.35 1:140.37	A:3434495131;C:3120669719;G:3036482303;T:3502963330;N:370966	140	140	3434495131	3120669719	3036482303	3502963330	370966	SRX19347579	SRS16745097	SRA1590470	Huazhong University of Science and Technology	Huazhong University of Science and Technology	2	0.89276	0.90193	0.352	0.3489	0.70905	0.70719	0.52165	0.52427	142	142	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2023-02-12	Undetermined	Embryo	Trunk	Surface Structure
74104	74104	SRR23433714	SRX19347578	SRS16745096	SRP422577	PRJNA934472	Mettl16 promotes hematopoietic stem and progenitor cell expansion in embryonic hematopoiesis [m6A Seq]	GSE225136	Other	The RNA N6 methyladenosine m6A modification has emerged as an essential regulator of vertebrate embryogenesis and malignancies. However its functions and underlying molecular mechanisms in the expansion of hematopoietic stem and progenitor cells HSPCs during early embryonic development remain elusive. Here we show that Mettl16 an RNA methyltransferase identified recently is specifically required for HSPC expansion during zebrafish early embryonic development in an m6A dependent manner. In mettl16 deficient embryos HSPCs exhibit defective proliferation capacity due to G0/G1 arrest. Mechanistically HSPC proliferation is blocked by impaired methyltransferase function of Mettl16 in vivo. We identify cell cycle gene mybl2b as a novel direct m6A target of Mettl16 and Mettl16 deficiency destabilizes mybl2b mRNA which is mediated by m6A reader Igf2bp1. Moreover we revealed that the METTL16 m6A MYBL2 IGF2BP1 signaling axis in G1/S progression is conserved in humans. Collectively our findings demonstrate the critical function of m6A modification deposited by Mettl16 in HSPC expansion during early embryonic development. Overall design: m6A seq profiles of sibling and mettl16 / zebrafish embryos at 3 dpf for triplicates	parent bioproject:PRJNA934075	pubmed:38605226	sibling IP rep1	GSM7039969	source name:trunk region of zebrafish embryos\|tissue:trunk region of zebrafish embryos\|genotype:mettl16+/+\|treatment:no treatment\|rip antibody:anti m6A\|geo loc name:missing\|collection date:missing	sibling IP rep1	Illumina Casava 1.8 software used for basecalling. fastp software were used to remove the reads that contained adaptor contamination low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp. HISAT2 was used to map reads to zebrafish reference genome Ensembl GRCz11. Mapped reads of IP and input libraries were provided for R package exomePeak which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software. StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM total exon fragments /mapped reads millions × exon length kB. The differentially expressed mRNAs were selected by R package edgeR. Assembly: GRCz11 Supplementary files format and content: BW files include peak files with quantitative data for each gene and each sample	trunk region of zebrafish embryos		Total RNA was isolated from the trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003 Synaptic Systems was applied for m6A immunoprecipitation. Then the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq		tissue:trunk region of zebrafish embryos\|genotype:mettl16+/+\|treatment:no treatment\|rip antibody:anti m6A	GSM7039969	GSM7039969: sibling IP rep1; Danio rerio; RIP Seq	GSM7039969 r1	GSM7039969	1	Total RNA was isolated from the trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003 Synaptic Systems was applied for m6A immunoprecipitation. Then the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq		RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP422577	loader:fastq load.py	sibling1_IP_R1.fastq.gz sibling1_IP_R2.fastq.gz	fastq fastq	12317957591.0	43954374.0	GSM7039969 r1	0:140.17 1:140.08	A:3509912915;C:2650796924;G:2663699373;T:3493137659;N:410720	140	140	3509912915	2650796924	2663699373	3493137659	410720	SRX19347578	SRS16745096	SRA1590470	Huazhong University of Science and Technology	Huazhong University of Science and Technology	2	0.87054	0.88058	0.30375	0.30421	0.67783	0.67584	0.44329	0.44327	142	142	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2023-02-12	Undetermined	Embryo	Trunk	Surface Structure
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

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