metadata: run_metadata: 259 rows where experiment.library_selection = "unspecified", experiment.library_source = "TRANSCRIPTOMIC" and technology = "iclip"

259 rows where experiment.library_selection = "unspecified", experiment.library_source = "TRANSCRIPTOMIC" and technology = "iclip"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	sample.title	sample.alias	sample.attributes	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.nofeature_rate.mate1	seqdetective.sparsity.mate1	seqdetective.pos_strand_rate.mate1	seqdetective.readlen.mate1	seqdetective.judgement.mate1	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
48384	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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
51374	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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
51430	51430	SRR8787629	SRX5577579	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	AGR001642	AGR001642	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP189499	AGR001642_R1.fastq.gz	fastq	1662744874.0	43230354.0	AGR001642 R1.fastq.gz	0:38.46 1:0	A:376736248;C:461813400;G:427305358;T:396834971;N:54897	38	0	376736248	461813400	427305358	396834971	54897	SRX5577579	SRS4539477	SRA866141	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.55062	0.18985	0.86139	0.52582	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
51431	51431	SRR8787630	SRX5577578	SRS4539427	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 B3	iCLIP iC pcbp2 B3 AGN001331	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:AGN001331\|replicate order:3\|barcode:CACA\|BioSampleModel:Model organism or animal	iCLIP iCLIP pcbp2 B3	AGR001639	AGR001639	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP189499	AGR001639_R1.fastq.gz	fastq	609630998.0	15554480.0	AGR001639 R1.fastq.gz	0:39.19 1:0	A:142471773;C:154695776;G:165182170;T:147275497;N:5782	39	0	142471773	154695776	165182170	147275497	5782	SRX5577578	SRS4539427	SRA866141	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.29147	0.09649	0.90281	0.5473	39	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
51432	51432	SRR8787631	SRX5577577	SRS4539468	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 rbm4.2 B2;iCLIP rbm4.2 B3;iCLIP rbm4.2 B4	Raw multiplex: iC rbm4.2 B2 AGN001423;iC rbm4.2 B3 AGN001424;iC rbm4.2 B4 AGN001425	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;AGN001424;AGN001425\|replicate order:2;3;4\|barcode:AGAG;CACA;TCTC\|BioSampleModel:Model organism or animal	Raw multiplex: iCLIP rbm4.2 B2;iCLIP rbm4.2 B3;iCLIP rbm4.2 B4	AGR001715;AGR001717;AGR001719	AGR001715;AGR001717;AGR001719	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP189499	HVJ7JADXX_rbm4_25_2E2_001_R1.fastq.gz	fastq	1219960740.0	16052115.0	HVJ7JADXX rbm4 25 2E2 001 R1.fastq.gz	0:76	A:369714292;C:350701070;G:276654597;T:222866423;N:24358	76		369714292	350701070	276654597	222866423	24358	SRX5577577	SRS4539468	SRA866141	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.0	0.0	1.0		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
51433	51433	SRR8787632	SRX5577576	SRS4539476	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 cth1 B1	iCLIP iC cth1 B1 AGN001184	strain:TU/AB\|age:4\|dev stage:sphere\|sex:pooled male and female\|tissue:embryo\|treatment:iCLIP\|molecule:RNA\|selection:FLAG antibody\|sample ref:AGS001028\|replicate ref:AGN001184\|replicate order:1\|barcode:AGAG\|BioSampleModel:Model organism or animal	iCLIP iCLIP cth1 B1	AGR001643	AGR001643	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP189499	AGR001643_R1.fastq.gz	fastq	91776005.0	3641660.0	AGR001643 R1.fastq.gz	0:25.20 1:0	A:22193145;C:20772397;G:27527831;T:21281950;N:682	25	0	22193145	20772397	27527831	21281950	682	SRX5577576	SRS4539476	SRA866141	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.10461	0.04738	0.95582	0.68421	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
51434	51434	SRR8787633	SRX5577575	SRS4539476	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 cth1 B1	iCLIP iC cth1 B1 AGN001184	strain:TU/AB\|age:4\|dev stage:sphere\|sex:pooled male and female\|tissue:embryo\|treatment:iCLIP\|molecule:RNA\|selection:FLAG antibody\|sample ref:AGS001028\|replicate ref:AGN001184\|replicate order:1\|barcode:AGAG\|BioSampleModel:Model organism or animal	iCLIP iCLIP cth1 B1	AGR001644	AGR001644	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP189499	AGR001644_R1.fastq.gz	fastq	26001199.0	1030254.0	AGR001644 R1.fastq.gz	0:25.24 1:0	A:6269459;C:5907813;G:7837997;T:5985925;N:5	25	0	6269459	5907813	7837997	5985925	5	SRX5577575	SRS4539476	SRA866141	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.10578	0.0478	0.95566	0.71537	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
51435	51435	SRR8787634	SRX5577574	SRS4539475	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 zff9 B2;iCLIP zff9 B3;iCLIP zff9 B4	Raw multiplex: iC zff9 B2 AGN001333;iC zff9 B3 AGN001334;iC zff9 B4 AGN001335	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:AGN001333;AGN001334;AGN001335\|replicate order:2;3;4\|barcode:AGAG;CACA;TCTC\|BioSampleModel:Model organism or animal	Raw multiplex: iCLIP zff9 B2;iCLIP zff9 B3;iCLIP zff9 B4	AGR001618;AGR001620;AGR001622	AGR001618;AGR001620;AGR001622	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP189499	HWJWWADXX_zff9_NOBCX_R1.fastq.gz	fastq	11688647392.0	153797992.0	HWJWWADXX zff9 NOBCX R1.fastq.gz	0:76	A:3371911412;C:2802203187;G:3257914678;T:2236941962;N:19676153	76		3371911412	2802203187	3257914678	2236941962	19676153	SRX5577574	SRS4539475	SRA866141	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	3e-05	0.0	0.99989	0.6	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
51436	51436	SRR8787635	SRX5577573	SRS4539475	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 zff9 B2;iCLIP zff9 B3;iCLIP zff9 B4	Raw multiplex: iC zff9 B2 AGN001333;iC zff9 B3 AGN001334;iC zff9 B4 AGN001335	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:AGN001333;AGN001334;AGN001335\|replicate order:2;3;4\|barcode:AGAG;CACA;TCTC\|BioSampleModel:Model organism or animal	Raw multiplex: iCLIP zff9 B2;iCLIP zff9 B3;iCLIP zff9 B4	AGR001617;AGR001619;AGR001621	AGR001617;AGR001619;AGR001621	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP189499	C70FKACXX_zff9_005_R1.fastq.gz	fastq	4372351592.0	57530942.0	C70FKACXX zff9 005 R1.fastq.gz	0:76	A:1263922877;C:1047723705;G:1221328368;T:839052313;N:324329	76		1263922877	1047723705	1221328368	839052313	324329	SRX5577573	SRS4539475	SRA866141	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	4e-05	1e-05	0.99993	0.33333	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
51437	51437	SRR8787636	SRX5577572	SRS4539474	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 zff9 B1;iCLIP org B1;iCLIP srsf4 B1;iCLIP hnrnpa0a B1	Raw multiplex: iC zff9 B1 AGN001179;iC org B1 AGN001180;iC srsf4 B1 AGN001181;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:AGS001023;AGS001024;AGS001025;AGS001026\|replicate ref:AGN001179;AGN001180;AGN001181;AGN001182\|replicate order:1\|barcode:CACA;AGAG;TCTC;GTGT\|BioSampleModel:Model organism or animal	Raw multiplex: iCLIP zff9 B1;iCLIP org B1;iCLIP srsf4 B1;iCLIP hnrnpa0a B1	AGR001615;AGR001623;AGR001625;AGR001627	AGR001615;AGR001623;AGR001625;AGR001627	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP189499	HHYLKADXX_A_001_R1.fastq.gz	fastq	6580292040.0	86582790.0	HHYLKADXX A 001 R1.fastq.gz	0:76	A:1993895906;C:1617758931;G:1655408496;T:1312928441;N:300266	76		1993895906	1617758931	1655408496	1312928441	300266	SRX5577572	SRS4539474	SRA866141	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.00032	0.00014	0.99943	0.66666	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
51438	51438	SRR8787637	SRX5577571	SRS4539474	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 zff9 B1;iCLIP org B1;iCLIP srsf4 B1;iCLIP hnrnpa0a B1	Raw multiplex: iC zff9 B1 AGN001179;iC org B1 AGN001180;iC srsf4 B1 AGN001181;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:AGS001023;AGS001024;AGS001025;AGS001026\|replicate ref:AGN001179;AGN001180;AGN001181;AGN001182\|replicate order:1\|barcode:CACA;AGAG;TCTC;GTGT\|BioSampleModel:Model organism or animal	Raw multiplex: iCLIP zff9 B1;iCLIP org B1;iCLIP srsf4 B1;iCLIP hnrnpa0a B1	AGR001616;AGR001624;AGR001626;AGR001628	AGR001616;AGR001624;AGR001626;AGR001628	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP189499	C78TPACXX_A_001_R1.fastq.gz	fastq	10301944248.0	135551898.0	C78TPACXX A 001 R1.fastq.gz	0:76	A:3081993818;C:2552332073;G:2597278544;T:2069986979;N:352834	76		3081993818	2552332073	2597278544	2069986979	352834	SRX5577571	SRS4539474	SRA866141	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.00026	0.00011	0.99953	0.55555	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
51439	51439	SRR8787638	SRX5577570	SRS4539473	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 pcbp2 B1;iCLIP cth1 B1;iCLIP hnrnpc B1;iCLIP hrnpd B1	Raw multiplex: iC pcbp2 B1 AGN001183;iC cth1 B1 AGN001184;iC hnrnpc B1 AGN001185;iC hrnpd B1 AGN001186	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;AGS001028;AGS001029;AGS001030\|replicate ref:AGN001183;AGN001184;AGN001185;AGN001186\|replicate order:1\|barcode:CACA;AGAG;TCTC;GTGT\|BioSampleModel:Model organism or animal	Raw multiplex: iCLIP pcbp2 B1;iCLIP cth1 B1;iCLIP hnrnpc B1;iCLIP hrnpd B1	AGR001635;AGR001643;AGR001645;AGR001653	AGR001635;AGR001643;AGR001645;AGR001653	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP189499	HHYLKADXX_BandG_002_R1.fastq.gz	fastq	11010240156.0	144871581.0	HHYLKADXX BandG 002 R1.fastq.gz	0:76	A:3310585877;C:2806637716;G:2821444471;T:2071066579;N:505513	76		3310585877	2806637716	2821444471	2071066579	505513	SRX5577570	SRS4539473	SRA866141	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.00812	0.00414	0.99188	0.60026	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
51440	51440	SRR8787639	SRX5577569	SRS4539473	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 pcbp2 B1;iCLIP cth1 B1;iCLIP hnrnpc B1;iCLIP hrnpd B1	Raw multiplex: iC pcbp2 B1 AGN001183;iC cth1 B1 AGN001184;iC hnrnpc B1 AGN001185;iC hrnpd B1 AGN001186	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;AGS001028;AGS001029;AGS001030\|replicate ref:AGN001183;AGN001184;AGN001185;AGN001186\|replicate order:1\|barcode:CACA;AGAG;TCTC;GTGT\|BioSampleModel:Model organism or animal	Raw multiplex: iCLIP pcbp2 B1;iCLIP cth1 B1;iCLIP hnrnpc B1;iCLIP hrnpd B1	AGR001636;AGR001644;AGR001646;AGR001654	AGR001636;AGR001644;AGR001646;AGR001654	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP189499	C78TPACXX_G_002_R1.fastq.gz	fastq	4709906808.0	61972458.0	C78TPACXX G 002 R1.fastq.gz	0:76	A:1331502358;C:1166992915;G:1269065993;T:942186509;N:159033	76		1331502358	1166992915	1269065993	942186509	159033	SRX5577569	SRS4539473	SRA866141	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.03254	0.01636	0.97753	0.63771	76	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
51441	51441	SRR8787640	SRX5577568	SRS4539472	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 hnrnpa0a B2;iCLIP hnrnpa0a B3;iCLIP hnrnpa0a B4	Raw multiplex: iC hnrnpa0a B2 AGN001312;iC hnrnpa0a B3 AGN001313;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:AGN001312;AGN001313;AGN001314\|replicate order:2;3;4\|barcode:AGAG;CACA;TCTC\|BioSampleModel:Model organism or animal	Raw multiplex: iCLIP hnrnpa0a B2;iCLIP hnrnpa0a B3;iCLIP hnrnpa0a B4	AGR001629;AGR001631;AGR001633	AGR001629;AGR001631;AGR001633	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP189499	C70FKACXX_hnrnpa0a_004_R1.fastq.gz	fastq	4998247996.0	65766421.0	C70FKACXX hnrnpa0a 004 R1.fastq.gz	0:76	A:1480688354;C:1217554263;G:1309119307;T:990671087;N:214985	76		1480688354	1217554263	1309119307	990671087	214985	SRX5577568	SRS4539472	SRA866141	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	1e-05	0.0	0.99997	1.0	76	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	unknown	unknown	bulk	clip	iclip	United States	2019-03-26	Blastula	Embryo	Embryo Imprecise	All anatomical structures
51442	51442	SRR8787641	SRX5577567	SRS4539472	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 hnrnpa0a B2;iCLIP hnrnpa0a B3;iCLIP hnrnpa0a B4	Raw multiplex: iC hnrnpa0a B2 AGN001312;iC hnrnpa0a B3 AGN001313;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:AGN001312;AGN001313;AGN001314\|replicate order:2;3;4\|barcode:AGAG;CACA;TCTC\|BioSampleModel:Model organism or animal	Raw multiplex: iCLIP hnrnpa0a B2;iCLIP hnrnpa0a B3;iCLIP hnrnpa0a B4	AGR001630;AGR001632;AGR001634	AGR001630;AGR001632;AGR001634	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP189499	C6CE9ACXX_hnrnpa0a_NOBCX_R1.fastq.gz	fastq	12207696384.0	160627584.0	C6CE9ACXX hnrnpa0a NOBCX R1.fastq.gz	0:76	A:3606404923;C:2974853507;G:3197013331;T:2424250418;N:5174205	76		3606404923	2974853507	3197013331	2424250418	5174205	SRX5577567	SRS4539472	SRA866141	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.0	0.0	1.0		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
51443	51443	SRR8787642	SRX5577566	SRS4539471	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 pcbp2 B2;iCLIP pcbp2 B3;iCLIP pcbp2 B4	Raw multiplex: iC pcbp2 B2 AGN001330;iC pcbp2 B3 AGN001331;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:AGN001330;AGN001331;AGN001332\|replicate order:2;3;4\|barcode:AGAG;CACA;TCTC\|BioSampleModel:Model organism or animal	Raw multiplex: iCLIP pcbp2 B2;iCLIP pcbp2 B3;iCLIP pcbp2 B4	AGR001637;AGR001639;AGR001641	AGR001637;AGR001639;AGR001641	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP189499	C70FKACXX_pcbp2_007_R1.fastq.gz	fastq	2972295096.0	39109146.0	C70FKACXX pcbp2 007 R1.fastq.gz	0:76	A:821089926;C:793387094;G:728463238;T:629225275;N:129563	76		821089926	793387094	728463238	629225275	129563	SRX5577566	SRS4539471	SRA866141	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.00027	6e-05	0.99937	0.47368	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
51444	51444	SRR8787643	SRX5577565	SRS4539471	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 pcbp2 B2;iCLIP pcbp2 B3;iCLIP pcbp2 B4	Raw multiplex: iC pcbp2 B2 AGN001330;iC pcbp2 B3 AGN001331;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:AGN001330;AGN001331;AGN001332\|replicate order:2;3;4\|barcode:AGAG;CACA;TCTC\|BioSampleModel:Model organism or animal	Raw multiplex: iCLIP pcbp2 B2;iCLIP pcbp2 B3;iCLIP pcbp2 B4	AGR001638;AGR001640;AGR001642	AGR001638;AGR001640;AGR001642	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP189499	C6CE9ACXX_pcbp2_NOBCX_R1.fastq.gz	fastq	11427874900.0	150366775.0	C6CE9ACXX pcbp2 NOBCX R1.fastq.gz	0:76	A:3142700009;C:3057107957;G:2796748090;T:2426486320;N:4832524	76		3142700009	3057107957	2796748090	2426486320	4832524	SRX5577565	SRS4539471	SRA866141	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.00034	6e-05	0.99924	0.47916	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
51445	51445	SRR8787644	SRX5577564	SRS4539469	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 B4	iCLIP iC hrnpd B4 AGN001326	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:AGN001326\|replicate order:4\|barcode:TCTC\|BioSampleModel:Model organism or animal	iCLIP iCLIP hrnpd B4	AGR001659	AGR001659	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP189499	AGR001659_R1.fastq.gz	fastq	401606803.0	13049141.0	AGR001659 R1.fastq.gz	0:30.78 1:0	A:120013041;C:76269300;G:84288752;T:121032164;N:3546	30	0	120013041	76269300	84288752	121032164	3546	SRX5577564	SRS4539469	SRA866141	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.42881	0.32719	0.85366	0.58367	20	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
51446	51446	SRR8787645	SRX5577563	SRS4539470	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 fubp1 B1;iCLIP fubp1 B2;iCLIP fubp1 B3	Raw multiplex: iC fubp1 B1 AGN001451;iC fubp1 B2 AGN001452;iC fubp1 B3 AGN001453	strain:TU/AB\|age:4\|dev stage:sphere\|sex:pooled male and female\|tissue:embryo\|treatment:iCLIP\|molecule:RNA\|selection:FLAG antibody\|sample ref:AGS001046\|replicate ref:AGN001451;AGN001452;AGN001453\|replicate order:1;2;3\|barcode:AGAG;CACA;TCTC\|BioSampleModel:Model organism or animal	Raw multiplex: iCLIP fubp1 B1;iCLIP fubp1 B2;iCLIP fubp1 B3	AGR001770;AGR001772;AGR001774	AGR001770;AGR001772;AGR001774	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP189499	C7MYYANXX_fubp1_004_R1.fastq.gz	fastq	4369468000.0	57493000.0	C7MYYANXX fubp1 004 R1.fastq.gz	0:76	A:1284532901;C:1198834587;G:993773404;T:891984959;N:342149	76		1284532901	1198834587	993773404	891984959	342149	SRX5577563	SRS4539470	SRA866141	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.00038	0.00033	0.99991	0.28571	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
51447	51447	SRR8787646	SRX5577562	SRS4539470	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 fubp1 B1;iCLIP fubp1 B2;iCLIP fubp1 B3	Raw multiplex: iC fubp1 B1 AGN001451;iC fubp1 B2 AGN001452;iC fubp1 B3 AGN001453	strain:TU/AB\|age:4\|dev stage:sphere\|sex:pooled male and female\|tissue:embryo\|treatment:iCLIP\|molecule:RNA\|selection:FLAG antibody\|sample ref:AGS001046\|replicate ref:AGN001451;AGN001452;AGN001453\|replicate order:1;2;3\|barcode:AGAG;CACA;TCTC\|BioSampleModel:Model organism or animal	Raw multiplex: iCLIP fubp1 B1;iCLIP fubp1 B2;iCLIP fubp1 B3	AGR001769;AGR001771;AGR001773	AGR001769;AGR001771;AGR001773	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP189499	C7JM0ANXX_fubp1_004_R1.fastq.gz	fastq	710289312.0	9345912.0	C7JM0ANXX fubp1 004 R1.fastq.gz	0:76	A:210471830;C:197185764;G:158758089;T:143754883;N:118746	76		210471830	197185764	158758089	143754883	118746	SRX5577562	SRS4539470	SRA866141	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.0	0.0	1.0		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
51448	51448	SRR8787647	SRX5577561	SRS4539469	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 B4	iCLIP iC hrnpd B4 AGN001326	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:AGN001326\|replicate order:4\|barcode:TCTC\|BioSampleModel:Model organism or animal	iCLIP iCLIP hrnpd B4	AGR001660	AGR001660	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP189499	AGR001660_R1.fastq.gz	fastq	1240761602.0	40191868.0	AGR001660 R1.fastq.gz	0:30.87 1:0	A:372471311;C:234191965;G:258261558;T:375767527;N:69241	30	0	372471311	234191965	258261558	375767527	69241	SRX5577561	SRS4539469	SRA866141	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.43577	0.3344	0.85435	0.59214	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
51449	51449	SRR8787648	SRX5577560	SRS4539468	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 rbm4.2 B2;iCLIP rbm4.2 B3;iCLIP rbm4.2 B4	Raw multiplex: iC rbm4.2 B2 AGN001423;iC rbm4.2 B3 AGN001424;iC rbm4.2 B4 AGN001425	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;AGN001424;AGN001425\|replicate order:2;3;4\|barcode:AGAG;CACA;TCTC\|BioSampleModel:Model organism or animal	Raw multiplex: iCLIP rbm4.2 B2;iCLIP rbm4.2 B3;iCLIP rbm4.2 B4	AGR001716;AGR001718;AGR001720	AGR001716;AGR001718;AGR001720	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP189499	HVJC2ADXX_rbm4_25_2E2_001_R1.fastq.gz	fastq	1299992920.0	17105170.0	HVJC2ADXX rbm4 25 2E2 001 R1.fastq.gz	0:76	A:394000623;C:372971384;G:294209171;T:238753675;N:58067	76		394000623	372971384	294209171	238753675	58067	SRX5577560	SRS4539468	SRA866141	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	2e-05	0.0	0.99995	0.5	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
51450	51450	SRR8787649	SRX5577559	SRS4539459	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 hug B1	iCLIP iC hug B1 AGN001187	strain:TU/AB\|age:4\|dev stage:sphere\|sex:pooled male and female\|tissue:embryo\|treatment:iCLIP\|molecule:RNA\|selection:FLAG antibody\|sample ref:AGS001031\|replicate ref:AGN001187\|replicate order:1\|barcode:CACA\|BioSampleModel:Model organism or animal	iCLIP iCLIP hug B1	AGR001661	AGR001661	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP189499	AGR001661_R1.fastq.gz	fastq	21474210.0	889521.0	AGR001661 R1.fastq.gz	0:24.14 1:0	A:5528771;C:3971626;G:5040195;T:6933448;N:170	24	0	5528771	3971626	5040195	6933448	170	SRX5577559	SRS4539459	SRA866141	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.34932	0.22099	0.84333	0.54545	22	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
51451	51451	SRR8787650	SRX5577558	SRS4539425	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 B4	iCLIP iC zff9 B4 AGN001335	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:AGN001335\|replicate order:4\|barcode:TCTC\|BioSampleModel:Model organism or animal	iCLIP iCLIP zff9 B4	AGR001621	AGR001621	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP189499	AGR001621_R1.fastq.gz	fastq	156943588.0	4846435.0	AGR001621 R1.fastq.gz	0:32.38 1:0	A:34733260;C:38377946;G:49689848;T:34142420;N:114	32	0	34733260	38377946	49689848	34142420	114	SRX5577558	SRS4539425	SRA866141	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.25453	0.06408	0.9246	0.702	48	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
51452	51452	SRR8787651	SRX5577557	SRS4539459	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 hug B1	iCLIP iC hug B1 AGN001187	strain:TU/AB\|age:4\|dev stage:sphere\|sex:pooled male and female\|tissue:embryo\|treatment:iCLIP\|molecule:RNA\|selection:FLAG antibody\|sample ref:AGS001031\|replicate ref:AGN001187\|replicate order:1\|barcode:CACA\|BioSampleModel:Model organism or animal	iCLIP iCLIP hug B1	AGR001662	AGR001662	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP189499	AGR001662_R1.fastq.gz	fastq	151566597.0	6312901.0	AGR001662 R1.fastq.gz	0:24.01 1:0	A:38923086;C:28142547;G:35612280;T:48884389;N:4295	24	0	38923086	28142547	35612280	48884389	4295	SRX5577557	SRS4539459	SRA866141	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.34625	0.21874	0.84719	0.55442	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
51453	51453	SRR8787652	SRX5577556	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	AGR001656	AGR001656	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP189499	AGR001656_R1.fastq.gz	fastq	668036295.0	21091210.0	AGR001656 R1.fastq.gz	0:31.67 1:0	A:198751615;C:123534983;G:137946363;T:207766995;N:36339	31	0	198751615	123534983	137946363	207766995	36339	SRX5577556	SRS4539467	SRA866141	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.51158	0.38017	0.84155	0.56678	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
51454	51454	SRR8787653	SRX5577555	SRS4539391	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 B2	iCLIP iC hnrnpab B2 AGN001318	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:AGN001318\|replicate order:2\|barcode:AGAG\|BioSampleModel:Model organism or animal	iCLIP iCLIP hnrnpab B2	AGR001673	AGR001673	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP189499	AGR001673_R1.fastq.gz	fastq	226960450.0	8639618.0	AGR001673 R1.fastq.gz	0:26.27 1:0	A:58567603;C:50420542;G:62028732;T:55942194;N:1379	26	0	58567603	50420542	62028732	55942194	1379	SRX5577555	SRS4539391	SRA866141	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.17033	0.10077	0.9582	0.6614	42	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
51455	51455	SRR8787654	SRX5577554	SRS4539463	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 patA B1	iCLIP iC purbb patA B1 AGN001500	strain:TU/AB\|age:4\|dev stage:sphere\|sex:pooled male and female\|tissue:embryo\|treatment:iCLIP pateamineA\|molecule:RNA\|selection:FLAG antibody\|sample ref:AGS001051\|replicate ref:AGN001500\|replicate order:1\|barcode:AGAG\|BioSampleModel:Model organism or animal	iCLIP iCLIP purbb patA B1	AGR001794	AGR001794	RNA	OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP189499	AGR001794_R1.fastq.gz	fastq	205643499.0	5249724.0	AGR001794 R1.fastq.gz	0:39.17 1:0	A:51597295;C:46180683;G:61808487;T:46050568;N:6466	39	0	51597295	46180683	61808487	46050568	6466	SRX5577554	SRS4539463	SRA866141	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.14694	0.02796	0.8785	0.55244	37	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

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