metadata: run_metadata: 502 rows where experiment.library_selection = "RT-PCR", experiment.library_source = "TRANSCRIPTOMIC" and technology = "unknown"

502 rows where experiment.library_selection = "RT-PCR", experiment.library_source = "TRANSCRIPTOMIC" and technology = "unknown"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	sample.description	sample.title	sample.alias	sample.attributes	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.spot_descriptor	experiment.study_ref	run.title	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
282	282	DRR179616	DRX170142	DRS185505	DRP007318	PRJDB8340	Gene expression analysis of zebrafish fin melanophores and xanthophores.	DRP007318	Other	Pigment cells melanophores and xanthophores were collected from zebrafish fin. Total RNAs were extracted from each melanophore and xanthophore and cDNA libraries were prepared using SMARTer Ultra Low Input RNA Kit for Sequencing v3 and Ion Xpress Plus gDNA Fragment Library Preparation. The libraries were sequenced using the Ion PGM with Ion PGM OT2 400 kit and Ion PGM Sequencing 400 kit.	Biological replicate 2	Fin xanthophore 03	SAMD00172019	sample name:Zebrafish pigment cell 06\|cell type:Xanthophore\|collection date:2015 11 12\|dev stage:Adult\|genotype:Wild type\|tissue:Caudal fin and anal fin	Ion Torrent PGM sequencing of SAMD00172019	DRX170142	Zebrafish fin xanthophore 01	1	1	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	SINGLE	ION_TORRENT	Ion Torrent PGM	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>232</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP007318	Ion Torrent PGM sequencing of SAMD00172019			376558775.0	1624500.0	DRR179616	0:231.80	A:107837072;C:79508449;G:79372899;T:109840355;N:0	231		107837072	79508449	79372899	109840355	0	DRX170142	DRS185505	DRA008445	OSAKA_FB\|Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University	Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University	1	0.86944		0.10951		0.90425		0.59385		311		B		usable mapping rate	ion_torrent	ion_torrent	full_length	other	smarter	bulk	unknown	unknown	Japan	2021-05-21	Adult	Adult	Fin	Surface Structure
283	283	DRR179615	DRX170141	DRS185504	DRP007318	PRJDB8340	Gene expression analysis of zebrafish fin melanophores and xanthophores.	DRP007318	Other	Pigment cells melanophores and xanthophores were collected from zebrafish fin. Total RNAs were extracted from each melanophore and xanthophore and cDNA libraries were prepared using SMARTer Ultra Low Input RNA Kit for Sequencing v3 and Ion Xpress Plus gDNA Fragment Library Preparation. The libraries were sequenced using the Ion PGM with Ion PGM OT2 400 kit and Ion PGM Sequencing 400 kit.	Biological replicate 1	Fin xanthophore 02	SAMD00172018	sample name:Zebrafish pigment cell 05\|cell type:Xanthophore\|collection date:2015 09 10\|dev stage:Adult\|genotype:Wild type\|tissue:Caudal fin and anal fin	Ion Torrent PGM sequencing of SAMD00172018	DRX170141	Zebrafish fin xanthophore 01	1	1	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	SINGLE	ION_TORRENT	Ion Torrent PGM	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>243</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP007318	Ion Torrent PGM sequencing of SAMD00172018			515115515.0	2124170.0	DRR179615	0:242.50	A:138421982;C:119032803;G:119412227;T:138248503;N:0	242		138421982	119032803	119412227	138248503	0	DRX170141	DRS185504	DRA008445	OSAKA_FB\|Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University	Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University	1	0.88998		0.05858		0.88051		0.50917		284		B		usable mapping rate	ion_torrent	ion_torrent	full_length	other	smarter	bulk	unknown	unknown	Japan	2021-05-21	Adult	Adult	Fin	Surface Structure
284	284	DRR179614	DRX170140	DRS185503	DRP007318	PRJDB8340	Gene expression analysis of zebrafish fin melanophores and xanthophores.	DRP007318	Other	Pigment cells melanophores and xanthophores were collected from zebrafish fin. Total RNAs were extracted from each melanophore and xanthophore and cDNA libraries were prepared using SMARTer Ultra Low Input RNA Kit for Sequencing v3 and Ion Xpress Plus gDNA Fragment Library Preparation. The libraries were sequenced using the Ion PGM with Ion PGM OT2 400 kit and Ion PGM Sequencing 400 kit.	Biological replicate 1	Fin xanthophore 01	SAMD00172017	sample name:Zebrafish pigment cell 04\|cell type:Xanthophore\|collection date:2015 09 10\|dev stage:Adult\|genotype:Wild type\|tissue:Caudal fin and anal fin	Ion Torrent PGM sequencing of SAMD00172017	DRX170140	Zebrafish fin xanthophore 01	1	1	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	SINGLE	ION_TORRENT	Ion Torrent PGM	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>247</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP007318	Ion Torrent PGM sequencing of SAMD00172017			371242152.0	1504407.0	DRR179614	0:246.77	A:99341086;C:86126839;G:86264882;T:99509345;N:0	246		99341086	86126839	86264882	99509345	0	DRX170140	DRS185503	DRA008445	OSAKA_FB\|Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University	Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University	1	0.88672		0.06422		0.85679		0.5066		56		B		usable mapping rate	ion_torrent	ion_torrent	full_length	other	smarter	bulk	unknown	unknown	Japan	2021-05-21	Adult	Adult	Fin	Surface Structure
285	285	DRR179613	DRX170139	DRS185502	DRP007318	PRJDB8340	Gene expression analysis of zebrafish fin melanophores and xanthophores.	DRP007318	Other	Pigment cells melanophores and xanthophores were collected from zebrafish fin. Total RNAs were extracted from each melanophore and xanthophore and cDNA libraries were prepared using SMARTer Ultra Low Input RNA Kit for Sequencing v3 and Ion Xpress Plus gDNA Fragment Library Preparation. The libraries were sequenced using the Ion PGM with Ion PGM OT2 400 kit and Ion PGM Sequencing 400 kit.	Biological replicate 2	Fin melanophore 03	SAMD00172016	sample name:Zebrafish pigment cell 03\|cell type:Melanophore\|collection date:2015 11 12\|dev stage:Adult\|genotype:Wild type\|tissue:Caudal fin and anal fin	Ion Torrent PGM sequencing of SAMD00172016	DRX170139	Zebrafish fin melanophore 03	1	1	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	SINGLE	ION_TORRENT	Ion Torrent PGM	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>248</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP007318	Ion Torrent PGM sequencing of SAMD00172016			342802993.0	1585538.0	DRR179613	0:216.21	A:90833658;C:80789744;G:80463233;T:90716358;N:0	216		90833658	80789744	80463233	90716358	0	DRX170139	DRS185502	DRA008445	OSAKA_FB\|Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University	Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University	1	0.8312		0.03528		0.88605		0.47299		285		B		usable mapping rate	ion_torrent	ion_torrent	full_length	other	smarter	bulk	unknown	unknown	Japan	2021-05-21	Adult	Adult	Fin	Surface Structure
286	286	DRR179612	DRX170138	DRS185501	DRP007318	PRJDB8340	Gene expression analysis of zebrafish fin melanophores and xanthophores.	DRP007318	Other	Pigment cells melanophores and xanthophores were collected from zebrafish fin. Total RNAs were extracted from each melanophore and xanthophore and cDNA libraries were prepared using SMARTer Ultra Low Input RNA Kit for Sequencing v3 and Ion Xpress Plus gDNA Fragment Library Preparation. The libraries were sequenced using the Ion PGM with Ion PGM OT2 400 kit and Ion PGM Sequencing 400 kit.	Biological replicate 1	Fin melanophore 02	SAMD00172015	sample name:Zebrafish pigment cell 02\|cell type:Melanophore\|collection date:2015 05 12\|dev stage:Adult\|genotype:Wild type\|tissue:Caudal fin and anal fin	Ion Torrent PGM sequencing of SAMD00172015	DRX170138	Zebrafish fin melanophore 02	1	1	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	SINGLE	ION_TORRENT	Ion Torrent PGM	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>216</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP007318	Ion Torrent PGM sequencing of SAMD00172015			538412675.0	2168231.0	DRR179612	0:248.32	A:147128403;C:121854818;G:121564109;T:147865345;N:0	248		147128403	121854818	121564109	147865345	0	DRX170138	DRS185501	DRA008445	OSAKA_FB\|Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University	Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University	1	0.89106		0.07081		0.89286		0.5935		283		B		usable mapping rate	ion_torrent	ion_torrent	full_length	other	smarter	bulk	unknown	unknown	Japan	2021-05-21	Adult	Adult	Fin	Surface Structure
287	287	DRR179611	DRX170137	DRS185500	DRP007318	PRJDB8340	Gene expression analysis of zebrafish fin melanophores and xanthophores.	DRP007318	Other	Pigment cells melanophores and xanthophores were collected from zebrafish fin. Total RNAs were extracted from each melanophore and xanthophore and cDNA libraries were prepared using SMARTer Ultra Low Input RNA Kit for Sequencing v3 and Ion Xpress Plus gDNA Fragment Library Preparation. The libraries were sequenced using the Ion PGM with Ion PGM OT2 400 kit and Ion PGM Sequencing 400 kit.	Biological replicate 1	Fin melanophore 01	SAMD00172014	sample name:Zebrafish pigment cell 01\|cell type:Melanophore\|collection date:2015 05 12\|dev stage:Adult\|genotype:Wild type\|tissue:Caudal fin and anal fin	Ion Torrent PGM sequencing of SAMD00172014	DRX170137	Zebrafish fin melanophore 01	1	1	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	SINGLE	ION_TORRENT	Ion Torrent PGM	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>215</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP007318	Ion Torrent PGM sequencing of SAMD00172014			282446840.0	1311431.0	DRR179611	0:215.37	A:74927237;C:66575483;G:66161471;T:74782649;N:0	215		74927237	66575483	66161471	74782649	0	DRX170137	DRS185500	DRA008445	OSAKA_FB\|Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University	Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University	1	0.85938		0.0335		0.89248		0.58813		274		B		usable mapping rate	ion_torrent	ion_torrent	full_length	other	smarter	bulk	unknown	unknown	Japan	2021-05-21	Adult	Adult	Fin	Surface Structure
29210	29210	SRR27489726	SRX23160983	SRS20111140	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.	polysome fraction	80S fraction 6hpf replica A	MPRA repA fractions 4 5 6hpf	strain:TLAB\|age:6 hpf\|dev stage:shield\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:10\|replicate:replicate A\|BioSampleModel:Model organism or animal	80S fraction 6hpf replica A	Library 10	Library 10	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.		OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP483112		BSSE_QGF_206645_HGWLYDSX3_3_MPRA_repA_fractions_4_5_6hpf_CTCTCGTC_TATAACCT_S10_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206645_HGWLYDSX3_3_MPRA_repA_fractions_4_5_6hpf_CTCTCGTC_TATAACCT_S10_L003_R2_001_MM_1.fastq.gz	fastq fastq	13762167482.0	45570091.0	BSSE QGF 206645 HGWLYDSX3 3 MPRA repA fractions 4 5 6hpf CTCTCGTC TATAACCT S10 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:3449173111;C:3620318973;G:3412595233;T:3279391764;N:688401	151	151	3449173111	3620318973	3412595233	3279391764	688401	SRX23160983	SRS20111140	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01348	9e-05	0.00033	1e-05	0.99151	0.99973	0.41104	0.57142	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Gastrula	Embryo	Whole Organism	All anatomical structures
29211	29211	SRR27489727	SRX23160982	SRS20111139	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.	input sample	Total 6hpf replica A	MPRA repA input 6hpf	strain:TLAB\|age:6 hpf\|dev stage:shield\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:9\|replicate:replicate A\|BioSampleModel:Model organism or animal	Total 6hpf replica A	Library 9	Library 9	Total RNA was extracted from input sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.		OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP483112		BSSE_QGF_206644_HGWLYDSX3_3_MPRA_repA_input_6hpf_TCTCTACT_CGCGGTTC_S9_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206644_HGWLYDSX3_3_MPRA_repA_input_6hpf_TCTCTACT_CGCGGTTC_S9_L003_R1_001_MM_1.fastq.gz	fastq fastq	13570263998.0	44934649.0	BSSE QGF 206644 HGWLYDSX3 3 MPRA repA input 6hpf TCTCTACT CGCGGTTC S9 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:3444180060;C:3577051220;G:3264051077;T:3284343514;N:638127	151	151	3444180060	3577051220	3264051077	3284343514	638127	SRX23160982	SRS20111139	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01809	5e-05	0.00042	0.0	0.99013	0.99985	0.41794	0.57142	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Gastrula	Embryo	Whole Organism	All anatomical structures
29212	29212	SRR27489728	SRX23160981	SRS20111138	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.	polysome fraction	HMW fraction 4hpf replica A	MPRA repA fractions 8 9 4hpf	strain:TLAB\|age:4 hpf\|dev stage:sphere\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:8\|replicate:replicate A\|BioSampleModel:Model organism or animal	HMW fraction 4hpf replica A	Library 8	Library 8	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.		OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP483112		BSSE_QGF_206643_HGWLYDSX3_3_MPRA_repA_fractions_8_9_4hpf_GACCTGAA_TTGGTGAG_S8_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206643_HGWLYDSX3_3_MPRA_repA_fractions_8_9_4hpf_GACCTGAA_TTGGTGAG_S8_L003_R1_001_MM_1.fastq.gz	fastq fastq	12066108000.0	39954000.0	BSSE QGF 206643 HGWLYDSX3 3 MPRA repA fractions 8 9 4hpf GACCTGAA TTGGTGAG S8 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:3060316371;C:3136678983;G:2965588104;T:2902920606;N:603936	151	151	3060316371	3136678983	2965588104	2902920606	603936	SRX23160981	SRS20111138	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01336	5e-05	0.00027	0.0	0.99143	0.99983	0.40418	0.125	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Blastula	Embryo	Whole Organism	All anatomical structures
29213	29213	SRR27489729	SRX23160980	SRS20111142	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.	polysome fraction	LMW fraction 4hpf replica A	MPRA repA fractions 6 7 4hpf	strain:TLAB\|age:4 hpf\|dev stage:sphere\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:7\|replicate:replicate A\|BioSampleModel:Model organism or animal	LMW fraction 4hpf replica A	Library 7	Library 7	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.		OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP483112		BSSE_QGF_206642_HGWLYDSX3_3_MPRA_repA_fractions_6_7_4hpf_AGTTCAGG_CCAACAGA_S7_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206642_HGWLYDSX3_3_MPRA_repA_fractions_6_7_4hpf_AGTTCAGG_CCAACAGA_S7_L003_R1_001_MM_1.fastq.gz	fastq fastq	11998643314.0	39730607.0	BSSE QGF 206642 HGWLYDSX3 3 MPRA repA fractions 6 7 4hpf AGTTCAGG CCAACAGA S7 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:3044270548;C:3145201016;G:2907229129;T:2901344613;N:598008	151	151	3044270548	3145201016	2907229129	2901344613	598008	SRX23160980	SRS20111142	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01631	0.00013	0.00035	1e-05	0.99101	0.99965	0.40542	0.33333	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Blastula	Embryo	Whole Organism	All anatomical structures
29214	29214	SRR27489730	SRX23160979	SRS20111137	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.	polysome fraction	80S fraction 4hpf replica A	MPRA repA fractions 4 5 4hpf	strain:TLAB\|age:4 hpf\|dev stage:sphere\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:6\|replicate:replicate A\|BioSampleModel:Model organism or animal	80S fraction 4hpf replica A	Library 6	Library 6	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.		OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP483112		BSSE_QGF_206641_HGWLYDSX3_3_MPRA_repA_fractions_4_5_4hpf_TGGATCGA_GTGCGATA_S6_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206641_HGWLYDSX3_3_MPRA_repA_fractions_4_5_4hpf_TGGATCGA_GTGCGATA_S6_L003_R2_001_MM_1.fastq.gz	fastq fastq	12838157410.0	42510455.0	BSSE QGF 206641 HGWLYDSX3 3 MPRA repA fractions 4 5 4hpf TGGATCGA GTGCGATA S6 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:3238698530;C:3377705608;G:3143460419;T:3077655243;N:637610	151	151	3238698530	3377705608	3143460419	3077655243	637610	SRX23160979	SRS20111137	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01549	3e-05	0.00042	1e-05	0.99097	0.99995	0.42138	0.5	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Blastula	Embryo	Whole Organism	All anatomical structures
29215	29215	SRR27489731	SRX23160978	SRS20111136	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.	RNA product	control RNA library	RNA mMessage MPRA library	strain:not applicable\|age:not applicable\|dev stage:not applicable\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:not applicable\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:not applicable\|growth protocol:not applicable\|sample type:IVT mRNA\|sample number:50\|replicate:unique sample\|BioSampleModel:Model organism or animal	control RNA library	Library 50	Library 50	PCR product was amplified from DNA plasmid pool with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.		OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP483112		BSSE_QGF_206685_HGWLYDSX3_3_RNA_mMessage_MPRA_library_test_GGTTATAA_GATATCGA_S50_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206685_HGWLYDSX3_3_RNA_mMessage_MPRA_library_test_GGTTATAA_GATATCGA_S50_L003_R2_001_MM_1.fastq.gz	fastq fastq	16695252486.0	55282293.0	BSSE QGF 206685 HGWLYDSX3 3 RNA mMessage MPRA library test GGTTATAA GATATCGA S50 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:4275447149;C:4413405571;G:3936523108;T:4069049357;N:827301	151	151	4275447149	4413405571	3936523108	4069049357	827301	SRX23160978	SRS20111136	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.02176	0.00021	0.00058	2e-05	0.99056	0.99933	0.41475	0.48571	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Undetermined	Embryo	Undetermined	Embryo Imprecise
29216	29216	SRR27489733	SRX23160976	SRS20111134	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.	polysome fraction	HMW fraction 10hpf replica C	MPRA repC fractions 8 9 10hpf	strain:TLAB\|age:10 hpf\|dev stage:bud\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:48\|replicate:replicate C\|BioSampleModel:Model organism or animal	HMW fraction 10hpf replica C	Library 48	Library 48	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.		OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP483112		BSSE_QGF_206683_HGWLYDSX3_3_MPRA_repC_fractions_8_9_10hpf_CAACAATG_CTTCACGG_S48_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206683_HGWLYDSX3_3_MPRA_repC_fractions_8_9_10hpf_CAACAATG_CTTCACGG_S48_L003_R2_001_MM_1.fastq.gz	fastq fastq	16074911568.0	53228184.0	BSSE QGF 206683 HGWLYDSX3 3 MPRA repC fractions 8 9 10hpf CAACAATG CTTCACGG S48 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:4029048727;C:4167204709;G:4036912991;T:3840941866;N:803275	151	151	4029048727	4167204709	4036912991	3840941866	803275	SRX23160976	SRS20111134	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.00795	0.00021	0.00019	2e-05	0.99263	0.99935	0.45247	0.62857	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Gastrula	Embryo	Whole Organism	All anatomical structures
29217	29217	SRR27489734	SRX23160975	SRS20111132	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.	polysome fraction	LMW fraction 10hpf replica C	MPRA repC fractions 6 7 10hpf	strain:TLAB\|age:10 hpf\|dev stage:bud\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:47\|replicate:replicate C\|BioSampleModel:Model organism or animal	LMW fraction 10hpf replica C	Library 47	Library 47	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.		OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP483112		BSSE_QGF_206682_HGWLYDSX3_3_MPRA_repC_fractions_6_7_10hpf_GGTGAACC_GCGTTGGA_S47_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206682_HGWLYDSX3_3_MPRA_repC_fractions_6_7_10hpf_GGTGAACC_GCGTTGGA_S47_L003_R2_001_MM_1.fastq.gz	fastq fastq	16211925948.0	53681874.0	BSSE QGF 206682 HGWLYDSX3 3 MPRA repC fractions 6 7 10hpf GGTGAACC GCGTTGGA S47 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:4078470905;C:4239434649;G:4000426230;T:3892801664;N:792500	151	151	4078470905	4239434649	4000426230	3892801664	792500	SRX23160975	SRS20111132	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01232	0.00028	0.00027	5e-05	0.99166	0.99926	0.4522	0.61904	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Gastrula	Embryo	Whole Organism	All anatomical structures
29218	29218	SRR27489735	SRX23160974	SRS20111131	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.	polysome fraction	80S fraction 10hpf replica C	MPRA repC fractions 4 5 10hpf	strain:TLAB\|age:10 hpf\|dev stage:bud\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:46\|replicate:replicate C\|BioSampleModel:Model organism or animal	80S fraction 10hpf replica C	Library 46	Library 46	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.		OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP483112		BSSE_QGF_206681_HGWLYDSX3_3_MPRA_repC_fractions_4_5_10hpf_AACAGGTT_ATACCAAG_S46_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206681_HGWLYDSX3_3_MPRA_repC_fractions_4_5_10hpf_AACAGGTT_ATACCAAG_S46_L003_R2_001_MM_1.fastq.gz	fastq fastq	18761117310.0	62122905.0	BSSE QGF 206681 HGWLYDSX3 3 MPRA repC fractions 4 5 10hpf AACAGGTT ATACCAAG S46 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:4746221682;C:4940258209;G:4549993563;T:4523714877;N:928979	151	151	4746221682	4940258209	4549993563	4523714877	928979	SRX23160974	SRS20111131	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01785	0.0002	0.00043	3e-05	0.9908	0.99951	0.45866	0.6	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Gastrula	Embryo	Whole Organism	All anatomical structures
29219	29219	SRR27489736	SRX23160973	SRS20111130	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.	input sample	Total 10hpf replica C	MPRA repC input 10hpf	strain:TLAB\|age:10 hpf\|dev stage:bud\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:45\|replicate:replicate C\|BioSampleModel:Model organism or animal	Total 10hpf replica C	Library 45	Library 45	Total RNA was extracted from input sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.		OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP483112		BSSE_QGF_206680_HGWLYDSX3_3_MPRA_repC_input_10hpf_GCGCTCTA_GCTCCGAC_S45_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206680_HGWLYDSX3_3_MPRA_repC_input_10hpf_GCGCTCTA_GCTCCGAC_S45_L003_R2_001_MM_1.fastq.gz	fastq fastq	15148053334.0	50159117.0	BSSE QGF 206680 HGWLYDSX3 3 MPRA repC input 10hpf GCGCTCTA GCTCCGAC S45 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:3877492548;C:4007711111;G:3560735163;T:3701356537;N:757975	151	151	3877492548	4007711111	3560735163	3701356537	757975	SRX23160973	SRS20111130	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.02196	3e-05	0.00062	1e-05	0.98944	0.99993	0.4404	0.66666	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Gastrula	Embryo	Whole Organism	All anatomical structures
29220	29220	SRR27489737	SRX23160972	SRS20111129	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.	polysome fraction	HMW fraction 6hpf replica C	MPRA repC fractions 8 9 6hpf	strain:TLAB\|age:6 hpf\|dev stage:shield\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:44\|replicate:replicate C\|BioSampleModel:Model organism or animal	HMW fraction 6hpf replica C	Library 44	Library 44	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.		OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP483112		BSSE_QGF_206679_HGWLYDSX3_3_MPRA_repC_fractions_8_9_6hpf_ATATCTCG_ATCTTAGT_S44_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206679_HGWLYDSX3_3_MPRA_repC_fractions_8_9_6hpf_ATATCTCG_ATCTTAGT_S44_L003_R1_001_MM_1.fastq.gz	fastq fastq	14506315716.0	48034158.0	BSSE QGF 206679 HGWLYDSX3 3 MPRA repC fractions 8 9 6hpf ATATCTCG ATCTTAGT S44 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:3655344763;C:3770081597;G:3599601074;T:3480562617;N:725665	151	151	3655344763	3770081597	3599601074	3480562617	725665	SRX23160972	SRS20111129	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01152	0.00012	0.00021	1e-05	0.99204	0.99963	0.40859	0.47368	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Gastrula	Embryo	Whole Organism	All anatomical structures
29221	29221	SRR27489738	SRX23160971	SRS20111128	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.	polysome fraction	LMW fraction 6hpf replica C	MPRA repC fractions 6 7 6hpf	strain:TLAB\|age:6 hpf\|dev stage:shield\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:43\|replicate:replicate C\|BioSampleModel:Model organism or animal	LMW fraction 6hpf replica C	Library 43	Library 43	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.		OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP483112		BSSE_QGF_206678_HGWLYDSX3_3_MPRA_repC_fractions_6_7_6hpf_ACCTTGGC_GGCCTCAT_S43_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206678_HGWLYDSX3_3_MPRA_repC_fractions_6_7_6hpf_ACCTTGGC_GGCCTCAT_S43_L003_R2_001_MM_1.fastq.gz	fastq fastq	14912162946.0	49378023.0	BSSE QGF 206678 HGWLYDSX3 3 MPRA repC fractions 6 7 6hpf ACCTTGGC GGCCTCAT S43 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:3752402181;C:3897191999;G:3682100517;T:3579734634;N:733615	151	151	3752402181	3897191999	3682100517	3579734634	733615	SRX23160971	SRS20111128	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01301	0.0001	0.00023	0.0	0.99131	0.99963	0.41128	0.44444	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Gastrula	Embryo	Whole Organism	All anatomical structures
29222	29222	SRR27489739	SRX23160970	SRS20111127	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.	polysome fraction	80S fraction 6hpf replica C	MPRA repC fractions 4 5 6hpf	strain:TLAB\|age:6 hpf\|dev stage:shield\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:42\|replicate:replicate C\|BioSampleModel:Model organism or animal	80S fraction 6hpf replica C	Library 42	Library 42	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.		OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP483112		BSSE_QGF_206677_HGWLYDSX3_3_MPRA_repC_fractions_4_5_6hpf_GTTCCAAT_AATTCTGC_S42_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206677_HGWLYDSX3_3_MPRA_repC_fractions_4_5_6hpf_GTTCCAAT_AATTCTGC_S42_L003_R1_001_MM_1.fastq.gz	fastq fastq	16464627468.0	54518634.0	BSSE QGF 206677 HGWLYDSX3 3 MPRA repC fractions 4 5 6hpf GTTCCAAT AATTCTGC S42 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:4169088631;C:4342123158;G:3994621055;T:3957976348;N:818276	151	151	4169088631	4342123158	3994621055	3957976348	818276	SRX23160970	SRS20111127	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01689	8e-05	0.00051	0.0	0.99107	0.99973	0.40071	0.53846	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Gastrula	Embryo	Whole Organism	All anatomical structures
29223	29223	SRR27489740	SRX23160969	SRS20111125	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.	input sample	Total 6hpf replica C	MPRA repC input 6hpf	strain:TLAB\|age:6 hpf\|dev stage:shield\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:41\|replicate:replicate C\|BioSampleModel:Model organism or animal	Total 6hpf replica C	Library 41	Library 41	Total RNA was extracted from input sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.		OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP483112		BSSE_QGF_206676_HGWLYDSX3_3_MPRA_repC_input_6hpf_GCAATGCA_GGAACGTT_S41_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206676_HGWLYDSX3_3_MPRA_repC_input_6hpf_GCAATGCA_GGAACGTT_S41_L003_R2_001_MM_1.fastq.gz	fastq fastq	10859083158.0	35957229.0	BSSE QGF 206676 HGWLYDSX3 3 MPRA repC input 6hpf GCAATGCA GGAACGTT S41 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:2762807814;C:2857106152;G:2613305234;T:2625327901;N:536057	151	151	2762807814	2857106152	2613305234	2625327901	536057	SRX23160969	SRS20111125	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01753	0.0	0.00047	0.0	0.9907	1.0	0.40097		151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Gastrula	Embryo	Whole Organism	All anatomical structures
29224	29224	SRR27489741	SRX23160968	SRS20111133	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.	input sample	Total 4hpf replica A	MPRA repA input 4hpf	strain:TLAB\|age:4 hpf\|dev stage:sphere\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:5\|replicate:replicate A\|BioSampleModel:Model organism or animal	Total 4hpf replica A	Library 5	Library 5	Total RNA was extracted from input sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.		OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP483112		BSSE_QGF_206640_HGWLYDSX3_3_MPRA_repA_input_4hpf_CAAGCTAG_ACATAGCG_S5_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206640_HGWLYDSX3_3_MPRA_repA_input_4hpf_CAAGCTAG_ACATAGCG_S5_L003_R2_001_MM_1.fastq.gz	fastq fastq	13631534966.0	45137533.0	BSSE QGF 206640 HGWLYDSX3 3 MPRA repA input 4hpf CAAGCTAG ACATAGCG S5 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:3486253250;C:3611078376;G:3219396920;T:3314128840;N:677580	151	151	3486253250	3611078376	3219396920	3314128840	677580	SRX23160968	SRS20111133	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.02225	2e-05	0.00066	0.0	0.98975	0.99993	0.40257	0.33333	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Blastula	Embryo	Whole Organism	All anatomical structures
29225	29225	SRR27489742	SRX23160967	SRS20111126	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.	polysome fraction	HMW fraction 4hpf replica C	MPRA repC fractions 8 9 4hpf	strain:TLAB\|age:4 hpf\|dev stage:sphere\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:40\|replicate:replicate C\|BioSampleModel:Model organism or animal	HMW fraction 4hpf replica C	Library 40	Library 40	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.		OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP483112		BSSE_QGF_206675_HGWLYDSX3_3_MPRA_repC_fractions_8_9_4hpf_ATGGCATG_AAGGTACC_S40_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206675_HGWLYDSX3_3_MPRA_repC_fractions_8_9_4hpf_ATGGCATG_AAGGTACC_S40_L003_R2_001_MM_1.fastq.gz	fastq fastq	16854209582.0	55808641.0	BSSE QGF 206675 HGWLYDSX3 3 MPRA repC fractions 8 9 4hpf ATGGCATG AAGGTACC S40 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:4270727222;C:4383022813;G:4143081915;T:4056541855;N:835777	151	151	4270727222	4383022813	4143081915	4056541855	835777	SRX23160967	SRS20111126	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01329	0.00015	0.00029	2e-05	0.99141	0.99953	0.4263	0.47826	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Blastula	Embryo	Whole Organism	All anatomical structures
29226	29226	SRR27489743	SRX23160966	SRS20111124	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.	polysome fraction	LMW fraction 4hpf replica C	MPRA repC fractions 6 7 4hpf	strain:TLAB\|age:4 hpf\|dev stage:sphere\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:39\|replicate:replicate C\|BioSampleModel:Model organism or animal	LMW fraction 4hpf replica C	Library 39	Library 39	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.		OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP483112		BSSE_QGF_206674_HGWLYDSX3_3_MPRA_repC_fractions_6_7_4hpf_GGAGCGTC_GTCCGTGC_S39_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206674_HGWLYDSX3_3_MPRA_repC_fractions_6_7_4hpf_GGAGCGTC_GTCCGTGC_S39_L003_R2_001_MM_1.fastq.gz	fastq fastq	12146174844.0	40219122.0	BSSE QGF 206674 HGWLYDSX3 3 MPRA repC fractions 6 7 4hpf GGAGCGTC GTCCGTGC S39 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:3060215849;C:3176615755;G:3002666854;T:2906066243;N:610143	151	151	3060215849	3176615755	3002666854	2906066243	610143	SRX23160966	SRS20111124	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01309	0.0002	0.00031	0.0	0.99164	0.99939	0.40018	0.57142	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Blastula	Embryo	Whole Organism	All anatomical structures
29227	29227	SRR27489744	SRX23160965	SRS20111123	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.	polysome fraction	80S fraction 4hpf replica C	MPRA repC fractions 4 5 4hpf	strain:TLAB\|age:4 hpf\|dev stage:sphere\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:38\|replicate:replicate C\|BioSampleModel:Model organism or animal	80S fraction 4hpf replica C	Library 38	Library 38	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.		OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP483112		BSSE_QGF_206673_HGWLYDSX3_3_MPRA_repC_fractions_4_5_4hpf_AAGATACT_ACTTACAT_S38_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206673_HGWLYDSX3_3_MPRA_repC_fractions_4_5_4hpf_AAGATACT_ACTTACAT_S38_L003_R1_001_MM_1.fastq.gz	fastq fastq	14100203330.0	46689415.0	BSSE QGF 206673 HGWLYDSX3 3 MPRA repC fractions 4 5 4hpf AAGATACT ACTTACAT S38 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:3544539088;C:3702795841;G:3493240125;T:3358929671;N:698605	151	151	3544539088	3702795841	3493240125	3358929671	698605	SRX23160965	SRS20111123	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01368	0.00016	0.00037	0.0	0.99107	0.99951	0.40864	0.5	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Blastula	Embryo	Whole Organism	All anatomical structures
29228	29228	SRR27489745	SRX23160964	SRS20111120	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.	input sample	Total 4hpf replica C	MPRA repC input 4hpf	strain:TLAB\|age:4 hpf\|dev stage:sphere\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:37\|replicate:replicate C\|BioSampleModel:Model organism or animal	Total 4hpf replica C	Library 37	Library 37	Total RNA was extracted from input sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.		OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP483112		BSSE_QGF_206672_HGWLYDSX3_3_MPRA_repC_input_4hpf_GCGCAAGC_TCACGCCG_S37_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206672_HGWLYDSX3_3_MPRA_repC_input_4hpf_GCGCAAGC_TCACGCCG_S37_L003_R2_001_MM_1.fastq.gz	fastq fastq	10925301792.0	36176496.0	BSSE QGF 206672 HGWLYDSX3 3 MPRA repC input 4hpf GCGCAAGC TCACGCCG S37 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:2802490901;C:2878602103;G:2592316062;T:2651349641;N:543085	151	151	2802490901	2878602103	2592316062	2651349641	543085	SRX23160964	SRS20111120	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.02108	3e-05	0.0006	0.0	0.98981	0.99991	0.42181	0.0	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Blastula	Embryo	Whole Organism	All anatomical structures
29229	29229	SRR27489746	SRX23160963	SRS20111121	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.	polysome fraction	HMW fraction 2hpf replica C	MPRA repC fractions 8 9 2hpf	strain:TLAB\|age:2 hpf\|dev stage:64 cells\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:36\|replicate:replicate C\|BioSampleModel:Model organism or animal	HMW fraction 2hpf replica C	Library 36	Library 36	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.		OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP483112		BSSE_QGF_206671_HGWLYDSX3_3_MPRA_repC_fractions_8_9_2hpf_ATATGGAT_CTGTATTA_S36_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206671_HGWLYDSX3_3_MPRA_repC_fractions_8_9_2hpf_ATATGGAT_CTGTATTA_S36_L003_R2_001_MM_1.fastq.gz	fastq fastq	13085558528.0	43329664.0	BSSE QGF 206671 HGWLYDSX3 3 MPRA repC fractions 8 9 2hpf ATATGGAT CTGTATTA S36 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:3305413622;C:3391845548;G:3249932870;T:3137708503;N:657985	151	151	3305413622	3391845548	3249932870	3137708503	657985	SRX23160963	SRS20111121	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01098	8e-05	0.00025	0.0	0.99216	0.99973	0.4317	0.61538	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Cleavage	Embryo	Whole Organism	All anatomical structures
29230	29230	SRR27489747	SRX23160962	SRS20111119	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.	polysome fraction	LMW fraction 2hpf replica C	MPRA repC fractions 6 7 2hpf	strain:TLAB\|age:2 hpf\|dev stage:64 cells\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:35\|replicate:replicate C\|BioSampleModel:Model organism or animal	LMW fraction 2hpf replica C	Library 35	Library 35	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.		OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP483112		BSSE_QGF_206670_HGWLYDSX3_3_MPRA_repC_fractions_6_7_2hpf_CGGACAAC_TCCGGATT_S35_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206670_HGWLYDSX3_3_MPRA_repC_fractions_6_7_2hpf_CGGACAAC_TCCGGATT_S35_L003_R1_001_MM_1.fastq.gz	fastq fastq	16647721914.0	55124907.0	BSSE QGF 206670 HGWLYDSX3 3 MPRA repC fractions 6 7 2hpf CGGACAAC TCCGGATT S35 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:4231542934;C:4348688006;G:4050131444;T:4016534422;N:825108	151	151	4231542934	4348688006	4050131444	4016534422	825108	SRX23160962	SRS20111119	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01514	0.00017	0.00035	3e-05	0.99109	0.99955	0.4372	0.30434	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Cleavage	Embryo	Whole Organism	All anatomical structures
29231	29231	SRR27489748	SRX23160961	SRS20111118	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.	polysome fraction	80S fraction 2hpf replica C	MPRA repC fractions 4 5 2hpf	strain:TLAB\|age:2 hpf\|dev stage:64 cells\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:34\|replicate:replicate C\|BioSampleModel:Model organism or animal	80S fraction 2hpf replica C	Library 34	Library 34	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.		OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP483112		BSSE_QGF_206669_HGWLYDSX3_3_MPRA_repC_fractions_4_5_2hpf_TAAGTGGT_CTTAAGCC_S34_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206669_HGWLYDSX3_3_MPRA_repC_fractions_4_5_2hpf_TAAGTGGT_CTTAAGCC_S34_L003_R2_001_MM_1.fastq.gz	fastq fastq	15431181052.0	51096626.0	BSSE QGF 206669 HGWLYDSX3 3 MPRA repC fractions 4 5 2hpf TAAGTGGT CTTAAGCC S34 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:3856018869;C:4036338306;G:3877988553;T:3660059325;N:775999	151	151	3856018869	4036338306	3877988553	3660059325	775999	SRX23160961	SRS20111118	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01114	8e-05	0.00028	0.0	0.99192	0.99975	0.42956	0.5	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Cleavage	Embryo	Whole Organism	All anatomical structures
29232	29232	SRR27489749	SRX23160960	SRS20111117	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.	input sample	Total 2hpf replica C	MPRA repC input 2hpf	strain:TLAB\|age:2 hpf\|dev stage:64 cells\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:33\|replicate:replicate C\|BioSampleModel:Model organism or animal	Total 2hpf replica C	Library 33	Library 33	Total RNA was extracted from input sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.		OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP483112		BSSE_QGF_206668_HGWLYDSX3_3_MPRA_repC_input_2hpf_CTACGACA_GAGTCCAA_S33_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206668_HGWLYDSX3_3_MPRA_repC_input_2hpf_CTACGACA_GAGTCCAA_S33_L003_R1_001_MM_1.fastq.gz	fastq fastq	11771229160.0	38977580.0	BSSE QGF 206668 HGWLYDSX3 3 MPRA repC input 2hpf CTACGACA GAGTCCAA S33 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:2999574420;C:3115525474;G:2806539264;T:2849003922;N:586080	151	151	2999574420	3115525474	2806539264	2849003922	586080	SRX23160960	SRS20111117	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01997	2e-05	0.00054	0.0	0.99022	0.99993	0.41853	0.33333	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Cleavage	Embryo	Whole Organism	All anatomical structures
29233	29233	SRR27489750	SRX23160959	SRS20111116	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.	polysome fraction	HMW fraction 10hpf replica B	MPRA repB fractions 8 9 10hpf	strain:TLAB\|age:10 hpf\|dev stage:bud\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:32\|replicate:replicate B\|BioSampleModel:Model organism or animal	HMW fraction 10hpf replica B	Library 32	Library 32	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.		OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP483112		BSSE_QGF_206667_HGWLYDSX3_3_MPRA_repB_fractions_8_9_10hpf_TCGTAGTG_AGACTTGG_S32_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206667_HGWLYDSX3_3_MPRA_repB_fractions_8_9_10hpf_TCGTAGTG_AGACTTGG_S32_L003_R2_001_MM_1.fastq.gz	fastq fastq	12683073766.0	41996933.0	BSSE QGF 206667 HGWLYDSX3 3 MPRA repB fractions 8 9 10hpf TCGTAGTG AGACTTGG S32 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:3165850297;C:3286094227;G:3205853472;T:3024640146;N:635624	151	151	3165850297	3286094227	3205853472	3024640146	635624	SRX23160959	SRS20111116	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.00973	0.00093	0.00036	0.00015	0.99265	0.99819	0.4701	0.61111	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Gastrula	Embryo	Whole Organism	All anatomical structures
29234	29234	SRR27489751	SRX23160958	SRS20111115	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.	polysome fraction	LMW fraction 10hpf replica B	MPRA repB fractions 6 7 10hpf	strain:TLAB\|age:10 hpf\|dev stage:bud\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:31\|replicate:replicate B\|BioSampleModel:Model organism or animal	LMW fraction 10hpf replica B	Library 31	Library 31	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.		OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP483112		BSSE_QGF_206666_HGWLYDSX3_3_MPRA_repB_fractions_6_7_10hpf_GATTCTGC_GACGAGAG_S31_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206666_HGWLYDSX3_3_MPRA_repB_fractions_6_7_10hpf_GATTCTGC_GACGAGAG_S31_L003_R2_001_MM_1.fastq.gz	fastq fastq	11187950286.0	37046193.0	BSSE QGF 206666 HGWLYDSX3 3 MPRA repB fractions 6 7 10hpf GATTCTGC GACGAGAG S31 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:2805602272;C:2927866458;G:2773076846;T:2680845208;N:559502	151	151	2805602272	2927866458	2773076846	2680845208	559502	SRX23160958	SRS20111115	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01142	0.0002	0.00018	2e-05	0.99243	0.99943	0.45894	0.54838	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Gastrula	Embryo	Whole Organism	All anatomical structures
29235	29235	SRR27489752	SRX23160957	SRS20111114	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.	polysome fraction	HMW fraction 2hpf replica A	MPRA repA fractions 8 9 2hpf	strain:TLAB\|age:2 hpf\|dev stage:64 cells\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:4\|replicate:replicate A\|BioSampleModel:Model organism or animal	HMW fraction 2hpf replica A	Library 4	Library 4	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.		OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP483112		BSSE_QGF_206639_HGWLYDSX3_3_MPRA_repA_fractions_8_9_2hpf_GCTTGTCA_GAACATAC_S4_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206639_HGWLYDSX3_3_MPRA_repA_fractions_8_9_2hpf_GCTTGTCA_GAACATAC_S4_L003_R1_001_MM_1.fastq.gz	fastq fastq	12108626278.0	40094789.0	BSSE QGF 206639 HGWLYDSX3 3 MPRA repA fractions 8 9 2hpf GCTTGTCA GAACATAC S4 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:3079403604;C:3149095123;G:2953175005;T:2926352278;N:600268	151	151	3079403604	3149095123	2953175005	2926352278	600268	SRX23160957	SRS20111114	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.014	5e-05	0.00032	0.0	0.99137	0.99987	0.45127	0.28571	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Cleavage	Embryo	Whole Organism	All anatomical structures
29236	29236	SRR27489753	SRX23160956	SRS20111113	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.	polysome fraction	80S fraction 10hpf replica B	MPRA repB fractions 4 5 10hpf	strain:TLAB\|age:10 hpf\|dev stage:bud\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:30\|replicate:replicate B\|BioSampleModel:Model organism or animal	80S fraction 10hpf replica B	Library 30	Library 30	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.		OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP483112		BSSE_QGF_206665_HGWLYDSX3_3_MPRA_repB_fractions_4_5_10hpf_AGCCTCAT_AGTAGAGA_S30_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206665_HGWLYDSX3_3_MPRA_repB_fractions_4_5_10hpf_AGCCTCAT_AGTAGAGA_S30_L003_R2_001_MM_1.fastq.gz	fastq fastq	15465851256.0	51211428.0	BSSE QGF 206665 HGWLYDSX3 3 MPRA repB fractions 4 5 10hpf AGCCTCAT AGTAGAGA S30 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:3889753740;C:4075740540;G:3791174754;T:3708409198;N:773024	151	151	3889753740	4075740540	3791174754	3708409198	773024	SRX23160956	SRS20111113	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01609	0.00014	0.0003	3e-05	0.99139	0.99959	0.4335	0.5	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Gastrula	Embryo	Whole Organism	All anatomical structures
29237	29237	SRR27489754	SRX23160955	SRS20111112	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.	input sample	Total 10hpf replica B	MPRA repB input 10hpf	strain:TLAB\|age:10 hpf\|dev stage:bud\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:29\|replicate:replicate B\|BioSampleModel:Model organism or animal	Total 10hpf replica B	Library 29	Library 29	Total RNA was extracted from input sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.		OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP483112		BSSE_QGF_206664_HGWLYDSX3_3_MPRA_repB_input_10hpf_CGTTAGAA_TTCAGGTC_S29_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206664_HGWLYDSX3_3_MPRA_repB_input_10hpf_CGTTAGAA_TTCAGGTC_S29_L003_R2_001_MM_1.fastq.gz	fastq fastq	12592035866.0	41695483.0	BSSE QGF 206664 HGWLYDSX3 3 MPRA repB input 10hpf CGTTAGAA TTCAGGTC S29 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:3220865280;C:3326103488;G:2978281202;T:3066156448;N:629448	151	151	3220865280	3326103488	2978281202	3066156448	629448	SRX23160955	SRS20111112	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.02168	1e-05	0.0006	0.0	0.98993	0.99997	0.41273	1.0	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Gastrula	Embryo	Whole Organism	All anatomical structures
29238	29238	SRR27489755	SRX23160954	SRS20111122	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.	polysome fraction	HMW fraction 6hpf replica B	MPRA repB fractions 8 9 6hpf	strain:TLAB\|age:6 hpf\|dev stage:shield\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:28\|replicate:replicate B\|BioSampleModel:Model organism or animal	HMW fraction 6hpf replica B	Library 28	Library 28	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.		OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP483112		BSSE_QGF_206663_HGWLYDSX3_3_MPRA_repB_fractions_8_9_6hpf_TACCGAGG_CCTGAACT_S28_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206663_HGWLYDSX3_3_MPRA_repB_fractions_8_9_6hpf_TACCGAGG_CCTGAACT_S28_L003_R2_001_MM_1.fastq.gz	fastq fastq	12606651156.0	41743878.0	BSSE QGF 206663 HGWLYDSX3 3 MPRA repB fractions 8 9 6hpf TACCGAGG CCTGAACT S28 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:3184687427;C:3283680489;G:3107570485;T:3030085619;N:627136	151	151	3184687427	3283680489	3107570485	3030085619	627136	SRX23160954	SRS20111122	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01219	7e-05	0.00028	0.0	0.99182	0.99977	0.42217	0.45454	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Gastrula	Embryo	Whole Organism	All anatomical structures
29239	29239	SRR27489756	SRX23160953	SRS20111110	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.	polysome fraction	LMW fraction 6hpf replica B	MPRA repB fractions 6 7 6hpf	strain:TLAB\|age:6 hpf\|dev stage:shield\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:27\|replicate:replicate B\|BioSampleModel:Model organism or animal	LMW fraction 6hpf replica B	Library 27	Library 27	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.		OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP483112		BSSE_QGF_206662_HGWLYDSX3_3_MPRA_repB_fractions_6_7_6hpf_AATGCCTC_TCGATCCA_S27_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206662_HGWLYDSX3_3_MPRA_repB_fractions_6_7_6hpf_AATGCCTC_TCGATCCA_S27_L003_R1_001_MM_1.fastq.gz	fastq fastq	13738263880.0	45490940.0	BSSE QGF 206662 HGWLYDSX3 3 MPRA repB fractions 6 7 6hpf AATGCCTC TCGATCCA S27 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:3463772316;C:3608023656;G:3363805269;T:3301974573;N:688066	151	151	3463772316	3608023656	3363805269	3301974573	688066	SRX23160953	SRS20111110	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01443	0.00014	0.00028	1e-05	0.99117	0.99957	0.38916	0.45833	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Gastrula	Embryo	Whole Organism	All anatomical structures
29240	29240	SRR27489757	SRX23160952	SRS20111111	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.	polysome fraction	80S fraction 6hpf replica B	MPRA repB fractions 4 5 6hpf	strain:TLAB\|age:6 hpf\|dev stage:shield\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:26\|replicate:replicate B\|BioSampleModel:Model organism or animal	80S fraction 6hpf replica B	Library 26	Library 26	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.		OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP483112		BSSE_QGF_206661_HGWLYDSX3_3_MPRA_repB_fractions_4_5_6hpf_GGCATTCT_CTAGCTTG_S26_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206661_HGWLYDSX3_3_MPRA_repB_fractions_4_5_6hpf_GGCATTCT_CTAGCTTG_S26_L003_R1_001_MM_1.fastq.gz	fastq fastq	10624262152.0	35179676.0	BSSE QGF 206661 HGWLYDSX3 3 MPRA repB fractions 4 5 6hpf GGCATTCT CTAGCTTG S26 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:2680084455;C:2804915710;G:2592024460;T:2546707250;N:530277	151	151	2680084455	2804915710	2592024460	2546707250	530277	SRX23160952	SRS20111111	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01636	0.00013	0.00046	0.0	0.99088	0.99959	0.39222	0.40909	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Gastrula	Embryo	Whole Organism	All anatomical structures
29241	29241	SRR27489758	SRX23160951	SRS20111109	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.	input sample	Total 6hpf replica B	MPRA repB input 6hpf	strain:TLAB\|age:6 hpf\|dev stage:shield\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:25\|replicate:replicate B\|BioSampleModel:Model organism or animal	Total 6hpf replica B	Library 25	Library 25	Total RNA was extracted from input sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.		OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP483112		BSSE_QGF_206660_HGWLYDSX3_3_MPRA_repB_input_6hpf_TTACAGGA_TGACAAGC_S25_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206660_HGWLYDSX3_3_MPRA_repB_input_6hpf_TTACAGGA_TGACAAGC_S25_L003_R2_001_MM_1.fastq.gz	fastq fastq	10153888998.0	33622149.0	BSSE QGF 206660 HGWLYDSX3 3 MPRA repB input 6hpf TTACAGGA TGACAAGC S25 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:2587160061;C:2673241688;G:2432503358;T:2460478928;N:504963	151	151	2587160061	2673241688	2432503358	2460478928	504963	SRX23160951	SRS20111109	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01911	2e-05	0.00061	0.0	0.99064	0.99995	0.42802	0.0	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Gastrula	Embryo	Whole Organism	All anatomical structures
29242	29242	SRR27489759	SRX23160950	SRS20111107	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.	polysome fraction	HMW fraction 4hpf replica B	MPRA repB fractions 8 9 4hpf	strain:TLAB\|age:4 hpf\|dev stage:sphere\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:24\|replicate:replicate B\|BioSampleModel:Model organism or animal	HMW fraction 4hpf replica B	Library 24	Library 24	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.		OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP483112		BSSE_QGF_206659_HGWLYDSX3_3_MPRA_repB_fractions_8_9_4hpf_CCGTGAAG_CAGTGGAT_S24_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206659_HGWLYDSX3_3_MPRA_repB_fractions_8_9_4hpf_CCGTGAAG_CAGTGGAT_S24_L003_R2_001_MM_1.fastq.gz	fastq fastq	11600767978.0	38413139.0	BSSE QGF 206659 HGWLYDSX3 3 MPRA repB fractions 8 9 4hpf CCGTGAAG CAGTGGAT S24 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:2943303855;C:3024500200;G:2833306086;T:2799077405;N:580432	151	151	2943303855	3024500200	2833306086	2799077405	580432	SRX23160950	SRS20111107	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01371	0.00013	0.00031	1e-05	0.99143	0.99955	0.41912	0.5909	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Blastula	Embryo	Whole Organism	All anatomical structures
29243	29243	SRR27489760	SRX23160949	SRS20111106	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.	polysome fraction	LMW fraction 4hpf replica B	MPRA repB fractions 6 7 4hpf	strain:TLAB\|age:4 hpf\|dev stage:sphere\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:23\|replicate:replicate B\|BioSampleModel:Model organism or animal	LMW fraction 4hpf replica B	Library 23	Library 23	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.		OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP483112		BSSE_QGF_206658_HGWLYDSX3_3_MPRA_repB_fractions_6_7_4hpf_CTTGGTAT_CCAAGTCC_S23_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206658_HGWLYDSX3_3_MPRA_repB_fractions_6_7_4hpf_CTTGGTAT_CCAAGTCC_S23_L003_R2_001_MM_1.fastq.gz	fastq fastq	13216553444.0	43763422.0	BSSE QGF 206658 HGWLYDSX3 3 MPRA repB fractions 6 7 4hpf CTTGGTAT CCAAGTCC S23 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:3339016083;C:3457419680;G:3233764657;T:3185687490;N:665534	151	151	3339016083	3457419680	3233764657	3185687490	665534	SRX23160949	SRS20111106	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01431	0.00024	0.00034	1e-05	0.99135	0.99924	0.41915	0.45238	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Blastula	Embryo	Whole Organism	All anatomical structures
29244	29244	SRR27489761	SRX23160948	SRS20111105	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.	polysome fraction	80S fraction 4hpf replica B	MPRA repB fractions 4 5 4hpf	strain:TLAB\|age:4 hpf\|dev stage:sphere\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:22\|replicate:replicate B\|BioSampleModel:Model organism or animal	80S fraction 4hpf replica B	Library 22	Library 22	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.		OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP483112		BSSE_QGF_206657_HGWLYDSX3_3_MPRA_repB_fractions_4_5_4hpf_ATGAGGCC_GTTAATTG_S22_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206657_HGWLYDSX3_3_MPRA_repB_fractions_4_5_4hpf_ATGAGGCC_GTTAATTG_S22_L003_R2_001_MM_1.fastq.gz	fastq fastq	11938250562.0	39530631.0	BSSE QGF 206657 HGWLYDSX3 3 MPRA repB fractions 4 5 4hpf ATGAGGCC GTTAATTG S22 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:3040684418;C:3144238599;G:2873359599;T:2879374531;N:593415	151	151	3040684418	3144238599	2873359599	2879374531	593415	SRX23160948	SRS20111105	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.0185	8e-05	0.00056	0.0	0.9903	0.99969	0.4376	0.4	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Blastula	Embryo	Whole Organism	All anatomical structures
29245	29245	SRR27489762	SRX23160947	SRS20111104	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.	input sample	Total 4hpf replica B	MPRA repB input 4hpf	strain:TLAB\|age:4 hpf\|dev stage:sphere\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:21\|replicate:replicate B\|BioSampleModel:Model organism or animal	Total 4hpf replica B	Library 21	Library 21	Total RNA was extracted from input sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.		OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP483112		BSSE_QGF_206656_HGWLYDSX3_3_MPRA_repB_input_4hpf_GCAGAATT_ACCGGCCA_S21_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206656_HGWLYDSX3_3_MPRA_repB_input_4hpf_GCAGAATT_ACCGGCCA_S21_L003_R1_001_MM_1.fastq.gz	fastq fastq	14482326346.0	47954723.0	BSSE QGF 206656 HGWLYDSX3 3 MPRA repB input 4hpf GCAGAATT ACCGGCCA S21 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:3697691325;C:3838972714;G:3432418300;T:3512522230;N:721777	151	151	3697691325	3838972714	3432418300	3512522230	721777	SRX23160947	SRS20111104	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.0211	2e-05	0.00055	0.0	0.9903	0.99993	0.42543	0.0	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Blastula	Embryo	Whole Organism	All anatomical structures
29246	29246	SRR27489763	SRX23160946	SRS20111108	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.	polysome fraction	LMW fraction 2hpf replica A	MPRA repA fractions 6 7 2hpf	strain:TLAB\|age:2 hpf\|dev stage:64 cells\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:3\|replicate:replicate A\|BioSampleModel:Model organism or animal	LMW fraction 2hpf replica A	Library 3	Library 3	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.		OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP483112		BSSE_QGF_206638_HGWLYDSX3_3_MPRA_repA_fractions_6_7_2hpf_ATCCACTG_AGGTGCGT_S3_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206638_HGWLYDSX3_3_MPRA_repA_fractions_6_7_2hpf_ATCCACTG_AGGTGCGT_S3_L003_R1_001_MM_1.fastq.gz	fastq fastq	12524202136.0	41470868.0	BSSE QGF 206638 HGWLYDSX3 3 MPRA repA fractions 6 7 2hpf ATCCACTG AGGTGCGT S3 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:3168466372;C:3269998328;G:3075956662;T:3009160932;N:619842	151	151	3168466372	3269998328	3075956662	3009160932	619842	SRX23160946	SRS20111108	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01351	7e-05	0.00028	0.0	0.99168	0.99977	0.43472	0.54545	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Cleavage	Embryo	Whole Organism	All anatomical structures
29247	29247	SRR27489764	SRX23160945	SRS20111103	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.	polysome fraction	HMW fraction 2hpf replica B	MPRA repB fractions 8 9 2hpf	strain:TLAB\|age:2 hpf\|dev stage:64 cells\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:20\|replicate:replicate B\|BioSampleModel:Model organism or animal	HMW fraction 2hpf replica B	Library 20	Library 20	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.		OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP483112		BSSE_QGF_206655_HGWLYDSX3_3_MPRA_repB_fractions_8_9_2hpf_AACGTTCC_GGAGTACT_S20_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206655_HGWLYDSX3_3_MPRA_repB_fractions_8_9_2hpf_AACGTTCC_GGAGTACT_S20_L003_R2_001_MM_1.fastq.gz	fastq fastq	12514444214.0	41438557.0	BSSE QGF 206655 HGWLYDSX3 3 MPRA repB fractions 8 9 2hpf AACGTTCC GGAGTACT S20 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:3174354240;C:3246812350;G:3082021359;T:3010633962;N:622303	151	151	3174354240	3246812350	3082021359	3010633962	622303	SRX23160945	SRS20111103	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01121	0.00016	0.00027	1e-05	0.99204	0.99953	0.43533	0.5	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Cleavage	Embryo	Whole Organism	All anatomical structures
29248	29248	SRR27489765	SRX23160944	SRS20111102	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.	polysome fraction	LMW fraction 2hpf replica B	MPRA repB fractions 6 7 2hpf	strain:TLAB\|age:2 hpf\|dev stage:64 cells\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:19\|replicate:replicate B\|BioSampleModel:Model organism or animal	LMW fraction 2hpf replica B	Library 19	Library 19	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.		OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP483112		BSSE_QGF_206654_HGWLYDSX3_3_MPRA_repB_fractions_6_7_2hpf_GGTACCTT_AAGACGTC_S19_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206654_HGWLYDSX3_3_MPRA_repB_fractions_6_7_2hpf_GGTACCTT_AAGACGTC_S19_L003_R1_001_MM_1.fastq.gz	fastq fastq	16535129670.0	54752085.0	BSSE QGF 206654 HGWLYDSX3 3 MPRA repB fractions 6 7 2hpf GGTACCTT AAGACGTC S19 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:4184643114;C:4312135767;G:4051628900;T:3985895468;N:826421	151	151	4184643114	4312135767	4051628900	3985895468	826421	SRX23160944	SRS20111102	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01416	0.00017	0.00031	1e-05	0.9917	0.99941	0.40732	0.6	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Cleavage	Embryo	Whole Organism	All anatomical structures
29249	29249	SRR27489766	SRX23160943	SRS20111101	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.	polysome fraction	80S fraction 2hpf replica B	MPRA repB fractions 4 5 2hpf	strain:TLAB\|age:2 hpf\|dev stage:64 cells\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:18\|replicate:replicate B\|BioSampleModel:Model organism or animal	80S fraction 2hpf replica B	Library 18	Library 18	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.		OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP483112		BSSE_QGF_206653_HGWLYDSX3_3_MPRA_repB_fractions_4_5_2hpf_GCACGGAC_GTCTCGCA_S18_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206653_HGWLYDSX3_3_MPRA_repB_fractions_4_5_2hpf_GCACGGAC_GTCTCGCA_S18_L003_R2_001_MM_1.fastq.gz	fastq fastq	12692870042.0	42029371.0	BSSE QGF 206653 HGWLYDSX3 3 MPRA repB fractions 4 5 2hpf GCACGGAC GTCTCGCA S18 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:3179006274;C:3325152682;G:3173386021;T:3014687781;N:637284	151	151	3179006274	3325152682	3173386021	3014687781	637284	SRX23160943	SRS20111101	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01199	8e-05	0.0003	1e-05	0.99145	0.99979	0.40897	0.36363	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Cleavage	Embryo	Whole Organism	All anatomical structures
29250	29250	SRR27489767	SRX23160942	SRS20111100	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.	input sample	Total 2hpf replica B	MPRA repB input 2hpf	strain:TLAB\|age:2 hpf\|dev stage:64 cells\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:17\|replicate:replicate B\|BioSampleModel:Model organism or animal	Total 2hpf replica B	Library 17	Library 17	Total RNA was extracted from input sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.		OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP483112		BSSE_QGF_206652_HGWLYDSX3_3_MPRA_repB_input_2hpf_ATGTAAGT_ACTCTATG_S17_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206652_HGWLYDSX3_3_MPRA_repB_input_2hpf_ATGTAAGT_ACTCTATG_S17_L003_R2_001_MM_1.fastq.gz	fastq fastq	13169436008.0	43607404.0	BSSE QGF 206652 HGWLYDSX3 3 MPRA repB input 2hpf ATGTAAGT ACTCTATG S17 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:3341908647;C:3485072739;G:3171200836;T:3170595031;N:658755	151	151	3341908647	3485072739	3171200836	3170595031	658755	SRX23160942	SRS20111100	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01868	5e-05	0.0006	0.0	0.99038	0.99983	0.41955	0.125	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Cleavage	Embryo	Whole Organism	All anatomical structures
29251	29251	SRR27489768	SRX23160941	SRS20111099	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.	polysome fraction	HMW fraction 10hpf replica A	MPRA repA fractions 8 9 10hpf	strain:TLAB\|age:10 hpf\|dev stage:bud\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:16\|replicate:replicate A\|BioSampleModel:Model organism or animal	HMW fraction 10hpf replica A	Library 16	Library 16	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.		OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP483112		BSSE_QGF_206651_HGWLYDSX3_3_MPRA_repA_fractions_8_9_10hpf_CGGCGTGA_GCGCCTGT_S16_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206651_HGWLYDSX3_3_MPRA_repA_fractions_8_9_10hpf_CGGCGTGA_GCGCCTGT_S16_L003_R2_001_MM_1.fastq.gz	fastq fastq	13501095730.0	44705615.0	BSSE QGF 206651 HGWLYDSX3 3 MPRA repA fractions 8 9 10hpf CGGCGTGA GCGCCTGT S16 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:3386778587;C:3499255836;G:3382745292;T:3231634315;N:681700	151	151	3386778587	3499255836	3382745292	3231634315	681700	SRX23160941	SRS20111099	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.00829	0.00016	0.00011	0.0	0.99265	0.99949	0.49527	0.48275	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Gastrula	Embryo	Whole Organism	All anatomical structures
29252	29252	SRR27489769	SRX23160940	SRS20111096	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.	polysome fraction	LMW fraction 10hpf replica A	MPRA repA fractions 6 7 10hpf	strain:TLAB\|age:10 hpf\|dev stage:bud\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:15\|replicate:replicate A\|BioSampleModel:Model organism or animal	LMW fraction 10hpf replica A	Library 15	Library 15	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.		OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP483112		BSSE_QGF_206650_HGWLYDSX3_3_MPRA_repA_fractions_6_7_10hpf_TAATACAG_ATATTCAC_S15_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206650_HGWLYDSX3_3_MPRA_repA_fractions_6_7_10hpf_TAATACAG_ATATTCAC_S15_L003_R2_001_MM_1.fastq.gz	fastq fastq	13046767232.0	43201216.0	BSSE QGF 206650 HGWLYDSX3 3 MPRA repA fractions 6 7 10hpf TAATACAG ATATTCAC S15 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:3290688159;C:3400409529;G:3214905336;T:3140115501;N:648707	151	151	3290688159	3400409529	3214905336	3140115501	648707	SRX23160940	SRS20111096	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01093	0.0001	0.00011	0.0	0.99249	0.99967	0.43443	0.77777	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Gastrula	Embryo	Whole Organism	All anatomical structures
29253	29253	SRR27489770	SRX23160939	SRS20111097	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.	polysome fraction	80S fraction 10hpf replica A	MPRA repA fractions 4 5 10hpf	strain:TLAB\|age:10 hpf\|dev stage:bud\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:14\|replicate:replicate A\|BioSampleModel:Model organism or animal	80S fraction 10hpf replica A	Library 14	Library 14	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.		OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP483112		BSSE_QGF_206649_HGWLYDSX3_3_MPRA_repA_fractions_4_5_10hpf_AATCCGGA_CTACAGTT_S14_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206649_HGWLYDSX3_3_MPRA_repA_fractions_4_5_10hpf_AATCCGGA_CTACAGTT_S14_L003_R2_001_MM_1.fastq.gz	fastq fastq	13986764580.0	46313790.0	BSSE QGF 206649 HGWLYDSX3 3 MPRA repA fractions 4 5 10hpf AATCCGGA CTACAGTT S14 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:3536884918;C:3676313944;G:3410122661;T:3362749616;N:693441	151	151	3536884918	3676313944	3410122661	3362749616	693441	SRX23160939	SRS20111097	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01503	7e-05	0.00035	0.0	0.99141	0.99983	0.43326	0.77777	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Gastrula	Embryo	Whole Organism	All anatomical structures
29254	29254	SRR27489771	SRX23160938	SRS20111095	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.	input sample	Total 10hpf replica A	MPRA repA input 10hpf	strain:TLAB\|age:10 hpf\|dev stage:bud\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:13\|replicate:replicate A\|BioSampleModel:Model organism or animal	Total 10hpf replica A	Library 13	Library 13	Total RNA was extracted from input sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.		OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP483112		BSSE_QGF_206648_HGWLYDSX3_3_MPRA_repA_input_10hpf_GGCTTAAG_TCGTGACC_S13_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206648_HGWLYDSX3_3_MPRA_repA_input_10hpf_GGCTTAAG_TCGTGACC_S13_L003_R2_001_MM_1.fastq.gz	fastq fastq	11263507666.0	37296383.0	BSSE QGF 206648 HGWLYDSX3 3 MPRA repA input 10hpf GGCTTAAG TCGTGACC S13 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:2881851385;C:2968960112;G:2663338223;T:2748794775;N:563171	151	151	2881851385	2968960112	2663338223	2748794775	563171	SRX23160938	SRS20111095	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.02096	1e-05	0.00058	0.0	0.99022	0.99997	0.43837	1.0	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Gastrula	Embryo	Whole Organism	All anatomical structures
29255	29255	SRR27489772	SRX23160937	SRS20111098	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.	polysome fraction	HMW fraction 6hpf replica A	MPRA repA fractions 8 9 6hpf	strain:TLAB\|age:6 hpf\|dev stage:shield\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:12\|replicate:replicate A\|BioSampleModel:Model organism or animal	HMW fraction 6hpf replica A	Library 12	Library 12	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.		OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP483112		BSSE_QGF_206647_HGWLYDSX3_3_MPRA_repA_fractions_8_9_6hpf_TTGGACTC_GGAAGCAG_S12_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206647_HGWLYDSX3_3_MPRA_repA_fractions_8_9_6hpf_TTGGACTC_GGAAGCAG_S12_L003_R2_001_MM_1.fastq.gz	fastq fastq	14724761980.0	48757490.0	BSSE QGF 206647 HGWLYDSX3 3 MPRA repA fractions 8 9 6hpf TTGGACTC GGAAGCAG S12 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:3711442998;C:3830334531;G:3642299006;T:3539948266;N:737179	151	151	3711442998	3830334531	3642299006	3539948266	737179	SRX23160937	SRS20111098	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01161	8e-05	0.0002	1e-05	0.99214	0.99985	0.4529	0.3	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Gastrula	Embryo	Whole Organism	All anatomical structures
29256	29256	SRR27489773	SRX23160936	SRS20111094	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.	polysome fraction	LMW fraction 6hpf replica A	MPRA repA fractions 6 7 6hpf	strain:TLAB\|age:6 hpf\|dev stage:shield\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:11\|replicate:replicate A\|BioSampleModel:Model organism or animal	LMW fraction 6hpf replica A	Library 11	Library 11	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.		OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP483112		BSSE_QGF_206646_HGWLYDSX3_3_MPRA_repA_fractions_6_7_6hpf_CCAAGTCT_AAGGATGA_S11_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206646_HGWLYDSX3_3_MPRA_repA_fractions_6_7_6hpf_CCAAGTCT_AAGGATGA_S11_L003_R2_001_MM_1.fastq.gz	fastq fastq	16713361312.0	55342256.0	BSSE QGF 206646 HGWLYDSX3 3 MPRA repA fractions 6 7 6hpf CCAAGTCT AAGGATGA S11 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:4183339886;C:4365661507;G:4181177026;T:3982339731;N:843162	151	151	4183339886	4365661507	4181177026	3982339731	843162	SRX23160936	SRS20111094	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01132	0.00011	0.00024	0.0	0.99174	0.99965	0.40968	0.47368	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Gastrula	Embryo	Whole Organism	All anatomical structures
29257	29257	SRR27489774	SRX23160935	SRS20111093	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.	polysome fraction	80S fraction 2hpf replica A	MPRA repA fractions 4 5 2hpf	strain:TLAB\|age:2 hpf\|dev stage:64 cells\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:2\|replicate:replicate A\|BioSampleModel:Model organism or animal	80S fraction 2hpf replica A	Library 2	Library 2	Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.		OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP483112		BSSE_QGF_206637_HGWLYDSX3_3_MPRA_repA_fractions_4_5_2hpf_TTGGACTT_TATGAGTA_S2_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206637_HGWLYDSX3_3_MPRA_repA_fractions_4_5_2hpf_TTGGACTT_TATGAGTA_S2_L003_R2_001_MM_1.fastq.gz	fastq fastq	16111078182.0	53347941.0	BSSE QGF 206637 HGWLYDSX3 3 MPRA repA fractions 4 5 2hpf TTGGACTT TATGAGTA S2 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:4069536779;C:4222816450;G:3957789955;T:3860129964;N:805034	151	151	4069536779	4222816450	3957789955	3860129964	805034	SRX23160935	SRS20111093	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.01511	5e-05	0.00034	0.0	0.99135	0.99985	0.41564	0.42857	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Cleavage	Embryo	Whole Organism	All anatomical structures
29258	29258	SRR27489775	SRX23160934	SRS20111092	SRP483112	PRJNA1056276	five prime UTR MPRA during early zebrafish embryogenesis	PRJNA1056276	Other	The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.	input sample	Total 2hpf replica A	MPRA repA input 2hpf	strain:TLAB\|age:2 hpf\|dev stage:64 cells\|collection date:2022 05 16\|geo loc name:Switzerland: Basel\|sex:not applicable\|tissue:whole embryo\|biomaterial provider:Schier lab\|collected by:Madalena M. Reimao Pinto\|genotype:WT\|growth protocol:E3 buffer standard conditions\|sample type:100 embryos\|sample number:1\|replicate:replicate A\|BioSampleModel:Model organism or animal	Total 2hpf replica A	Library 1	Library 1	Total RNA was extracted from input sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.		OTHER	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP483112		BSSE_QGF_206636_HGWLYDSX3_3_MPRA_repA_input_2hpf_GGACTTGG_CGCAGACG_S1_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206636_HGWLYDSX3_3_MPRA_repA_input_2hpf_GGACTTGG_CGCAGACG_S1_L003_R2_001_MM_1.fastq.gz	fastq fastq	9769305890.0	32348695.0	BSSE QGF 206636 HGWLYDSX3 3 MPRA repA input 2hpf GGACTTGG CGCAGACG S1 L003 R1 001 MM 1.fastq.gz	0:151 1:151	A:2477269774;C:2598109179;G:2338444856;T:2354997596;N:484485	151	151	2477269774	2598109179	2338444856	2354997596	484485	SRX23160934	SRS20111092	SRA1775336	University of Basel\|Biozentrum Basel	University of Basel	2	0.0205	4e-05	0.00059	0.0	0.99013	0.99987	0.41957	0.33333	151	151	T	T	mates < 9% mapping rate	illumina	novaseq_era	5prime	other	unknown	bulk	unknown	unknown	Switzerland	2024-01-11	Cleavage	Embryo	Whole Organism	All anatomical structures
30599	30599	SRR27865238	SRX23527802	SRS20377517	SRP488009	PRJNA1073183	Transcriptome of SEMA5A MT ATP6 ZNF662 and KDM4C in zebrafish embryos	PRJNA1073183	Other			Embryos transcriptome	Embryos transcriptome	strain:AB\|breed:Egg water\|age:5hpf\|dev stage:5hpf\|sex:not applicable\|tissue:Embryos\|collection date:not applicable\|geo loc name:not applicable\|BioSampleModel:Model organism or animal	con MO	6	6	con MO		RNA-Seq	TRANSCRIPTOMIC	RT-PCR	SINGLE	ILLUMINA	Illumina HiSeq 4000		SRP488009		con-KDM_1.fq.gz con-KDM_2.fq.gz	fastq fastq	7088132100.0	23627107.0	con KDM 1.fq.gz	0:150 1:150	A:1893419600;C:1649526065;G:1662549202;T:1882459200;N:178033	150	150	1893419600	1649526065	1662549202	1882459200	178033	SRX23527802	SRS20377517	SRA1797184	Sichuan University\|West China Second University Hospital	Sichuan University												B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-02-04	Blastula	Embryo	Embryo Imprecise	All anatomical structures
30600	30600	SRR27865239	SRX23527801	SRS20377517	SRP488009	PRJNA1073183	Transcriptome of SEMA5A MT ATP6 ZNF662 and KDM4C in zebrafish embryos	PRJNA1073183	Other			Embryos transcriptome	Embryos transcriptome	strain:AB\|breed:Egg water\|age:5hpf\|dev stage:5hpf\|sex:not applicable\|tissue:Embryos\|collection date:not applicable\|geo loc name:not applicable\|BioSampleModel:Model organism or animal	KDM4C MO	5	5	KDM4C MO		RNA-Seq	TRANSCRIPTOMIC	RT-PCR	SINGLE	ILLUMINA	Illumina HiSeq 4000		SRP488009		KDM-MO_1.fq.gz KDM-MO_2.fq.gz	fastq fastq	7876840500.0	26256135.0	KDM MO 1.fq.gz	0:150 1:150	A:2104173142;C:1831662159;G:1843980192;T:2096831538;N:193469	150	150	2104173142	1831662159	1843980192	2096831538	193469	SRX23527801	SRS20377517	SRA1797184	Sichuan University\|West China Second University Hospital	Sichuan University												B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-02-04	Blastula	Embryo	Embryo Imprecise	All anatomical structures
30601	30601	SRR27865240	SRX23527800	SRS20377517	SRP488009	PRJNA1073183	Transcriptome of SEMA5A MT ATP6 ZNF662 and KDM4C in zebrafish embryos	PRJNA1073183	Other			Embryos transcriptome	Embryos transcriptome	strain:AB\|breed:Egg water\|age:5hpf\|dev stage:5hpf\|sex:not applicable\|tissue:Embryos\|collection date:not applicable\|geo loc name:not applicable\|BioSampleModel:Model organism or animal	ZNF662 MO	4	4	ZNF662 MO		RNA-Seq	TRANSCRIPTOMIC	RT-PCR	SINGLE	ILLUMINA	Illumina HiSeq 4000		SRP488009		znf547-MO_1.fq.gz znf547-MO_2.fq.gz	fastq fastq	7573815300.0	25246051.0	znf547 MO 1.fq.gz	0:150 1:150	A:2014197761;C:1766587259;G:1782217029;T:2010540623;N:272628	150	150	2014197761	1766587259	1782217029	2010540623	272628	SRX23527800	SRS20377517	SRA1797184	Sichuan University\|West China Second University Hospital	Sichuan University												B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-02-04	Blastula	Embryo	Embryo Imprecise	All anatomical structures
30602	30602	SRR27865241	SRX23527799	SRS20377517	SRP488009	PRJNA1073183	Transcriptome of SEMA5A MT ATP6 ZNF662 and KDM4C in zebrafish embryos	PRJNA1073183	Other			Embryos transcriptome	Embryos transcriptome	strain:AB\|breed:Egg water\|age:5hpf\|dev stage:5hpf\|sex:not applicable\|tissue:Embryos\|collection date:not applicable\|geo loc name:not applicable\|BioSampleModel:Model organism or animal	SEMA5A RNA	3	3	SEMA5A RNA		RNA-Seq	TRANSCRIPTOMIC	RT-PCR	SINGLE	ILLUMINA	Illumina HiSeq 4000		SRP488009		semRNA_1.fq.gz semRNA_2.fq.gz	fastq fastq	5575566000.0	18585220.0	semRNA 1.fq.gz	0:150 1:150	A:1456001758;C:1325628099;G:1339796989;T:1454076989;N:62165	150	150	1456001758	1325628099	1339796989	1454076989	62165	SRX23527799	SRS20377517	SRA1797184	Sichuan University\|West China Second University Hospital	Sichuan University												B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-02-04	Blastula	Embryo	Embryo Imprecise	All anatomical structures
30603	30603	SRR27865242	SRX23527798	SRS20377517	SRP488009	PRJNA1073183	Transcriptome of SEMA5A MT ATP6 ZNF662 and KDM4C in zebrafish embryos	PRJNA1073183	Other			Embryos transcriptome	Embryos transcriptome	strain:AB\|breed:Egg water\|age:5hpf\|dev stage:5hpf\|sex:not applicable\|tissue:Embryos\|collection date:not applicable\|geo loc name:not applicable\|BioSampleModel:Model organism or animal	MT ATP6 RNA	2	2	MT ATP6 RNA		RNA-Seq	TRANSCRIPTOMIC	RT-PCR	SINGLE	ILLUMINA	Illumina HiSeq 4000		SRP488009		ATP6-RNA_1.fq.gz ATP6-RNA_2.fq.gz	fastq fastq	5437771200.0	18125904.0	ATP6 RNA 1.fq.gz	0:150 1:150	A:1438540045;C:1272310670;G:1290121053;T:1436739799;N:59633	150	150	1438540045	1272310670	1290121053	1436739799	59633	SRX23527798	SRS20377517	SRA1797184	Sichuan University\|West China Second University Hospital	Sichuan University												B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-02-04	Blastula	Embryo	Embryo Imprecise	All anatomical structures
30604	30604	SRR27865243	SRX23527797	SRS20377517	SRP488009	PRJNA1073183	Transcriptome of SEMA5A MT ATP6 ZNF662 and KDM4C in zebrafish embryos	PRJNA1073183	Other			Embryos transcriptome	Embryos transcriptome	strain:AB\|breed:Egg water\|age:5hpf\|dev stage:5hpf\|sex:not applicable\|tissue:Embryos\|collection date:not applicable\|geo loc name:not applicable\|BioSampleModel:Model organism or animal	con RNA	1	1	con RNA		RNA-Seq	TRANSCRIPTOMIC	RT-PCR	SINGLE	ILLUMINA	Illumina HiSeq 4000		SRP488009		con-RNA_1.fq.gz con-RNA_2.fq.gz	fastq fastq	6733158900.0	22443863.0	con RNA 1.fq.gz	0:150 1:150	A:1766014369;C:1595337569;G:1610127771;T:1761604971;N:74220	150	150	1766014369	1595337569	1610127771	1761604971	74220	SRX23527797	SRS20377517	SRA1797184	Sichuan University\|West China Second University Hospital	Sichuan University												B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-02-04	Blastula	Embryo	Embryo Imprecise	All anatomical structures
30716	30716	SRR28342048	SRX23948605	SRS20750294	SRP495203	PRJNA1087701	UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP.	PRJNA1087701	Other	Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.		3xflag RESA CLIP input B3	3xflag RESA CLIP input B3 AGN003279	strain:TU/AB\|age:3.5 hpf\|dev stage:1k cell\|collection date:2022 10 04\|geo loc name:USA\|sex:pooled male and female\|tissue:embryo\|genotype:wt\|strain maternal:wt\|strain paternal:wt\|molecule:mRNA\|selection:flag bead PD post crosslinking\|sample ref:AGS002510\|replicate ref:AGN003279\|replicate order:1\|project label long:3x flag upf1 mutants plasmids 3735 3736 3737 3650 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper\|project label short:upf1 mutant RESA HITS CLIP\|sample label short:RESA CLIP Upf1 #3737 input\|replicate label short:RESA CLIP Upf1 #3737 input B1\|BioSampleModel:Model organism or animal	3xflag RESA HITS CLIP input B3	AGR004059	AGR004059	PCR from library specific RT		RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP495203		AGR004059_R1.fastq AGR004059_R2.fastq	fastq fastq	15446715026.0	51148063.0	AGR004059 R1.fastq.zst	0:151 1:151	A:4298384942;C:3080575022;G:4004069877;T:4063619821;N:65364	151	151	4298384942	3080575022	4004069877	4063619821	65364	SRX23948605	SRS20750294	SRA1824033	Yale University\|Genetics	Yale University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2024-03-14	Blastula	Embryo	Embryo Imprecise	All anatomical structures
30717	30717	SRR28342039	SRX23948614	SRS20750302	SRP495203	PRJNA1087701	UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP.	PRJNA1087701	Other	Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.		3xflag upf1 R843C RESA HITS CLIP B1	3xflag upf1 R843C RESA HITS CLIP B1 AGN003273	strain:TU/AB\|age:3.5 hpf\|dev stage:1k cell\|collection date:2022 10 04\|geo loc name:USA\|sex:pooled male and female\|tissue:embryo\|genotype:wt\|strain maternal:wt\|strain paternal:wt\|molecule:mRNA\|selection:flag bead PD post crosslinking\|sample ref:AGS002507\|replicate ref:AGN003273\|replicate order:1\|project label long:3x flag upf1 mutants plasmids 3735 3736 3737 3650 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper\|project label short:upf1 mutant RESA HITS CLIP\|sample label short:RESA CLIP Upf1 #3735 IP\|replicate label short:RESA CLIP Upf1 #3735 IP B1\|BioSampleModel:Model organism or animal	3xflag upf1 R843C RESA HITS CLIP B1	AGR004053	AGR004053	PCR from library specific RT		RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP495203		AGR004053_R1.fastq AGR004053_R2.fastq	fastq fastq	10545264992.0	34918096.0	AGR004053 R1.fastq.zst	0:151 1:151	A:2943441620;C:2155828506;G:2709854276;T:2736095568;N:45022	151	151	2943441620	2155828506	2709854276	2736095568	45022	SRX23948614	SRS20750302	SRA1824033	Yale University\|Genetics	Yale University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2024-03-14	Blastula	Embryo	Embryo Imprecise	All anatomical structures
30718	30718	SRR28342040	SRX23948613	SRS20750303	SRP495203	PRJNA1087701	UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP.	PRJNA1087701	Other	Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.		3xflag upf1 C126S RESA HITS CLIP B2	3xflag upf1 C126S RESA HITS CLIP B2 AGN003282	strain:TU/AB\|age:3.5 hpf\|dev stage:1k cell\|collection date:2022 10 04\|geo loc name:USA\|sex:pooled male and female\|tissue:embryo\|genotype:wt\|strain maternal:wt\|strain paternal:wt\|molecule:mRNA\|selection:flag bead PD post crosslinking\|sample ref:AGS002511\|replicate ref:AGN003282\|replicate order:2\|project label long:3x flag upf1 mutants plasmids 3735 3736 3737 3650 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper\|project label short:upf1 mutant RESA HITS CLIP\|sample label short:RESA CLIP Upf1 #3737 IP\|replicate label short:RESA CLIP Upf1 #3737 IP B2\|BioSampleModel:Model organism or animal	3xflag upf1 C126S RESA HITS CLIP B2	AGR004062	AGR004062	PCR from library specific RT		RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP495203		AGR004062_R1.fastq AGR004062_R2.fastq	fastq fastq	11134300590.0	36868545.0	AGR004062 R1.fastq.zst	0:151 1:151	A:3063023630;C:2386509106;G:2925940275;T:2758782993;N:44586	151	151	3063023630	2386509106	2925940275	2758782993	44586	SRX23948613	SRS20750303	SRA1824033	Yale University\|Genetics	Yale University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2024-03-14	Blastula	Embryo	Embryo Imprecise	All anatomical structures
30719	30719	SRR28342041	SRX23948612	SRS20750301	SRP495203	PRJNA1087701	UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP.	PRJNA1087701	Other	Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.		3xflag upf1 C126S RESA HITS CLIP B1	3xflag upf1 C126S RESA HITS CLIP B1 AGN003281	strain:TU/AB\|age:3.5 hpf\|dev stage:1k cell\|collection date:2022 10 04\|geo loc name:USA\|sex:pooled male and female\|tissue:embryo\|genotype:wt\|strain maternal:wt\|strain paternal:wt\|molecule:mRNA\|selection:flag bead PD post crosslinking\|sample ref:AGS002511\|replicate ref:AGN003281\|replicate order:1\|project label long:3x flag upf1 mutants plasmids 3735 3736 3737 3650 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper\|project label short:upf1 mutant RESA HITS CLIP\|sample label short:RESA CLIP Upf1 #3737 IP\|replicate label short:RESA CLIP Upf1 #3737 IP B1\|BioSampleModel:Model organism or animal	3xflag upf1 C126S RESA HITS CLIP B1	AGR004061	AGR004061	PCR from library specific RT		RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP495203		AGR004061_R1.fastq AGR004061_R2.fastq	fastq fastq	13368435586.0	44266343.0	AGR004061 R1.fastq.zst	0:151 1:151	A:3603822055;C:2659540495;G:3591989409;T:3513026539;N:57088	151	151	3603822055	2659540495	3591989409	3513026539	57088	SRX23948612	SRS20750301	SRA1824033	Yale University\|Genetics	Yale University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2024-03-14	Blastula	Embryo	Embryo Imprecise	All anatomical structures
30720	30720	SRR28342042	SRX23948611	SRS20750300	SRP495203	PRJNA1087701	UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP.	PRJNA1087701	Other	Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.		3xflag upf1 G495R/G497E RESA HITS CLIP B2	3xflag upf1 G495R/G497E RESA HITS CLIP B2 AGN003278	strain:TU/AB\|age:3.5 hpf\|dev stage:1k cell\|collection date:2022 10 04\|geo loc name:USA\|sex:pooled male and female\|tissue:embryo\|genotype:wt\|strain maternal:wt\|strain paternal:wt\|molecule:mRNA\|selection:flag bead PD post crosslinking\|sample ref:AGS002509\|replicate ref:AGN003278\|replicate order:2\|project label long:3x flag upf1 mutants plasmids 3735 3736 3737 3650 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper\|project label short:upf1 mutant RESA HITS CLIP\|sample label short:RESA CLIP Upf1 #3736 IP\|replicate label short:RESA CLIP Upf1 #3736 IP B2\|BioSampleModel:Model organism or animal	3xflag upf1 G495R/G497E RESA HITS CLIP B2	AGR004058	AGR004058	PCR from library specific RT		RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP495203		AGR004058_R1.fastq AGR004058_R2.fastq	fastq fastq	13750586084.0	45531742.0	AGR004058 R1.fastq.zst	0:151 1:151	A:3775460380;C:2748834924;G:3672092546;T:3554141983;N:56251	151	151	3775460380	2748834924	3672092546	3554141983	56251	SRX23948611	SRS20750300	SRA1824033	Yale University\|Genetics	Yale University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2024-03-14	Blastula	Embryo	Embryo Imprecise	All anatomical structures
30721	30721	SRR28342043	SRX23948610	SRS20750299	SRP495203	PRJNA1087701	UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP.	PRJNA1087701	Other	Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.		3xflag upf1 G495R/G497E RESA HITS CLIP B1	3xflag upf1 G495R/G497E RESA HITS CLIP B1 AGN003277	strain:TU/AB\|age:3.5 hpf\|dev stage:1k cell\|collection date:2022 10 04\|geo loc name:USA\|sex:pooled male and female\|tissue:embryo\|genotype:wt\|strain maternal:wt\|strain paternal:wt\|molecule:mRNA\|selection:flag bead PD post crosslinking\|sample ref:AGS002509\|replicate ref:AGN003277\|replicate order:1\|project label long:3x flag upf1 mutants plasmids 3735 3736 3737 3650 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper\|project label short:upf1 mutant RESA HITS CLIP\|sample label short:RESA CLIP Upf1 #3736 IP\|replicate label short:RESA CLIP Upf1 #3736 IP B1\|BioSampleModel:Model organism or animal	3xflag upf1 G495R/G497E RESA HITS CLIP B1	AGR004057	AGR004057	PCR from library specific RT		RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP495203		AGR004057_R1.fastq AGR004057_R2.fastq	fastq fastq	10708529212.0	35458706.0	AGR004057 R1.fastq.zst	0:151 1:151	A:2983511099;C:2231542625;G:2842811089;T:2650619142;N:45257	151	151	2983511099	2231542625	2842811089	2650619142	45257	SRX23948610	SRS20750299	SRA1824033	Yale University\|Genetics	Yale University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2024-03-14	Blastula	Embryo	Embryo Imprecise	All anatomical structures
30722	30722	SRR28342044	SRX23948609	SRS20750297	SRP495203	PRJNA1087701	UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP.	PRJNA1087701	Other	Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.		3xflag gfp RESA HITS CLIP B1	3xflag gfp RESA HITS CLIP B1 AGN002579	strain:TU/AB\|age:3.5 hpf\|dev stage:1k cell\|collection date:2021 01 05\|geo loc name:USA\|sex:pooled male and female\|tissue:embryo\|genotype:wt\|strain maternal:wt\|strain paternal:wt\|molecule:mRNA\|selection:flag bead PD post crosslinking\|sample ref:AGS001970\|replicate ref:AGN002579\|replicate order:1\|project label long:3x flag upf1 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper. Control is 3x flag gfp\|project label short:3xflag upf1 RESA HITS CLIP\|sample label short:gfp CLIP\|replicate label short:gfp CLIP B1\|BioSampleModel:Model organism or animal	3xflag gfp RESA HITS CLIP B1	AGR003308	AGR003308	PCR from library specific RT		RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP495203		AGR003308_R1.fastq AGR003308_R2.fastq	fastq fastq	507167460.0	2510730.0	AGR003308 R1.fastq.zst	0:101 1:101	A:156207937;C:97169427;G:111291367;T:142479104;N:19625	101	101	156207937	97169427	111291367	142479104	19625	SRX23948609	SRS20750297	SRA1824033	Yale University\|Genetics	Yale University												B	B	mate2-mate1 similar by mapping diff	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2024-03-14	Blastula	Embryo	Embryo Imprecise	All anatomical structures
30723	30723	SRR28342045	SRX23948608	SRS20750298	SRP495203	PRJNA1087701	UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP.	PRJNA1087701	Other	Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.		3xflag RESA HITS CLIP input B4	3xflag RESA CLIP input B4 AGN003267	strain:TU/AB\|age:3.5 hpf\|dev stage:1k cell\|collection date:2022 10 04\|geo loc name:USA\|sex:pooled male and female\|tissue:embryo\|genotype:wt\|strain maternal:wt\|strain paternal:wt\|molecule:mRNA\|selection:flag bead PD post crosslinking\|sample ref:AGS002504\|replicate ref:AGN003267\|replicate order:1\|project label long:3x flag upf1 mutants plasmids 3735 3736 3737 3650 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper\|project label short:upf1 mutant RESA HITS CLIP\|sample label short:RESA CLIP Upf1 #3650 input\|replicate label short:RESA CLIP Upf1 #3650 input B1\|BioSampleModel:Model organism or animal	3xflag RESA HITS CLIP input B4	AGR004047	AGR004047	PCR from library specific RT		RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP495203		AGR004047_R2.fastq AGR004047_R1.fastq	fastq fastq	19396379142.0	64226421.0	AGR004047 R1.fastq.zst	0:151 1:151	A:5606633601;C:3872715770;G:4910603410;T:5006345083;N:81278	151	151	5606633601	3872715770	4910603410	5006345083	81278	SRX23948608	SRS20750298	SRA1824033	Yale University\|Genetics	Yale University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2024-03-14	Blastula	Embryo	Embryo Imprecise	All anatomical structures
30724	30724	SRR28342046	SRX23948607	SRS20750295	SRP495203	PRJNA1087701	UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP.	PRJNA1087701	Other	Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.		3xflag upf3b RESA HITS CLIP B2	3xflag upf3b RESA HITS CLIP B2 AGN002796	strain:TU/AB\|age:3.5 hpf\|dev stage:1k cell\|collection date:2021 08 19\|geo loc name:USA\|sex:pooled male and female\|tissue:embryo\|genotype:wt\|strain maternal:wt\|strain paternal:wt\|molecule:mRNA\|selection:flag bead PD post crosslinking\|sample ref:AGS002161\|replicate ref:AGN002796\|replicate order:2\|project label long:3x flag upf1 2 3a 3b RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper\|project label short:3xflag upf1 RESA HITS CLIP\|sample label short:Upf3b pulldown\|replicate label short:Upf3b pulldown B2\|BioSampleModel:Model organism or animal	3xflag upf3b RESA HITS CLIP B2	AGR003554	AGR003554	PCR from library specific RT		RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP495203		AGR003554_R1.fastq AGR003554_R2.fastq	fastq fastq	9047261244.0	44788422.0	AGR003554 R1.fastq.zst	0:101 1:101	A:2711585737;C:1825740983;G:2076537283;T:2433050799;N:346442	101	101	2711585737	1825740983	2076537283	2433050799	346442	SRX23948607	SRS20750295	SRA1824033	Yale University\|Genetics	Yale University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2024-03-14	Blastula	Embryo	Embryo Imprecise	All anatomical structures
30725	30725	SRR28342047	SRX23948606	SRS20750296	SRP495203	PRJNA1087701	UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP.	PRJNA1087701	Other	Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.		3xflag upf3b RESA HITS CLIP B1	3xflag upf3b RESA HITS CLIP B1 AGN002795	strain:TU/AB\|age:3.5 hpf\|dev stage:1k cell\|collection date:2021 08 19\|geo loc name:USA\|sex:pooled male and female\|tissue:embryo\|genotype:wt\|strain maternal:wt\|strain paternal:wt\|molecule:mRNA\|selection:flag bead PD post crosslinking\|sample ref:AGS002161\|replicate ref:AGN002795\|replicate order:1\|project label long:3x flag upf1 2 3a 3b RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper\|project label short:3xflag upf1 RESA HITS CLIP\|sample label short:Upf3b pulldown\|replicate label short:Upf3b pulldown B1\|BioSampleModel:Model organism or animal	3xflag upf3b RESA HITS CLIP B1	AGR003549	AGR003549	PCR from library specific RT		RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP495203		AGR003549_R1.fastq AGR003549_R2.fastq	fastq fastq	9617196770.0	47609885.0	AGR003549 R1.fastq.zst	0:101 1:101	A:2856263963;C:1963091501;G:2218118010;T:2579364306;N:358990	101	101	2856263963	1963091501	2218118010	2579364306	358990	SRX23948606	SRS20750296	SRA1824033	Yale University\|Genetics	Yale University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2024-03-14	Blastula	Embryo	Embryo Imprecise	All anatomical structures
30726	30726	SRR28342049	SRX23948604	SRS20750292	SRP495203	PRJNA1087701	UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP.	PRJNA1087701	Other	Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.		3xflag upf3a RESA HITS CLIP B2	3xflag upf3a RESA HITS CLIP B2 AGN002792	strain:TU/AB\|age:3.5 hpf\|dev stage:1k cell\|collection date:2021 08 19\|geo loc name:USA\|sex:pooled male and female\|tissue:embryo\|genotype:wt\|strain maternal:wt\|strain paternal:wt\|molecule:mRNA\|selection:flag bead PD post crosslinking\|sample ref:AGS002159\|replicate ref:AGN002792\|replicate order:2\|project label long:3x flag upf1 2 3a 3b RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper\|project label short:3xflag upf1 RESA HITS CLIP\|sample label short:Upf3a pulldown\|replicate label short:Upf3a pulldown B2\|BioSampleModel:Model organism or animal	3xflag upf3a RESA HITS CLIP B2	AGR003566	AGR003566	PCR from library specific RT		RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP495203		AGR003566_R1.fastq AGR003566_R2.fastq	fastq fastq	50318544410.0	249101705.0	AGR003566 R1.fastq.zst	0:101 1:101	A:14930547705;C:10295739682;G:11624332741;T:13466693890;N:1230392	101	101	14930547705	10295739682	11624332741	13466693890	1230392	SRX23948604	SRS20750292	SRA1824033	Yale University\|Genetics	Yale University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2024-03-14	Blastula	Embryo	Embryo Imprecise	All anatomical structures
30727	30727	SRR28342050	SRX23948603	SRS20750293	SRP495203	PRJNA1087701	UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP.	PRJNA1087701	Other	Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.		3xflag upf3a RESA HITS CLIP B1	3xflag upf3a RESA HITS CLIP B1 AGN002791	strain:TU/AB\|age:3.5 hpf\|dev stage:1k cell\|collection date:2021 08 19\|geo loc name:USA\|sex:pooled male and female\|tissue:embryo\|genotype:wt\|strain maternal:wt\|strain paternal:wt\|molecule:mRNA\|selection:flag bead PD post crosslinking\|sample ref:AGS002159\|replicate ref:AGN002791\|replicate order:1\|project label long:3x flag upf1 2 3a 3b RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper\|project label short:3xflag upf1 RESA HITS CLIP\|sample label short:Upf3a pulldown\|replicate label short:Upf3a pulldown B1\|BioSampleModel:Model organism or animal	3xflag upf3a RESA HITS CLIP B1	AGR003545	AGR003545	PCR from library specific RT		RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP495203		AGR003545_R1.fastq AGR003545_R2.fastq	fastq fastq	10770959564.0	53321582.0	AGR003545 R1.fastq.zst	0:101 1:101	A:3207646854;C:2186852059;G:2481889724;T:2894165865;N:405062	101	101	3207646854	2186852059	2481889724	2894165865	405062	SRX23948603	SRS20750293	SRA1824033	Yale University\|Genetics	Yale University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2024-03-14	Blastula	Embryo	Embryo Imprecise	All anatomical structures
30728	30728	SRR28342051	SRX23948602	SRS20750291	SRP495203	PRJNA1087701	UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP.	PRJNA1087701	Other	Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.		3xflag upf2 RESA HITS CLIP B2	3xflag upf2 RESA HITS CLIP B2 AGN002788	strain:TU/AB\|age:3.5 hpf\|dev stage:1k cell\|collection date:2021 08 19\|geo loc name:USA\|sex:pooled male and female\|tissue:embryo\|genotype:wt\|strain maternal:wt\|strain paternal:wt\|molecule:mRNA\|selection:flag bead PD post crosslinking\|sample ref:AGS002157\|replicate ref:AGN002788\|replicate order:2\|project label long:3x flag upf1 2 3a 3b RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper\|project label short:3xflag upf1 RESA HITS CLIP\|sample label short:Upf2 pulldown\|replicate label short:Upf2 pulldown B2\|BioSampleModel:Model organism or animal	3xflag upf2 RESA HITS CLIP B2	AGR003541	AGR003541	PCR from library specific RT		RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP495203		AGR003541_R1.fastq AGR003541_R2.fastq	fastq fastq	9471117440.0	46886720.0	AGR003541 R1.fastq.zst	0:101 1:101	A:2852420143;C:1898246719;G:2136843599;T:2583254674;N:352305	101	101	2852420143	1898246719	2136843599	2583254674	352305	SRX23948602	SRS20750291	SRA1824033	Yale University\|Genetics	Yale University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2024-03-14	Blastula	Embryo	Embryo Imprecise	All anatomical structures
30729	30729	SRR28342052	SRX23948601	SRS20750290	SRP495203	PRJNA1087701	UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP.	PRJNA1087701	Other	Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.		3xflag upf2 RESA HITS CLIP B1	3xflag upf2 RESA HITS CLIP B1 AGN002787	strain:TU/AB\|age:3.5 hpf\|dev stage:1k cell\|collection date:2021 08 19\|geo loc name:USA\|sex:pooled male and female\|tissue:embryo\|genotype:wt\|strain maternal:wt\|strain paternal:wt\|molecule:mRNA\|selection:flag bead PD post crosslinking\|sample ref:AGS002157\|replicate ref:AGN002787\|replicate order:1\|project label long:3x flag upf1 2 3a 3b RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper\|project label short:3xflag upf1 RESA HITS CLIP\|sample label short:Upf2 pulldown\|replicate label short:Upf2 pulldown B1\|BioSampleModel:Model organism or animal	3xflag upf2 RESA HITS CLIP B1	AGR003542	AGR003542	PCR from library specific RT		RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP495203		AGR003542_R1.fastq AGR003542_R2.fastq	fastq fastq	10845546044.0	53690822.0	AGR003542 R1.fastq.zst	0:101 1:101	A:3277705832;C:2154122837;G:2449408891;T:2963913264;N:395220	101	101	3277705832	2154122837	2449408891	2963913264	395220	SRX23948601	SRS20750290	SRA1824033	Yale University\|Genetics	Yale University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2024-03-14	Blastula	Embryo	Embryo Imprecise	All anatomical structures
30730	30730	SRR28342053	SRX23948600	SRS20750289	SRP495203	PRJNA1087701	UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP.	PRJNA1087701	Other	Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.		3xflag upf1 RESA HITS CLIP B5	3xflag upf1 RESA HITS CLIP B5 AGN003270	strain:TU/AB\|age:3.5 hpf\|dev stage:1k cell\|collection date:2022 10 04\|geo loc name:USA\|sex:pooled male and female\|tissue:embryo\|genotype:wt\|strain maternal:wt\|strain paternal:wt\|molecule:mRNA\|selection:flag bead PD post crosslinking\|sample ref:AGS002505\|replicate ref:AGN003270\|replicate order:2\|project label long:3x flag upf1 mutants plasmids 3735 3736 3737 3650 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper\|project label short:upf1 mutant RESA HITS CLIP\|sample label short:RESA CLIP Upf1 #3650 IP\|replicate label short:RESA CLIP Upf1 #3650 IP B2\|BioSampleModel:Model organism or animal	3xflag upf1 RESA HITS CLIP B5	AGR004050	AGR004050	PCR from library specific RT		RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP495203		AGR004050_R1.fastq AGR004050_R2.fastq	fastq fastq	11823214534.0	39149717.0	AGR004050 R1.fastq.zst	0:151 1:151	A:3184473505;C:2558650081;G:3236214151;T:2843828317;N:48480	151	151	3184473505	2558650081	3236214151	2843828317	48480	SRX23948600	SRS20750289	SRA1824033	Yale University\|Genetics	Yale University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2024-03-14	Blastula	Embryo	Embryo Imprecise	All anatomical structures
30731	30731	SRR28342054	SRX23948599	SRS20750288	SRP495203	PRJNA1087701	UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP.	PRJNA1087701	Other	Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.		3xflag upf1 RESA HITS CLIP B4	3xflag upf1 RESA HITS CLIP B4 AGN003269	strain:TU/AB\|age:3.5 hpf\|dev stage:1k cell\|collection date:2022 10 04\|geo loc name:USA\|sex:pooled male and female\|tissue:embryo\|genotype:wt\|strain maternal:wt\|strain paternal:wt\|molecule:mRNA\|selection:flag bead PD post crosslinking\|sample ref:AGS002505\|replicate ref:AGN003269\|replicate order:1\|project label long:3x flag upf1 mutants plasmids 3735 3736 3737 3650 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper\|project label short:upf1 mutant RESA HITS CLIP\|sample label short:RESA CLIP Upf1 #3650 IP\|replicate label short:RESA CLIP Upf1 #3650 IP B1\|BioSampleModel:Model organism or animal	3xflag upf1 RESA HITS CLIP B4	AGR004049	AGR004049	PCR from library specific RT		RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP495203		AGR004049_R1.fastq AGR004049_R2.fastq	fastq fastq	14371221754.0	47586827.0	AGR004049 R1.fastq.zst	0:151 1:151	A:3983698498;C:2912453835;G:3805806498;T:3669203887;N:59036	151	151	3983698498	2912453835	3805806498	3669203887	59036	SRX23948599	SRS20750288	SRA1824033	Yale University\|Genetics	Yale University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2024-03-14	Blastula	Embryo	Embryo Imprecise	All anatomical structures
30732	30732	SRR28342055	SRX23948598	SRS20750287	SRP495203	PRJNA1087701	UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP.	PRJNA1087701	Other	Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.		3xflag upf1 RESA HITS CLIP B3	3xflag upf1 RESA HITS CLIP B3 AGN002798	strain:TU/AB\|age:3.5 hpf\|dev stage:1k cell\|collection date:2021 08 19\|geo loc name:USA\|sex:pooled male and female\|tissue:embryo\|genotype:wt\|strain maternal:wt\|strain paternal:wt\|molecule:mRNA\|selection:flag bead PD post crosslinking\|sample ref:AGS002154\|replicate ref:AGN002798\|replicate order:2\|project label long:3x flag upf1 2 3a 3b RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper\|project label short:3xflag upf1 RESA HITS CLIP\|sample label short:Upf1 pulldown\|replicate label short:Upf1 pulldown B2\|BioSampleModel:Model organism or animal	3xflag upf1 RESA HITS CLIP B3	AGR003555	AGR003555	PCR from library specific RT		RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP495203		AGR003555_R1.fastq AGR003555_R2.fastq	fastq fastq	13605076932.0	67351866.0	AGR003555 R1.fastq.zst	0:101 1:101	A:3996372048;C:2823464384;G:3156030119;T:3628752419;N:457962	101	101	3996372048	2823464384	3156030119	3628752419	457962	SRX23948598	SRS20750287	SRA1824033	Yale University\|Genetics	Yale University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2024-03-14	Blastula	Embryo	Embryo Imprecise	All anatomical structures
30733	30733	SRR28342056	SRX23948597	SRS20750283	SRP495203	PRJNA1087701	UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP.	PRJNA1087701	Other	Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.		3xflag upf1 RESA HITS CLIP B2	3xflag upf1 RESA HITS CLIP B2 AGN002784	strain:TU/AB\|age:3.5 hpf\|dev stage:1k cell\|collection date:2021 08 19\|geo loc name:USA\|sex:pooled male and female\|tissue:embryo\|genotype:wt\|strain maternal:wt\|strain paternal:wt\|molecule:mRNA\|selection:flag bead PD post crosslinking\|sample ref:AGS002154\|replicate ref:AGN002784\|replicate order:1\|project label long:3x flag upf1 2 3a 3b RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper\|project label short:3xflag upf1 RESA HITS CLIP\|sample label short:Upf1 pulldown\|replicate label short:Upf1 pulldown B1\|BioSampleModel:Model organism or animal	3xflag upf1 RESA HITS CLIP B2	AGR003552	AGR003552	PCR from library specific RT		RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP495203		AGR003552_R1.fastq AGR003552_R2.fastq	fastq fastq	10762870878.0	53281539.0	AGR003552 R1.fastq.zst	0:101 1:101	A:3170047840;C:2223795927;G:2504911576;T:2863700088;N:415447	101	101	3170047840	2223795927	2504911576	2863700088	415447	SRX23948597	SRS20750283	SRA1824033	Yale University\|Genetics	Yale University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2024-03-14	Blastula	Embryo	Embryo Imprecise	All anatomical structures
30734	30734	SRR28342057	SRX23948596	SRS20750286	SRP495203	PRJNA1087701	UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP.	PRJNA1087701	Other	Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.		3xflag upf1 RESA HITS CLIP B1	3xflag upf1 RESA HITS CLIP B1 AGN002577	strain:TU/AB\|age:3.5 hpf\|dev stage:1k cell\|collection date:2021 01 05\|geo loc name:USA\|sex:pooled male and female\|tissue:embryo\|genotype:wt\|strain maternal:wt\|strain paternal:wt\|molecule:mRNA\|selection:flag bead PD post crosslinking\|sample ref:AGS001968\|replicate ref:AGN002577\|replicate order:1\|project label long:3x flag upf1 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper. Control is 3x flag gfp\|project label short:3xflag upf1 RESA HITS CLIP\|sample label short:upf1 CLIP\|replicate label short:upf1 CLIP B1\|BioSampleModel:Model organism or animal	3xflag upf1 RESA HITS CLIP B1	AGR003306	AGR003306	PCR from library specific RT		RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP495203		AGR003306_R1.fastq AGR003306_R2.fastq	fastq fastq	529433718.0	2620959.0	AGR003306 R1.fastq.zst	0:101 1:101	A:157881697;C:106579975;G:122214915;T:142736640;N:20491	101	101	157881697	106579975	122214915	142736640	20491	SRX23948596	SRS20750286	SRA1824033	Yale University\|Genetics	Yale University												B	B	mate2-mate1 similar by mapping diff	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2024-03-14	Blastula	Embryo	Embryo Imprecise	All anatomical structures
30735	30735	SRR28342058	SRX23948595	SRS20750284	SRP495203	PRJNA1087701	UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP.	PRJNA1087701	Other	Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.		3xflag upf1 R843C RESA HITS CLIP B2	3xflag upf1 R843C RESA HITS CLIP B2 AGN003274	strain:TU/AB\|age:3.5 hpf\|dev stage:1k cell\|collection date:2022 10 04\|geo loc name:USA\|sex:pooled male and female\|tissue:embryo\|genotype:wt\|strain maternal:wt\|strain paternal:wt\|molecule:mRNA\|selection:flag bead PD post crosslinking\|sample ref:AGS002507\|replicate ref:AGN003274\|replicate order:2\|project label long:3x flag upf1 mutants plasmids 3735 3736 3737 3650 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper\|project label short:upf1 mutant RESA HITS CLIP\|sample label short:RESA CLIP Upf1 #3735 IP\|replicate label short:RESA CLIP Upf1 #3735 IP B2\|BioSampleModel:Model organism or animal	3xflag upf1 R843C RESA HITS CLIP B2	AGR004054	AGR004054	PCR from library specific RT		RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP495203		AGR004054_R1.fastq AGR004054_R2.fastq	fastq fastq	12067359790.0	39958145.0	AGR004054 R1.fastq.zst	0:151 1:151	A:3301899297;C:2532414363;G:3161463027;T:3071532640;N:50463	151	151	3301899297	2532414363	3161463027	3071532640	50463	SRX23948595	SRS20750284	SRA1824033	Yale University\|Genetics	Yale University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2024-03-14	Blastula	Embryo	Embryo Imprecise	All anatomical structures
30736	30736	SRR28342059	SRX23948594	SRS20750282	SRP495203	PRJNA1087701	UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP.	PRJNA1087701	Other	Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.		3xflag RESA CLIP input B2	3xflag RESA CLIP input B2 AGN003275	strain:TU/AB\|age:3.5 hpf\|dev stage:1k cell\|collection date:2022 10 04\|geo loc name:USA\|sex:pooled male and female\|tissue:embryo\|genotype:wt\|strain maternal:wt\|strain paternal:wt\|molecule:mRNA\|selection:flag bead PD post crosslinking\|sample ref:AGS002508\|replicate ref:AGN003275\|replicate order:1\|project label long:3x flag upf1 mutants plasmids 3735 3736 3737 3650 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper\|project label short:upf1 mutant RESA HITS CLIP\|sample label short:RESA CLIP Upf1 #3736 input\|replicate label short:RESA CLIP Upf1 #3736 input B1\|BioSampleModel:Model organism or animal	3xflag RESA HITS CLIP input B2	AGR004055	AGR004055	PCR from library specific RT		RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP495203		AGR004055_R1.fastq AGR004055_R2.fastq	fastq fastq	13295917534.0	44026217.0	AGR004055 R1.fastq.zst	0:151 1:151	A:3866188367;C:2751508227;G:3344357660;T:3333805406;N:57874	151	151	3866188367	2751508227	3344357660	3333805406	57874	SRX23948594	SRS20750282	SRA1824033	Yale University\|Genetics	Yale University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2024-03-14	Blastula	Embryo	Embryo Imprecise	All anatomical structures
30737	30737	SRR28342060	SRX23948593	SRS20750285	SRP495203	PRJNA1087701	UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP.	PRJNA1087701	Other	Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.		3xflag RESA CLIP input B1	3xflag RESA CLIP input B1 AGN003271	strain:TU/AB\|age:3.5 hpf\|dev stage:1k cell\|collection date:2022 10 04\|geo loc name:USA\|sex:pooled male and female\|tissue:embryo\|genotype:wt\|strain maternal:wt\|strain paternal:wt\|molecule:mRNA\|selection:flag bead PD post crosslinking\|sample ref:AGS002506\|replicate ref:AGN003271\|replicate order:1\|project label long:3x flag upf1 mutants plasmids 3735 3736 3737 3650 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper\|project label short:upf1 mutant RESA HITS CLIP\|sample label short:RESA CLIP Upf1 #3735 input\|replicate label short:RESA CLIP Upf1 #3735 input B1\|BioSampleModel:Model organism or animal	3xflag RESA HITS CLIP input B1	AGR004051	AGR004051	PCR from library specific RT		RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP495203		AGR004051_R1.fastq AGR004051_R2.fastq	fastq fastq	14891006336.0	49307968.0	AGR004051 R1.fastq.zst	0:151 1:151	A:4241333172;C:3027167277;G:3764089225;T:3858355544;N:61118	151	151	4241333172	3027167277	3764089225	3858355544	61118	SRX23948593	SRS20750285	SRA1824033	Yale University\|Genetics	Yale University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2024-03-14	Blastula	Embryo	Embryo Imprecise	All anatomical structures
31884	31884	SRR28747851	SRX24313483	SRS21075233	SRP502930	PRJNA1102048	Danio rerio Raw sequence reads	PRJNA1102048	Whole Genome Sequencing	This experimental study aimed to investigate a role of Irg1l/itaconate axis in zebrafish neuromast development using RNA seq analysis. At 5dpf Larvae treated with 4 octyl itaconate was preformed to subsequent transcriptomic analysis.		Model organism or animal sample from Danio rerio	Zebrafish control sample3	strain:TgBrn3C:mGFP\|age:5dpf\|collection date:2022 09 25\|geo loc name:China\|sex:pooled male and female\|tissue:larvae\|BioSampleModel:Model organism or animal	Zebrafish control 3	Ctrl 3	Ctrl 3	DNA barcode		RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP502930		Ctrl-3_S26_L004_R2_001.fastq.gz Ctrl-3_S26_L004_R1_001.fastq.gz	fastq fastq	6658139400.0	22193798.0	Ctrl 3 S26 L004 R1 001.fastq.gz	0:150 1:150	A:1953050910;C:1380426193;G:1413459206;T:1911166654;N:36437	150	150	1953050910	1380426193	1413459206	1911166654	36437	SRX24313483	SRS21075233	SRA1849567	Nantong University\|Institute of Special Environmental Medicine	Nantong University	2	0.94694	0.94695	0.14305	0.14206	0.70412	0.70473	0.59878	0.59922	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-04-19	Larval	Larval	Whole Organism	All anatomical structures
31885	31885	SRR28747852	SRX24313482	SRS21075231	SRP502930	PRJNA1102048	Danio rerio Raw sequence reads	PRJNA1102048	Whole Genome Sequencing	This experimental study aimed to investigate a role of Irg1l/itaconate axis in zebrafish neuromast development using RNA seq analysis. At 5dpf Larvae treated with 4 octyl itaconate was preformed to subsequent transcriptomic analysis.		Model organism or animal sample from Danio rerio	Zebrafish control sample2	strain:TgBrn3C:mGFP\|age:5dpf\|collection date:2022 09 25\|geo loc name:China\|sex:pooled male and female\|tissue:larvae\|BioSampleModel:Model organism or animal	Zebrafish control 2	Ctrl 2	Ctrl 2	DNA barcode		RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP502930		Ctrl-2_S25_L004_R1_001.fastq.gz Ctrl-2_S25_L004_R2_001.fastq.gz	fastq fastq	7515161100.0	25050537.0	Ctrl 2 S25 L004 R1 001.fastq.gz	0:150 1:150	A:2218032458;C:1545198589;G:1580900913;T:2170988635;N:40505	150	150	2218032458	1545198589	1580900913	2170988635	40505	SRX24313482	SRS21075231	SRA1849567	Nantong University\|Institute of Special Environmental Medicine	Nantong University	2	0.94205	0.94032	0.15138	0.15085	0.69578	0.69645	0.5641	0.56481	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-04-19	Larval	Larval	Whole Organism	All anatomical structures
31886	31886	SRR28747853	SRX24313481	SRS21075234	SRP502930	PRJNA1102048	Danio rerio Raw sequence reads	PRJNA1102048	Whole Genome Sequencing	This experimental study aimed to investigate a role of Irg1l/itaconate axis in zebrafish neuromast development using RNA seq analysis. At 5dpf Larvae treated with 4 octyl itaconate was preformed to subsequent transcriptomic analysis.		Model organism or animal sample from Danio rerio	Zebrafish control sample1	strain:TgBrn3C:mGFP\|age:5dpf\|collection date:2022 09 25\|geo loc name:China\|sex:pooled male and female\|tissue:larvae\|BioSampleModel:Model organism or animal	Zebrafish control 1	Ctrl 1	Ctrl 1	DNA barcode		RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP502930		Ctrl-1_S24_L004_R1_001.fastq.gz Ctrl-1_S24_L004_R2_001.fastq.gz	fastq fastq	9747041100.0	32490137.0	Ctrl 1 S24 L004 R1 001.fastq.gz	0:150 1:150	A:2863031605;C:2014131410;G:2067943208;T:2801881561;N:53316	150	150	2863031605	2014131410	2067943208	2801881561	53316	SRX24313481	SRS21075234	SRA1849567	Nantong University\|Institute of Special Environmental Medicine	Nantong University	2	0.94378	0.94419	0.14935	0.14934	0.70749	0.7069	0.60161	0.59912	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-04-19	Larval	Larval	Whole Organism	All anatomical structures
31887	31887	SRR28747854	SRX24313480	SRS21075232	SRP502930	PRJNA1102048	Danio rerio Raw sequence reads	PRJNA1102048	Whole Genome Sequencing	This experimental study aimed to investigate a role of Irg1l/itaconate axis in zebrafish neuromast development using RNA seq analysis. At 5dpf Larvae treated with 4 octyl itaconate was preformed to subsequent transcriptomic analysis.		Model organism or animal sample from Danio rerio	Zebrafish 4 octyl itaconate sample3	strain:TgBrn3C:mGFP\|age:5dpf\|collection date:2022 09 25\|geo loc name:China\|sex:pooled male and female\|tissue:larvae\|BioSampleModel:Model organism or animal	Zebrafish 4 octyl itaconate 3	4OI 3	4OI 3	DNA barcode		RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP502930		4OI-3_S23_L004_R1_001.fastq.gz 4OI-3_S23_L004_R2_001.fastq.gz	fastq fastq	8273990400.0	27579968.0	4OI 3 S23 L004 R1 001.fastq.gz	0:150 1:150	A:2162937415;C:1975194532;G:2012089890;T:2123723196;N:45367	150	150	2162937415	1975194532	2012089890	2123723196	45367	SRX24313480	SRS21075232	SRA1849567	Nantong University\|Institute of Special Environmental Medicine	Nantong University	2	0.96535	0.96542	0.03083	0.03097	0.71279	0.71295	0.48276	0.47927	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-04-19	Larval	Larval	Whole Organism	All anatomical structures
31888	31888	SRR28747855	SRX24313479	SRS21075230	SRP502930	PRJNA1102048	Danio rerio Raw sequence reads	PRJNA1102048	Whole Genome Sequencing	This experimental study aimed to investigate a role of Irg1l/itaconate axis in zebrafish neuromast development using RNA seq analysis. At 5dpf Larvae treated with 4 octyl itaconate was preformed to subsequent transcriptomic analysis.		Model organism or animal sample from Danio rerio	Zebrafish 4 octyl itaconate sample2	strain:TgBrn3C:mGFP\|age:5dpf\|collection date:2022 09 25\|geo loc name:China\|sex:pooled male and female\|tissue:larvae\|BioSampleModel:Model organism or animal	Zebrafish 4 octyl itaconate 2	4OI 2	4OI 2	DNA barcode		RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP502930		4OI-2_S28_L003_R1_001.fastq.gz 4OI-2_S28_L003_R2_001.fastq.gz	fastq fastq	6579714300.0	21932381.0	4OI 2 S28 L003 R1 001.fastq.gz	0:150 1:150	A:1710345718;C:1580260893;G:1608081826;T:1680921918;N:103945	150	150	1710345718	1580260893	1608081826	1680921918	103945	SRX24313479	SRS21075230	SRA1849567	Nantong University\|Institute of Special Environmental Medicine	Nantong University	2	0.96511	0.96418	0.03843	0.0384	0.70179	0.7027	0.49174	0.5066	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-04-19	Larval	Larval	Whole Organism	All anatomical structures
31889	31889	SRR28747856	SRX24313478	SRS21075229	SRP502930	PRJNA1102048	Danio rerio Raw sequence reads	PRJNA1102048	Whole Genome Sequencing	This experimental study aimed to investigate a role of Irg1l/itaconate axis in zebrafish neuromast development using RNA seq analysis. At 5dpf Larvae treated with 4 octyl itaconate was preformed to subsequent transcriptomic analysis.		Model organism or animal sample from Danio rerio	Zebrafish 4 octyl itaconate sample1	strain:TgBrn3C:mGFP\|age:5dpf\|collection date:2022 09 25\|geo loc name:China\|sex:pooled male and female\|tissue:larvae\|BioSampleModel:Model organism or animal	Zebrafish 4 octyl itaconate 1	4OI 1	4OI 1	DNA barcode		RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP502930		4OI-1_S27_L003_R1_001.fastq.gz 4OI-1_S27_L003_R2_001.fastq.gz	fastq fastq	7099570500.0	23665235.0	4OI 1 S27 L003 R1 001.fastq.gz	0:150 1:150	A:1858012411;C:1693592911;G:1723374425;T:1824476953;N:113800	150	150	1858012411	1693592911	1723374425	1824476953	113800	SRX24313478	SRS21075229	SRA1849567	Nantong University\|Institute of Special Environmental Medicine	Nantong University	2	0.96619	0.96559	0.04154	0.04152	0.70386	0.70412	0.48321	0.49372	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-04-19	Larval	Larval	Whole Organism	All anatomical structures
32617	32617	SRR29366294	SRX24880743	SRS21589520	SRP513315	PRJNA1122875	Transcriptome of zebrafish Danio rerio larvae exposed to MPs at xxx dpf	PRJNA1122875	Other	This study aims to figure out the NPs toxicity on zebrafish at early stages especially on visual system development.			NPs4	strain:TU\|isolate:NPs4\|age:5dpf\|collection date:2023 07 30\|geo loc name:China:Zhejiang\|sex:pooled male and female\|tissue:the front part of larvae\|BioSampleModel:Model organism or animal	RNA Seq of zebrafish larvae	NPs4	NPs4	A total amount of 9 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual mode mRNA Library Prep Kit for Illumina Yeasen Biotechnology Shanghai Co. Ltd. following x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000…		RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP513315		Unknown_BO623-04T0022_good_1.fq.gz Unknown_BO623-04T0022_good_2.fq.gz	fastq fastq	6748273836.0	22592809.0	Unknown BO623 04T0022 good 1.fq.gz	0:149.35 1:149.35	A:1774719919;C:1597377190;G:1614927098;T:1761071358;N:178271	149	149	1774719919	1597377190	1614927098	1761071358	178271	SRX24880743	SRS21589520	SRA1896007	Zhejiang University\|College of Animal Science	Zhejiang University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-06-11	Larval	Larval	Whole Organism	All anatomical structures
32618	32618	SRR29366295	SRX24880742	SRS21589518	SRP513315	PRJNA1122875	Transcriptome of zebrafish Danio rerio larvae exposed to MPs at xxx dpf	PRJNA1122875	Other	This study aims to figure out the NPs toxicity on zebrafish at early stages especially on visual system development.			NPs3	strain:TU\|isolate:NPs3\|age:5dpf\|collection date:2023 07 30\|geo loc name:China:Zhejiang\|sex:pooled male and female\|tissue:the front part of larvae\|BioSampleModel:Model organism or animal	RNA Seq of zebrafish larvae	NPs3	NPs3	A total amount of 8 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual mode mRNA Library Prep Kit for Illumina Yeasen Biotechnology Shanghai Co. Ltd. following x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000…		RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP513315		Unknown_BO623-04T0021_good_1.fq.gz Unknown_BO623-04T0021_good_2.fq.gz	fastq fastq	6529485490.0	21847936.0	Unknown BO623 04T0021 good 1.fq.gz	0:149.43 1:149.43	A:1717039978;C:1547743896;G:1563982349;T:1700522682;N:196585	149	149	1717039978	1547743896	1563982349	1700522682	196585	SRX24880742	SRS21589518	SRA1896007	Zhejiang University\|College of Animal Science	Zhejiang University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-06-11	Larval	Larval	Whole Organism	All anatomical structures
32619	32619	SRR29366296	SRX24880741	SRS21589519	SRP513315	PRJNA1122875	Transcriptome of zebrafish Danio rerio larvae exposed to MPs at xxx dpf	PRJNA1122875	Other	This study aims to figure out the NPs toxicity on zebrafish at early stages especially on visual system development.			NPs2	strain:TU\|isolate:NPs2\|age:5dpf\|collection date:2023 07 30\|geo loc name:China:Zhejiang\|sex:pooled male and female\|tissue:the front part of larvae\|BioSampleModel:Model organism or animal	RNA Seq of zebrafish larvae	NPs2	NPs2	A total amount of 7 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual mode mRNA Library Prep Kit for Illumina Yeasen Biotechnology Shanghai Co. Ltd. following x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000…		RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP513315		Unknown_BO623-04T0020_good_1.fq.gz Unknown_BO623-04T0020_good_2.fq.gz	fastq fastq	6699049910.0	22407080.0	Unknown BO623 04T0020 good 1.fq.gz	0:149.49 1:149.49	A:1761959579;C:1586799482;G:1603631340;T:1746520369;N:139140	149	149	1761959579	1586799482	1603631340	1746520369	139140	SRX24880741	SRS21589519	SRA1896007	Zhejiang University\|College of Animal Science	Zhejiang University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-06-11	Larval	Larval	Whole Organism	All anatomical structures
32620	32620	SRR29366297	SRX24880740	SRS21589517	SRP513315	PRJNA1122875	Transcriptome of zebrafish Danio rerio larvae exposed to MPs at xxx dpf	PRJNA1122875	Other	This study aims to figure out the NPs toxicity on zebrafish at early stages especially on visual system development.			NPs1	strain:TU\|isolate:NPs1\|age:5dpf\|collection date:2023 07 30\|geo loc name:China:Zhejiang\|sex:pooled male and female\|tissue:the front part of larvae\|BioSampleModel:Model organism or animal	RNA Seq of zebrafish larvae	NPs1	NPs1	A total amount of 6 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual mode mRNA Library Prep Kit for Illumina Yeasen Biotechnology Shanghai Co. Ltd. following x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000…		RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP513315		Unknown_BO623-04T0019_good_1.fq.gz Unknown_BO623-04T0019_good_2.fq.gz	fastq fastq	6132468788.0	20516184.0	Unknown BO623 04T0019 good 1.fq.gz	0:149.45 1:149.45	A:1607332987;C:1458658424;G:1471957341;T:1594421337;N:98699	149	149	1607332987	1458658424	1471957341	1594421337	98699	SRX24880740	SRS21589517	SRA1896007	Zhejiang University\|College of Animal Science	Zhejiang University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-06-11	Larval	Larval	Whole Organism	All anatomical structures
32621	32621	SRR29366298	SRX24880739	SRS21589516	SRP513315	PRJNA1122875	Transcriptome of zebrafish Danio rerio larvae exposed to MPs at xxx dpf	PRJNA1122875	Other	This study aims to figure out the NPs toxicity on zebrafish at early stages especially on visual system development.			C6	strain:TU\|isolate:Control6\|age:5dpf\|collection date:2023 07 30\|geo loc name:China:Zhejiang\|sex:pooled male and female\|tissue:the front part of larvae\|BioSampleModel:Model organism or animal	RNA Seq of zebrafish larvae	C6	C6	A total amount of 5 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual mode mRNA Library Prep Kit for Illumina Yeasen Biotechnology Shanghai Co. Ltd. following x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000…		RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP513315		Unknown_BO623-04T0018_good_1.fq.gz Unknown_BO623-04T0018_good_2.fq.gz	fastq fastq	5940082248.0	19857041.0	Unknown BO623 04T0018 good 1.fq.gz	0:149.57 1:149.57	A:1533707674;C:1435538751;G:1452812826;T:1517833025;N:189972	149	149	1533707674	1435538751	1452812826	1517833025	189972	SRX24880739	SRS21589516	SRA1896007	Zhejiang University\|College of Animal Science	Zhejiang University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-06-11	Larval	Larval	Whole Organism	All anatomical structures
32622	32622	SRR29366299	SRX24880738	SRS21589515	SRP513315	PRJNA1122875	Transcriptome of zebrafish Danio rerio larvae exposed to MPs at xxx dpf	PRJNA1122875	Other	This study aims to figure out the NPs toxicity on zebrafish at early stages especially on visual system development.			C5	strain:TU\|isolate:Control5\|age:5dpf\|collection date:2023 07 30\|geo loc name:China:Zhejiang\|sex:pooled male and female\|tissue:the front part of larvae\|BioSampleModel:Model organism or animal	RNA Seq of zebrafish larvae	C5	C5	A total amount of 4 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual mode mRNA Library Prep Kit for Illumina Yeasen Biotechnology Shanghai Co. Ltd. following x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000…		RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP513315		Unknown_BO623-04T0017_good_1.fq.gz Unknown_BO623-04T0017_good_2.fq.gz	fastq fastq	6758002932.0	22599590.0	Unknown BO623 04T0017 good 1.fq.gz	0:149.52 1:149.52	A:1739766340;C:1637642157;G:1652002401;T:1728330255;N:261779	149	149	1739766340	1637642157	1652002401	1728330255	261779	SRX24880738	SRS21589515	SRA1896007	Zhejiang University\|College of Animal Science	Zhejiang University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-06-11	Larval	Larval	Whole Organism	All anatomical structures
32623	32623	SRR29366300	SRX24880737	SRS21589514	SRP513315	PRJNA1122875	Transcriptome of zebrafish Danio rerio larvae exposed to MPs at xxx dpf	PRJNA1122875	Other	This study aims to figure out the NPs toxicity on zebrafish at early stages especially on visual system development.			C4	strain:TU\|isolate:Control4\|age:5dpf\|collection date:2023 07 30\|geo loc name:China:Zhejiang\|sex:pooled male and female\|tissue:the front part of larvae\|BioSampleModel:Model organism or animal	RNA Seq of zebrafish larvae	C4	C4	A total amount of 3 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual mode mRNA Library Prep Kit for Illumina Yeasen Biotechnology Shanghai Co. Ltd. following x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000…		RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP513315		Unknown_BO623-04T0016_good_1.fq.gz Unknown_BO623-04T0016_good_2.fq.gz	fastq fastq	6210972784.0	20767744.0	Unknown BO623 04T0016 good 1.fq.gz	0:149.53 1:149.53	A:1591917700;C:1506245368;G:1529628371;T:1583090947;N:90398	149	149	1591917700	1506245368	1529628371	1583090947	90398	SRX24880737	SRS21589514	SRA1896007	Zhejiang University\|College of Animal Science	Zhejiang University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-06-11	Larval	Larval	Whole Organism	All anatomical structures
32624	32624	SRR29366301	SRX24880736	SRS21589513	SRP513315	PRJNA1122875	Transcriptome of zebrafish Danio rerio larvae exposed to MPs at xxx dpf	PRJNA1122875	Other	This study aims to figure out the NPs toxicity on zebrafish at early stages especially on visual system development.			C3	strain:TU\|isolate:Control3\|age:5dpf\|collection date:2023 07 30\|geo loc name:China:Zhejiang\|sex:pooled male and female\|tissue:the front part of larvae\|BioSampleModel:Model organism or animal	RNA Seq of zebrafish larvae	C3	C3	A total amount of 2 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual mode mRNA Library Prep Kit for Illumina Yeasen Biotechnology Shanghai Co. Ltd. following x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000…		RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP513315		Unknown_BO623-04T0015_good_1.fq.gz Unknown_BO623-04T0015_good_2.fq.gz	fastq fastq	6666249022.0	22284306.0	Unknown BO623 04T0015 good 1.fq.gz	0:149.57 1:149.57	A:1722337869;C:1610144787;G:1630507947;T:1703082771;N:175648	149	149	1722337869	1610144787	1630507947	1703082771	175648	SRX24880736	SRS21589513	SRA1896007	Zhejiang University\|College of Animal Science	Zhejiang University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-06-11	Larval	Larval	Whole Organism	All anatomical structures
32625	32625	SRR29366302	SRX24880735	SRS21589512	SRP513315	PRJNA1122875	Transcriptome of zebrafish Danio rerio larvae exposed to MPs at xxx dpf	PRJNA1122875	Other	This study aims to figure out the NPs toxicity on zebrafish at early stages especially on visual system development.			NPs6	strain:TU\|isolate:NPs6\|age:5dpf\|collection date:2023 07 30\|geo loc name:China:Zhejiang\|sex:pooled male and female\|tissue:the front part of larvae\|BioSampleModel:Model organism or animal	RNA Seq of zebrafish larvae	NPs6	NPs6	A total amount of11 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual mode mRNA Library Prep Kit for Illumina Yeasen Biotechnology Shanghai Co. Ltd. following x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000…		RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP513315		Unknown_BO623-04T0024_good_1.fq.gz Unknown_BO623-04T0024_good_2.fq.gz	fastq fastq	6819262402.0	22797722.0	Unknown BO623 04T0024 good 1.fq.gz	0:149.56 1:149.56	A:1781861689;C:1629655448;G:1645382478;T:1762184452;N:178335	149	149	1781861689	1629655448	1645382478	1762184452	178335	SRX24880735	SRS21589512	SRA1896007	Zhejiang University\|College of Animal Science	Zhejiang University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-06-11	Larval	Larval	Whole Organism	All anatomical structures
32626	32626	SRR29366303	SRX24880734	SRS21589511	SRP513315	PRJNA1122875	Transcriptome of zebrafish Danio rerio larvae exposed to MPs at xxx dpf	PRJNA1122875	Other	This study aims to figure out the NPs toxicity on zebrafish at early stages especially on visual system development.			NPs5	strain:TU\|isolate:NPs5\|age:5dpf\|collection date:2023 07 30\|geo loc name:China:Zhejiang\|sex:pooled male and female\|tissue:the front part of larvae\|BioSampleModel:Model organism or animal	RNA Seq of zebrafish larvae	NPs5	NPs5	A total amount of10 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual mode mRNA Library Prep Kit for Illumina Yeasen Biotechnology Shanghai Co. Ltd. following x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000…		RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP513315		Unknown_BO623-04T0023_good_1.fq.gz Unknown_BO623-04T0023_good_2.fq.gz	fastq fastq	6773730348.0	22673915.0	Unknown BO623 04T0023 good 1.fq.gz	0:149.37 1:149.37	A:1779182337;C:1607164031;G:1624141377;T:1763062617;N:179986	149	149	1779182337	1607164031	1624141377	1763062617	179986	SRX24880734	SRS21589511	SRA1896007	Zhejiang University\|College of Animal Science	Zhejiang University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-06-11	Larval	Larval	Whole Organism	All anatomical structures
32627	32627	SRR29366304	SRX24880733	SRS21589509	SRP513315	PRJNA1122875	Transcriptome of zebrafish Danio rerio larvae exposed to MPs at xxx dpf	PRJNA1122875	Other	This study aims to figure out the NPs toxicity on zebrafish at early stages especially on visual system development.			C2	strain:TU\|isolate:Control2\|age:5dpf\|collection date:2023 07 30\|geo loc name:China:Zhejiang\|sex:pooled male and female\|tissue:the front part of larvae\|BioSampleModel:Model organism or animal	RNA Seq of zebrafish larvae	C2	C2	A total amount of 1 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual mode mRNA Library Prep Kit for Illumina Yeasen Biotechnology Shanghai Co. Ltd. following manufacturers recommendations and index codes were added to attribute sequences to each sample. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads.First strand cDNA was synthesized and second strand cDNA synthesis was subsequently performed. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of 3 ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then 3 l USER Enzyme NEB USA was used with size selected adaptor ligated cDNA at 37C for 15 min followed by 5 min at 95C before PCR. Then PCR was performed with Phusion High Fidelity DNA polymerase Universal PCR primers and Index X Primer. At last PCR products were purified AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system.		RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP513315		Unknown_BO623-04T0014_good_1.fq.gz Unknown_BO623-04T0014_good_2.fq.gz	fastq fastq	6805354296.0	22755187.0	Unknown BO623 04T0014 good 1.fq.gz	0:149.53 1:149.53	A:1742825793;C:1651738009;G:1677448209;T:1733168084;N:174201	149	149	1742825793	1651738009	1677448209	1733168084	174201	SRX24880733	SRS21589509	SRA1896007	Zhejiang University\|College of Animal Science	Zhejiang University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	nebnext	bulk	unknown	unknown	China	2024-06-11	Larval	Larval	Whole Organism	All anatomical structures

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