rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.title,run.attributes,run.filename,run.semantic_name,run.total_bases,run.total_spots,run.alias,run.read_lengths,run.base_counts,run.r1_length,run.r2_length,run.r3_length,run.r4_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,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse
40249,SRR3038049,SRX1494244,SRS1217111,SRP067641,PRJNA306648,Dynamic RNA protein interactions underlie the zebrafish maternal to zygotic transition,GSE76212,Other,We adapted the iCLIP method to zebrafish embryos to investigate activities of Hnrnpa1 during the maternal to zygotic transition Overall design: 3 and 4 biological replicates from zebrafish embryos before preZGA and during ZGA zygotic genome activation  respectively  post UV crosslinking. Negative control samples include 3 IgG replicates of UV crosslinked samples for both developmental stages examined,,pubmed:28381614,,IgG iCLIP zf ZGA rep3,GSM1976593,,tissue:zebrafish embryo|developmental stage:ZGA 1K cell stage|antibody:anti IgG|barcode sequence:NNNTGGCNN,IgG iCLIP zf ZGA rep3,Basecalls performed using CASAVA version 1.4 For detail on data processing see: König et al. 2010: iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959 Genome build: Zv9 version 75 Supplementary files format and content: .bed files describing significant crosslink sites derived from unique contain G in the file name and multi mapped contain M in the file name reads for combined replicates for each individual developmental stages and negative controls.,zebrafish embryo,Zebrafish embryos at the desired developmental stages were irradiated with UV light 254 nm to in vivo crosslink RNA protein interactions.,Zebrafish embryos were lysed and lysates treated with RNaseI to obtain optimal length of RNA fragments for cDNA library preparation. hnRNP A1 RNA complexes were immunopurified using mouse anti hnRNP A1 antibody and protein G dynabeads Invitrogen. Anti IgG antibody Sigma was used for negative control immunopurifications. post RNA dephosphorylation  three prime end linker ligation was performed. Protein RNA complexes were resolved on SDS PAGE and transferred to the nitrocellulose membrane. Region of the membrane above the predicted size of hnRNP A1 was cut and RNA extracted using proteise K treatment. Subsequently  RNA was reverse transcribed using RT primers harboring a barcode. cDNA was separated into three size selected fractions using 6% TBE Urea gel Life Technologies and circularized by ssDNA circligase. Specific oligo was annealed for BamHI restriction site formation. cDNA was linearized by BamHI digestion. Final cDNA libraries were generated by PCR amplification.. For more details see: König et al. 2010: iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959,Zebrafish embryos were raised from WT AB strain and maintained using standard conditions.,developmental stage:ZGA 1K cell stage|antibody:anti IgG|barcode sequence:NNNTGGCNN,GSM1976593,GSM1976593: IgG iCLIP zf ZGA rep3; Danio rerio; OTHER,GSM1976593,,1,Zebrafish embryos were lysed and lysates treated with RNaseI to obtain optimal length of RNA fragments for cDNA library preparation. hnRNP A1 RNA complexes were immunopurified using mouse anti hnRNP A1 antibody and protein G dynabeads Invitrogen. Anti IgG antibody Sigma was used for negative control immunopurifications. post RNA dephosphorylation  three prime end linker ligation was performed. Protein RNA complexes were resolved on SDS PAGE and transferred to the nitrocellulose membrane. Region of the membrane above the predicted size of hnRNP A1 was cut and RNA extracted using proteise K treatment. Subsequently  RNA was reverse transcribed using RT primers harboring a barcode. cDNA was separated into three size selected fractions using 6% TBE Urea gel Life Technologies and circularized by ssDNA circligase. Specific oligo was annealed for BamHI restriction site formation. cDNA was linearized by BamHI digestion. Final cDNA libraries were generated by PCR amplification.. For more details see: König et al. 2010: iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959,GEO Accession:GSM1976593,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP067641,,,iCLIP_IgG_zebrafishembryo_wt_1K_IgGcontrol_Dr_NNNTGGCNN_20140613_L4333_4.fq.gz,fastq,82722124.0,1088449.0,GSM1976593 r1,0:76,A:21959870;C:19048567;G:22289272;T:19403630;N:20785,76,,,,21959870,19048567,22289272,19403630,20785,SRX1494244,SRS1217111,SRA320959,GEO,"Molecular Biophysics and Biochemistry, Yale University",1,0.08124,,0.02181,,0.98591,,0.59183,,76,,B,,usable mapping rate,illumina,hiseq_era,3prime,other,unknown,bulk,clip,iclip,,United States,2015-12-21,Blastula,Embryo,Embryo Imprecise,All anatomical structures
40250,SRR3038048,SRX1494243,SRS1217112,SRP067641,PRJNA306648,Dynamic RNA protein interactions underlie the zebrafish maternal to zygotic transition,GSE76212,Other,We adapted the iCLIP method to zebrafish embryos to investigate activities of Hnrnpa1 during the maternal to zygotic transition Overall design: 3 and 4 biological replicates from zebrafish embryos before preZGA and during ZGA zygotic genome activation  respectively  post UV crosslinking. Negative control samples include 3 IgG replicates of UV crosslinked samples for both developmental stages examined,,pubmed:28381614,,IgG iCLIP zf ZGA rep2,GSM1976592,,tissue:zebrafish embryo|developmental stage:ZGA 1K cell stage|antibody:anti IgG|barcode sequence:NNNCCACNN,IgG iCLIP zf ZGA rep2,Basecalls performed using CASAVA version 1.4 For detail on data processing see: König et al. 2010: iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959 Genome build: Zv9 version 75 Supplementary files format and content: .bed files describing significant crosslink sites derived from unique contain G in the file name and multi mapped contain M in the file name reads for combined replicates for each individual developmental stages and negative controls.,zebrafish embryo,Zebrafish embryos at the desired developmental stages were irradiated with UV light 254 nm to in vivo crosslink RNA protein interactions.,Zebrafish embryos were lysed and lysates treated with RNaseI to obtain optimal length of RNA fragments for cDNA library preparation. hnRNP A1 RNA complexes were immunopurified using mouse anti hnRNP A1 antibody and protein G dynabeads Invitrogen. Anti IgG antibody Sigma was used for negative control immunopurifications. post RNA dephosphorylation  three prime end linker ligation was performed. Protein RNA complexes were resolved on SDS PAGE and transferred to the nitrocellulose membrane. Region of the membrane above the predicted size of hnRNP A1 was cut and RNA extracted using proteise K treatment. Subsequently  RNA was reverse transcribed using RT primers harboring a barcode. cDNA was separated into three size selected fractions using 6% TBE Urea gel Life Technologies and circularized by ssDNA circligase. Specific oligo was annealed for BamHI restriction site formation. cDNA was linearized by BamHI digestion. Final cDNA libraries were generated by PCR amplification.. For more details see: König et al. 2010: iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959,Zebrafish embryos were raised from WT AB strain and maintained using standard conditions.,developmental stage:ZGA 1K cell stage|antibody:anti IgG|barcode sequence:NNNCCACNN,GSM1976592,GSM1976592: IgG iCLIP zf ZGA rep2; Danio rerio; OTHER,GSM1976592,,1,Zebrafish embryos were lysed and lysates treated with RNaseI to obtain optimal length of RNA fragments for cDNA library preparation. hnRNP A1 RNA complexes were immunopurified using mouse anti hnRNP A1 antibody and protein G dynabeads Invitrogen. Anti IgG antibody Sigma was used for negative control immunopurifications. post RNA dephosphorylation  three prime end linker ligation was performed. Protein RNA complexes were resolved on SDS PAGE and transferred to the nitrocellulose membrane. Region of the membrane above the predicted size of hnRNP A1 was cut and RNA extracted using proteise K treatment. Subsequently  RNA was reverse transcribed using RT primers harboring a barcode. cDNA was separated into three size selected fractions using 6% TBE Urea gel Life Technologies and circularized by ssDNA circligase. Specific oligo was annealed for BamHI restriction site formation. cDNA was linearized by BamHI digestion. Final cDNA libraries were generated by PCR amplification.. For more details see: König et al. 2010: iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959,GEO Accession:GSM1976592,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP067641,,,iCLIP_IgG_zebrafishembryo_wt_1K_IgGcontrol_Dr_NNNCCACNN_20140613_L4333_2.fq.gz,fastq,50195036.0,660461.0,GSM1976592 r1,0:76,A:14249581;C:12927029;G:12969451;T:10036400;N:12575,76,,,,14249581,12927029,12969451,10036400,12575,SRX1494243,SRS1217112,SRA320959,GEO,"Molecular Biophysics and Biochemistry, Yale University",1,0.25447,,0.03871,,0.94556,,0.7523,,76,,B,,usable mapping rate,illumina,hiseq_era,3prime,other,unknown,bulk,clip,iclip,,United States,2015-12-21,Blastula,Embryo,Embryo Imprecise,All anatomical structures
40251,SRR3038047,SRX1494242,SRS1217113,SRP067641,PRJNA306648,Dynamic RNA protein interactions underlie the zebrafish maternal to zygotic transition,GSE76212,Other,We adapted the iCLIP method to zebrafish embryos to investigate activities of Hnrnpa1 during the maternal to zygotic transition Overall design: 3 and 4 biological replicates from zebrafish embryos before preZGA and during ZGA zygotic genome activation  respectively  post UV crosslinking. Negative control samples include 3 IgG replicates of UV crosslinked samples for both developmental stages examined,,pubmed:28381614,,IgG iCLIP zf ZGA rep1,GSM1976591,,tissue:zebrafish embryo|developmental stage:ZGA 1K cell stage|antibody:anti IgG|barcode sequence:NNNGGCGNN,IgG iCLIP zf ZGA rep1,Basecalls performed using CASAVA version 1.4 For detail on data processing see: König et al. 2010: iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959 Genome build: Zv9 version 75 Supplementary files format and content: .bed files describing significant crosslink sites derived from unique contain G in the file name and multi mapped contain M in the file name reads for combined replicates for each individual developmental stages and negative controls.,zebrafish embryo,Zebrafish embryos at the desired developmental stages were irradiated with UV light 254 nm to in vivo crosslink RNA protein interactions.,Zebrafish embryos were lysed and lysates treated with RNaseI to obtain optimal length of RNA fragments for cDNA library preparation. hnRNP A1 RNA complexes were immunopurified using mouse anti hnRNP A1 antibody and protein G dynabeads Invitrogen. Anti IgG antibody Sigma was used for negative control immunopurifications. post RNA dephosphorylation  three prime end linker ligation was performed. Protein RNA complexes were resolved on SDS PAGE and transferred to the nitrocellulose membrane. Region of the membrane above the predicted size of hnRNP A1 was cut and RNA extracted using proteise K treatment. Subsequently  RNA was reverse transcribed using RT primers harboring a barcode. cDNA was separated into three size selected fractions using 6% TBE Urea gel Life Technologies and circularized by ssDNA circligase. Specific oligo was annealed for BamHI restriction site formation. cDNA was linearized by BamHI digestion. Final cDNA libraries were generated by PCR amplification.. For more details see: König et al. 2010: iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959,Zebrafish embryos were raised from WT AB strain and maintained using standard conditions.,developmental stage:ZGA 1K cell stage|antibody:anti IgG|barcode sequence:NNNGGCGNN,GSM1976591,GSM1976591: IgG iCLIP zf ZGA rep1; Danio rerio; OTHER,GSM1976591,,1,Zebrafish embryos were lysed and lysates treated with RNaseI to obtain optimal length of RNA fragments for cDNA library preparation. hnRNP A1 RNA complexes were immunopurified using mouse anti hnRNP A1 antibody and protein G dynabeads Invitrogen. Anti IgG antibody Sigma was used for negative control immunopurifications. post RNA dephosphorylation  three prime end linker ligation was performed. Protein RNA complexes were resolved on SDS PAGE and transferred to the nitrocellulose membrane. Region of the membrane above the predicted size of hnRNP A1 was cut and RNA extracted using proteise K treatment. Subsequently  RNA was reverse transcribed using RT primers harboring a barcode. cDNA was separated into three size selected fractions using 6% TBE Urea gel Life Technologies and circularized by ssDNA circligase. Specific oligo was annealed for BamHI restriction site formation. cDNA was linearized by BamHI digestion. Final cDNA libraries were generated by PCR amplification.. For more details see: König et al. 2010: iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959,GEO Accession:GSM1976591,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP067641,,,iCLIP_IgG_zebrafishembryo_wt_1K_IgGcontrol_Dr_NNNGGCGNN_20140613_L4333_5.fq.gz,fastq,453449136.0,5966436.0,GSM1976591 r1,0:76,A:124726528;C:101139098;G:135573575;T:91900507;N:109428,76,,,,124726528,101139098,135573575,91900507,109428,SRX1494242,SRS1217113,SRA320959,GEO,"Molecular Biophysics and Biochemistry, Yale University",1,0.51353,,0.10729,,0.88069,,0.7159,,76,,B,,usable mapping rate,illumina,hiseq_era,3prime,other,unknown,bulk,clip,iclip,,United States,2015-12-21,Blastula,Embryo,Embryo Imprecise,All anatomical structures
40255,SRR3038043,SRX1494238,SRS1217117,SRP067641,PRJNA306648,Dynamic RNA protein interactions underlie the zebrafish maternal to zygotic transition,GSE76212,Other,We adapted the iCLIP method to zebrafish embryos to investigate activities of Hnrnpa1 during the maternal to zygotic transition Overall design: 3 and 4 biological replicates from zebrafish embryos before preZGA and during ZGA zygotic genome activation  respectively  post UV crosslinking. Negative control samples include 3 IgG replicates of UV crosslinked samples for both developmental stages examined,,pubmed:28381614,,hnRNP A1 iCLIP zf ZGA rep4,GSM1976587,,tissue:zebrafish embryo|developmental stage:ZGA 1K cell stage|antibody:anti hnRNP A1|barcode sequence:NNNGGTCNN,hnRNP A1 iCLIP zf ZGA rep4,Basecalls performed using CASAVA version 1.4 For detail on data processing see: König et al. 2010: iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959 Genome build: Zv9 version 75 Supplementary files format and content: .bed files describing significant crosslink sites derived from unique contain G in the file name and multi mapped contain M in the file name reads for combined replicates for each individual developmental stages and negative controls.,zebrafish embryo,Zebrafish embryos at the desired developmental stages were irradiated with UV light 254 nm to in vivo crosslink RNA protein interactions.,Zebrafish embryos were lysed and lysates treated with RNaseI to obtain optimal length of RNA fragments for cDNA library preparation. hnRNP A1 RNA complexes were immunopurified using mouse anti hnRNP A1 antibody and protein G dynabeads Invitrogen. Anti IgG antibody Sigma was used for negative control immunopurifications. post RNA dephosphorylation  three prime end linker ligation was performed. Protein RNA complexes were resolved on SDS PAGE and transferred to the nitrocellulose membrane. Region of the membrane above the predicted size of hnRNP A1 was cut and RNA extracted using proteise K treatment. Subsequently  RNA was reverse transcribed using RT primers harboring a barcode. cDNA was separated into three size selected fractions using 6% TBE Urea gel Life Technologies and circularized by ssDNA circligase. Specific oligo was annealed for BamHI restriction site formation. cDNA was linearized by BamHI digestion. Final cDNA libraries were generated by PCR amplification.. For more details see: König et al. 2010: iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959,Zebrafish embryos were raised from WT AB strain and maintained using standard conditions.,developmental stage:ZGA 1K cell stage|antibody:anti hnRNP A1|barcode sequence:NNNGGTCNN,GSM1976587,GSM1976587: hnRNP A1 iCLIP zf ZGA rep4; Danio rerio; OTHER,GSM1976587,,1,Zebrafish embryos were lysed and lysates treated with RNaseI to obtain optimal length of RNA fragments for cDNA library preparation. hnRNP A1 RNA complexes were immunopurified using mouse anti hnRNP A1 antibody and protein G dynabeads Invitrogen. Anti IgG antibody Sigma was used for negative control immunopurifications. post RNA dephosphorylation  three prime end linker ligation was performed. Protein RNA complexes were resolved on SDS PAGE and transferred to the nitrocellulose membrane. Region of the membrane above the predicted size of hnRNP A1 was cut and RNA extracted using proteise K treatment. Subsequently  RNA was reverse transcribed using RT primers harboring a barcode. cDNA was separated into three size selected fractions using 6% TBE Urea gel Life Technologies and circularized by ssDNA circligase. Specific oligo was annealed for BamHI restriction site formation. cDNA was linearized by BamHI digestion. Final cDNA libraries were generated by PCR amplification.. For more details see: König et al. 2010: iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959,GEO Accession:GSM1976587,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP067641,,,iCLIP_hnRNPA1_zebrafishembryo_wt_1K_hnRNPA1_Dr_NNNGGTCNN_20140613_L4333_6.fq.gz,fastq,2884007568.0,37947468.0,GSM1976587 r1,0:76,A:936463452;C:557587142;G:746595510;T:642623181;N:738283,76,,,,936463452,557587142,746595510,642623181,738283,SRX1494238,SRS1217117,SRA320959,GEO,"Molecular Biophysics and Biochemistry, Yale University",1,0.38306,,0.08291,,0.80568,,0.62132,,76,,B,,usable mapping rate,illumina,hiseq_era,3prime,other,unknown,bulk,clip,iclip,,United States,2015-12-21,Blastula,Embryo,Embryo Imprecise,All anatomical structures
40256,SRR3038042,SRX1494237,SRS1217118,SRP067641,PRJNA306648,Dynamic RNA protein interactions underlie the zebrafish maternal to zygotic transition,GSE76212,Other,We adapted the iCLIP method to zebrafish embryos to investigate activities of Hnrnpa1 during the maternal to zygotic transition Overall design: 3 and 4 biological replicates from zebrafish embryos before preZGA and during ZGA zygotic genome activation  respectively  post UV crosslinking. Negative control samples include 3 IgG replicates of UV crosslinked samples for both developmental stages examined,,pubmed:28381614,,hnRNP A1 iCLIP zf ZGA rep3,GSM1976586,,tissue:zebrafish embryo|developmental stage:ZGA 1K cell stage|antibody:anti hnRNP A1|barcode sequence:NNNCAATNN,hnRNP A1 iCLIP zf ZGA rep3,Basecalls performed using CASAVA version 1.4 For detail on data processing see: König et al. 2010: iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959 Genome build: Zv9 version 75 Supplementary files format and content: .bed files describing significant crosslink sites derived from unique contain G in the file name and multi mapped contain M in the file name reads for combined replicates for each individual developmental stages and negative controls.,zebrafish embryo,Zebrafish embryos at the desired developmental stages were irradiated with UV light 254 nm to in vivo crosslink RNA protein interactions.,Zebrafish embryos were lysed and lysates treated with RNaseI to obtain optimal length of RNA fragments for cDNA library preparation. hnRNP A1 RNA complexes were immunopurified using mouse anti hnRNP A1 antibody and protein G dynabeads Invitrogen. Anti IgG antibody Sigma was used for negative control immunopurifications. post RNA dephosphorylation  three prime end linker ligation was performed. Protein RNA complexes were resolved on SDS PAGE and transferred to the nitrocellulose membrane. Region of the membrane above the predicted size of hnRNP A1 was cut and RNA extracted using proteise K treatment. Subsequently  RNA was reverse transcribed using RT primers harboring a barcode. cDNA was separated into three size selected fractions using 6% TBE Urea gel Life Technologies and circularized by ssDNA circligase. Specific oligo was annealed for BamHI restriction site formation. cDNA was linearized by BamHI digestion. Final cDNA libraries were generated by PCR amplification.. For more details see: König et al. 2010: iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959,Zebrafish embryos were raised from WT AB strain and maintained using standard conditions.,developmental stage:ZGA 1K cell stage|antibody:anti hnRNP A1|barcode sequence:NNNCAATNN,GSM1976586,GSM1976586: hnRNP A1 iCLIP zf ZGA rep3; Danio rerio; OTHER,GSM1976586,,1,Zebrafish embryos were lysed and lysates treated with RNaseI to obtain optimal length of RNA fragments for cDNA library preparation. hnRNP A1 RNA complexes were immunopurified using mouse anti hnRNP A1 antibody and protein G dynabeads Invitrogen. Anti IgG antibody Sigma was used for negative control immunopurifications. post RNA dephosphorylation  three prime end linker ligation was performed. Protein RNA complexes were resolved on SDS PAGE and transferred to the nitrocellulose membrane. Region of the membrane above the predicted size of hnRNP A1 was cut and RNA extracted using proteise K treatment. Subsequently  RNA was reverse transcribed using RT primers harboring a barcode. cDNA was separated into three size selected fractions using 6% TBE Urea gel Life Technologies and circularized by ssDNA circligase. Specific oligo was annealed for BamHI restriction site formation. cDNA was linearized by BamHI digestion. Final cDNA libraries were generated by PCR amplification.. For more details see: König et al. 2010: iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959,GEO Accession:GSM1976586,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP067641,,,iCLIP_hnRNPA1_zebrafishembryo_wt_1K_hnRNPA1_Dr_NNNCAATNN_20140613_L4333_3.fq.gz,fastq,3875071508.0,50987783.0,GSM1976586 r1,0:76,A:1328984506;C:775814536;G:956147632;T:813109146;N:1015688,76,,,,1328984506,775814536,956147632,813109146,1015688,SRX1494237,SRS1217118,SRA320959,GEO,"Molecular Biophysics and Biochemistry, Yale University",1,0.35787,,0.0904,,0.81874,,0.64706,,76,,B,,usable mapping rate,illumina,hiseq_era,3prime,other,unknown,bulk,clip,iclip,,United States,2015-12-21,Blastula,Embryo,Embryo Imprecise,All anatomical structures
40257,SRR3038041,SRX1494236,SRS1217119,SRP067641,PRJNA306648,Dynamic RNA protein interactions underlie the zebrafish maternal to zygotic transition,GSE76212,Other,We adapted the iCLIP method to zebrafish embryos to investigate activities of Hnrnpa1 during the maternal to zygotic transition Overall design: 3 and 4 biological replicates from zebrafish embryos before preZGA and during ZGA zygotic genome activation  respectively  post UV crosslinking. Negative control samples include 3 IgG replicates of UV crosslinked samples for both developmental stages examined,,pubmed:28381614,,hnRNP A1 iCLIP zf ZGA rep2,GSM1976585,,tissue:zebrafish embryo|developmental stage:ZGA 1K cell stage|antibody:anti hnRNP A1|barcode sequence:NNNTTGTNN,hnRNP A1 iCLIP zf ZGA rep2,Basecalls performed using CASAVA version 1.4 For detail on data processing see: König et al. 2010: iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959 Genome build: Zv9 version 75 Supplementary files format and content: .bed files describing significant crosslink sites derived from unique contain G in the file name and multi mapped contain M in the file name reads for combined replicates for each individual developmental stages and negative controls.,zebrafish embryo,Zebrafish embryos at the desired developmental stages were irradiated with UV light 254 nm to in vivo crosslink RNA protein interactions.,Zebrafish embryos were lysed and lysates treated with RNaseI to obtain optimal length of RNA fragments for cDNA library preparation. hnRNP A1 RNA complexes were immunopurified using mouse anti hnRNP A1 antibody and protein G dynabeads Invitrogen. Anti IgG antibody Sigma was used for negative control immunopurifications. post RNA dephosphorylation  three prime end linker ligation was performed. Protein RNA complexes were resolved on SDS PAGE and transferred to the nitrocellulose membrane. Region of the membrane above the predicted size of hnRNP A1 was cut and RNA extracted using proteise K treatment. Subsequently  RNA was reverse transcribed using RT primers harboring a barcode. cDNA was separated into three size selected fractions using 6% TBE Urea gel Life Technologies and circularized by ssDNA circligase. Specific oligo was annealed for BamHI restriction site formation. cDNA was linearized by BamHI digestion. Final cDNA libraries were generated by PCR amplification.. For more details see: König et al. 2010: iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959,Zebrafish embryos were raised from WT AB strain and maintained using standard conditions.,developmental stage:ZGA 1K cell stage|antibody:anti hnRNP A1|barcode sequence:NNNTTGTNN,GSM1976585,GSM1976585: hnRNP A1 iCLIP zf ZGA rep2; Danio rerio; OTHER,GSM1976585,,1,Zebrafish embryos were lysed and lysates treated with RNaseI to obtain optimal length of RNA fragments for cDNA library preparation. hnRNP A1 RNA complexes were immunopurified using mouse anti hnRNP A1 antibody and protein G dynabeads Invitrogen. Anti IgG antibody Sigma was used for negative control immunopurifications. post RNA dephosphorylation  three prime end linker ligation was performed. Protein RNA complexes were resolved on SDS PAGE and transferred to the nitrocellulose membrane. Region of the membrane above the predicted size of hnRNP A1 was cut and RNA extracted using proteise K treatment. Subsequently  RNA was reverse transcribed using RT primers harboring a barcode. cDNA was separated into three size selected fractions using 6% TBE Urea gel Life Technologies and circularized by ssDNA circligase. Specific oligo was annealed for BamHI restriction site formation. cDNA was linearized by BamHI digestion. Final cDNA libraries were generated by PCR amplification.. For more details see: König et al. 2010: iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959,GEO Accession:GSM1976585,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP067641,,,iCLIP_hnRNPA1_zebrafishembryo_wt_1K_hnRNPA1_Dr_NNNTTGTNN_20140613_L4333_1.fq.gz,fastq,3482039180.0,45816305.0,GSM1976585 r1,0:76,A:1093877493;C:647486562;G:914636686;T:825135975;N:902464,76,,,,1093877493,647486562,914636686,825135975,902464,SRX1494236,SRS1217119,SRA320959,GEO,"Molecular Biophysics and Biochemistry, Yale University",1,0.29908,,0.07356,,0.83459,,0.62976,,76,,B,,usable mapping rate,illumina,hiseq_era,3prime,other,unknown,bulk,clip,iclip,,United States,2015-12-21,Blastula,Embryo,Embryo Imprecise,All anatomical structures
40258,SRR3038040,SRX1494235,SRS1217120,SRP067641,PRJNA306648,Dynamic RNA protein interactions underlie the zebrafish maternal to zygotic transition,GSE76212,Other,We adapted the iCLIP method to zebrafish embryos to investigate activities of Hnrnpa1 during the maternal to zygotic transition Overall design: 3 and 4 biological replicates from zebrafish embryos before preZGA and during ZGA zygotic genome activation  respectively  post UV crosslinking. Negative control samples include 3 IgG replicates of UV crosslinked samples for both developmental stages examined,,pubmed:28381614,,hnRNP A1 iCLIP zf ZGA rep1,GSM1976584,,tissue:zebrafish embryo|developmental stage:ZGA 1K cell stage|antibody:anti hnRNP A1|barcode sequence:NNNGGTTNN,hnRNP A1 iCLIP zf ZGA rep1,Basecalls performed using CASAVA version 1.4 For detail on data processing see: König et al. 2010: iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959 Genome build: Zv9 version 75 Supplementary files format and content: .bed files describing significant crosslink sites derived from unique contain G in the file name and multi mapped contain M in the file name reads for combined replicates for each individual developmental stages and negative controls.,zebrafish embryo,Zebrafish embryos at the desired developmental stages were irradiated with UV light 254 nm to in vivo crosslink RNA protein interactions.,Zebrafish embryos were lysed and lysates treated with RNaseI to obtain optimal length of RNA fragments for cDNA library preparation. hnRNP A1 RNA complexes were immunopurified using mouse anti hnRNP A1 antibody and protein G dynabeads Invitrogen. Anti IgG antibody Sigma was used for negative control immunopurifications. post RNA dephosphorylation  three prime end linker ligation was performed. Protein RNA complexes were resolved on SDS PAGE and transferred to the nitrocellulose membrane. Region of the membrane above the predicted size of hnRNP A1 was cut and RNA extracted using proteise K treatment. Subsequently  RNA was reverse transcribed using RT primers harboring a barcode. cDNA was separated into three size selected fractions using 6% TBE Urea gel Life Technologies and circularized by ssDNA circligase. Specific oligo was annealed for BamHI restriction site formation. cDNA was linearized by BamHI digestion. Final cDNA libraries were generated by PCR amplification.. For more details see: König et al. 2010: iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959,Zebrafish embryos were raised from WT AB strain and maintained using standard conditions.,developmental stage:ZGA 1K cell stage|antibody:anti hnRNP A1|barcode sequence:NNNGGTTNN,GSM1976584,GSM1976584: hnRNP A1 iCLIP zf ZGA rep1; Danio rerio; OTHER,GSM1976584,,1,Zebrafish embryos were lysed and lysates treated with RNaseI to obtain optimal length of RNA fragments for cDNA library preparation. hnRNP A1 RNA complexes were immunopurified using mouse anti hnRNP A1 antibody and protein G dynabeads Invitrogen. Anti IgG antibody Sigma was used for negative control immunopurifications. post RNA dephosphorylation  three prime end linker ligation was performed. Protein RNA complexes were resolved on SDS PAGE and transferred to the nitrocellulose membrane. Region of the membrane above the predicted size of hnRNP A1 was cut and RNA extracted using proteise K treatment. Subsequently  RNA was reverse transcribed using RT primers harboring a barcode. cDNA was separated into three size selected fractions using 6% TBE Urea gel Life Technologies and circularized by ssDNA circligase. Specific oligo was annealed for BamHI restriction site formation. cDNA was linearized by BamHI digestion. Final cDNA libraries were generated by PCR amplification.. For more details see: König et al. 2010: iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959,GEO Accession:GSM1976584,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP067641,,,iCLIP_hnRNPA1_zebrafishembryo_wt_1K_hnRNPA1_Dr_NNNGGTTNN_20140613_L4333_7.fq.gz,fastq,3547711920.0,46680420.0,GSM1976584 r1,0:76,A:1105542969;C:658172853;G:958654426;T:824422930;N:918742,76,,,,1105542969,658172853,958654426,824422930,918742,SRX1494235,SRS1217120,SRA320959,GEO,"Molecular Biophysics and Biochemistry, Yale University",1,0.34257,,0.08694,,0.83055,,0.64965,,76,,B,,usable mapping rate,illumina,hiseq_era,3prime,other,unknown,bulk,clip,iclip,,United States,2015-12-21,Blastula,Embryo,Embryo Imprecise,All anatomical structures
48384,SRR7236655,SRX4142917,SRS3356704,SRP149368,PRJNA473836,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: KHSRP iCLIP,PRJNA473836,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis. This is the endogenous KHSRP iCLIP part of the study.,,,,Raw multiplex: KHSRP iCLIP   iCLIP Khsrp Ab B2;KHSRP iCLIP   iCLIP Khsrp noAb B2,Raw multiplex: KHSRP iCLIP   iC Khsrp Ab B2 AG01175;KHSRP iCLIP   iC Khsrp noAb B2 AG01176,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:KHSRP antibody;|replicate group:1;2|replicate:2|barcode:TCTC;GTGT|BioSampleModel:Model organism or animal,,,,,,,,,Raw multiplex: KHSRP iCLIP   iCLIP Khsrp Ab B2;KHSRP iCLIP   iCLIP Khsrp noAb B2,AG01175.2;AG01176.2,AG01175.2;AG01176.2,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP149368,,,HHLV3ADXX_kh2_NOBCX_R1.fastq.gz,fastq,7675050912.0,100987512.0,HHLV3ADXX kh2 NOBCX R1.fastq.gz,0:76,A:2241934669;C:1774343310;G:1727825603;T:1912212373;N:18734957,76,,,,2241934669,1774343310,1727825603,1912212373,18734957,SRX4142917,SRS3356704,SRA712863,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.00123,,0.00083,,0.99939,,0.47297,,76,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,clip,iclip,,United States,2018-06-07,Blastula,Embryo,Embryo Imprecise,All anatomical structures
48385,SRR7236656,SRX4142916,SRS3356704,SRP149368,PRJNA473836,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: KHSRP iCLIP,PRJNA473836,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis. This is the endogenous KHSRP iCLIP part of the study.,,,,Raw multiplex: KHSRP iCLIP   iCLIP Khsrp Ab B2;KHSRP iCLIP   iCLIP Khsrp noAb B2,Raw multiplex: KHSRP iCLIP   iC Khsrp Ab B2 AG01175;KHSRP iCLIP   iC Khsrp noAb B2 AG01176,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:KHSRP antibody;|replicate group:1;2|replicate:2|barcode:TCTC;GTGT|BioSampleModel:Model organism or animal,,,,,,,,,Raw multiplex: KHSRP iCLIP   iCLIP Khsrp Ab B2;KHSRP iCLIP   iCLIP Khsrp noAb B2,AG01175.1;AG01176.1,AG01175.1;AG01176.1,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP149368,,,HHLY2ADXX_kh2_NOBCX_R1.fastq.gz,fastq,10199922760.0,134209510.0,HHLY2ADXX kh2 NOBCX R1.fastq.gz,0:76,A:2990232290;C:2350693064;G:2293777949;T:2554099449;N:11120008,76,,,,2990232290,2350693064,2293777949,2554099449,11120008,SRX4142916,SRS3356704,SRA712863,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.00128,,0.00076,,0.99945,,0.43877,,76,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,clip,iclip,,United States,2018-06-07,Blastula,Embryo,Embryo Imprecise,All anatomical structures
48386,SRR7236657,SRX4142915,SRS3356703,SRP149368,PRJNA473836,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: KHSRP iCLIP,PRJNA473836,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis. This is the endogenous KHSRP iCLIP part of the study.,,,,Raw multiplex: KHSRP iCLIP   iCLIP Khsrp noAb B3;KHSRP iCLIP   iCLIP Khsrp Ab B3,Raw multiplex: KHSRP iCLIP   iC Khsrp noAb B3 AG01177;KHSRP iCLIP   iC Khsrp Ab B3 AG01178,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:;KHSRP antibody|replicate group:2;1|replicate:3|barcode:CACA;AGAG|BioSampleModel:Model organism or animal,,,,,,,,,Raw multiplex: KHSRP iCLIP   iCLIP Khsrp noAb B3;KHSRP iCLIP   iCLIP Khsrp Ab B3,AG01177.2;AG01178.2,AG01177.2;AG01178.2,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP149368,,,HHLTFADXX_kh3_022_R1.fastq.gz,fastq,5612942988.0,73854513.0,HHLTFADXX kh3 022 R1.fastq.gz,0:76,A:1761182916;C:1273000548;G:1339715056;T:1238748082;N:296386,76,,,,1761182916,1273000548,1339715056,1238748082,296386,SRX4142915,SRS3356703,SRA712863,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.00125,,0.00069,,0.99831,,0.5566,,76,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,clip,iclip,,United States,2018-06-07,Blastula,Embryo,Embryo Imprecise,All anatomical structures
48387,SRR7236658,SRX4142914,SRS3356703,SRP149368,PRJNA473836,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: KHSRP iCLIP,PRJNA473836,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis. This is the endogenous KHSRP iCLIP part of the study.,,,,Raw multiplex: KHSRP iCLIP   iCLIP Khsrp noAb B3;KHSRP iCLIP   iCLIP Khsrp Ab B3,Raw multiplex: KHSRP iCLIP   iC Khsrp noAb B3 AG01177;KHSRP iCLIP   iC Khsrp Ab B3 AG01178,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:;KHSRP antibody|replicate group:2;1|replicate:3|barcode:CACA;AGAG|BioSampleModel:Model organism or animal,,,,,,,,,Raw multiplex: KHSRP iCLIP   iCLIP Khsrp noAb B3;KHSRP iCLIP   iCLIP Khsrp Ab B3,AG01177.1;AG01178.1,AG01177.1;AG01178.1,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP149368,,,HHLV3ADXX_kh3_NOBCX_R1.fastq.gz,fastq,7810653532.0,102771757.0,HHLV3ADXX kh3 NOBCX R1.fastq.gz,0:76,A:2439317937;C:1775190292;G:1863760875;T:1714265680;N:18118748,76,,,,2439317937,1775190292,1863760875,1714265680,18118748,SRX4142914,SRS3356703,SRA712863,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.00121,,0.00071,,0.99864,,0.54444,,76,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,clip,iclip,,United States,2018-06-07,Blastula,Embryo,Embryo Imprecise,All anatomical structures
48388,SRR7236659,SRX4142913,SRS3356702,SRP149368,PRJNA473836,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: KHSRP iCLIP,PRJNA473836,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis. This is the endogenous KHSRP iCLIP part of the study.,,,,KHSRP iCLIP   iCLIP Khsrp Ab B3,KHSRP iCLIP   iC Khsrp Ab B3 AG01178,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:KHSRP antibody|replicate group:1|replicate:3|barcode:AGAG|BioSampleModel:Model organism or animal,,,,,,,,,KHSRP iCLIP   iCLIP Khsrp Ab B3,AG01178.2,AG01178.2,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP149368,,,AG01178.2_R1.fastq.gz,fastq,1046051929.0,35061189.0,AG01178.2 R1.fastq.gz,0:29.84 1:0,A:304629557;C:170568838;G:208541597;T:362307791;N:4146,29,0,,,304629557,170568838,208541597,362307791,4146,SRX4142913,SRS3356702,SRA712863,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.68324,,0.4824,,0.78139,,0.51734,,20,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,clip,iclip,,United States,2018-06-07,Blastula,Embryo,Embryo Imprecise,All anatomical structures
48389,SRR7236660,SRX4142912,SRS3356702,SRP149368,PRJNA473836,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: KHSRP iCLIP,PRJNA473836,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis. This is the endogenous KHSRP iCLIP part of the study.,,,,KHSRP iCLIP   iCLIP Khsrp Ab B3,KHSRP iCLIP   iC Khsrp Ab B3 AG01178,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:KHSRP antibody|replicate group:1|replicate:3|barcode:AGAG|BioSampleModel:Model organism or animal,,,,,,,,,KHSRP iCLIP   iCLIP Khsrp Ab B3,AG01178.1,AG01178.1,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP149368,,,AG01178.1_R1.fastq.gz,fastq,1429865561.0,47958542.0,AG01178.1 R1.fastq.gz,0:29.81 1:0,A:416462367;C:233529708;G:285810572;T:494062288;N:626,29,0,,,416462367,233529708,285810572,494062288,626,SRX4142912,SRS3356702,SRA712863,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.67776,,0.47933,,0.782,,0.52337,,31,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,clip,iclip,,United States,2018-05-30,Blastula,Embryo,Embryo Imprecise,All anatomical structures
48390,SRR7236661,SRX4142911,SRS3356701,SRP149368,PRJNA473836,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: KHSRP iCLIP,PRJNA473836,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis. This is the endogenous KHSRP iCLIP part of the study.,,,,Raw multiplex: KHSRP iCLIP   iCLIP Khsrp Ab B1;KHSRP iCLIP   iCLIP Khsrp noAb B1,Raw multiplex: KHSRP iCLIP   iC Khsrp Ab B1 AG01173;KHSRP iCLIP   iC Khsrp noAb B1 AG01174,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:KHSRP antibody;|replicate group:1;2|replicate:1|barcode:CACA;AGAG|BioSampleModel:Model organism or animal,,,,,,,,,Raw multiplex: KHSRP iCLIP   iCLIP Khsrp Ab B1;KHSRP iCLIP   iCLIP Khsrp noAb B1,AG01173.2;AG01174.2,AG01173.2;AG01174.2,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP149368,,,HHMMTADXX_kh1_020_R1.fastq.gz,fastq,5281915868.0,69498893.0,HHMMTADXX kh1 020 R1.fastq.gz,0:76,A:1639173476;C:1196546385;G:1285461861;T:1160482436;N:251710,76,,,,1639173476,1196546385,1285461861,1160482436,251710,SRX4142911,SRS3356701,SRA712863,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.00021,,0.00011,,0.99973,,0.64705,,76,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,clip,iclip,,United States,2018-06-07,Blastula,Embryo,Embryo Imprecise,All anatomical structures
48391,SRR7236662,SRX4142910,SRS3356701,SRP149368,PRJNA473836,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: KHSRP iCLIP,PRJNA473836,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis. This is the endogenous KHSRP iCLIP part of the study.,,,,Raw multiplex: KHSRP iCLIP   iCLIP Khsrp Ab B1;KHSRP iCLIP   iCLIP Khsrp noAb B1,Raw multiplex: KHSRP iCLIP   iC Khsrp Ab B1 AG01173;KHSRP iCLIP   iC Khsrp noAb B1 AG01174,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:KHSRP antibody;|replicate group:1;2|replicate:1|barcode:CACA;AGAG|BioSampleModel:Model organism or animal,,,,,,,,,Raw multiplex: KHSRP iCLIP   iCLIP Khsrp Ab B1;KHSRP iCLIP   iCLIP Khsrp noAb B1,AG01173.1;AG01174.1,AG01173.1;AG01174.1,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP149368,,,HHLY2ADXX_kh1_NOBCX_R1.fastq.gz,fastq,9991920032.0,131472632.0,HHLY2ADXX kh1 NOBCX R1.fastq.gz,0:76,A:3100849614;C:2254998457;G:2420727161;T:2205131206;N:10213594,76,,,,3100849614,2254998457,2420727161,2205131206,10213594,SRX4142910,SRS3356701,SRA712863,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.00019,,0.0001,,0.99975,,0.46666,,76,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,clip,iclip,,United States,2018-05-31,Blastula,Embryo,Embryo Imprecise,All anatomical structures
48392,SRR7236663,SRX4142909,SRS3356700,SRP149368,PRJNA473836,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: KHSRP iCLIP,PRJNA473836,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis. This is the endogenous KHSRP iCLIP part of the study.,,,,KHSRP iCLIP   iCLIP Khsrp noAb B3,KHSRP iCLIP   iC Khsrp noAb B3 AG01177,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|replicate group:2|replicate:3|barcode:CACA|BioSampleModel:Model organism or animal,,,,,,,,,KHSRP iCLIP   iCLIP Khsrp noAb B3,AG01177.2,AG01177.2,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP149368,,,AG01177.2_R1.fastq.gz,fastq,885888031.0,33497952.0,AG01177.2 R1.fastq.gz,0:26.45 1:0,A:206425913;C:174763971;G:243957147;T:260737810;N:3190,26,0,,,206425913,174763971,243957147,260737810,3190,SRX4142909,SRS3356700,SRA712863,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.06832,,0.02459,,0.98098,,0.60923,,28,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,clip,iclip,,United States,2018-05-30,Blastula,Embryo,Embryo Imprecise,All anatomical structures
48393,SRR7236664,SRX4142908,SRS3356700,SRP149368,PRJNA473836,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: KHSRP iCLIP,PRJNA473836,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis. This is the endogenous KHSRP iCLIP part of the study.,,,,KHSRP iCLIP   iCLIP Khsrp noAb B3,KHSRP iCLIP   iC Khsrp noAb B3 AG01177,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|replicate group:2|replicate:3|barcode:CACA|BioSampleModel:Model organism or animal,,,,,,,,,KHSRP iCLIP   iCLIP Khsrp noAb B3,AG01177.1,AG01177.1,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP149368,,,AG01177.1_R1.fastq.gz,fastq,1222226291.0,46319107.0,AG01177.1 R1.fastq.gz,0:26.39 1:0,A:284330952;C:241163311;G:337366164;T:359365256;N:608,26,0,,,284330952,241163311,337366164,359365256,608,SRX4142908,SRS3356700,SRA712863,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.06321,,0.02496,,0.99541,,0.59566,,24,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,clip,iclip,,United States,2018-06-07,Blastula,Embryo,Embryo Imprecise,All anatomical structures
48394,SRR7236665,SRX4142907,SRS3356699,SRP149368,PRJNA473836,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: KHSRP iCLIP,PRJNA473836,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis. This is the endogenous KHSRP iCLIP part of the study.,,,,KHSRP iCLIP   iCLIP Khsrp noAb B2,KHSRP iCLIP   iC Khsrp noAb B2 AG01176,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|replicate group:2|replicate:2|barcode:GTGT|BioSampleModel:Model organism or animal,,,,,,,,,KHSRP iCLIP   iCLIP Khsrp noAb B2,AG01176.2,AG01176.2,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP149368,,,AG01176.2_R1.fastq.gz,fastq,233885454.0,7281208.0,AG01176.2 R1.fastq.gz,0:32.12 1:0,A:54788902;C:54168846;G:66577250;T:58350443;N:13,32,0,,,54788902,54168846,66577250,58350443,13,SRX4142907,SRS3356699,SRA712863,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.10795,,0.04438,,0.97516,,0.69327,,38,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,clip,iclip,,United States,2018-06-07,Blastula,Embryo,Embryo Imprecise,All anatomical structures
48395,SRR7236666,SRX4142906,SRS3356699,SRP149368,PRJNA473836,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: KHSRP iCLIP,PRJNA473836,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis. This is the endogenous KHSRP iCLIP part of the study.,,,,KHSRP iCLIP   iCLIP Khsrp noAb B2,KHSRP iCLIP   iC Khsrp noAb B2 AG01176,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|replicate group:2|replicate:2|barcode:GTGT|BioSampleModel:Model organism or animal,,,,,,,,,KHSRP iCLIP   iCLIP Khsrp noAb B2,AG01176.1,AG01176.1,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP149368,,,AG01176.1_R1.fastq.gz,fastq,311212095.0,9672607.0,AG01176.1 R1.fastq.gz,0:32.17 1:0,A:73018762;C:72027124;G:88456228;T:77709256;N:725,32,0,,,73018762,72027124,88456228,77709256,725,SRX4142906,SRS3356699,SRA712863,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.10719,,0.04462,,0.97498,,0.70725,,37,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,clip,iclip,,United States,2018-05-30,Blastula,Embryo,Embryo Imprecise,All anatomical structures
48396,SRR7236667,SRX4142905,SRS3356698,SRP149368,PRJNA473836,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: KHSRP iCLIP,PRJNA473836,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis. This is the endogenous KHSRP iCLIP part of the study.,,,,KHSRP iCLIP   iCLIP Khsrp Ab B2,KHSRP iCLIP   iC Khsrp Ab B2 AG01175,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:KHSRP antibody|replicate group:1|replicate:2|barcode:TCTC|BioSampleModel:Model organism or animal,,,,,,,,,KHSRP iCLIP   iCLIP Khsrp Ab B2,AG01175.2,AG01175.2,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP149368,,,AG01175.2_R1.fastq.gz,fastq,2466162835.0,77779195.0,AG01175.2 R1.fastq.gz,0:31.71 1:0,A:716944933;C:413092452;G:514707831;T:821417411;N:208,31,0,,,716944933,413092452,514707831,821417411,208,SRX4142905,SRS3356698,SRA712863,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.64577,,0.4225,,0.77516,,0.52286,,23,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,clip,iclip,,United States,2018-06-07,Blastula,Embryo,Embryo Imprecise,All anatomical structures
48397,SRR7236668,SRX4142904,SRS3356698,SRP149368,PRJNA473836,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: KHSRP iCLIP,PRJNA473836,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis. This is the endogenous KHSRP iCLIP part of the study.,,,,KHSRP iCLIP   iCLIP Khsrp Ab B2,KHSRP iCLIP   iC Khsrp Ab B2 AG01175,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:KHSRP antibody|replicate group:1|replicate:2|barcode:TCTC|BioSampleModel:Model organism or animal,,,,,,,,,KHSRP iCLIP   iCLIP Khsrp Ab B2,AG01175.1,AG01175.1,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP149368,,,AG01175.1_R1.fastq.gz,fastq,3316001149.0,104496257.0,AG01175.1 R1.fastq.gz,0:31.73 1:0,A:964563720;C:554605513;G:690144862;T:1106678088;N:8966,31,0,,,964563720,554605513,690144862,1106678088,8966,SRX4142904,SRS3356698,SRA712863,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.64794,,0.42598,,0.77719,,0.53602,,31,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,clip,iclip,,United States,2018-05-31,Blastula,Embryo,Embryo Imprecise,All anatomical structures
48398,SRR7236669,SRX4142903,SRS3356697,SRP149368,PRJNA473836,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: KHSRP iCLIP,PRJNA473836,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis. This is the endogenous KHSRP iCLIP part of the study.,,,,KHSRP iCLIP   iCLIP Khsrp noAb B1,KHSRP iCLIP   iC Khsrp noAb B1 AG01174,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|replicate group:2|replicate:1|barcode:AGAG|BioSampleModel:Model organism or animal,,,,,,,,,KHSRP iCLIP   iCLIP Khsrp noAb B1,AG01174.2,AG01174.2,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP149368,,,AG01174.2_R1.fastq.gz,fastq,997707611.0,35501164.0,AG01174.2 R1.fastq.gz,0:28.10 1:0,A:234873124;C:200942687;G:273279747;T:288611385;N:668,28,0,,,234873124,200942687,273279747,288611385,668,SRX4142903,SRS3356697,SRA712863,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.05803,,0.02195,,0.99632,,0.62645,,26,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,clip,iclip,,United States,2018-06-07,Blastula,Embryo,Embryo Imprecise,All anatomical structures
48399,SRR7236670,SRX4142902,SRS3356697,SRP149368,PRJNA473836,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: KHSRP iCLIP,PRJNA473836,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis. This is the endogenous KHSRP iCLIP part of the study.,,,,KHSRP iCLIP   iCLIP Khsrp noAb B1,KHSRP iCLIP   iC Khsrp noAb B1 AG01174,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|replicate group:2|replicate:1|barcode:AGAG|BioSampleModel:Model organism or animal,,,,,,,,,KHSRP iCLIP   iCLIP Khsrp noAb B1,AG01174.1,AG01174.1,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP149368,,,AG01174.1_R1.fastq.gz,fastq,1864739454.0,66313666.0,AG01174.1 R1.fastq.gz,0:28.12 1:0,A:439206469;C:375517297;G:509810941;T:540192256;N:12491,28,0,,,439206469,375517297,509810941,540192256,12491,SRX4142902,SRS3356697,SRA712863,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.0573,,0.02132,,0.99618,,0.52433,,34,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,clip,iclip,,United States,2018-06-07,Blastula,Embryo,Embryo Imprecise,All anatomical structures
48400,SRR7236671,SRX4142901,SRS3356696,SRP149368,PRJNA473836,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: KHSRP iCLIP,PRJNA473836,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis. This is the endogenous KHSRP iCLIP part of the study.,,,,KHSRP iCLIP   iCLIP Khsrp Ab B1,KHSRP iCLIP   iC Khsrp Ab B1 AG01173,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:KHSRP antibody|replicate group:1|replicate:1|barcode:CACA|BioSampleModel:Model organism or animal,,,,,,,,,KHSRP iCLIP   iCLIP Khsrp Ab B1,AG01173.2,AG01173.2,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP149368,,,AG01173.2_R1.fastq.gz,fastq,867830730.0,28259963.0,AG01173.2 R1.fastq.gz,0:30.71 1:0,A:248512374;C:137460842;G:175204067;T:306652878;N:569,30,0,,,248512374,137460842,175204067,306652878,569,SRX4142901,SRS3356696,SRA712863,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.67622,,0.4515,,0.76765,,0.52978,,31,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,clip,iclip,,United States,2018-06-07,Blastula,Embryo,Embryo Imprecise,All anatomical structures
48401,SRR7236672,SRX4142900,SRS3356696,SRP149368,PRJNA473836,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: KHSRP iCLIP,PRJNA473836,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis. This is the endogenous KHSRP iCLIP part of the study.,,,,KHSRP iCLIP   iCLIP Khsrp Ab B1,KHSRP iCLIP   iC Khsrp Ab B1 AG01173,,strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:KHSRP antibody|replicate group:1|replicate:1|barcode:CACA|BioSampleModel:Model organism or animal,,,,,,,,,KHSRP iCLIP   iCLIP Khsrp Ab B1,AG01173.1,AG01173.1,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP149368,,,AG01173.1_R1.fastq.gz,fastq,1644979798.0,53548650.0,AG01173.1 R1.fastq.gz,0:30.72 1:0,A:471457103;C:259804358;G:331035207;T:582672297;N:10833,30,0,,,471457103,259804358,331035207,582672297,10833,SRX4142900,SRS3356696,SRA712863,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.67964,,0.45484,,0.77147,,0.52736,,27,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,clip,iclip,,United States,2018-05-30,Blastula,Embryo,Embryo Imprecise,All anatomical structures
49537,SRR8937007,SRX5717520,SRS4655940,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/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 TURBOâ„¢ 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. RNA RIP BisSeq: 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 purified mRNA was used for RNA BisSeq library construction. Around 200 ng mRNA premixed with the in vitro transcribed Dhfr mRNA at a ratio of 300:1 Dhfr mRNA serves as methylation conversion control was fragmented to 100 nt fragments for 1 min at 90°C in 10× RNA Fragmentation Reagent Ambion  then stopped by 10× RNA stop solution Ambion  and precipitated with 100% ethanol. The RNA pellet was resuspended in 100 µl bisulfite solution pH 5.1  which is a 100:1 mixture of 40% sodium bisulfite Sigma and 600 µM hydroquinone Sigma and subjected to heat incubation at 75°C for 4.5 h. The reaction mixture was desalted by passing through Nanosep with 3K Omega 500/pk columns PALL Corporation with centrifugation. post washed with nuclease free water and centrifuged for five times  the RNA was finally disolved in 75 ?l nuclease free water and then desulfonated by incubation with an equal volume of 1 M Tris HCl pH 9.0 at 75 °C for 1 h. post ethanol precipitation  the RNA was resuspended in 11 µl of RNase free water and subjected to library construction. Reverse transcription was carried out with superscript II Reverse Transcriptase Invitrogen and ACT random hexamers. The following procedures were performed with the KAPA Stranded mRNA Seq Kit KAPA according to the manufacturer?s instructions.Libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 125 bp.,parent bioproject:PRJNA534030,,,RIP BS 3hpf,GSM3732427,,source name:Zebrafish embryo|strain:AB strain|age:3 hpf|tissue:whole embryo|rip antibody:polyclonal anti Ybx1 antibody,RIP BS 3hpf,library strategy: RNA RIP BisSeq Reads were aligned to the zv9 genome assembly using meRanTK v1.2.0 m5C sites were called by meRanCall v1.2.0 and annotated by applying BEDTools’ intersectBed. 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 m5C sites in one biological replicates.,Zebrafish embryo,,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. Thus purified mRNA was used for RNA BisSeq library construction. Around 200 ng mRNA premixed with the in vitro transcribed Dhfr mRNA at a ratio of 300:1 Dhfr mRNA serves as methylation conversion control was fragmented to 100 nt fragments for 1 min at 90°C in 10× RNA Fragmentation Reagent Ambion  then stopped by 10× RNA stop solution Ambion  and precipitated with 100% ethanol. The RNA pellet was resuspended in 100 µl bisulfite solution pH 5.1  which is a 100:1 mixture of 40% sodium bisulfite Sigma and 600 µM hydroquinone Sigma and subjected to heat incubation at 75°C for 4.5 h. The reaction mixture was desalted by passing through Nanosep with 3K Omega 500/pk columns PALL Corporation with centrifugation. post washed with nuclease free water and centrifuged for five times  the RNA was finally disolved in 75 μl nuclease free water and then desulfonated by incubation with an equal volume of 1 M Tris HCl pH 9.0 at 75 °C for 1 h. post ethanol precipitation  the RNA was resuspended in 11 µl of RNase free water and subjected to library construction. Reverse transcription was carried out with superscript II Reverse Transcriptase Invitrogen and ACT random hexamers. The following procedures were performed with the KAPA Stranded mRNA Seq Kit KAPA according to the manufacturer’s instructions.Libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 125 bp.,,strain:AB strain|age:3 hpf|tissue:whole embryo|rip antibody:polyclonal anti Ybx1 antibody,GSM3732427,GSM3732427: RIP BS 3hpf; Danio rerio; OTHER,GSM3732427,,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. Thus purified mRNA was used for RNA BisSeq library construction. Around 200 ng mRNA premixed with the in vitro transcribed Dhfr mRNA at a ratio of 300:1 Dhfr mRNA serves as methylation conversion control was fragmented to 100 nt fragments for 1 min at 90°C in 10× RNA Fragmentation Reagent Ambion  then stopped by 10× RNA stop solution Ambion  and precipitated with 100% ethanol. The RNA pellet was resuspended in 100 µl bisulfite solution pH 5.1  which is a 100:1 mixture of 40% sodium bisulfite Sigma and 600 µM hydroquinone Sigma and subjected to heat incubation at 75°C for 4.5 h. The reaction mixture was desalted by passing through Nanosep with 3K Omega 500/pk columns PALL Corporation with centrifugation. post washed with nuclease free water and centrifuged for five times  the RNA was finally disolved in 75 μl nuclease free water and then desulfonated by incubation with an equal volume of 1 M Tris HCl pH 9.0 at 75 °C for 1 h. post ethanol precipitation  the RNA was resuspended in 11 µl of RNase free water and subjected to library construction. Reverse transcription was carried out with superscript II Reverse Transcriptase Invitrogen and ACT random hexamers. The following procedures were performed with the KAPA Stranded mRNA Seq Kit KAPA according to the manufacturer's instructions.Libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 125 bp.,GEO Accession:GSM3732427,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP162876,,,RIP-BS_3hpf_R1.fastq.gz RIP-BS_3hpf_R2.fastq.gz,fastq fastq,46222984200.0,154076614.0,GSM3732427 r1,0:150 1:150,A:13069130635;C:10120441406;G:10858372086;T:12169793951;N:5246122,150,150,,,13069130635,10120441406,10858372086,12169793951,5246122,SRX5717520,SRS4655940,SRA786939,GEO,Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS),2,0.0063,0.00488,0.00135,0.00112,0.99736,0.99801,0.66703,0.76167,150,150,T,T,mates < 9% mapping rate,illumina,hiseq_era,full_length,random_priming,smarter,bulk,clip,iclip,,China,2019-04-22,Blastula,Embryo,Whole Organism,All anatomical structures
49547,SRR7942638,SRX4776903,SRS3857464,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/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 TURBOâ„¢ 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. RNA RIP BisSeq: 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 purified mRNA was used for RNA BisSeq library construction. Around 200 ng mRNA premixed with the in vitro transcribed Dhfr mRNA at a ratio of 300:1 Dhfr mRNA serves as methylation conversion control was fragmented to 100 nt fragments for 1 min at 90°C in 10× RNA Fragmentation Reagent Ambion  then stopped by 10× RNA stop solution Ambion  and precipitated with 100% ethanol. The RNA pellet was resuspended in 100 µl bisulfite solution pH 5.1  which is a 100:1 mixture of 40% sodium bisulfite Sigma and 600 µM hydroquinone Sigma and subjected to heat incubation at 75°C for 4.5 h. The reaction mixture was desalted by passing through Nanosep with 3K Omega 500/pk columns PALL Corporation with centrifugation. post washed with nuclease free water and centrifuged for five times  the RNA was finally disolved in 75 ?l nuclease free water and then desulfonated by incubation with an equal volume of 1 M Tris HCl pH 9.0 at 75 °C for 1 h. post ethanol precipitation  the RNA was resuspended in 11 µl of RNase free water and subjected to library construction. Reverse transcription was carried out with superscript II Reverse Transcriptase Invitrogen and ACT random hexamers. The following procedures were performed with the KAPA Stranded mRNA Seq Kit KAPA according to the manufacturer?s instructions.Libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 125 bp.,parent bioproject:PRJNA534030,,,iCLIP 4hpf rep2,GSM3406904,,source name:Zebrafish embryo|strain:AB strain|cell type:Zebrafish embryo|age:4 hpf|tissue:whole embryo,iCLIP 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,GSM3406904,GSM3406904: iCLIP 4hpf rep2; Danio rerio; OTHER,GSM3406904,,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:GSM3406904,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP162876,,,iCLIP_4hpf_rep2_R1.fastq.gz iCLIP_4hpf_rep2_R2.fastq.gz,fastq fastq,17432004900.0,58106683.0,GSM3406904 r1,0:150 1:150,A:5027776225;C:3413769313;G:3531157280;T:5459126811;N:175271,150,150,,,5027776225,3413769313,3531157280,5459126811,175271,SRX4776903,SRS3857464,SRA786939,GEO,Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS),2,0.62059,0.61563,0.02838,0.02072,0.95298,0.9628,0.94729,0.94715,150,150,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,smarter,bulk,clip,iclip,,China,2018-09-28,Blastula,Embryo,Whole Organism,All anatomical structures
49548,SRR7942637,SRX4776902,SRS3857447,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/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 TURBOâ„¢ 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. RNA RIP BisSeq: 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 purified mRNA was used for RNA BisSeq library construction. Around 200 ng mRNA premixed with the in vitro transcribed Dhfr mRNA at a ratio of 300:1 Dhfr mRNA serves as methylation conversion control was fragmented to 100 nt fragments for 1 min at 90°C in 10× RNA Fragmentation Reagent Ambion  then stopped by 10× RNA stop solution Ambion  and precipitated with 100% ethanol. The RNA pellet was resuspended in 100 µl bisulfite solution pH 5.1  which is a 100:1 mixture of 40% sodium bisulfite Sigma and 600 µM hydroquinone Sigma and subjected to heat incubation at 75°C for 4.5 h. The reaction mixture was desalted by passing through Nanosep with 3K Omega 500/pk columns PALL Corporation with centrifugation. post washed with nuclease free water and centrifuged for five times  the RNA was finally disolved in 75 ?l nuclease free water and then desulfonated by incubation with an equal volume of 1 M Tris HCl pH 9.0 at 75 °C for 1 h. post ethanol precipitation  the RNA was resuspended in 11 µl of RNase free water and subjected to library construction. Reverse transcription was carried out with superscript II Reverse Transcriptase Invitrogen and ACT random hexamers. The following procedures were performed with the KAPA Stranded mRNA Seq Kit KAPA according to the manufacturer?s instructions.Libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 125 bp.,parent bioproject:PRJNA534030,,,iCLIP 4hpf rep1,GSM3406903,,source name:Zebrafish embryo|strain:AB strain|cell type:Zebrafish embryo|age:4 hpf|tissue:whole embryo,iCLIP 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,GSM3406903,GSM3406903: iCLIP 4hpf rep1; Danio rerio; OTHER,GSM3406903,,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:GSM3406903,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP162876,,,iCLIP_4hpf_rep1_R1.fastq.gz iCLIP_4hpf_rep1_R2.fastq.gz,fastq fastq,18547407600.0,61824692.0,GSM3406903 r1,0:150 1:150,A:5264017245;C:3699523947;G:3688768985;T:5894912242;N:185181,150,150,,,5264017245,3699523947,3688768985,5894912242,185181,SRX4776902,SRS3857447,SRA786939,GEO,Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS),2,0.68368,0.67882,0.0342,0.02328,0.95375,0.96623,0.962,0.9572,150,150,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,smarter,bulk,clip,iclip,,China,2018-09-28,Blastula,Embryo,Whole Organism,All anatomical structures
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/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 TURBOâ„¢ 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. RNA RIP BisSeq: 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 purified mRNA was used for RNA BisSeq library construction. Around 200 ng mRNA premixed with the in vitro transcribed Dhfr mRNA at a ratio of 300:1 Dhfr mRNA serves as methylation conversion control was fragmented to 100 nt fragments for 1 min at 90°C in 10× RNA Fragmentation Reagent Ambion  then stopped by 10× RNA stop solution Ambion  and precipitated with 100% ethanol. The RNA pellet was resuspended in 100 µl bisulfite solution pH 5.1  which is a 100:1 mixture of 40% sodium bisulfite Sigma and 600 µM hydroquinone Sigma and subjected to heat incubation at 75°C for 4.5 h. The reaction mixture was desalted by passing through Nanosep with 3K Omega 500/pk columns PALL Corporation with centrifugation. post washed with nuclease free water and centrifuged for five times  the RNA was finally disolved in 75 ?l nuclease free water and then desulfonated by incubation with an equal volume of 1 M Tris HCl pH 9.0 at 75 °C for 1 h. post ethanol precipitation  the RNA was resuspended in 11 µl of RNase free water and subjected to library construction. Reverse transcription was carried out with superscript II Reverse Transcriptase Invitrogen and ACT random hexamers. The following procedures were performed with the KAPA Stranded mRNA Seq Kit KAPA according to the manufacturer?s instructions.Libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 125 bp.,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,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/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 TURBOâ„¢ 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. RNA RIP BisSeq: 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 purified mRNA was used for RNA BisSeq library construction. Around 200 ng mRNA premixed with the in vitro transcribed Dhfr mRNA at a ratio of 300:1 Dhfr mRNA serves as methylation conversion control was fragmented to 100 nt fragments for 1 min at 90°C in 10× RNA Fragmentation Reagent Ambion  then stopped by 10× RNA stop solution Ambion  and precipitated with 100% ethanol. The RNA pellet was resuspended in 100 µl bisulfite solution pH 5.1  which is a 100:1 mixture of 40% sodium bisulfite Sigma and 600 µM hydroquinone Sigma and subjected to heat incubation at 75°C for 4.5 h. The reaction mixture was desalted by passing through Nanosep with 3K Omega 500/pk columns PALL Corporation with centrifugation. post washed with nuclease free water and centrifuged for five times  the RNA was finally disolved in 75 ?l nuclease free water and then desulfonated by incubation with an equal volume of 1 M Tris HCl pH 9.0 at 75 °C for 1 h. post ethanol precipitation  the RNA was resuspended in 11 µl of RNase free water and subjected to library construction. Reverse transcription was carried out with superscript II Reverse Transcriptase Invitrogen and ACT random hexamers. The following procedures were performed with the KAPA Stranded mRNA Seq Kit KAPA according to the manufacturer?s instructions.Libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 125 bp.,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
49569,SRR11537840,SRX8108895,SRS6473981,SRP163087,PRJNA494251,Dynamic landscapes and regulome of mRNA structure during zebrafish early embryogenesis,GSE120724,Other,We resolved the RNA secondary structure during zebrafish early embryogenesis based on  in vivo click selective 2' hydroxyl acylation and profiling experiment icSHAPE. We analyzed the RNA structure dynamics among different development stages.  Also  we studied which factors regulate maternal gene decay by RNA structure switch. Overall design: icSHAPE of 12 samples from zebrafish embryos at six different early development stages and 4 samples from Elavl1a deficient zebrafish embryos at sphere and shield stages  including two treated with DMSO as control and two treated with NAIN3 for each stage or condition. RNA seq of 6 samples from zebrafish embryos at 2  4  6 h.p.f. and 4 samples from Elavl1a deficient zebrafish embryos at 4 and 6 h.p.f. including two biological replicates. iCLIP seq of 4 samples from flag elavl1a mRNA injected zebrafish embryos at xxx and 6 h.p.f. including two biological replicates.,,pubmed:32423473,,Sphere Elavl1a MO NAIN3.rep2,GSM4473288,,tissue:Sphere Elavl1a MO NAIN3|strain background:AB|age:4hpf|cell type:elavl1a morphants zebrafish embryos cells|treatment:NAI N3,Sphere Elavl1a MO NAIN3.rep2,Library strategy: icSHAPE trimmed three prime adaptor from reads by cutadapt trimmed low quality bases by trimmomatic collapsed duplicated reads as icSHAPE pipeline trimmed the leading 13nt UMI mapping reads to zebrafish reference transcriptomez10 by bowtie2 using the same parameters in icSHAPE pipeline calculate rpkm as icshape pipeline calulate reverse transcription stop sitesRT stop as icshape pipeline RT stop was normalized by using sliding window  then icSHAPE score was calculated as icshape pipeline Genome build: z10 Supplementary files format and content: tab delimited text files for icshape files. First column is the Refseq ID  second is transcript length  third is RPKM  then every column is the nucleotide resolution icSHAPE score. NULL means no confident score. Tab delimited text files for read counts and rpkm files. First column is the Refseq ID  second is  transcript length  third is the unique mapped reads count  fourth is the mulitple mapped reads count  fifth is the RPKM.,Sphere Elavl1a MO NAIN3,For Elavl1a morphants generation  morpholino oligonucleotides of elavl1a were injected into one cell stage embryos  then embryos were harvested at desired stages. For in vivo treatment  cells was incubated with NAI N3 or DMSO at 28.5°C for 5min,The  RNA or modified RNA was extracted or cleaned up and eluted in RNase free water by using TRIzol® Reagent invitrogen.To enrich polyA RNA  the total RNA was subjected to polyA selection. For icSHAPE  the in vivo modified RNA and unmodified RNA were biotinylated by copper free click reaction  followed by fragmentation. The fragmented RNA was end repaired by incubation at 37℃ for 1 hours with the following mix 70 mM Tris 7.0  18mM MgCl2  5mM DTT  4 U/µl RiboLock  0.1 U/µl FastAP Life Technology  2 U/µl T4 PNKNEB before 3’ adapter ligation with addition of 10 µl ligation mix 5mM DTT  0.5µM 5’ adenylated and 3’ blocked linker 3’ bio for unmodified  3’ ddc for modified  0.66 U/µl T4 RNA ligase NEB  M0437M  15% PEG8000  1X RNA ligase buffer and incubation at 25℃ for extra 3 hours. Then the excess adaptor was removed as described below. The purified RNA was incubated in the mix of 1µl FastAP  0.2µl SSB Promega  0.8µl Ribolock and 1µl 5’ Deadenylase NEB in 1X NEB buffer 2 NEB at 30℃ for 90 min. And then 1µl RecJf NEB was added with another incubation at 37℃ for 1 hour. The following procedures  including reverse transcription  biotin streptavadin enrichment  size selection of cDNA  circularization and PCR amplification  were the same as described in the standard protocol. For RNA seq， Fragmented mRNA was used for library construction using the KAPA Stranded mRNA Seq Kit KAPA according to manufacturer’s protocol.,Zebrafish wild type strain AB was raised in system water at 28.5°C under standard conditions.,strain background:AB|age:4hpf|cell type:elavl1a morphants zebrafish embryos cells|treatment:NAI N3,GSM4473288,GSM4473288: Sphere Elavl1a MO NAIN3.rep2; Danio rerio; OTHER,GSM4473288,,1,The  RNA or modified RNA was extracted or cleaned up and eluted in RNase free water by using TRIzol® Reagent invitrogen. For icSHAPE  the in vivo modified RNA and unmodified RNA were biotinylated by copper free click reaction  followed by fragmentation. The fragmented RNA was end repaired by incubation at 37℃ for 1 hours with the following mix 70 mM Tris 7.0  18mM MgCl2  5mM DTT  4 U/µl RiboLock  0.1 U/µl FastAP Life Technology  2 U/µl T4 PNKNEB before three prime adapter ligation with addition of 10 µl ligation mix 5mM DTT  0.5µM five prime adenylated and three prime blocked linker three prime bio for unmodified  three prime ddc for modified  0.66 U/µl T4 RNA ligase NEB  M0437M  15% PEG8000  1X RNA ligase buffer and incubation at 25℃ for extra 3 hours. Then the excess adaptor was removed as described below. The purified RNA was incubated in the mix of 1µl FastAP  0.2µl SSB Promega  0.8µl Ribolock and 1µl five prime Deadenylase NEB in 1X NEB buffer 2 NEB at 30℃ for 90 min. And then 1µl RecJf NEB was added with another incubation at 37℃ for 1 hour. The following procedures  including reverse transcription  biotin streptavadin enrichment  size selection of cDNA  circularization and PCR amplification  were the same as described in the standard protocol. For RNA seq， Fragmented mRNA was used for library construction using the KAPA Stranded mRNA Seq Kit KAPA according to manufacturer's protocol.,GEO Accession:GSM4473288,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP163087,,,Sphere_Elavl1a_MO_NAIN3.rep2.fastq.gz,fastq,83266825200.0,555112168.0,GSM4473288 r1,0:150 1:0,A:20621422257;C:17635819340;G:29266248375;T:15742691319;N:643909,150,0,,,20621422257,17635819340,29266248375,15742691319,643909,SRX8108895,SRS6473981,SRA787572,GEO,"Life Science, Tsinghua University",1,0.13635,,0.01536,,0.88586,,0.72417,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,clip,iclip,,China,2020-04-12,Blastula,Embryo,Embryo Imprecise,All anatomical structures
49570,SRR11537839,SRX8108894,SRS6473980,SRP163087,PRJNA494251,Dynamic landscapes and regulome of mRNA structure during zebrafish early embryogenesis,GSE120724,Other,We resolved the RNA secondary structure during zebrafish early embryogenesis based on  in vivo click selective 2' hydroxyl acylation and profiling experiment icSHAPE. We analyzed the RNA structure dynamics among different development stages.  Also  we studied which factors regulate maternal gene decay by RNA structure switch. Overall design: icSHAPE of 12 samples from zebrafish embryos at six different early development stages and 4 samples from Elavl1a deficient zebrafish embryos at sphere and shield stages  including two treated with DMSO as control and two treated with NAIN3 for each stage or condition. RNA seq of 6 samples from zebrafish embryos at 2  4  6 h.p.f. and 4 samples from Elavl1a deficient zebrafish embryos at 4 and 6 h.p.f. including two biological replicates. iCLIP seq of 4 samples from flag elavl1a mRNA injected zebrafish embryos at xxx and 6 h.p.f. including two biological replicates.,,pubmed:32423473,,Sphere Elavl1a MO NAIN3.rep1,GSM4473287,,tissue:Sphere Elavl1a MO NAIN3|strain background:AB|age:4hpf|cell type:elavl1a morphants zebrafish embryos cells|treatment:NAI N3,Sphere Elavl1a MO NAIN3.rep1,Library strategy: icSHAPE trimmed three prime adaptor from reads by cutadapt trimmed low quality bases by trimmomatic collapsed duplicated reads as icSHAPE pipeline trimmed the leading 13nt UMI mapping reads to zebrafish reference transcriptomez10 by bowtie2 using the same parameters in icSHAPE pipeline calculate rpkm as icshape pipeline calulate reverse transcription stop sitesRT stop as icshape pipeline RT stop was normalized by using sliding window  then icSHAPE score was calculated as icshape pipeline Genome build: z10 Supplementary files format and content: tab delimited text files for icshape files. First column is the Refseq ID  second is transcript length  third is RPKM  then every column is the nucleotide resolution icSHAPE score. NULL means no confident score. Tab delimited text files for read counts and rpkm files. First column is the Refseq ID  second is  transcript length  third is the unique mapped reads count  fourth is the mulitple mapped reads count  fifth is the RPKM.,Sphere Elavl1a MO NAIN3,For Elavl1a morphants generation  morpholino oligonucleotides of elavl1a were injected into one cell stage embryos  then embryos were harvested at desired stages. For in vivo treatment  cells was incubated with NAI N3 or DMSO at 28.5°C for 5min,The  RNA or modified RNA was extracted or cleaned up and eluted in RNase free water by using TRIzol® Reagent invitrogen.To enrich polyA RNA  the total RNA was subjected to polyA selection. For icSHAPE  the in vivo modified RNA and unmodified RNA were biotinylated by copper free click reaction  followed by fragmentation. The fragmented RNA was end repaired by incubation at 37℃ for 1 hours with the following mix 70 mM Tris 7.0  18mM MgCl2  5mM DTT  4 U/µl RiboLock  0.1 U/µl FastAP Life Technology  2 U/µl T4 PNKNEB before 3’ adapter ligation with addition of 10 µl ligation mix 5mM DTT  0.5µM 5’ adenylated and 3’ blocked linker 3’ bio for unmodified  3’ ddc for modified  0.66 U/µl T4 RNA ligase NEB  M0437M  15% PEG8000  1X RNA ligase buffer and incubation at 25℃ for extra 3 hours. Then the excess adaptor was removed as described below. The purified RNA was incubated in the mix of 1µl FastAP  0.2µl SSB Promega  0.8µl Ribolock and 1µl 5’ Deadenylase NEB in 1X NEB buffer 2 NEB at 30℃ for 90 min. And then 1µl RecJf NEB was added with another incubation at 37℃ for 1 hour. The following procedures  including reverse transcription  biotin streptavadin enrichment  size selection of cDNA  circularization and PCR amplification  were the same as described in the standard protocol. For RNA seq， Fragmented mRNA was used for library construction using the KAPA Stranded mRNA Seq Kit KAPA according to manufacturer’s protocol.,Zebrafish wild type strain AB was raised in system water at 28.5°C under standard conditions.,strain background:AB|age:4hpf|cell type:elavl1a morphants zebrafish embryos cells|treatment:NAI N3,GSM4473287,GSM4473287: Sphere Elavl1a MO NAIN3.rep1; Danio rerio; OTHER,GSM4473287,,1,The  RNA or modified RNA was extracted or cleaned up and eluted in RNase free water by using TRIzol® Reagent invitrogen. For icSHAPE  the in vivo modified RNA and unmodified RNA were biotinylated by copper free click reaction  followed by fragmentation. The fragmented RNA was end repaired by incubation at 37℃ for 1 hours with the following mix 70 mM Tris 7.0  18mM MgCl2  5mM DTT  4 U/µl RiboLock  0.1 U/µl FastAP Life Technology  2 U/µl T4 PNKNEB before three prime adapter ligation with addition of 10 µl ligation mix 5mM DTT  0.5µM five prime adenylated and three prime blocked linker three prime bio for unmodified  three prime ddc for modified  0.66 U/µl T4 RNA ligase NEB  M0437M  15% PEG8000  1X RNA ligase buffer and incubation at 25℃ for extra 3 hours. Then the excess adaptor was removed as described below. The purified RNA was incubated in the mix of 1µl FastAP  0.2µl SSB Promega  0.8µl Ribolock and 1µl five prime Deadenylase NEB in 1X NEB buffer 2 NEB at 30℃ for 90 min. And then 1µl RecJf NEB was added with another incubation at 37℃ for 1 hour. The following procedures  including reverse transcription  biotin streptavadin enrichment  size selection of cDNA  circularization and PCR amplification  were the same as described in the standard protocol. For RNA seq， Fragmented mRNA was used for library construction using the KAPA Stranded mRNA Seq Kit KAPA according to manufacturer's protocol.,GEO Accession:GSM4473287,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP163087,,,Sphere_Elavl1a_MO_NAIN3.rep1.fastq.gz,fastq,75408648300.0,502724322.0,GSM4473287 r1,0:150 1:0,A:19590532626;C:15494788593;G:26125416257;T:14197330642;N:580182,150,0,,,19590532626,15494788593,26125416257,14197330642,580182,SRX8108894,SRS6473980,SRA787572,GEO,"Life Science, Tsinghua University",1,0.0048,,0.00055,,0.99502,,0.81456,,150,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,clip,iclip,,China,2020-04-12,Blastula,Embryo,Embryo Imprecise,All anatomical structures
49571,SRR11537838,SRX8108893,SRS6473979,SRP163087,PRJNA494251,Dynamic landscapes and regulome of mRNA structure during zebrafish early embryogenesis,GSE120724,Other,We resolved the RNA secondary structure during zebrafish early embryogenesis based on  in vivo click selective 2' hydroxyl acylation and profiling experiment icSHAPE. We analyzed the RNA structure dynamics among different development stages.  Also  we studied which factors regulate maternal gene decay by RNA structure switch. Overall design: icSHAPE of 12 samples from zebrafish embryos at six different early development stages and 4 samples from Elavl1a deficient zebrafish embryos at sphere and shield stages  including two treated with DMSO as control and two treated with NAIN3 for each stage or condition. RNA seq of 6 samples from zebrafish embryos at 2  4  6 h.p.f. and 4 samples from Elavl1a deficient zebrafish embryos at 4 and 6 h.p.f. including two biological replicates. iCLIP seq of 4 samples from flag elavl1a mRNA injected zebrafish embryos at xxx and 6 h.p.f. including two biological replicates.,,pubmed:32423473,,Sphere Elavl1a MO DMSO.rep2,GSM4473286,,tissue:Sphere Elavl1a MO DMSO|strain background:AB|age:4hpf|cell type:elavl1a morphants zebrafish embryos cells|treatment:DMSO,Sphere Elavl1a MO DMSO.rep2,Library strategy: icSHAPE trimmed three prime adaptor from reads by cutadapt trimmed low quality bases by trimmomatic collapsed duplicated reads as icSHAPE pipeline trimmed the leading 13nt UMI mapping reads to zebrafish reference transcriptomez10 by bowtie2 using the same parameters in icSHAPE pipeline calculate rpkm as icshape pipeline calulate reverse transcription stop sitesRT stop as icshape pipeline RT stop was normalized by using sliding window  then icSHAPE score was calculated as icshape pipeline Genome build: z10 Supplementary files format and content: tab delimited text files for icshape files. First column is the Refseq ID  second is transcript length  third is RPKM  then every column is the nucleotide resolution icSHAPE score. NULL means no confident score. Tab delimited text files for read counts and rpkm files. First column is the Refseq ID  second is  transcript length  third is the unique mapped reads count  fourth is the mulitple mapped reads count  fifth is the RPKM.,Sphere Elavl1a MO DMSO,For Elavl1a morphants generation  morpholino oligonucleotides of elavl1a were injected into one cell stage embryos  then embryos were harvested at desired stages. For in vivo treatment  cells was incubated with NAI N3 or DMSO at 28.5°C for 5min,The  RNA or modified RNA was extracted or cleaned up and eluted in RNase free water by using TRIzol® Reagent invitrogen.To enrich polyA RNA  the total RNA was subjected to polyA selection. For icSHAPE  the in vivo modified RNA and unmodified RNA were biotinylated by copper free click reaction  followed by fragmentation. The fragmented RNA was end repaired by incubation at 37℃ for 1 hours with the following mix 70 mM Tris 7.0  18mM MgCl2  5mM DTT  4 U/µl RiboLock  0.1 U/µl FastAP Life Technology  2 U/µl T4 PNKNEB before 3’ adapter ligation with addition of 10 µl ligation mix 5mM DTT  0.5µM 5’ adenylated and 3’ blocked linker 3’ bio for unmodified  3’ ddc for modified  0.66 U/µl T4 RNA ligase NEB  M0437M  15% PEG8000  1X RNA ligase buffer and incubation at 25℃ for extra 3 hours. Then the excess adaptor was removed as described below. The purified RNA was incubated in the mix of 1µl FastAP  0.2µl SSB Promega  0.8µl Ribolock and 1µl 5’ Deadenylase NEB in 1X NEB buffer 2 NEB at 30℃ for 90 min. And then 1µl RecJf NEB was added with another incubation at 37℃ for 1 hour. The following procedures  including reverse transcription  biotin streptavadin enrichment  size selection of cDNA  circularization and PCR amplification  were the same as described in the standard protocol. For RNA seq， Fragmented mRNA was used for library construction using the KAPA Stranded mRNA Seq Kit KAPA according to manufacturer’s protocol.,Zebrafish wild type strain AB was raised in system water at 28.5°C under standard conditions.,strain background:AB|age:4hpf|cell type:elavl1a morphants zebrafish embryos cells|treatment:DMSO,GSM4473286,GSM4473286: Sphere Elavl1a MO DMSO.rep2; Danio rerio; OTHER,GSM4473286,,1,The  RNA or modified RNA was extracted or cleaned up and eluted in RNase free water by using TRIzol® Reagent invitrogen. For icSHAPE  the in vivo modified RNA and unmodified RNA were biotinylated by copper free click reaction  followed by fragmentation. The fragmented RNA was end repaired by incubation at 37℃ for 1 hours with the following mix 70 mM Tris 7.0  18mM MgCl2  5mM DTT  4 U/µl RiboLock  0.1 U/µl FastAP Life Technology  2 U/µl T4 PNKNEB before three prime adapter ligation with addition of 10 µl ligation mix 5mM DTT  0.5µM five prime adenylated and three prime blocked linker three prime bio for unmodified  three prime ddc for modified  0.66 U/µl T4 RNA ligase NEB  M0437M  15% PEG8000  1X RNA ligase buffer and incubation at 25℃ for extra 3 hours. Then the excess adaptor was removed as described below. The purified RNA was incubated in the mix of 1µl FastAP  0.2µl SSB Promega  0.8µl Ribolock and 1µl five prime Deadenylase NEB in 1X NEB buffer 2 NEB at 30℃ for 90 min. And then 1µl RecJf NEB was added with another incubation at 37℃ for 1 hour. The following procedures  including reverse transcription  biotin streptavadin enrichment  size selection of cDNA  circularization and PCR amplification  were the same as described in the standard protocol. For RNA seq， Fragmented mRNA was used for library construction using the KAPA Stranded mRNA Seq Kit KAPA according to manufacturer's protocol.,GEO Accession:GSM4473286,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP163087,,,Sphere_Elavl1a_MO_DMSO.rep2.fastq.gz,fastq,21843179550.0,145621197.0,GSM4473286 r1,0:150 1:0,A:5896736067;C:4594959790;G:6585009703;T:4766305398;N:168592,150,0,,,5896736067,4594959790,6585009703,4766305398,168592,SRX8108893,SRS6473979,SRA787572,GEO,"Life Science, Tsinghua University",1,0.21638,,0.03521,,0.84902,,0.66034,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,clip,iclip,,China,2020-04-12,Blastula,Embryo,Embryo Imprecise,All anatomical structures
49572,SRR11537837,SRX8108892,SRS6473978,SRP163087,PRJNA494251,Dynamic landscapes and regulome of mRNA structure during zebrafish early embryogenesis,GSE120724,Other,We resolved the RNA secondary structure during zebrafish early embryogenesis based on  in vivo click selective 2' hydroxyl acylation and profiling experiment icSHAPE. We analyzed the RNA structure dynamics among different development stages.  Also  we studied which factors regulate maternal gene decay by RNA structure switch. Overall design: icSHAPE of 12 samples from zebrafish embryos at six different early development stages and 4 samples from Elavl1a deficient zebrafish embryos at sphere and shield stages  including two treated with DMSO as control and two treated with NAIN3 for each stage or condition. RNA seq of 6 samples from zebrafish embryos at 2  4  6 h.p.f. and 4 samples from Elavl1a deficient zebrafish embryos at 4 and 6 h.p.f. including two biological replicates. iCLIP seq of 4 samples from flag elavl1a mRNA injected zebrafish embryos at xxx and 6 h.p.f. including two biological replicates.,,pubmed:32423473,,Sphere Elavl1a MO DMSO.rep1,GSM4473285,,tissue:Sphere Elavl1a MO DMSO|strain background:AB|age:4hpf|cell type:elavl1a morphants zebrafish embryos cells|treatment:DMSO,Sphere Elavl1a MO DMSO.rep1,Library strategy: icSHAPE trimmed three prime adaptor from reads by cutadapt trimmed low quality bases by trimmomatic collapsed duplicated reads as icSHAPE pipeline trimmed the leading 13nt UMI mapping reads to zebrafish reference transcriptomez10 by bowtie2 using the same parameters in icSHAPE pipeline calculate rpkm as icshape pipeline calulate reverse transcription stop sitesRT stop as icshape pipeline RT stop was normalized by using sliding window  then icSHAPE score was calculated as icshape pipeline Genome build: z10 Supplementary files format and content: tab delimited text files for icshape files. First column is the Refseq ID  second is transcript length  third is RPKM  then every column is the nucleotide resolution icSHAPE score. NULL means no confident score. Tab delimited text files for read counts and rpkm files. First column is the Refseq ID  second is  transcript length  third is the unique mapped reads count  fourth is the mulitple mapped reads count  fifth is the RPKM.,Sphere Elavl1a MO DMSO,For Elavl1a morphants generation  morpholino oligonucleotides of elavl1a were injected into one cell stage embryos  then embryos were harvested at desired stages. For in vivo treatment  cells was incubated with NAI N3 or DMSO at 28.5°C for 5min,The  RNA or modified RNA was extracted or cleaned up and eluted in RNase free water by using TRIzol® Reagent invitrogen.To enrich polyA RNA  the total RNA was subjected to polyA selection. For icSHAPE  the in vivo modified RNA and unmodified RNA were biotinylated by copper free click reaction  followed by fragmentation. The fragmented RNA was end repaired by incubation at 37℃ for 1 hours with the following mix 70 mM Tris 7.0  18mM MgCl2  5mM DTT  4 U/µl RiboLock  0.1 U/µl FastAP Life Technology  2 U/µl T4 PNKNEB before 3’ adapter ligation with addition of 10 µl ligation mix 5mM DTT  0.5µM 5’ adenylated and 3’ blocked linker 3’ bio for unmodified  3’ ddc for modified  0.66 U/µl T4 RNA ligase NEB  M0437M  15% PEG8000  1X RNA ligase buffer and incubation at 25℃ for extra 3 hours. Then the excess adaptor was removed as described below. The purified RNA was incubated in the mix of 1µl FastAP  0.2µl SSB Promega  0.8µl Ribolock and 1µl 5’ Deadenylase NEB in 1X NEB buffer 2 NEB at 30℃ for 90 min. And then 1µl RecJf NEB was added with another incubation at 37℃ for 1 hour. The following procedures  including reverse transcription  biotin streptavadin enrichment  size selection of cDNA  circularization and PCR amplification  were the same as described in the standard protocol. For RNA seq， Fragmented mRNA was used for library construction using the KAPA Stranded mRNA Seq Kit KAPA according to manufacturer’s protocol.,Zebrafish wild type strain AB was raised in system water at 28.5°C under standard conditions.,strain background:AB|age:4hpf|cell type:elavl1a morphants zebrafish embryos cells|treatment:DMSO,GSM4473285,GSM4473285: Sphere Elavl1a MO DMSO.rep1; Danio rerio; OTHER,GSM4473285,,1,The  RNA or modified RNA was extracted or cleaned up and eluted in RNase free water by using TRIzol® Reagent invitrogen. For icSHAPE  the in vivo modified RNA and unmodified RNA were biotinylated by copper free click reaction  followed by fragmentation. The fragmented RNA was end repaired by incubation at 37℃ for 1 hours with the following mix 70 mM Tris 7.0  18mM MgCl2  5mM DTT  4 U/µl RiboLock  0.1 U/µl FastAP Life Technology  2 U/µl T4 PNKNEB before three prime adapter ligation with addition of 10 µl ligation mix 5mM DTT  0.5µM five prime adenylated and three prime blocked linker three prime bio for unmodified  three prime ddc for modified  0.66 U/µl T4 RNA ligase NEB  M0437M  15% PEG8000  1X RNA ligase buffer and incubation at 25℃ for extra 3 hours. Then the excess adaptor was removed as described below. The purified RNA was incubated in the mix of 1µl FastAP  0.2µl SSB Promega  0.8µl Ribolock and 1µl five prime Deadenylase NEB in 1X NEB buffer 2 NEB at 30℃ for 90 min. And then 1µl RecJf NEB was added with another incubation at 37℃ for 1 hour. The following procedures  including reverse transcription  biotin streptavadin enrichment  size selection of cDNA  circularization and PCR amplification  were the same as described in the standard protocol. For RNA seq， Fragmented mRNA was used for library construction using the KAPA Stranded mRNA Seq Kit KAPA according to manufacturer's protocol.,GEO Accession:GSM4473285,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP163087,,,Sphere_Elavl1a_MO_DMSO.rep1.fastq.gz,fastq,39150278250.0,261001855.0,GSM4473285 r1,0:150 1:0,A:10112519472;C:8251284950;G:12148560750;T:8637610037;N:303041,150,0,,,10112519472,8251284950,12148560750,8637610037,303041,SRX8108892,SRS6473978,SRA787572,GEO,"Life Science, Tsinghua University",1,0.24867,,0.03662,,0.83402,,0.65435,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,clip,iclip,,China,2020-04-12,Blastula,Embryo,Embryo Imprecise,All anatomical structures
49575,SRR10434660,SRX7130630,SRS5639974,SRP163087,PRJNA494251,Dynamic landscapes and regulome of mRNA structure during zebrafish early embryogenesis,GSE120724,Other,We resolved the RNA secondary structure during zebrafish early embryogenesis based on  in vivo click selective 2' hydroxyl acylation and profiling experiment icSHAPE. We analyzed the RNA structure dynamics among different development stages.  Also  we studied which factors regulate maternal gene decay by RNA structure switch. Overall design: icSHAPE of 12 samples from zebrafish embryos at six different early development stages and 4 samples from Elavl1a deficient zebrafish embryos at sphere and shield stages  including two treated with DMSO as control and two treated with NAIN3 for each stage or condition. RNA seq of 6 samples from zebrafish embryos at 2  4  6 h.p.f. and 4 samples from Elavl1a deficient zebrafish embryos at 4 and 6 h.p.f. including two biological replicates. iCLIP seq of 4 samples from flag elavl1a mRNA injected zebrafish embryos at xxx and 6 h.p.f. including two biological replicates.,,pubmed:32423473,,sphere Flag Elavl1a iCLIP rep2,GSM4157937,,tissue:zebrafish embryos|strain:zebrafish embryos|cell type:normal zebrafish embryos cells|age:4hpf,sphere Flag Elavl1a iCLIP rep2,"The proceesing procedure is similar to CTK toolhttps://zhanglab.c2b2.columbia.edu/index.php/ICLIP data analysis using CTK. First  we trimmed three prime adaptor from reads by cutadapt collapsed duplicated reads by fastq2collapse.pl in CTK tool stripped  5’ degenerated barcode mapped clean reads to zebrafish reference genomez10 by bwav0.7.17. data from replicates was merged for peak calling We use CTK tool CITS mode to call the peaks. Reads were clustered using tag2cluster.pl with parameters  big  s  maxgap "" 1"" peaks are identified using tag2peak.pl with parameters  big  ss  v   prefix ""CITS""  gap 25  p 0.05 Genome build: z10 Supplementary files format and content: iCLIP peaks identified by CTK tool were provided in bed file format. The first three columns represent the 0 based location of the peak in the genome and the last column represents the strand.The fourth column reprents the peak ID and describes the gene locus  peak heightPH  expected PH/backgroundPH0 and pvalueP. The fifth  column represents the peak height.",zebrafish embryos,,iCLIP seq was carried out as previously described Despic et al.  2017. Breifly  flag elavl1a mRNA injected embryos were collected at xxx h.p.f. and 6 h.p.f.. 400 zebrafish embryos were irradiated twice with 0.8 J/cm2 Stratalinker 2400  Stratagene  lysed  and subjected to mild RNA fragmentation. Crosslinked RNA proteins complexes were immunopurified using Anti FLAG M2 Magnetic Beads Merck  M8823 for 4 h.p.f. and 6 h.p.f. at 4 °C. RNA was extracted Library construction was performed by using Smarter smRNA Seq kit Clontech Laboratories Inc,Zebrafish wild type strain AB was raised in system water at 28.5°C under standard conditions.,strain:zebrafish embryos|cell type:normal zebrafish embryos cells|age:4hpf,GSM4157937,GSM4157937: sphere Flag Elavl1a iCLIP rep2; Danio rerio; OTHER,GSM4157937,,1,iCLIP seq was carried out as previously described Despic et al.  2017. Breifly  flag elavl1a mRNA injected embryos were collected at xxx h.p.f. and 6 h.p.f.. 400 zebrafish embryos were irradiated twice with 0.8 J/cm2 Stratalinker 2400  Stratagene  lysed  and subjected to mild RNA fragmentation. Crosslinked RNA proteins complexes were immunopurified using Anti FLAG M2 Magnetic Beads Merck  M8823 for 4 h.p.f. and 6 h.p.f. at 4 °C. RNA was extracted Library construction was performed by using Smarter smRNA Seq kit Clontech Laboratories Inc,GEO Accession:GSM4157937,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,HiSeq X Ten,,SRP163087,,,Sphere_Elavl1a_iCLIP_rep2.R1.fq.gz Sphere_Elavl1a_iCLIP_rep2.R2.fq.gz,fastq fastq,22090855200.0,73636184.0,GSM4157937 r1,0:150 1:150,A:5631298996;C:5114935575;G:5742247735;T:5600647498;N:1725396,150,150,,,5631298996,5114935575,5742247735,5600647498,1725396,SRX7130630,SRS5639974,SRA787572,GEO,"Life Science, Tsinghua University",2,0.23476,0.17586,0.06861,0.08859,0.99563,0.98873,0.95465,0.79994,150,150,B,B,mate2-mate1 similar by mapping diff,illumina,hiseq_era,full_length,poly_a,smarter,bulk,clip,iclip,,China,2019-11-12,Blastula,Embryo,Embryo Imprecise,All anatomical structures
49576,SRR10434659,SRX7130629,SRS5639973,SRP163087,PRJNA494251,Dynamic landscapes and regulome of mRNA structure during zebrafish early embryogenesis,GSE120724,Other,We resolved the RNA secondary structure during zebrafish early embryogenesis based on  in vivo click selective 2' hydroxyl acylation and profiling experiment icSHAPE. We analyzed the RNA structure dynamics among different development stages.  Also  we studied which factors regulate maternal gene decay by RNA structure switch. Overall design: icSHAPE of 12 samples from zebrafish embryos at six different early development stages and 4 samples from Elavl1a deficient zebrafish embryos at sphere and shield stages  including two treated with DMSO as control and two treated with NAIN3 for each stage or condition. RNA seq of 6 samples from zebrafish embryos at 2  4  6 h.p.f. and 4 samples from Elavl1a deficient zebrafish embryos at 4 and 6 h.p.f. including two biological replicates. iCLIP seq of 4 samples from flag elavl1a mRNA injected zebrafish embryos at xxx and 6 h.p.f. including two biological replicates.,,pubmed:32423473,,sphere Flag Elavl1a iCLIP rep1,GSM4157936,,tissue:zebrafish embryos|strain:zebrafish embryos|cell type:normal zebrafish embryos cells|age:4hpf,sphere Flag Elavl1a iCLIP rep1,"The proceesing procedure is similar to CTK toolhttps://zhanglab.c2b2.columbia.edu/index.php/ICLIP data analysis using CTK. First  we trimmed three prime adaptor from reads by cutadapt collapsed duplicated reads by fastq2collapse.pl in CTK tool stripped  5’ degenerated barcode mapped clean reads to zebrafish reference genomez10 by bwav0.7.17. data from replicates was merged for peak calling We use CTK tool CITS mode to call the peaks. Reads were clustered using tag2cluster.pl with parameters  big  s  maxgap "" 1"" peaks are identified using tag2peak.pl with parameters  big  ss  v   prefix ""CITS""  gap 25  p 0.05 Genome build: z10 Supplementary files format and content: iCLIP peaks identified by CTK tool were provided in bed file format. The first three columns represent the 0 based location of the peak in the genome and the last column represents the strand.The fourth column reprents the peak ID and describes the gene locus  peak heightPH  expected PH/backgroundPH0 and pvalueP. The fifth  column represents the peak height.",zebrafish embryos,,iCLIP seq was carried out as previously described Despic et al.  2017. Breifly  flag elavl1a mRNA injected embryos were collected at xxx h.p.f. and 6 h.p.f.. 400 zebrafish embryos were irradiated twice with 0.8 J/cm2 Stratalinker 2400  Stratagene  lysed  and subjected to mild RNA fragmentation. Crosslinked RNA proteins complexes were immunopurified using Anti FLAG M2 Magnetic Beads Merck  M8823 for 4 h.p.f. and 6 h.p.f. at 4 °C. RNA was extracted Library construction was performed by using Smarter smRNA Seq kit Clontech Laboratories Inc,Zebrafish wild type strain AB was raised in system water at 28.5°C under standard conditions.,strain:zebrafish embryos|cell type:normal zebrafish embryos cells|age:4hpf,GSM4157936,GSM4157936: sphere Flag Elavl1a iCLIP rep1; Danio rerio; OTHER,GSM4157936,,1,iCLIP seq was carried out as previously described Despic et al.  2017. Breifly  flag elavl1a mRNA injected embryos were collected at xxx h.p.f. and 6 h.p.f.. 400 zebrafish embryos were irradiated twice with 0.8 J/cm2 Stratalinker 2400  Stratagene  lysed  and subjected to mild RNA fragmentation. Crosslinked RNA proteins complexes were immunopurified using Anti FLAG M2 Magnetic Beads Merck  M8823 for 4 h.p.f. and 6 h.p.f. at 4 °C. RNA was extracted Library construction was performed by using Smarter smRNA Seq kit Clontech Laboratories Inc,GEO Accession:GSM4157936,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,HiSeq X Ten,,SRP163087,,,Sphere_Elavl1a_iCLIP_rep1.R2.fq.gz Sphere_Elavl1a_iCLIP_rep1.R1.fq.gz,fastq fastq,15794202300.0,52647341.0,GSM4157936 r1,0:150 1:150,A:4443931911;C:3527112429;G:3707720167;T:4114188890;N:1248903,150,150,,,4443931911,3527112429,3707720167,4114188890,1248903,SRX7130629,SRS5639973,SRA787572,GEO,"Life Science, Tsinghua University",2,0.06877,0.10388,0.02139,0.07135,0.99776,0.98413,0.87145,0.57456,150,150,B,B,mate1-mate2 similar by mapping diff,illumina,hiseq_era,full_length,poly_a,smarter,bulk,clip,iclip,,China,2019-11-12,Blastula,Embryo,Embryo Imprecise,All anatomical structures
49579,SRR7947924,SRX4781873,SRS3862065,SRP163087,PRJNA494251,Dynamic landscapes and regulome of mRNA structure during zebrafish early embryogenesis,GSE120724,Other,We resolved the RNA secondary structure during zebrafish early embryogenesis based on  in vivo click selective 2' hydroxyl acylation and profiling experiment icSHAPE. We analyzed the RNA structure dynamics among different development stages.  Also  we studied which factors regulate maternal gene decay by RNA structure switch. Overall design: icSHAPE of 12 samples from zebrafish embryos at six different early development stages and 4 samples from Elavl1a deficient zebrafish embryos at sphere and shield stages  including two treated with DMSO as control and two treated with NAIN3 for each stage or condition. RNA seq of 6 samples from zebrafish embryos at 2  4  6 h.p.f. and 4 samples from Elavl1a deficient zebrafish embryos at 4 and 6 h.p.f. including two biological replicates. iCLIP seq of 4 samples from flag elavl1a mRNA injected zebrafish embryos at xxx and 6 h.p.f. including two biological replicates.,,pubmed:32423473,,elavl1a morphant 4h rna seq rep2,GSM3409397,,source name:elavl1a morphant 4h rna seq rep2|strain:AB|tissue:zebrafish embryos|genotype/variation:elavl1a morphants zebrafish embryos cells|age:4hpf,elavl1a morphant 4h rna seq rep2,trimmed three prime adaptor from reads by cutadapt trimmed low quality bases by trimmomatic collapsed duplicated reads as icSHAPE pipeline trimmed the leading 13nt UMI mapping reads to zebrafish reference transcriptomez10 by bowtie2 using the same parameters in icSHAPE pipeline calculate rpkm as icshape pipeline calculate reverse transcription stop sitesRT stop as icshape pipeline RT stop was normalized by using sliding window  then icSHAPE score was calculated as icshape pipeline Genome build: z10 Supplementary files format and content: tab delimited text files for icshape files. First column is the Refseq ID  second is transcript length  third is RPKM  then every column is the nucleotide resolution icSHAPE score. NULL means no confident score. Tab delimited text files for read counts and rpkm files. First column is the Refseq ID  second is  transcript length  third is the unique mapped reads count  fourth is the mulitple mapped reads count  fifth is the RPKM.,elavl1a morphant 4h rna seq rep2,For Elavl1a morphants generation  morpholino oligonucleotides of elavl1a were injected into one cell stage embryos  then embryos were harvested at desired stages,The  RNA or modified RNA was extracted or cleaned up and eluted in RNase free water by using TRIzol® Reagent invitrogen.To enrich polyA RNA  the total RNA was subjected to polyA selection. For icSHAPE  the in vivo modified RNA and unmodified RNA were biotinylated by copper free click reaction  followed by fragmentation. The fragmented RNA was end repaired by incubation at 37°C for 1 hours with the following mix 70 mM Tris 7.0  18mM MgCl2  5mM DTT  4 U/µl RiboLock  0.1 U/µl FastAP Life Technology  2 U/µl T4 PNKNEB before 3’ adapter ligation with addition of 10 µl ligation mix 5mM DTT  0.5µM 5’ adenylated and 3’ blocked linker 3’ bio for unmodified  3’ ddc for modified  0.66 U/µl T4 RNA ligase NEB  M0437M  15% PEG8000  1X RNA ligase buffer and incubation at 25°C for extra 3 hours. Then the excess adaptor was removed as described below. The purified RNA was incubated in the mix of 1µl FastAP  0.2µl SSB Promega  0.8µl Ribolock and 1µl 5’ Deadenylase NEB in 1X NEB buffer 2 NEB at 30°C for 90 min. And then 1µl RecJf NEB was added with another incubation at 37°C for 1 hour. The following procedures  including reverse transcription  biotin streptavadin enrichment  size selection of cDNA  circularization and PCR amplification  were the same as described in the standard protocol. For RNA seq， Fragmented mRNA was used for library construction using the KAPA Stranded mRNA Seq Kit KAPA according to manufacturer’s protocol.,Zebrafish wild type strain AB was raised in system water at 28.5°C under standard conditions.,strain:AB|tissue:zebrafish embryos|genotype/variation:elavl1a morphants zebrafish embryos cells|age:4hpf,GSM3409397,GSM3409397: elavl1a morphant 4h rna seq rep2; Danio rerio; RNA Seq,GSM3409397,,1,The  RNA or modified RNA was extracted or cleaned up and eluted in RNase free water by using TRIzol® Reagent invitrogen. For icSHAPE  the in vivo modified RNA and unmodified RNA were biotinylated by copper free click reaction  followed by fragmentation. The fragmented RNA was end repaired by incubation at 37°C for 1 hours with the following mix 70 mM Tris 7.0  18mM MgCl2  5mM DTT  4 U/µl RiboLock  0.1 U/µl FastAP Life Technology  2 U/µl T4 PNKNEB before three prime adapter ligation with addition of 10 µl ligation mix 5mM DTT  0.5µM five prime adenylated and three prime blocked linker three prime bio for unmodified  three prime ddc for modified  0.66 U/µl T4 RNA ligase NEB  M0437M  15% PEG8000  1X RNA ligase buffer and incubation at 25°C for extra 3 hours. Then the excess adaptor was removed as described below. The purified RNA was incubated in the mix of 1µl FastAP  0.2µl SSB Promega  0.8µl Ribolock and 1µl five prime Deadenylase NEB in 1X NEB buffer 2 NEB at 30°C for 90 min. And then 1µl RecJf NEB was added with another incubation at 37°C for 1 hour. The following procedures  including reverse transcription  biotin streptavadin enrichment  size selection of cDNA  circularization and PCR amplification  were the same as described in the standard protocol. For RNA seq， Fragmented mRNA was used for library construction using the KAPA Stranded mRNA Seq Kit KAPA according to manufacturer's protocol.,GEO Accession:GSM3409397,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP163087,,,elavl1a_morphant_4h_rna-seq_rep2.R2.fastq.gz elavl1a_morphant_4h_rna-seq_rep2.R1.fastq.gz,fastq fastq,38764196400.0,129213988.0,GSM3409397 r1,0:150 1:150,A:10980499317;C:8394995318;G:8739322914;T:10645637187;N:3741664,150,150,,,10980499317,8394995318,8739322914,10645637187,3741664,SRX4781873,SRS3862065,SRA787572,GEO,"Life Science, Tsinghua University",2,0.94567,0.94509,0.06713,0.06614,0.76191,0.76508,0.73283,0.74007,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,clip,iclip,,China,2018-10-01,Blastula,Embryo,Embryo Imprecise,All anatomical structures
49580,SRR7947923,SRX4781872,SRS3862064,SRP163087,PRJNA494251,Dynamic landscapes and regulome of mRNA structure during zebrafish early embryogenesis,GSE120724,Other,We resolved the RNA secondary structure during zebrafish early embryogenesis based on  in vivo click selective 2' hydroxyl acylation and profiling experiment icSHAPE. We analyzed the RNA structure dynamics among different development stages.  Also  we studied which factors regulate maternal gene decay by RNA structure switch. Overall design: icSHAPE of 12 samples from zebrafish embryos at six different early development stages and 4 samples from Elavl1a deficient zebrafish embryos at sphere and shield stages  including two treated with DMSO as control and two treated with NAIN3 for each stage or condition. RNA seq of 6 samples from zebrafish embryos at 2  4  6 h.p.f. and 4 samples from Elavl1a deficient zebrafish embryos at 4 and 6 h.p.f. including two biological replicates. iCLIP seq of 4 samples from flag elavl1a mRNA injected zebrafish embryos at xxx and 6 h.p.f. including two biological replicates.,,pubmed:32423473,,elavl1a morphant 4h rna seq rep1,GSM3409396,,source name:elavl1a morphant 4h rna seq rep1|strain:AB|tissue:zebrafish embryos|genotype/variation:elavl1a morphants zebrafish embryos cells|age:4hpf,elavl1a morphant 4h rna seq rep1,trimmed three prime adaptor from reads by cutadapt trimmed low quality bases by trimmomatic collapsed duplicated reads as icSHAPE pipeline trimmed the leading 13nt UMI mapping reads to zebrafish reference transcriptomez10 by bowtie2 using the same parameters in icSHAPE pipeline calculate rpkm as icshape pipeline calculate reverse transcription stop sitesRT stop as icshape pipeline RT stop was normalized by using sliding window  then icSHAPE score was calculated as icshape pipeline Genome build: z10 Supplementary files format and content: tab delimited text files for icshape files. First column is the Refseq ID  second is transcript length  third is RPKM  then every column is the nucleotide resolution icSHAPE score. NULL means no confident score. Tab delimited text files for read counts and rpkm files. First column is the Refseq ID  second is  transcript length  third is the unique mapped reads count  fourth is the mulitple mapped reads count  fifth is the RPKM.,elavl1a morphant 4h rna seq rep1,For Elavl1a morphants generation  morpholino oligonucleotides of elavl1a were injected into one cell stage embryos  then embryos were harvested at desired stages,The  RNA or modified RNA was extracted or cleaned up and eluted in RNase free water by using TRIzol® Reagent invitrogen.To enrich polyA RNA  the total RNA was subjected to polyA selection. For icSHAPE  the in vivo modified RNA and unmodified RNA were biotinylated by copper free click reaction  followed by fragmentation. The fragmented RNA was end repaired by incubation at 37°C for 1 hours with the following mix 70 mM Tris 7.0  18mM MgCl2  5mM DTT  4 U/µl RiboLock  0.1 U/µl FastAP Life Technology  2 U/µl T4 PNKNEB before 3’ adapter ligation with addition of 10 µl ligation mix 5mM DTT  0.5µM 5’ adenylated and 3’ blocked linker 3’ bio for unmodified  3’ ddc for modified  0.66 U/µl T4 RNA ligase NEB  M0437M  15% PEG8000  1X RNA ligase buffer and incubation at 25°C for extra 3 hours. Then the excess adaptor was removed as described below. The purified RNA was incubated in the mix of 1µl FastAP  0.2µl SSB Promega  0.8µl Ribolock and 1µl 5’ Deadenylase NEB in 1X NEB buffer 2 NEB at 30°C for 90 min. And then 1µl RecJf NEB was added with another incubation at 37°C for 1 hour. The following procedures  including reverse transcription  biotin streptavadin enrichment  size selection of cDNA  circularization and PCR amplification  were the same as described in the standard protocol. For RNA seq， Fragmented mRNA was used for library construction using the KAPA Stranded mRNA Seq Kit KAPA according to manufacturer’s protocol.,Zebrafish wild type strain AB was raised in system water at 28.5°C under standard conditions.,strain:AB|tissue:zebrafish embryos|genotype/variation:elavl1a morphants zebrafish embryos cells|age:4hpf,GSM3409396,GSM3409396: elavl1a morphant 4h rna seq rep1; Danio rerio; RNA Seq,GSM3409396,,1,The  RNA or modified RNA was extracted or cleaned up and eluted in RNase free water by using TRIzol® Reagent invitrogen. For icSHAPE  the in vivo modified RNA and unmodified RNA were biotinylated by copper free click reaction  followed by fragmentation. The fragmented RNA was end repaired by incubation at 37°C for 1 hours with the following mix 70 mM Tris 7.0  18mM MgCl2  5mM DTT  4 U/µl RiboLock  0.1 U/µl FastAP Life Technology  2 U/µl T4 PNKNEB before three prime adapter ligation with addition of 10 µl ligation mix 5mM DTT  0.5µM five prime adenylated and three prime blocked linker three prime bio for unmodified  three prime ddc for modified  0.66 U/µl T4 RNA ligase NEB  M0437M  15% PEG8000  1X RNA ligase buffer and incubation at 25°C for extra 3 hours. Then the excess adaptor was removed as described below. The purified RNA was incubated in the mix of 1µl FastAP  0.2µl SSB Promega  0.8µl Ribolock and 1µl five prime Deadenylase NEB in 1X NEB buffer 2 NEB at 30°C for 90 min. And then 1µl RecJf NEB was added with another incubation at 37°C for 1 hour. The following procedures  including reverse transcription  biotin streptavadin enrichment  size selection of cDNA  circularization and PCR amplification  were the same as described in the standard protocol. For RNA seq， Fragmented mRNA was used for library construction using the KAPA Stranded mRNA Seq Kit KAPA according to manufacturer's protocol.,GEO Accession:GSM3409396,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP163087,,,elavl1a_morphant_4h_rna-seq_rep1.R1.fastq.gz elavl1a_morphant_4h_rna-seq_rep1.R2.fastq.gz,fastq fastq,34417602600.0,114725342.0,GSM3409396 r1,0:150 1:150,A:9798364920;C:7402367067;G:7677976380;T:9534399996;N:4494237,150,150,,,9798364920,7402367067,7677976380,9534399996,4494237,SRX4781872,SRS3862064,SRA787572,GEO,"Life Science, Tsinghua University",2,0.94663,0.94701,0.06442,0.06367,0.76264,0.7655,0.73483,0.74221,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,clip,iclip,,China,2018-10-01,Blastula,Embryo,Embryo Imprecise,All anatomical structures
49583,SRR7947920,SRX4781869,SRS3862061,SRP163087,PRJNA494251,Dynamic landscapes and regulome of mRNA structure during zebrafish early embryogenesis,GSE120724,Other,We resolved the RNA secondary structure during zebrafish early embryogenesis based on  in vivo click selective 2' hydroxyl acylation and profiling experiment icSHAPE. We analyzed the RNA structure dynamics among different development stages.  Also  we studied which factors regulate maternal gene decay by RNA structure switch. Overall design: icSHAPE of 12 samples from zebrafish embryos at six different early development stages and 4 samples from Elavl1a deficient zebrafish embryos at sphere and shield stages  including two treated with DMSO as control and two treated with NAIN3 for each stage or condition. RNA seq of 6 samples from zebrafish embryos at 2  4  6 h.p.f. and 4 samples from Elavl1a deficient zebrafish embryos at 4 and 6 h.p.f. including two biological replicates. iCLIP seq of 4 samples from flag elavl1a mRNA injected zebrafish embryos at xxx and 6 h.p.f. including two biological replicates.,,pubmed:32423473,,control 4h rna seq rep2,GSM3409393,,source name:control 4h rna seq rep2|strain:AB|tissue:zebrafish embryos|genotype/variation:normal zebrafish embryos cells|age:4hpf,control 4h rna seq rep2,trimmed three prime adaptor from reads by cutadapt trimmed low quality bases by trimmomatic collapsed duplicated reads as icSHAPE pipeline trimmed the leading 13nt UMI mapping reads to zebrafish reference transcriptomez10 by bowtie2 using the same parameters in icSHAPE pipeline calculate rpkm as icshape pipeline calculate reverse transcription stop sitesRT stop as icshape pipeline RT stop was normalized by using sliding window  then icSHAPE score was calculated as icshape pipeline Genome build: z10 Supplementary files format and content: tab delimited text files for icshape files. First column is the Refseq ID  second is transcript length  third is RPKM  then every column is the nucleotide resolution icSHAPE score. NULL means no confident score. Tab delimited text files for read counts and rpkm files. First column is the Refseq ID  second is  transcript length  third is the unique mapped reads count  fourth is the mulitple mapped reads count  fifth is the RPKM.,control 4h rna seq rep2,For Elavl1a morphants generation  morpholino oligonucleotides of elavl1a were injected into one cell stage embryos  then embryos were harvested at desired stages,The  RNA or modified RNA was extracted or cleaned up and eluted in RNase free water by using TRIzol® Reagent invitrogen.To enrich polyA RNA  the total RNA was subjected to polyA selection. For icSHAPE  the in vivo modified RNA and unmodified RNA were biotinylated by copper free click reaction  followed by fragmentation. The fragmented RNA was end repaired by incubation at 37°C for 1 hours with the following mix 70 mM Tris 7.0  18mM MgCl2  5mM DTT  4 U/µl RiboLock  0.1 U/µl FastAP Life Technology  2 U/µl T4 PNKNEB before 3’ adapter ligation with addition of 10 µl ligation mix 5mM DTT  0.5µM 5’ adenylated and 3’ blocked linker 3’ bio for unmodified  3’ ddc for modified  0.66 U/µl T4 RNA ligase NEB  M0437M  15% PEG8000  1X RNA ligase buffer and incubation at 25°C for extra 3 hours. Then the excess adaptor was removed as described below. The purified RNA was incubated in the mix of 1µl FastAP  0.2µl SSB Promega  0.8µl Ribolock and 1µl 5’ Deadenylase NEB in 1X NEB buffer 2 NEB at 30°C for 90 min. And then 1µl RecJf NEB was added with another incubation at 37°C for 1 hour. The following procedures  including reverse transcription  biotin streptavadin enrichment  size selection of cDNA  circularization and PCR amplification  were the same as described in the standard protocol. For RNA seq， Fragmented mRNA was used for library construction using the KAPA Stranded mRNA Seq Kit KAPA according to manufacturer’s protocol.,Zebrafish wild type strain AB was raised in system water at 28.5°C under standard conditions.,strain:AB|tissue:zebrafish embryos|genotype/variation:normal zebrafish embryos cells|age:4hpf,GSM3409393,GSM3409393: control 4h rna seq rep2; Danio rerio; RNA Seq,GSM3409393,,1,The  RNA or modified RNA was extracted or cleaned up and eluted in RNase free water by using TRIzol® Reagent invitrogen. For icSHAPE  the in vivo modified RNA and unmodified RNA were biotinylated by copper free click reaction  followed by fragmentation. The fragmented RNA was end repaired by incubation at 37°C for 1 hours with the following mix 70 mM Tris 7.0  18mM MgCl2  5mM DTT  4 U/µl RiboLock  0.1 U/µl FastAP Life Technology  2 U/µl T4 PNKNEB before three prime adapter ligation with addition of 10 µl ligation mix 5mM DTT  0.5µM five prime adenylated and three prime blocked linker three prime bio for unmodified  three prime ddc for modified  0.66 U/µl T4 RNA ligase NEB  M0437M  15% PEG8000  1X RNA ligase buffer and incubation at 25°C for extra 3 hours. Then the excess adaptor was removed as described below. The purified RNA was incubated in the mix of 1µl FastAP  0.2µl SSB Promega  0.8µl Ribolock and 1µl five prime Deadenylase NEB in 1X NEB buffer 2 NEB at 30°C for 90 min. And then 1µl RecJf NEB was added with another incubation at 37°C for 1 hour. The following procedures  including reverse transcription  biotin streptavadin enrichment  size selection of cDNA  circularization and PCR amplification  were the same as described in the standard protocol. For RNA seq， Fragmented mRNA was used for library construction using the KAPA Stranded mRNA Seq Kit KAPA according to manufacturer's protocol.,GEO Accession:GSM3409393,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP163087,,,control_4h_rna-seq_rep2.R1.fastq.gz control_4h_rna-seq_rep2.R2.fastq.gz,fastq fastq,33462197400.0,111540658.0,GSM3409393 r1,0:150 1:150,A:9246596683;C:7497270682;G:7798285753;T:8916810951;N:3233331,150,150,,,9246596683,7497270682,7798285753,8916810951,3233331,SRX4781869,SRS3862061,SRA787572,GEO,"Life Science, Tsinghua University",2,0.94792,0.94861,0.0862,0.08529,0.76084,0.76309,0.73536,0.73703,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,clip,iclip,,China,2018-10-01,Blastula,Embryo,Embryo Imprecise,All anatomical structures
49584,SRR7947919,SRX4781868,SRS3862060,SRP163087,PRJNA494251,Dynamic landscapes and regulome of mRNA structure during zebrafish early embryogenesis,GSE120724,Other,We resolved the RNA secondary structure during zebrafish early embryogenesis based on  in vivo click selective 2' hydroxyl acylation and profiling experiment icSHAPE. We analyzed the RNA structure dynamics among different development stages.  Also  we studied which factors regulate maternal gene decay by RNA structure switch. Overall design: icSHAPE of 12 samples from zebrafish embryos at six different early development stages and 4 samples from Elavl1a deficient zebrafish embryos at sphere and shield stages  including two treated with DMSO as control and two treated with NAIN3 for each stage or condition. RNA seq of 6 samples from zebrafish embryos at 2  4  6 h.p.f. and 4 samples from Elavl1a deficient zebrafish embryos at 4 and 6 h.p.f. including two biological replicates. iCLIP seq of 4 samples from flag elavl1a mRNA injected zebrafish embryos at xxx and 6 h.p.f. including two biological replicates.,,pubmed:32423473,,control 4h rna seq rep1,GSM3409392,,source name:control 4h rna seq rep1|strain:AB|tissue:zebrafish embryos|genotype/variation:normal zebrafish embryos cells|age:4hpf,control 4h rna seq rep1,trimmed three prime adaptor from reads by cutadapt trimmed low quality bases by trimmomatic collapsed duplicated reads as icSHAPE pipeline trimmed the leading 13nt UMI mapping reads to zebrafish reference transcriptomez10 by bowtie2 using the same parameters in icSHAPE pipeline calculate rpkm as icshape pipeline calculate reverse transcription stop sitesRT stop as icshape pipeline RT stop was normalized by using sliding window  then icSHAPE score was calculated as icshape pipeline Genome build: z10 Supplementary files format and content: tab delimited text files for icshape files. First column is the Refseq ID  second is transcript length  third is RPKM  then every column is the nucleotide resolution icSHAPE score. NULL means no confident score. Tab delimited text files for read counts and rpkm files. First column is the Refseq ID  second is  transcript length  third is the unique mapped reads count  fourth is the mulitple mapped reads count  fifth is the RPKM.,control 4h rna seq rep1,For Elavl1a morphants generation  morpholino oligonucleotides of elavl1a were injected into one cell stage embryos  then embryos were harvested at desired stages,The  RNA or modified RNA was extracted or cleaned up and eluted in RNase free water by using TRIzol® Reagent invitrogen.To enrich polyA RNA  the total RNA was subjected to polyA selection. For icSHAPE  the in vivo modified RNA and unmodified RNA were biotinylated by copper free click reaction  followed by fragmentation. The fragmented RNA was end repaired by incubation at 37°C for 1 hours with the following mix 70 mM Tris 7.0  18mM MgCl2  5mM DTT  4 U/µl RiboLock  0.1 U/µl FastAP Life Technology  2 U/µl T4 PNKNEB before 3’ adapter ligation with addition of 10 µl ligation mix 5mM DTT  0.5µM 5’ adenylated and 3’ blocked linker 3’ bio for unmodified  3’ ddc for modified  0.66 U/µl T4 RNA ligase NEB  M0437M  15% PEG8000  1X RNA ligase buffer and incubation at 25°C for extra 3 hours. Then the excess adaptor was removed as described below. The purified RNA was incubated in the mix of 1µl FastAP  0.2µl SSB Promega  0.8µl Ribolock and 1µl 5’ Deadenylase NEB in 1X NEB buffer 2 NEB at 30°C for 90 min. And then 1µl RecJf NEB was added with another incubation at 37°C for 1 hour. The following procedures  including reverse transcription  biotin streptavadin enrichment  size selection of cDNA  circularization and PCR amplification  were the same as described in the standard protocol. For RNA seq， Fragmented mRNA was used for library construction using the KAPA Stranded mRNA Seq Kit KAPA according to manufacturer’s protocol.,Zebrafish wild type strain AB was raised in system water at 28.5°C under standard conditions.,strain:AB|tissue:zebrafish embryos|genotype/variation:normal zebrafish embryos cells|age:4hpf,GSM3409392,GSM3409392: control 4h rna seq rep1; Danio rerio; RNA Seq,GSM3409392,,1,The  RNA or modified RNA was extracted or cleaned up and eluted in RNase free water by using TRIzol® Reagent invitrogen. For icSHAPE  the in vivo modified RNA and unmodified RNA were biotinylated by copper free click reaction  followed by fragmentation. The fragmented RNA was end repaired by incubation at 37°C for 1 hours with the following mix 70 mM Tris 7.0  18mM MgCl2  5mM DTT  4 U/µl RiboLock  0.1 U/µl FastAP Life Technology  2 U/µl T4 PNKNEB before three prime adapter ligation with addition of 10 µl ligation mix 5mM DTT  0.5µM five prime adenylated and three prime blocked linker three prime bio for unmodified  three prime ddc for modified  0.66 U/µl T4 RNA ligase NEB  M0437M  15% PEG8000  1X RNA ligase buffer and incubation at 25°C for extra 3 hours. Then the excess adaptor was removed as described below. The purified RNA was incubated in the mix of 1µl FastAP  0.2µl SSB Promega  0.8µl Ribolock and 1µl five prime Deadenylase NEB in 1X NEB buffer 2 NEB at 30°C for 90 min. And then 1µl RecJf NEB was added with another incubation at 37°C for 1 hour. The following procedures  including reverse transcription  biotin streptavadin enrichment  size selection of cDNA  circularization and PCR amplification  were the same as described in the standard protocol. For RNA seq， Fragmented mRNA was used for library construction using the KAPA Stranded mRNA Seq Kit KAPA according to manufacturer's protocol.,GEO Accession:GSM3409392,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP163087,,,control_4h_rna-seq_rep1.R1.fastq.gz control_4h_rna-seq_rep1.R2.fastq.gz,fastq fastq,38719753500.0,129065845.0,GSM3409392 r1,0:150 1:150,A:10763970685;C:8606443742;G:8961006857;T:10383272808;N:5059408,150,150,,,10763970685,8606443742,8961006857,10383272808,5059408,SRX4781868,SRS3862060,SRA787572,GEO,"Life Science, Tsinghua University",2,0.94748,0.948,0.08608,0.08505,0.76023,0.76357,0.72873,0.73242,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,clip,iclip,,China,2018-10-01,Blastula,Embryo,Embryo Imprecise,All anatomical structures
49591,SRR7947907,SRX4781861,SRS3862053,SRP163087,PRJNA494251,Dynamic landscapes and regulome of mRNA structure during zebrafish early embryogenesis,GSE120724,Other,We resolved the RNA secondary structure during zebrafish early embryogenesis based on  in vivo click selective 2' hydroxyl acylation and profiling experiment icSHAPE. We analyzed the RNA structure dynamics among different development stages.  Also  we studied which factors regulate maternal gene decay by RNA structure switch. Overall design: icSHAPE of 12 samples from zebrafish embryos at six different early development stages and 4 samples from Elavl1a deficient zebrafish embryos at sphere and shield stages  including two treated with DMSO as control and two treated with NAIN3 for each stage or condition. RNA seq of 6 samples from zebrafish embryos at 2  4  6 h.p.f. and 4 samples from Elavl1a deficient zebrafish embryos at 4 and 6 h.p.f. including two biological replicates. iCLIP seq of 4 samples from flag elavl1a mRNA injected zebrafish embryos at xxx and 6 h.p.f. including two biological replicates.,,pubmed:32423473,,sphere NAIN3 icSHAPE,GSM3409385,,source name:sphere NAIN3|strain:AB|tissue:zebrafish embryos|genotype/variation:normal zebrafish embryos cells|age:4hpf,sphere NAIN3 icSHAPE,Library strategy: icSHAPE icSHAPE computational pipeline reference: PubMedID: 26766114  DOI: 10.1038/nprot.2016.011 trimmed three prime adaptor from reads by cutadapt trimmed low quality bases by trimmomatic collapsed duplicated reads as icSHAPE pipeline trimmed the leading 13nt UMI mapping reads to zebrafish reference transcriptomez10 by bowtie2 using the same parameters in icSHAPE pipeline calculate rpkm as icshape pipeline calculate reverse transcription stop sitesRT stop as icshape pipeline RT stop was normalized by using sliding window  then icSHAPE score was calculated as icshape pipeline Genome build: z10 Supplementary files format and content: tab delimited text files for icshape files. First column is the Refseq ID  second is transcript length  third is RPKM  then every column is the nucleotide resolution icSHAPE score. NULL means no confident score. Tab delimited text files for read counts and rpkm files. First column is the Refseq ID  second is  transcript length  third is the unique mapped reads count  fourth is the mulitple mapped reads count  fifth is the RPKM.,sphere NAIN3,For in vivo treatment  cells was incubated with NAI N3 or DMSO at 28.5  C for 5min.,The  RNA or modified RNA was extracted or cleaned up and eluted in RNase free water by using TRIzol® Reagent invitrogen.To enrich polyA RNA  the total RNA was subjected to polyA selection. For icSHAPE  the in vivo modified RNA and unmodified RNA were biotinylated by copper free click reaction  followed by fragmentation. The fragmented RNA was end repaired by incubation at 37°C for 1 hours with the following mix 70 mM Tris 7.0  18mM MgCl2  5mM DTT  4 U/µl RiboLock  0.1 U/µl FastAP Life Technology  2 U/µl T4 PNKNEB before 3’ adapter ligation with addition of 10 µl ligation mix 5mM DTT  0.5µM 5’ adenylated and 3’ blocked linker 3’ bio for unmodified  3’ ddc for modified  0.66 U/µl T4 RNA ligase NEB  M0437M  15% PEG8000  1X RNA ligase buffer and incubation at 25°C for extra 3 hours. Then the excess adaptor was removed as described below. The purified RNA was incubated in the mix of 1µl FastAP  0.2µl SSB Promega  0.8µl Ribolock and 1µl 5’ Deadenylase NEB in 1X NEB buffer 2 NEB at 30°C for 90 min. And then 1µl RecJf NEB was added with another incubation at 37°C for 1 hour. The following procedures  including reverse transcription  biotin streptavadin enrichment  size selection of cDNA  circularization and PCR amplification  were the same as described in the standard protocol. For RNA seq， Fragmented mRNA was used for library construction using the KAPA Stranded mRNA Seq Kit KAPA according to manufacturer’s protocol.,Zebrafish wild type strain AB was raised in system water at 28.5°C under standard conditions.,strain:AB|tissue:zebrafish embryos|genotype/variation:normal zebrafish embryos cells|age:4hpf,GSM3409385,GSM3409385: sphere NAIN3; Danio rerio; OTHER,GSM3409385,,1,The  RNA or modified RNA was extracted or cleaned up and eluted in RNase free water by using TRIzol® Reagent invitrogen. For icSHAPE  the in vivo modified RNA and unmodified RNA were biotinylated by copper free click reaction  followed by fragmentation. The fragmented RNA was end repaired by incubation at 37°C for 1 hours with the following mix 70 mM Tris 7.0  18mM MgCl2  5mM DTT  4 U/µl RiboLock  0.1 U/µl FastAP Life Technology  2 U/µl T4 PNKNEB before three prime adapter ligation with addition of 10 µl ligation mix 5mM DTT  0.5µM five prime adenylated and three prime blocked linker three prime bio for unmodified  three prime ddc for modified  0.66 U/µl T4 RNA ligase NEB  M0437M  15% PEG8000  1X RNA ligase buffer and incubation at 25°C for extra 3 hours. Then the excess adaptor was removed as described below. The purified RNA was incubated in the mix of 1µl FastAP  0.2µl SSB Promega  0.8µl Ribolock and 1µl five prime Deadenylase NEB in 1X NEB buffer 2 NEB at 30°C for 90 min. And then 1µl RecJf NEB was added with another incubation at 37°C for 1 hour. The following procedures  including reverse transcription  biotin streptavadin enrichment  size selection of cDNA  circularization and PCR amplification  were the same as described in the standard protocol. For RNA seq， Fragmented mRNA was used for library construction using the KAPA Stranded mRNA Seq Kit KAPA according to manufacturer's protocol.,GEO Accession:GSM3409385,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP163087,,loader:latf load,sphere_NAIN3_rep1.fastq.gz,fastq,146089426800.0,973929512.0,GSM3409385 r1,0:150 1:0,A:42514514559;C:39238639903;G:29724694125;T:34595978556;N:15599657,150,0,,,42514514559,39238639903,29724694125,34595978556,15599657,SRX4781861,SRS3862053,SRA787572,GEO,"Life Science, Tsinghua University",1,0.02746,,0.01225,,0.97013,,0.77486,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,clip,iclip,,China,2018-10-01,Blastula,Embryo,Embryo Imprecise,All anatomical structures
49592,SRR7947908,SRX4781861,SRS3862053,SRP163087,PRJNA494251,Dynamic landscapes and regulome of mRNA structure during zebrafish early embryogenesis,GSE120724,Other,We resolved the RNA secondary structure during zebrafish early embryogenesis based on  in vivo click selective 2' hydroxyl acylation and profiling experiment icSHAPE. We analyzed the RNA structure dynamics among different development stages.  Also  we studied which factors regulate maternal gene decay by RNA structure switch. Overall design: icSHAPE of 12 samples from zebrafish embryos at six different early development stages and 4 samples from Elavl1a deficient zebrafish embryos at sphere and shield stages  including two treated with DMSO as control and two treated with NAIN3 for each stage or condition. RNA seq of 6 samples from zebrafish embryos at 2  4  6 h.p.f. and 4 samples from Elavl1a deficient zebrafish embryos at 4 and 6 h.p.f. including two biological replicates. iCLIP seq of 4 samples from flag elavl1a mRNA injected zebrafish embryos at xxx and 6 h.p.f. including two biological replicates.,,pubmed:32423473,,sphere NAIN3 icSHAPE,GSM3409385,,source name:sphere NAIN3|strain:AB|tissue:zebrafish embryos|genotype/variation:normal zebrafish embryos cells|age:4hpf,sphere NAIN3 icSHAPE,Library strategy: icSHAPE icSHAPE computational pipeline reference: PubMedID: 26766114  DOI: 10.1038/nprot.2016.011 trimmed three prime adaptor from reads by cutadapt trimmed low quality bases by trimmomatic collapsed duplicated reads as icSHAPE pipeline trimmed the leading 13nt UMI mapping reads to zebrafish reference transcriptomez10 by bowtie2 using the same parameters in icSHAPE pipeline calculate rpkm as icshape pipeline calculate reverse transcription stop sitesRT stop as icshape pipeline RT stop was normalized by using sliding window  then icSHAPE score was calculated as icshape pipeline Genome build: z10 Supplementary files format and content: tab delimited text files for icshape files. First column is the Refseq ID  second is transcript length  third is RPKM  then every column is the nucleotide resolution icSHAPE score. NULL means no confident score. Tab delimited text files for read counts and rpkm files. First column is the Refseq ID  second is  transcript length  third is the unique mapped reads count  fourth is the mulitple mapped reads count  fifth is the RPKM.,sphere NAIN3,For in vivo treatment  cells was incubated with NAI N3 or DMSO at 28.5  C for 5min.,The  RNA or modified RNA was extracted or cleaned up and eluted in RNase free water by using TRIzol® Reagent invitrogen.To enrich polyA RNA  the total RNA was subjected to polyA selection. For icSHAPE  the in vivo modified RNA and unmodified RNA were biotinylated by copper free click reaction  followed by fragmentation. The fragmented RNA was end repaired by incubation at 37°C for 1 hours with the following mix 70 mM Tris 7.0  18mM MgCl2  5mM DTT  4 U/µl RiboLock  0.1 U/µl FastAP Life Technology  2 U/µl T4 PNKNEB before 3’ adapter ligation with addition of 10 µl ligation mix 5mM DTT  0.5µM 5’ adenylated and 3’ blocked linker 3’ bio for unmodified  3’ ddc for modified  0.66 U/µl T4 RNA ligase NEB  M0437M  15% PEG8000  1X RNA ligase buffer and incubation at 25°C for extra 3 hours. Then the excess adaptor was removed as described below. The purified RNA was incubated in the mix of 1µl FastAP  0.2µl SSB Promega  0.8µl Ribolock and 1µl 5’ Deadenylase NEB in 1X NEB buffer 2 NEB at 30°C for 90 min. And then 1µl RecJf NEB was added with another incubation at 37°C for 1 hour. The following procedures  including reverse transcription  biotin streptavadin enrichment  size selection of cDNA  circularization and PCR amplification  were the same as described in the standard protocol. For RNA seq， Fragmented mRNA was used for library construction using the KAPA Stranded mRNA Seq Kit KAPA according to manufacturer’s protocol.,Zebrafish wild type strain AB was raised in system water at 28.5°C under standard conditions.,strain:AB|tissue:zebrafish embryos|genotype/variation:normal zebrafish embryos cells|age:4hpf,GSM3409385,GSM3409385: sphere NAIN3; Danio rerio; OTHER,GSM3409385,,1,The  RNA or modified RNA was extracted or cleaned up and eluted in RNase free water by using TRIzol® Reagent invitrogen. For icSHAPE  the in vivo modified RNA and unmodified RNA were biotinylated by copper free click reaction  followed by fragmentation. The fragmented RNA was end repaired by incubation at 37°C for 1 hours with the following mix 70 mM Tris 7.0  18mM MgCl2  5mM DTT  4 U/µl RiboLock  0.1 U/µl FastAP Life Technology  2 U/µl T4 PNKNEB before three prime adapter ligation with addition of 10 µl ligation mix 5mM DTT  0.5µM five prime adenylated and three prime blocked linker three prime bio for unmodified  three prime ddc for modified  0.66 U/µl T4 RNA ligase NEB  M0437M  15% PEG8000  1X RNA ligase buffer and incubation at 25°C for extra 3 hours. Then the excess adaptor was removed as described below. The purified RNA was incubated in the mix of 1µl FastAP  0.2µl SSB Promega  0.8µl Ribolock and 1µl five prime Deadenylase NEB in 1X NEB buffer 2 NEB at 30°C for 90 min. And then 1µl RecJf NEB was added with another incubation at 37°C for 1 hour. The following procedures  including reverse transcription  biotin streptavadin enrichment  size selection of cDNA  circularization and PCR amplification  were the same as described in the standard protocol. For RNA seq， Fragmented mRNA was used for library construction using the KAPA Stranded mRNA Seq Kit KAPA according to manufacturer's protocol.,GEO Accession:GSM3409385,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP163087,,,sphere_NAIN3_rep2.fastq.gz,fastq,129289327500.0,861928850.0,GSM3409385 r2,0:150 1:0,A:36336840338;C:31424534096;G:31054195778;T:30457153761;N:16603527,150,0,,,36336840338,31424534096,31054195778,30457153761,16603527,SRX4781861,SRS3862053,SRA787572,GEO,"Life Science, Tsinghua University",1,0.02812,,0.00884,,0.95887,,0.7364,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,clip,iclip,,China,2018-10-01,Blastula,Embryo,Embryo Imprecise,All anatomical structures
49593,SRR7947905,SRX4781860,SRS3862052,SRP163087,PRJNA494251,Dynamic landscapes and regulome of mRNA structure during zebrafish early embryogenesis,GSE120724,Other,We resolved the RNA secondary structure during zebrafish early embryogenesis based on  in vivo click selective 2' hydroxyl acylation and profiling experiment icSHAPE. We analyzed the RNA structure dynamics among different development stages.  Also  we studied which factors regulate maternal gene decay by RNA structure switch. Overall design: icSHAPE of 12 samples from zebrafish embryos at six different early development stages and 4 samples from Elavl1a deficient zebrafish embryos at sphere and shield stages  including two treated with DMSO as control and two treated with NAIN3 for each stage or condition. RNA seq of 6 samples from zebrafish embryos at 2  4  6 h.p.f. and 4 samples from Elavl1a deficient zebrafish embryos at 4 and 6 h.p.f. including two biological replicates. iCLIP seq of 4 samples from flag elavl1a mRNA injected zebrafish embryos at xxx and 6 h.p.f. including two biological replicates.,,pubmed:32423473,,sphere DMSO icSHAPE,GSM3409384,,source name:sphere DMSO|strain:AB|tissue:zebrafish embryos|genotype/variation:normal zebrafish embryos cells|age:4hpf,sphere DMSO icSHAPE,Library strategy: icSHAPE icSHAPE computational pipeline reference: PubMedID: 26766114  DOI: 10.1038/nprot.2016.011 trimmed three prime adaptor from reads by cutadapt trimmed low quality bases by trimmomatic collapsed duplicated reads as icSHAPE pipeline trimmed the leading 13nt UMI mapping reads to zebrafish reference transcriptomez10 by bowtie2 using the same parameters in icSHAPE pipeline calculate rpkm as icshape pipeline calculate reverse transcription stop sitesRT stop as icshape pipeline RT stop was normalized by using sliding window  then icSHAPE score was calculated as icshape pipeline Genome build: z10 Supplementary files format and content: tab delimited text files for icshape files. First column is the Refseq ID  second is transcript length  third is RPKM  then every column is the nucleotide resolution icSHAPE score. NULL means no confident score. Tab delimited text files for read counts and rpkm files. First column is the Refseq ID  second is  transcript length  third is the unique mapped reads count  fourth is the mulitple mapped reads count  fifth is the RPKM.,sphere DMSO,For in vivo treatment  cells was incubated with NAI N3 or DMSO at 28.5  C for 5min.,The  RNA or modified RNA was extracted or cleaned up and eluted in RNase free water by using TRIzol® Reagent invitrogen.To enrich polyA RNA  the total RNA was subjected to polyA selection. For icSHAPE  the in vivo modified RNA and unmodified RNA were biotinylated by copper free click reaction  followed by fragmentation. The fragmented RNA was end repaired by incubation at 37°C for 1 hours with the following mix 70 mM Tris 7.0  18mM MgCl2  5mM DTT  4 U/µl RiboLock  0.1 U/µl FastAP Life Technology  2 U/µl T4 PNKNEB before 3’ adapter ligation with addition of 10 µl ligation mix 5mM DTT  0.5µM 5’ adenylated and 3’ blocked linker 3’ bio for unmodified  3’ ddc for modified  0.66 U/µl T4 RNA ligase NEB  M0437M  15% PEG8000  1X RNA ligase buffer and incubation at 25°C for extra 3 hours. Then the excess adaptor was removed as described below. The purified RNA was incubated in the mix of 1µl FastAP  0.2µl SSB Promega  0.8µl Ribolock and 1µl 5’ Deadenylase NEB in 1X NEB buffer 2 NEB at 30°C for 90 min. And then 1µl RecJf NEB was added with another incubation at 37°C for 1 hour. The following procedures  including reverse transcription  biotin streptavadin enrichment  size selection of cDNA  circularization and PCR amplification  were the same as described in the standard protocol. For RNA seq， Fragmented mRNA was used for library construction using the KAPA Stranded mRNA Seq Kit KAPA according to manufacturer’s protocol.,Zebrafish wild type strain AB was raised in system water at 28.5°C under standard conditions.,strain:AB|tissue:zebrafish embryos|genotype/variation:normal zebrafish embryos cells|age:4hpf,GSM3409384,GSM3409384: sphere DMSO; Danio rerio; OTHER,GSM3409384,,1,The  RNA or modified RNA was extracted or cleaned up and eluted in RNase free water by using TRIzol® Reagent invitrogen. For icSHAPE  the in vivo modified RNA and unmodified RNA were biotinylated by copper free click reaction  followed by fragmentation. The fragmented RNA was end repaired by incubation at 37°C for 1 hours with the following mix 70 mM Tris 7.0  18mM MgCl2  5mM DTT  4 U/µl RiboLock  0.1 U/µl FastAP Life Technology  2 U/µl T4 PNKNEB before three prime adapter ligation with addition of 10 µl ligation mix 5mM DTT  0.5µM five prime adenylated and three prime blocked linker three prime bio for unmodified  three prime ddc for modified  0.66 U/µl T4 RNA ligase NEB  M0437M  15% PEG8000  1X RNA ligase buffer and incubation at 25°C for extra 3 hours. Then the excess adaptor was removed as described below. The purified RNA was incubated in the mix of 1µl FastAP  0.2µl SSB Promega  0.8µl Ribolock and 1µl five prime Deadenylase NEB in 1X NEB buffer 2 NEB at 30°C for 90 min. And then 1µl RecJf NEB was added with another incubation at 37°C for 1 hour. The following procedures  including reverse transcription  biotin streptavadin enrichment  size selection of cDNA  circularization and PCR amplification  were the same as described in the standard protocol. For RNA seq， Fragmented mRNA was used for library construction using the KAPA Stranded mRNA Seq Kit KAPA according to manufacturer's protocol.,GEO Accession:GSM3409384,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP163087,,,sphere_DMSO_rep1.fastq.gz,fastq,57691963050.0,384613087.0,GSM3409384 r1,0:150 1:0,A:16432201667;C:13571913193;G:12837196407;T:14845080025;N:5571758,150,0,,,16432201667,13571913193,12837196407,14845080025,5571758,SRX4781860,SRS3862052,SRA787572,GEO,"Life Science, Tsinghua University",1,0.1036,,0.01136,,0.87645,,0.65935,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,clip,iclip,,China,2018-10-01,Blastula,Embryo,Embryo Imprecise,All anatomical structures
49594,SRR7947906,SRX4781860,SRS3862052,SRP163087,PRJNA494251,Dynamic landscapes and regulome of mRNA structure during zebrafish early embryogenesis,GSE120724,Other,We resolved the RNA secondary structure during zebrafish early embryogenesis based on  in vivo click selective 2' hydroxyl acylation and profiling experiment icSHAPE. We analyzed the RNA structure dynamics among different development stages.  Also  we studied which factors regulate maternal gene decay by RNA structure switch. Overall design: icSHAPE of 12 samples from zebrafish embryos at six different early development stages and 4 samples from Elavl1a deficient zebrafish embryos at sphere and shield stages  including two treated with DMSO as control and two treated with NAIN3 for each stage or condition. RNA seq of 6 samples from zebrafish embryos at 2  4  6 h.p.f. and 4 samples from Elavl1a deficient zebrafish embryos at 4 and 6 h.p.f. including two biological replicates. iCLIP seq of 4 samples from flag elavl1a mRNA injected zebrafish embryos at xxx and 6 h.p.f. including two biological replicates.,,pubmed:32423473,,sphere DMSO icSHAPE,GSM3409384,,source name:sphere DMSO|strain:AB|tissue:zebrafish embryos|genotype/variation:normal zebrafish embryos cells|age:4hpf,sphere DMSO icSHAPE,Library strategy: icSHAPE icSHAPE computational pipeline reference: PubMedID: 26766114  DOI: 10.1038/nprot.2016.011 trimmed three prime adaptor from reads by cutadapt trimmed low quality bases by trimmomatic collapsed duplicated reads as icSHAPE pipeline trimmed the leading 13nt UMI mapping reads to zebrafish reference transcriptomez10 by bowtie2 using the same parameters in icSHAPE pipeline calculate rpkm as icshape pipeline calculate reverse transcription stop sitesRT stop as icshape pipeline RT stop was normalized by using sliding window  then icSHAPE score was calculated as icshape pipeline Genome build: z10 Supplementary files format and content: tab delimited text files for icshape files. First column is the Refseq ID  second is transcript length  third is RPKM  then every column is the nucleotide resolution icSHAPE score. NULL means no confident score. Tab delimited text files for read counts and rpkm files. First column is the Refseq ID  second is  transcript length  third is the unique mapped reads count  fourth is the mulitple mapped reads count  fifth is the RPKM.,sphere DMSO,For in vivo treatment  cells was incubated with NAI N3 or DMSO at 28.5  C for 5min.,The  RNA or modified RNA was extracted or cleaned up and eluted in RNase free water by using TRIzol® Reagent invitrogen.To enrich polyA RNA  the total RNA was subjected to polyA selection. For icSHAPE  the in vivo modified RNA and unmodified RNA were biotinylated by copper free click reaction  followed by fragmentation. The fragmented RNA was end repaired by incubation at 37°C for 1 hours with the following mix 70 mM Tris 7.0  18mM MgCl2  5mM DTT  4 U/µl RiboLock  0.1 U/µl FastAP Life Technology  2 U/µl T4 PNKNEB before 3’ adapter ligation with addition of 10 µl ligation mix 5mM DTT  0.5µM 5’ adenylated and 3’ blocked linker 3’ bio for unmodified  3’ ddc for modified  0.66 U/µl T4 RNA ligase NEB  M0437M  15% PEG8000  1X RNA ligase buffer and incubation at 25°C for extra 3 hours. Then the excess adaptor was removed as described below. The purified RNA was incubated in the mix of 1µl FastAP  0.2µl SSB Promega  0.8µl Ribolock and 1µl 5’ Deadenylase NEB in 1X NEB buffer 2 NEB at 30°C for 90 min. And then 1µl RecJf NEB was added with another incubation at 37°C for 1 hour. The following procedures  including reverse transcription  biotin streptavadin enrichment  size selection of cDNA  circularization and PCR amplification  were the same as described in the standard protocol. For RNA seq， Fragmented mRNA was used for library construction using the KAPA Stranded mRNA Seq Kit KAPA according to manufacturer’s protocol.,Zebrafish wild type strain AB was raised in system water at 28.5°C under standard conditions.,strain:AB|tissue:zebrafish embryos|genotype/variation:normal zebrafish embryos cells|age:4hpf,GSM3409384,GSM3409384: sphere DMSO; Danio rerio; OTHER,GSM3409384,,1,The  RNA or modified RNA was extracted or cleaned up and eluted in RNase free water by using TRIzol® Reagent invitrogen. For icSHAPE  the in vivo modified RNA and unmodified RNA were biotinylated by copper free click reaction  followed by fragmentation. The fragmented RNA was end repaired by incubation at 37°C for 1 hours with the following mix 70 mM Tris 7.0  18mM MgCl2  5mM DTT  4 U/µl RiboLock  0.1 U/µl FastAP Life Technology  2 U/µl T4 PNKNEB before three prime adapter ligation with addition of 10 µl ligation mix 5mM DTT  0.5µM five prime adenylated and three prime blocked linker three prime bio for unmodified  three prime ddc for modified  0.66 U/µl T4 RNA ligase NEB  M0437M  15% PEG8000  1X RNA ligase buffer and incubation at 25°C for extra 3 hours. Then the excess adaptor was removed as described below. The purified RNA was incubated in the mix of 1µl FastAP  0.2µl SSB Promega  0.8µl Ribolock and 1µl five prime Deadenylase NEB in 1X NEB buffer 2 NEB at 30°C for 90 min. And then 1µl RecJf NEB was added with another incubation at 37°C for 1 hour. The following procedures  including reverse transcription  biotin streptavadin enrichment  size selection of cDNA  circularization and PCR amplification  were the same as described in the standard protocol. For RNA seq， Fragmented mRNA was used for library construction using the KAPA Stranded mRNA Seq Kit KAPA according to manufacturer's protocol.,GEO Accession:GSM3409384,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP163087,,,sphere_DMSO_rep2.fastq.gz,fastq,67804917750.0,452032785.0,GSM3409384 r2,0:150 1:0,A:18522337687;C:17556962469;G:15356031761;T:16361409956;N:8175877,150,0,,,18522337687,17556962469,15356031761,16361409956,8175877,SRX4781860,SRS3862052,SRA787572,GEO,"Life Science, Tsinghua University",1,0.04269,,0.00601,,0.92652,,0.69825,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,clip,iclip,,China,2018-10-01,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51374,SRR8787779,SRX5577635,SRS4539399,SRP189499,PRJNA529224,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: iCLIP,PRJNA529224,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the iCLIP part of the study.,,,,iCLIP   iCLIP purbb B2,iCLIP   iC purbb B2 AGN001421,,strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001043|replicate ref:AGN001421|replicate order:2|barcode:CACA|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP purbb B2,AGR001754,AGR001754,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001754_R1.fastq.gz,fastq,335887114.0,14991395.0,AGR001754 R1.fastq.gz,0:22.41 1:0,A:74180345;C:83232406;G:106310215;T:72164148;N:0,22,0,,,74180345,83232406,106310215,72164148,0,SRX5577635,SRS4539399,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.24414,,0.06603,,0.86592,,0.61809,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-03-26,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51375,SRR8787573,SRX5577634,SRS4539488,SRP189499,PRJNA529224,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: iCLIP,PRJNA529224,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the iCLIP part of the study.,,,,iCLIP   iCLIP purbb B3,iCLIP   iC purbb B3 AGN001422,,strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001043|replicate ref:AGN001422|replicate order:3|barcode:TCTC|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP purbb B3,AGR001755,AGR001755,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001755_R1.fastq.gz,fastq,15677181.0,668468.0,AGR001755 R1.fastq.gz,0:23.45 1:0,A:4016903;C:3934951;G:4279760;T:3445518;N:49,23,0,,,4016903,3934951,4279760,3445518,49,SRX5577634,SRS4539488,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.19896,,0.05474,,0.89536,,0.6044,,29,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-05-31,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51376,SRR8787574,SRX5577633,SRS4539386,SRP189499,PRJNA529224,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: iCLIP,PRJNA529224,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the iCLIP part of the study.,,,,iCLIP   iCLIP hnrnpc B3,iCLIP   iC hnrnpc B3 AGN001322,,strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001029|replicate ref:AGN001322|replicate order:3|barcode:CACA|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP hnrnpc B3,AGR001650,AGR001650,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001650_R1.fastq.gz,fastq,629466824.0,18814705.0,AGR001650 R1.fastq.gz,0:33.46 1:0,A:156340325;C:132972003;G:151531068;T:188592616;N:30812,33,0,,,156340325,132972003,151531068,188592616,30812,SRX5577633,SRS4539386,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.49077,,0.31564,,0.92155,,0.52626,,27,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-05-31,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51377,SRR8787575,SRX5577632,SRS4539496,SRP189499,PRJNA529224,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: iCLIP,PRJNA529224,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the iCLIP part of the study.,,,,iCLIP   iCLIP hnrnpa0a B4,iCLIP   iC hnrnpa0a B4 AGN001314,,strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001026|replicate ref:AGN001314|replicate order:4|barcode:TCTC|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP hnrnpa0a B4,AGR001634,AGR001634,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001634_R1.fastq.gz,fastq,906990390.0,29842065.0,AGR001634 R1.fastq.gz,0:30.39 1:0,A:217828894;C:216233390;G:248751189;T:224136392;N:40525,30,0,,,217828894,216233390,248751189,224136392,40525,SRX5577632,SRS4539496,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.17185,,0.10489,,0.93478,,0.59354,,29,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-05-31,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51378,SRR8787576,SRX5577631,SRS4539496,SRP189499,PRJNA529224,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: iCLIP,PRJNA529224,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the iCLIP part of the study.,,,,iCLIP   iCLIP hnrnpa0a B4,iCLIP   iC hnrnpa0a B4 AGN001314,,strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001026|replicate ref:AGN001314|replicate order:4|barcode:TCTC|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP hnrnpa0a B4,AGR001633,AGR001633,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001633_R1.fastq.gz,fastq,372658652.0,12289936.0,AGR001633 R1.fastq.gz,0:30.32 1:0,A:89390910;C:89012247;G:102629829;T:91622338;N:3328,30,0,,,89390910,89012247,102629829,91622338,3328,SRX5577631,SRS4539496,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.1687,,0.10317,,0.93413,,0.61549,,25,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-05-31,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51379,SRR8787577,SRX5577630,SRS4539495,SRP189499,PRJNA529224,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: iCLIP,PRJNA529224,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the iCLIP part of the study.,,,,iCLIP   iCLIP hnrnpa0a B1,iCLIP   iC hnrnpa0a B1 AGN001182,,strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001026|replicate ref:AGN001182|replicate order:1|barcode:GTGT|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP hnrnpa0a B1,AGR001628,AGR001628,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001628_R1.fastq.gz,fastq,952894634.0,33140562.0,AGR001628 R1.fastq.gz,0:28.75 1:0,A:272894148;C:180655712;G:221297329;T:278047211;N:234,28,0,,,272894148,180655712,221297329,278047211,234,SRX5577630,SRS4539495,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.46793,,0.34168,,0.80734,,0.5874,,32,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-03-26,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51380,SRR8787578,SRX5577629,SRS4539495,SRP189499,PRJNA529224,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: iCLIP,PRJNA529224,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the iCLIP part of the study.,,,,iCLIP   iCLIP hnrnpa0a B1,iCLIP   iC hnrnpa0a B1 AGN001182,,strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001026|replicate ref:AGN001182|replicate order:1|barcode:GTGT|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP hnrnpa0a B1,AGR001627,AGR001627,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001627_R1.fastq.gz,fastq,626649019.0,21785135.0,AGR001627 R1.fastq.gz,0:28.76 1:0,A:180978164;C:117664846;G:144093534;T:183906538;N:5937,28,0,,,180978164,117664846,144093534,183906538,5937,SRX5577629,SRS4539495,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.47116,,0.3442,,0.80655,,0.58888,,19,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-05-31,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51381,SRR8787579,SRX5577628,SRS4539494,SRP189499,PRJNA529224,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: iCLIP,PRJNA529224,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the iCLIP part of the study.,,,,iCLIP   iCLIP srsf4 B1,iCLIP   iC srsf4 B1 AGN001181,,strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001025|replicate ref:AGN001181|replicate order:1|barcode:TCTC|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP srsf4 B1,AGR001626,AGR001626,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001626_R1.fastq.gz,fastq,26882055.0,1016708.0,AGR001626 R1.fastq.gz,0:26.44 1:0,A:7601629;C:6720961;G:6312349;T:6247110;N:6,26,0,,,7601629,6720961,6312349,6247110,6,SRX5577628,SRS4539494,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.12624,,0.05031,,0.92099,,0.62874,,25,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-03-26,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51382,SRR8787580,SRX5577627,SRS4539494,SRP189499,PRJNA529224,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: iCLIP,PRJNA529224,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the iCLIP part of the study.,,,,iCLIP   iCLIP srsf4 B1,iCLIP   iC srsf4 B1 AGN001181,,strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001025|replicate ref:AGN001181|replicate order:1|barcode:TCTC|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP srsf4 B1,AGR001625,AGR001625,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001625_R1.fastq.gz,fastq,19022228.0,719302.0,AGR001625 R1.fastq.gz,0:26.45 1:0,A:5340294;C:4692571;G:4510708;T:4478517;N:138,26,0,,,5340294,4692571,4510708,4478517,138,SRX5577627,SRS4539494,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.12739,,0.05334,,0.9205,,0.61225,,27,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-05-31,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51383,SRR8787581,SRX5577626,SRS4539493,SRP189499,PRJNA529224,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: iCLIP,PRJNA529224,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the iCLIP part of the study.,,,,iCLIP   iCLIP hnrnpa0a B3,iCLIP   iC hnrnpa0a B3 AGN001313,,strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001026|replicate ref:AGN001313|replicate order:3|barcode:CACA|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP hnrnpa0a B3,AGR001631,AGR001631,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001631_R1.fastq.gz,fastq,435541691.0,14051366.0,AGR001631 R1.fastq.gz,0:31.00 1:0,A:105298647;C:96108748;G:121537884;T:112592275;N:4137,31,0,,,105298647,96108748,121537884,112592275,4137,SRX5577626,SRS4539493,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.29884,,0.17976,,0.87375,,0.55383,,28,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-03-26,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51384,SRR8787582,SRX5577625,SRS4539493,SRP189499,PRJNA529224,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: iCLIP,PRJNA529224,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the iCLIP part of the study.,,,,iCLIP   iCLIP hnrnpa0a B3,iCLIP   iC hnrnpa0a B3 AGN001313,,strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001026|replicate ref:AGN001313|replicate order:3|barcode:CACA|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP hnrnpa0a B3,AGR001632,AGR001632,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001632_R1.fastq.gz,fastq,1060447048.0,34132191.0,AGR001632 R1.fastq.gz,0:31.07 1:0,A:257105081;C:233141636;G:294479896;T:275674763;N:45672,31,0,,,257105081,233141636,294479896,275674763,45672,SRX5577625,SRS4539493,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.30432,,0.18534,,0.87251,,0.52719,,26,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-05-31,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51385,SRR8787583,SRX5577624,SRS4539492,SRP189499,PRJNA529224,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: iCLIP,PRJNA529224,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the iCLIP part of the study.,,,,iCLIP   iCLIP hnrnpa0a B2,iCLIP   iC hnrnpa0a B2 AGN001312,,strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001026|replicate ref:AGN001312|replicate order:2|barcode:AGAG|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP hnrnpa0a B2,AGR001630,AGR001630,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001630_R1.fastq.gz,fastq,2555423901.0,80936768.0,AGR001630 R1.fastq.gz,0:31.57 1:0,A:580749928;C:601107101;G:763488952;T:609969537;N:108383,31,0,,,580749928,601107101,763488952,609969537,108383,SRX5577624,SRS4539492,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.29202,,0.15612,,0.87129,,0.61251,,44,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-03-26,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51386,SRR8787584,SRX5577623,SRS4539492,SRP189499,PRJNA529224,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: iCLIP,PRJNA529224,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the iCLIP part of the study.,,,,iCLIP   iCLIP hnrnpa0a B2,iCLIP   iC hnrnpa0a B2 AGN001312,,strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001026|replicate ref:AGN001312|replicate order:2|barcode:AGAG|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP hnrnpa0a B2,AGR001629,AGR001629,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001629_R1.fastq.gz,fastq,1042798712.0,33115269.0,AGR001629 R1.fastq.gz,0:31.49 1:0,A:236683651;C:245768203;G:312527702;T:247809090;N:10066,31,0,,,236683651,245768203,312527702,247809090,10066,SRX5577623,SRS4539492,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.28928,,0.15496,,0.87144,,0.61147,,33,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-03-26,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51387,SRR8787585,SRX5577622,SRS4539433,SRP189499,PRJNA529224,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: iCLIP,PRJNA529224,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the iCLIP part of the study.,,,,iCLIP   iCLIP control bottom B2,iCLIP   iC control b B2 AGN001447,,strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001045|replicate ref:AGN001447|replicate order:2|barcode:CACA|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP control bottom B2,AGR001765,AGR001765,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001765_R1.fastq.gz,fastq,362465747.0,14812513.0,AGR001765 R1.fastq.gz,0:24.47 1:0,A:68023633;C:96574680;G:114779246;T:83084749;N:3439,24,0,,,68023633,96574680,114779246,83084749,3439,SRX5577622,SRS4539433,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.1152,,0.03907,,0.98273,,0.72986,,24,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-03-26,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51388,SRR8787586,SRX5577621,SRS4539491,SRP189499,PRJNA529224,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: iCLIP,PRJNA529224,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the iCLIP part of the study.,,,,iCLIP   iCLIP control bottom B1,iCLIP   iC control b B1 AGN001446,,strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001045|replicate ref:AGN001446|replicate order:1|barcode:AGAG|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP control bottom B1,AGR001764,AGR001764,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001764_R1.fastq.gz,fastq,27765428.0,1056289.0,AGR001764 R1.fastq.gz,0:26.29 1:0,A:6050547;C:7009678;G:8303763;T:6401395;N:45,26,0,,,6050547,7009678,8303763,6401395,45,SRX5577621,SRS4539491,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.13469,,0.04057,,0.94608,,0.70282,,39,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-03-26,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51389,SRR8787587,SRX5577620,SRS4539491,SRP189499,PRJNA529224,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: iCLIP,PRJNA529224,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the iCLIP part of the study.,,,,iCLIP   iCLIP control bottom B1,iCLIP   iC control b B1 AGN001446,,strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001045|replicate ref:AGN001446|replicate order:1|barcode:AGAG|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP control bottom B1,AGR001763,AGR001763,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001763_R1.fastq.gz,fastq,103514920.0,3921032.0,AGR001763 R1.fastq.gz,0:26.40 1:0,A:22317034;C:26280973;G:31189774;T:23726065;N:1074,26,0,,,22317034,26280973,31189774,23726065,1074,SRX5577620,SRS4539491,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.12313,,0.0399,,0.97029,,0.6883,,21,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-05-31,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51390,SRR8787588,SRX5577619,SRS4539490,SRP189499,PRJNA529224,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: iCLIP,PRJNA529224,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the iCLIP part of the study.,,,,iCLIP   iCLIP control top B3,iCLIP   iC control t B3 AGN001445,,strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001044|replicate ref:AGN001445|replicate order:3|barcode:TCTC|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP control top B3,AGR001761,AGR001761,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001761_R1.fastq.gz,fastq,308262242.0,11618165.0,AGR001761 R1.fastq.gz,0:26.53 1:0,A:72671738;C:75399601;G:85879404;T:74309442;N:2057,26,0,,,72671738,75399601,85879404,74309442,2057,SRX5577619,SRS4539490,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.08645,,0.03066,,0.98283,,0.62503,,25,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-03-26,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51391,SRR8787589,SRX5577618,SRS4539490,SRP189499,PRJNA529224,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: iCLIP,PRJNA529224,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the iCLIP part of the study.,,,,iCLIP   iCLIP control top B3,iCLIP   iC control t B3 AGN001445,,strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001044|replicate ref:AGN001445|replicate order:3|barcode:TCTC|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP control top B3,AGR001762,AGR001762,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001762_R1.fastq.gz,fastq,869838345.0,32810303.0,AGR001762 R1.fastq.gz,0:26.51 1:0,A:203859110;C:213741664;G:243239675;T:208995731;N:2165,26,0,,,203859110,213741664,243239675,208995731,2165,SRX5577618,SRS4539490,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.08728,,0.03148,,0.9822,,0.6655,,34,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-05-31,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51392,SRR8787590,SRX5577617,SRS4539489,SRP189499,PRJNA529224,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: iCLIP,PRJNA529224,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the iCLIP part of the study.,,,,iCLIP   iCLIP control top B2,iCLIP   iC control t B2 AGN001444,,strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001044|replicate ref:AGN001444|replicate order:2|barcode:CACA|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP control top B2,AGR001760,AGR001760,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001760_R1.fastq.gz,fastq,1205268185.0,43628823.0,AGR001760 R1.fastq.gz,0:27.63 1:0,A:273019991;C:288986651;G:371900988;T:271357235;N:3320,27,0,,,273019991,288986651,371900988,271357235,3320,SRX5577617,SRS4539489,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.21687,,0.07509,,0.95396,,0.74949,,31,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-05-31,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51393,SRR8787591,SRX5577616,SRS4539489,SRP189499,PRJNA529224,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: iCLIP,PRJNA529224,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the iCLIP part of the study.,,,,iCLIP   iCLIP control top B2,iCLIP   iC control t B2 AGN001444,,strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001044|replicate ref:AGN001444|replicate order:2|barcode:CACA|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP control top B2,AGR001759,AGR001759,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001759_R1.fastq.gz,fastq,424013394.0,15328091.0,AGR001759 R1.fastq.gz,0:27.66 1:0,A:96563799;C:101163907;G:130484726;T:95798325;N:2637,27,0,,,96563799,101163907,130484726,95798325,2637,SRX5577616,SRS4539489,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.21671,,0.07618,,0.95846,,0.75387,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-05-31,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51394,SRR8787592,SRX5577615,SRS4539487,SRP189499,PRJNA529224,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: iCLIP,PRJNA529224,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the iCLIP part of the study.,,,,iCLIP   iCLIP control top B1,iCLIP   iC control t B1 AGN001443,,strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001044|replicate ref:AGN001443|replicate order:1|barcode:AGAG|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP control top B1,AGR001758,AGR001758,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001758_R1.fastq.gz,fastq,176786449.0,6344415.0,AGR001758 R1.fastq.gz,0:27.86 1:0,A:42909849;C:41469192;G:48710202;T:43696695;N:511,27,0,,,42909849,41469192,48710202,43696695,511,SRX5577615,SRS4539487,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.09087,,0.03187,,0.95349,,0.61728,,18,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-03-26,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51395,SRR8787593,SRX5577614,SRS4539487,SRP189499,PRJNA529224,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: iCLIP,PRJNA529224,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the iCLIP part of the study.,,,,iCLIP   iCLIP control top B1,iCLIP   iC control t B1 AGN001443,,strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001044|replicate ref:AGN001443|replicate order:1|barcode:AGAG|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP control top B1,AGR001757,AGR001757,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001757_R1.fastq.gz,fastq,61732792.0,2199809.0,AGR001757 R1.fastq.gz,0:28.06 1:0,A:15043206;C:14403091;G:16980323;T:15305796;N:376,28,0,,,15043206,14403091,16980323,15305796,376,SRX5577614,SRS4539487,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.07655,,0.03057,,0.98281,,0.65988,,29,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-05-31,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51396,SRR8787594,SRX5577613,SRS4539488,SRP189499,PRJNA529224,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: iCLIP,PRJNA529224,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the iCLIP part of the study.,,,,iCLIP   iCLIP purbb B3,iCLIP   iC purbb B3 AGN001422,,strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001043|replicate ref:AGN001422|replicate order:3|barcode:TCTC|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP purbb B3,AGR001756,AGR001756,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001756_R1.fastq.gz,fastq,11979990.0,504603.0,AGR001756 R1.fastq.gz,0:23.74 1:0,A:3095627;C:3021461;G:3242167;T:2620735;N:0,23,0,,,3095627,3021461,3242167,2620735,0,SRX5577613,SRS4539488,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.1939,,0.04936,,0.88903,,0.61793,,15,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-05-31,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51397,SRR8787595,SRX5577612,SRS4539426,SRP189499,PRJNA529224,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: iCLIP,PRJNA529224,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the iCLIP part of the study.,,,,iCLIP   iCLIP khdrbs1b B1,iCLIP   iC khdrbs1b B1 AGN001191,,strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001034|replicate ref:AGN001191|replicate order:1|barcode:CACA|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP khdrbs1b B1,AGR001693,AGR001693,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001693_R1.fastq.gz,fastq,314259347.0,13565614.0,AGR001693 R1.fastq.gz,0:23.17 1:0,A:76808223;C:70993486;G:91975035;T:74482570;N:33,23,0,,,76808223,70993486,91975035,74482570,33,SRX5577612,SRS4539426,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.06743,,0.03739,,0.97398,,0.70489,,17,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-05-31,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51398,SRR8787596,SRX5577611,SRS4539397,SRP189499,PRJNA529224,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: iCLIP,PRJNA529224,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the iCLIP part of the study.,,,,iCLIP   iCLIP hrnpd B3,iCLIP   iC hrnpd B3 AGN001325,,strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001030|replicate ref:AGN001325|replicate order:3|barcode:CACA|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP hrnpd B3,AGR001657,AGR001657,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001657_R1.fastq.gz,fastq,867656031.0,28112818.0,AGR001657 R1.fastq.gz,0:30.86 1:0,A:224043556;C:181203954;G:220707900;T:241693037;N:7584,30,0,,,224043556,181203954,220707900,241693037,7584,SRX5577611,SRS4539397,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.28099,,0.19543,,0.89889,,0.59527,,23,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-05-31,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51399,SRR8787597,SRX5577610,SRS4539486,SRP189499,PRJNA529224,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: iCLIP,PRJNA529224,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the iCLIP part of the study.,,,,iCLIP   iCLIP khdrbs1a B4,iCLIP   iC khdrbs1a B4 AGN001465,,strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001035|replicate ref:AGN001465|replicate order:4|barcode:TCTC|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP khdrbs1a B4,AGR001711,AGR001711,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001711_R1.fastq.gz,fastq,541123373.0,17615172.0,AGR001711 R1.fastq.gz,0:30.72 1:0,A:137763109;C:132270165;G:149121558;T:121966548;N:1993,30,0,,,137763109,132270165,149121558,121966548,1993,SRX5577610,SRS4539486,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.03093,,0.01351,,0.99007,,0.70114,,21,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-03-26,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51400,SRR8787598,SRX5577609,SRS4539486,SRP189499,PRJNA529224,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: iCLIP,PRJNA529224,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the iCLIP part of the study.,,,,iCLIP   iCLIP khdrbs1a B4,iCLIP   iC khdrbs1a B4 AGN001465,,strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001035|replicate ref:AGN001465|replicate order:4|barcode:TCTC|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP khdrbs1a B4,AGR001710,AGR001710,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001710_R1.fastq.gz,fastq,406544347.0,13224732.0,AGR001710 R1.fastq.gz,0:30.74 1:0,A:102907782;C:99582045;G:112587331;T:91451339;N:15850,30,0,,,102907782,99582045,112587331,91451339,15850,SRX5577609,SRS4539486,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.03018,,0.01279,,0.99005,,0.69694,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-05-31,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51401,SRR8787599,SRX5577608,SRS4539485,SRP189499,PRJNA529224,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: iCLIP,PRJNA529224,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the iCLIP part of the study.,,,,iCLIP   iCLIP khdrbs1a B2,iCLIP   iC khdrbs1a B2 AGN001463,,strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001035|replicate ref:AGN001463|replicate order:2|barcode:AGAG|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP khdrbs1a B2,AGR001706,AGR001706,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001706_R1.fastq.gz,fastq,152835854.0,4809820.0,AGR001706 R1.fastq.gz,0:31.78 1:0,A:37376227;C:36454925;G:44014978;T:34984060;N:5664,31,0,,,37376227,36454925,44014978,34984060,5664,SRX5577608,SRS4539485,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.07451,,0.03434,,0.98492,,0.60421,,31,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-05-31,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51402,SRR8787600,SRX5577607,SRS4539485,SRP189499,PRJNA529224,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: iCLIP,PRJNA529224,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the iCLIP part of the study.,,,,iCLIP   iCLIP khdrbs1a B2,iCLIP   iC khdrbs1a B2 AGN001463,,strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001035|replicate ref:AGN001463|replicate order:2|barcode:AGAG|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP khdrbs1a B2,AGR001707,AGR001707,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001707_R1.fastq.gz,fastq,204887506.0,6461278.0,AGR001707 R1.fastq.gz,0:31.71 1:0,A:50375661;C:48727553;G:58725735;T:47057683;N:874,31,0,,,50375661,48727553,58725735,47057683,874,SRX5577607,SRS4539485,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.07573,,0.03512,,0.98478,,0.62498,,32,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-03-26,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51403,SRR8787601,SRX5577606,SRS4539467,SRP189499,PRJNA529224,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: iCLIP,PRJNA529224,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the iCLIP part of the study.,,,,iCLIP   iCLIP hrnpd B2,iCLIP   iC hrnpd B2 AGN001324,,strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001030|replicate ref:AGN001324|replicate order:2|barcode:AGAG|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP hrnpd B2,AGR001655,AGR001655,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001655_R1.fastq.gz,fastq,217810065.0,6901524.0,AGR001655 R1.fastq.gz,0:31.56 1:0,A:64395958;C:40591509;G:45500452;T:67320152;N:1994,31,0,,,64395958,40591509,45500452,67320152,1994,SRX5577606,SRS4539467,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.50195,,0.37284,,0.84303,,0.5813,,29,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-03-26,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51404,SRR8787602,SRX5577605,SRS4539460,SRP189499,PRJNA529224,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: iCLIP,PRJNA529224,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the iCLIP part of the study.,,,,iCLIP   iCLIP khdrbs1a B3,iCLIP   iC khdrbs1a B3 AGN001464,,strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001035|replicate ref:AGN001464|replicate order:3|barcode:CACA|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP khdrbs1a B3,AGR001709,AGR001709,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001709_R1.fastq.gz,fastq,234626230.0,7363890.0,AGR001709 R1.fastq.gz,0:31.86 1:0,A:55309873;C:56843756;G:72058339;T:50413267;N:995,31,0,,,55309873,56843756,72058339,50413267,995,SRX5577605,SRS4539460,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.11777,,0.03537,,0.97064,,0.64099,,29,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-05-31,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51405,SRR8787603,SRX5577604,SRS4539430,SRP189499,PRJNA529224,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: iCLIP,PRJNA529224,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the iCLIP part of the study.,,,,iCLIP   iCLIP khdrbs1b B4,iCLIP   iC khdrbs1b B4 AGN001418,,strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001034|replicate ref:AGN001418|replicate order:4|barcode:CACA|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP khdrbs1b B4,AGR001700,AGR001700,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001700_R1.fastq.gz,fastq,22350255.0,1006114.0,AGR001700 R1.fastq.gz,0:22.21 1:0,A:5628009;C:5059585;G:6244615;T:5417642;N:404,22,0,,,5628009,5059585,6244615,5417642,404,SRX5577604,SRS4539430,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.22864,,0.0628,,0.83035,,0.541,,26,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-03-26,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51406,SRR8787604,SRX5577603,SRS4539381,SRP189499,PRJNA529224,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: iCLIP,PRJNA529224,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the iCLIP part of the study.,,,,Raw multiplex: iCLIP ddx6 B1;iCLIP ddx6 B3;unrelated,Raw multiplex: iC ddx6 B1 AGN001506;iC ddx6 B3 AGN001508;unrelated,,strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:ddx6 antibody ab40684|sample ref:AGS001053|replicate ref:AGN001506;AGN001508|replicate order:1;3|barcode:AGAG;TCTC;CACA|BioSampleModel:Model organism or animal,,,,,,,,,Raw multiplex: iCLIP ddx6 B1;iCLIP ddx6 B3;unrelated,AGR001803;AGR001807;unrelated,AGR001803;AGR001807;unrelated,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,HWT72ADXX_ddx6_R1.fastq.gz,fastq,2505025208.0,32960858.0,HWT72ADXX ddx6 R1.fastq.gz,0:76,A:702767294;C:648109554;G:640517758;T:513439350;N:191252,76,,,,702767294,648109554,640517758,513439350,191252,SRX5577603,SRS4539381,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.00197,,0.00129,,0.99835,,0.67692,,76,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-05-31,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51407,SRR8787605,SRX5577602,SRS4539444,SRP189499,PRJNA529224,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: iCLIP,PRJNA529224,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the iCLIP part of the study.,,,,iCLIP   iCLIP khdrbs1a B1,iCLIP   iC khdrbs1a B1 AGN001192,,strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001035|replicate ref:AGN001192|replicate order:1|barcode:AGAG|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP khdrbs1a B1,AGR001704,AGR001704,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001704_R1.fastq.gz,fastq,437569479.0,19056946.0,AGR001704 R1.fastq.gz,0:22.96 1:0,A:94607548;C:102540048;G:124760453;T:115648159;N:13271,22,0,,,94607548,102540048,124760453,115648159,13271,SRX5577602,SRS4539444,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.07926,,0.03719,,0.98796,,0.69201,,30,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-05-31,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51408,SRR8787606,SRX5577601,SRS4539444,SRP189499,PRJNA529224,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: iCLIP,PRJNA529224,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the iCLIP part of the study.,,,,iCLIP   iCLIP khdrbs1a B1,iCLIP   iC khdrbs1a B1 AGN001192,,strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001035|replicate ref:AGN001192|replicate order:1|barcode:AGAG|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP khdrbs1a B1,AGR001705,AGR001705,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001705_R1.fastq.gz,fastq,1351079354.0,58530019.0,AGR001705 R1.fastq.gz,0:23.08 1:0,A:292040050;C:317081079;G:385603010;T:356355048;N:167,23,0,,,292040050,317081079,385603010,356355048,167,SRX5577601,SRS4539444,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.0803,,0.03749,,0.98742,,0.66532,,19,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-05-31,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51409,SRR8787607,SRX5577600,SRS4539394,SRP189499,PRJNA529224,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: iCLIP,PRJNA529224,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the iCLIP part of the study.,,,,iCLIP   iCLIP g3bp1 B2,iCLIP   iC g3bp1 B2 AGN001460,,strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001038|replicate ref:AGN001460|replicate order:2|barcode:AGAG|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP g3bp1 B2,AGR001732,AGR001732,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001732_R1.fastq.gz,fastq,163107117.0,5298268.0,AGR001732 R1.fastq.gz,0:30.78 1:0,A:33354170;C:43559190;G:48781505;T:37411775;N:477,30,0,,,33354170,43559190,48781505,37411775,477,SRX5577600,SRS4539394,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.08461,,0.02422,,0.99123,,0.74488,,24,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-03-26,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51410,SRR8787608,SRX5577599,SRS4539403,SRP189499,PRJNA529224,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: iCLIP,PRJNA529224,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the iCLIP part of the study.,,,,iCLIP   iCLIP khsrp B1,iCLIP   iC khsrp B1 AGN001198,,strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001040|replicate ref:AGN001198|replicate order:1|barcode:CACA|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP khsrp B1,AGR001745,AGR001745,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001745_R1.fastq.gz,fastq,285887990.0,11709957.0,AGR001745 R1.fastq.gz,0:24.41 1:0,A:65508336;C:66208695;G:88420897;T:65748079;N:1983,24,0,,,65508336,66208695,88420897,65748079,1983,SRX5577599,SRS4539403,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.19628,,0.07223,,0.91841,,0.74316,,17,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-03-26,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51411,SRR8787610,SRX5577598,SRS4539481,SRP189499,PRJNA529224,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: iCLIP,PRJNA529224,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the iCLIP part of the study.,,,,iCLIP   iCLIP celf1 B4,iCLIP   iC celf1 B4 AGN001311,,strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001039|replicate ref:AGN001311|replicate order:4|barcode:TCTC|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP celf1 B4,AGR001744,AGR001744,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001744_R1.fastq.gz,fastq,2425007610.0,74638556.0,AGR001744 R1.fastq.gz,0:32.49 1:0,A:539664360;C:554945183;G:710446403;T:619866454;N:85210,32,0,,,539664360,554945183,710446403,619866454,85210,SRX5577598,SRS4539481,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.25544,,0.11088,,0.89124,,0.60343,,29,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-03-26,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51412,SRR8787611,SRX5577597,SRS4539438,SRP189499,PRJNA529224,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: iCLIP,PRJNA529224,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the iCLIP part of the study.,,,,iCLIP   iCLIP zff9 B3,iCLIP   iC zff9 B3 AGN001334,,strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001023|replicate ref:AGN001334|replicate order:3|barcode:CACA|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP zff9 B3,AGR001619,AGR001619,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001619_R1.fastq.gz,fastq,86999039.0,2589305.0,AGR001619 R1.fastq.gz,0:33.60 1:0,A:19053907;C:21162420;G:26968505;T:19814135;N:72,33,0,,,19053907,21162420,26968505,19814135,72,SRX5577597,SRS4539438,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.33633,,0.09881,,0.89351,,0.60132,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-05-31,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51413,SRR8787612,SRX5577596,SRS4539420,SRP189499,PRJNA529224,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: iCLIP,PRJNA529224,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the iCLIP part of the study.,,,,iCLIP   iCLIP rbm4.2 B2,iCLIP   iC rbm4.2 B2 AGN001423,,strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001036|replicate ref:AGN001423|replicate order:2|barcode:AGAG|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP rbm4.2 B2,AGR001715,AGR001715,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001715_R1.fastq.gz,fastq,12554363.0,617374.0,AGR001715 R1.fastq.gz,0:20.34 1:0,A:3385742;C:2960391;G:3425822;T:2782375;N:33,20,0,,,3385742,2960391,3425822,2782375,33,SRX5577596,SRS4539420,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.05903,,0.02701,,0.96351,,0.5801,,16,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-05-31,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51414,SRR8787613,SRX5577595,SRS4539484,SRP189499,PRJNA529224,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: iCLIP,PRJNA529224,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the iCLIP part of the study.,,,,iCLIP   iCLIP g3bp1 B4,iCLIP   iC g3bp1 B4 AGN001462,,strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001038|replicate ref:AGN001462|replicate order:4|barcode:TCTC|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP g3bp1 B4,AGR001735,AGR001735,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001735_R1.fastq.gz,fastq,247075127.0,7592473.0,AGR001735 R1.fastq.gz,0:32.54 1:0,A:62688002;C:62122034;G:68568573;T:53687219;N:9299,32,0,,,62688002,62122034,68568573,53687219,9299,SRX5577595,SRS4539484,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.19077,,0.0772,,0.96589,,0.69063,,32,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-05-31,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51415,SRR8787614,SRX5577594,SRS4539398,SRP189499,PRJNA529224,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: iCLIP,PRJNA529224,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the iCLIP part of the study.,,,,iCLIP   iCLIP g3bp1 B3,iCLIP   iC g3bp1 B3 AGN001461,,strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001038|replicate ref:AGN001461|replicate order:3|barcode:CACA|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP g3bp1 B3,AGR001734,AGR001734,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001734_R1.fastq.gz,fastq,887137829.0,25627772.0,AGR001734 R1.fastq.gz,0:34.62 1:0,A:201012457;C:220567528;G:275539909;T:190013755;N:4180,34,0,,,201012457,220567528,275539909,190013755,4180,SRX5577594,SRS4539398,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.09857,,0.02992,,0.97039,,0.70593,,28,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-03-26,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51416,SRR8787615,SRX5577593,SRS4539483,SRP189499,PRJNA529224,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: iCLIP,PRJNA529224,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the iCLIP part of the study.,,,,iCLIP   iCLIP celf1 B2,iCLIP   iC celf1 B2 AGN001309,,strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001039|replicate ref:AGN001309|replicate order:2|barcode:AGAG|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP celf1 B2,AGR001739,AGR001739,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001739_R1.fastq.gz,fastq,422946772.0,12941276.0,AGR001739 R1.fastq.gz,0:32.68 1:0,A:95259342;C:95780964;G:117839895;T:114062884;N:3687,32,0,,,95259342,95780964,117839895,114062884,3687,SRX5577593,SRS4539483,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.26402,,0.08194,,0.88929,,0.54528,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-05-31,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51417,SRR8787616,SRX5577592,SRS4539484,SRP189499,PRJNA529224,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: iCLIP,PRJNA529224,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the iCLIP part of the study.,,,,iCLIP   iCLIP g3bp1 B4,iCLIP   iC g3bp1 B4 AGN001462,,strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001038|replicate ref:AGN001462|replicate order:4|barcode:TCTC|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP g3bp1 B4,AGR001736,AGR001736,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001736_R1.fastq.gz,fastq,423934699.0,13058064.0,AGR001736 R1.fastq.gz,0:32.47 1:0,A:108323229;C:106199854;G:116868860;T:92541123;N:1633,32,0,,,108323229,106199854,116868860,92541123,1633,SRX5577592,SRS4539484,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.1867,,0.07517,,0.96587,,0.65779,,29,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-05-31,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51418,SRR8787617,SRX5577591,SRS4539482,SRP189499,PRJNA529224,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: iCLIP,PRJNA529224,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the iCLIP part of the study.,,,,iCLIP   iCLIP celf1 B3,iCLIP   iC celf1 B3 AGN001310,,strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001039|replicate ref:AGN001310|replicate order:3|barcode:CACA|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP celf1 B3,AGR001741,AGR001741,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001741_R1.fastq.gz,fastq,181225092.0,5582528.0,AGR001741 R1.fastq.gz,0:32.46 1:0,A:41569628;C:39480057;G:49760560;T:50413257;N:1590,32,0,,,41569628,39480057,49760560,50413257,1590,SRX5577591,SRS4539482,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.30171,,0.13079,,0.91171,,0.51467,,31,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-05-31,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51419,SRR8787618,SRX5577590,SRS4539483,SRP189499,PRJNA529224,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: iCLIP,PRJNA529224,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the iCLIP part of the study.,,,,iCLIP   iCLIP celf1 B2,iCLIP   iC celf1 B2 AGN001309,,strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001039|replicate ref:AGN001309|replicate order:2|barcode:AGAG|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP celf1 B2,AGR001740,AGR001740,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001740_R1.fastq.gz,fastq,1088689397.0,33184042.0,AGR001740 R1.fastq.gz,0:32.81 1:0,A:245214271;C:245849853;G:302277422;T:295309750;N:38101,32,0,,,245214271,245849853,302277422,295309750,38101,SRX5577590,SRS4539483,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.26846,,0.08387,,0.88801,,0.52508,,30,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-03-26,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51420,SRR8787619,SRX5577589,SRS4539481,SRP189499,PRJNA529224,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: iCLIP,PRJNA529224,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the iCLIP part of the study.,,,,iCLIP   iCLIP celf1 B4,iCLIP   iC celf1 B4 AGN001311,,strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001039|replicate ref:AGN001311|replicate order:4|barcode:TCTC|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP celf1 B4,AGR001743,AGR001743,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001743_R1.fastq.gz,fastq,945810011.0,29221727.0,AGR001743 R1.fastq.gz,0:32.37 1:0,A:210419683;C:217059856;G:278223751;T:240098280;N:8441,32,0,,,210419683,217059856,278223751,240098280,8441,SRX5577589,SRS4539481,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.25295,,0.10746,,0.89055,,0.60934,,33,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-03-26,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51421,SRR8787620,SRX5577588,SRS4539482,SRP189499,PRJNA529224,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: iCLIP,PRJNA529224,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the iCLIP part of the study.,,,,iCLIP   iCLIP celf1 B3,iCLIP   iC celf1 B3 AGN001310,,strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001039|replicate ref:AGN001310|replicate order:3|barcode:CACA|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP celf1 B3,AGR001742,AGR001742,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001742_R1.fastq.gz,fastq,463117997.0,14195587.0,AGR001742 R1.fastq.gz,0:32.62 1:0,A:106081984;C:100650003;G:126651450;T:129718379;N:16181,32,0,,,106081984,100650003,126651450,129718379,16181,SRX5577588,SRS4539482,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.30723,,0.13235,,0.9109,,0.5134,,45,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-05-31,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51422,SRR8787621,SRX5577587,SRS4539480,SRP189499,PRJNA529224,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: iCLIP,PRJNA529224,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the iCLIP part of the study.,,,,iCLIP   iCLIP org B1,iCLIP   iC org B1 AGN001180,,strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001024|replicate ref:AGN001180|replicate order:1|barcode:AGAG|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP org B1,AGR001624,AGR001624,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001624_R1.fastq.gz,fastq,217287715.0,8511226.0,AGR001624 R1.fastq.gz,0:25.53 1:0,A:48591949;C:50049079;G:62556651;T:56090011;N:25,25,0,,,48591949,50049079,62556651,56090011,25,SRX5577587,SRS4539480,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.0737,,0.02748,,0.98851,,0.64118,,23,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-05-31,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51423,SRR8787622,SRX5577586,SRS4539446,SRP189499,PRJNA529224,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: iCLIP,PRJNA529224,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the iCLIP part of the study.,,,,iCLIP   iCLIP hnrnpab B3,iCLIP   iC hnrnpab B3 AGN001319,,strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001032|replicate ref:AGN001319|replicate order:3|barcode:CACA|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP hnrnpab B3,AGR001675,AGR001675,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001675_R1.fastq.gz,fastq,358380946.0,13835552.0,AGR001675 R1.fastq.gz,0:25.90 1:0,A:105251250;C:66483444;G:82986382;T:103657768;N:2102,25,0,,,105251250,66483444,82986382,103657768,2102,SRX5577586,SRS4539446,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.53325,,0.4045,,0.86253,,0.6278,,26,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-05-31,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51424,SRR8787623,SRX5577585,SRS4539480,SRP189499,PRJNA529224,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: iCLIP,PRJNA529224,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the iCLIP part of the study.,,,,iCLIP   iCLIP org B1,iCLIP   iC org B1 AGN001180,,strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001024|replicate ref:AGN001180|replicate order:1|barcode:AGAG|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP org B1,AGR001623,AGR001623,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001623_R1.fastq.gz,fastq,145155252.0,5699027.0,AGR001623 R1.fastq.gz,0:25.47 1:0,A:32629718;C:33291713;G:41593699;T:37638976;N:1146,25,0,,,32629718,33291713,41593699,37638976,1146,SRX5577585,SRS4539480,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.07375,,0.02737,,0.98727,,0.60319,,21,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-05-31,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51425,SRR8787624,SRX5577584,SRS4539479,SRP189499,PRJNA529224,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: iCLIP,PRJNA529224,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the iCLIP part of the study.,,,,iCLIP   iCLIP pcbp2 B2,iCLIP   iC pcbp2 B2 AGN001330,,strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001027|replicate ref:AGN001330|replicate order:2|barcode:AGAG|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP pcbp2 B2,AGR001637,AGR001637,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001637_R1.fastq.gz,fastq,218084426.0,5598648.0,AGR001637 R1.fastq.gz,0:38.95 1:0,A:48672180;C:58396537;G:59431202;T:51582265;N:2242,38,0,,,48672180,58396537,59431202,51582265,2242,SRX5577584,SRS4539479,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.37399,,0.12141,,0.91985,,0.56399,,47,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-05-31,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51426,SRR8787625,SRX5577583,SRS4539479,SRP189499,PRJNA529224,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: iCLIP,PRJNA529224,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the iCLIP part of the study.,,,,iCLIP   iCLIP pcbp2 B2,iCLIP   iC pcbp2 B2 AGN001330,,strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001027|replicate ref:AGN001330|replicate order:2|barcode:AGAG|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP pcbp2 B2,AGR001638,AGR001638,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001638_R1.fastq.gz,fastq,821694004.0,20996017.0,AGR001638 R1.fastq.gz,0:39.14 1:0,A:183671412;C:219966645;G:222634680;T:195395147;N:26120,39,0,,,183671412,219966645,222634680,195395147,26120,SRX5577583,SRS4539479,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.37881,,0.11984,,0.91987,,0.55653,,34,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-05-31,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51427,SRR8787626,SRX5577582,SRS4539478,SRP189499,PRJNA529224,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: iCLIP,PRJNA529224,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the iCLIP part of the study.,,,,iCLIP   iCLIP pcbp2 B1,iCLIP   iC pcbp2 B1 AGN001183,,strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001027|replicate ref:AGN001183|replicate order:1|barcode:CACA|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP pcbp2 B1,AGR001635,AGR001635,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001635_R1.fastq.gz,fastq,2828355923.0,111576369.0,AGR001635 R1.fastq.gz,0:25.35 1:0,A:674445935;C:624662659;G:903485722;T:625739648;N:21959,25,0,,,674445935,624662659,903485722,625739648,21959,SRX5577582,SRS4539478,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.02786,,0.00938,,0.97163,,0.63882,,23,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-05-31,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51428,SRR8787627,SRX5577581,SRS4539478,SRP189499,PRJNA529224,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: iCLIP,PRJNA529224,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the iCLIP part of the study.,,,,iCLIP   iCLIP pcbp2 B1,iCLIP   iC pcbp2 B1 AGN001183,,strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001027|replicate ref:AGN001183|replicate order:1|barcode:CACA|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP pcbp2 B1,AGR001636,AGR001636,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001636_R1.fastq.gz,fastq,835160635.0,32947083.0,AGR001636 R1.fastq.gz,0:25.35 1:0,A:197796256;C:185188396;G:267722041;T:184453831;N:111,25,0,,,197796256,185188396,267722041,184453831,111,SRX5577581,SRS4539478,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.02806,,0.01008,,0.97319,,0.65071,,16,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-05-31,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51429,SRR8787628,SRX5577580,SRS4539477,SRP189499,PRJNA529224,Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: iCLIP,PRJNA529224,Other,Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the iCLIP part of the study.,,,,iCLIP   iCLIP pcbp2 B4,iCLIP   iC pcbp2 B4 AGN001332,,strain:TU/AB|age:4|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:iCLIP|molecule:RNA|selection:FLAG antibody|sample ref:AGS001027|replicate ref:AGN001332|replicate order:4|barcode:TCTC|BioSampleModel:Model organism or animal,,,,,,,,,iCLIP   iCLIP pcbp2 B4,AGR001641,AGR001641,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP189499,,,AGR001641_R1.fastq.gz,fastq,437000360.0,11388719.0,AGR001641 R1.fastq.gz,0:38.37 1:0,A:98908205;C:121480376;G:112815929;T:103791543;N:4307,38,0,,,98908205,121480376,112815929,103791543,4307,SRX5577580,SRS4539477,SRA866141,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.55116,,0.19197,,0.86095,,0.53929,,27,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,clip,iclip,,United States,2019-05-31,Blastula,Embryo,Embryo Imprecise,All anatomical structures