metadata: run_metadata: 8,175 rows where experiment.library_layout = "SINGLE", experiment.library_selection = "cDNA" and technology = "unknown"

8,175 rows where experiment.library_layout = "SINGLE", experiment.library_selection = "cDNA" and technology = "unknown"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	sample.description	sample.title	sample.alias	sample.centername	sample.attributes	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.spot_descriptor	experiment.study_ref	run.title	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.nofeature_rate.mate1	seqdetective.sparsity.mate1	seqdetective.pos_strand_rate.mate1	seqdetective.readlen.mate1	seqdetective.judgement.mate1	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
14	14	DRR334977	DRX323973	DRS217313	DRP008001	PRJDB12578	Allometric scaling of RNA abundance from genes to communities	DRP008001	Other	The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole body RNA content in organisms. However testing RNA allometric scaling with next generation sequencing is yet to be done. Here we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling while the assumed temperature dependence appeared to be weak. Lastly allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.		totalRNA metatranscriptomic sequences from mock communities consist of five model species	rRNA mock community at 28 degrees rep 3	SAMD00422597		sample name:rRNA mock community 28 degrees rep 3\|biological replicate:3\|collection date:2021 01 15\|dev stage:Adult\|technical replicate:3\|temp:28\|treatment:rRNA	NextSeq 2000 sequencing of SAMD00422597	DRX323973	t28 3 tRNA.fastq	1	NEBNext Kit for Illumina		RNA-Seq	METATRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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>	DRP008001	NextSeq 2000 sequencing of SAMD00422597				3791170746.0	37701921.0	DRR334977	0:100.56 1:0	A:967477491;C:926887571;G:898697642;T:998107868;N:174	100	0	967477491	926887571	898697642	998107868	174	DRX323973	DRS217313	DRA013226	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	1	0.31527	0.06446	0.88844	0.62118	101	B	usable mapping rate	illumina	nextseq_v2	unknown	random_priming	nebnext	bulk	unknown	unknown	Taiwan	2021-12-23	Adult	Adult	Undetermined	Undetermined
15	15	DRR334976	DRX323972	DRS217312	DRP008001	PRJDB12578	Allometric scaling of RNA abundance from genes to communities	DRP008001	Other	The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole body RNA content in organisms. However testing RNA allometric scaling with next generation sequencing is yet to be done. Here we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling while the assumed temperature dependence appeared to be weak. Lastly allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.		totalRNA metatranscriptomic sequences from mock communities consist of five model species	rRNA mock community at 28 degrees rep 2	SAMD00422596		sample name:rRNA mock community 28 degrees rep 2\|biological replicate:3\|collection date:2021 01 15\|dev stage:Adult\|technical replicate:2\|temp:28\|treatment:rRNA	NextSeq 2000 sequencing of SAMD00422596	DRX323972	t28 2 tRNA.fastq	1	NEBNext Kit for Illumina		RNA-Seq	METATRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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>	DRP008001	NextSeq 2000 sequencing of SAMD00422596				2801693695.0	27860658.0	DRR334976	0:100.56 1:0	A:700189496;C:702936549;G:679920984;T:718646067;N:599	100	0	700189496	702936549	679920984	718646067	599	DRX323972	DRS217312	DRA013226	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	1	0.43508	0.08819	0.85859	0.69447	101	B	usable mapping rate	illumina	nextseq_v2	unknown	random_priming	nebnext	bulk	unknown	unknown	Taiwan	2021-12-23	Adult	Adult	Undetermined	Undetermined
16	16	DRR334975	DRX323971	DRS217311	DRP008001	PRJDB12578	Allometric scaling of RNA abundance from genes to communities	DRP008001	Other	The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole body RNA content in organisms. However testing RNA allometric scaling with next generation sequencing is yet to be done. Here we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling while the assumed temperature dependence appeared to be weak. Lastly allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.		totalRNA metatranscriptomic sequences from mock communities consist of five model species	rRNA mock community at 28 degrees rep 1	SAMD00422595		sample name:rRNA mock community 28 degrees rep 1\|biological replicate:3\|collection date:2021 01 15\|dev stage:Adult\|technical replicate:1\|temp:28\|treatment:rRNA	NextSeq 2000 sequencing of SAMD00422595	DRX323971	t28 1 tRNA.fastq	1	NEBNext Kit for Illumina		RNA-Seq	METATRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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>	DRP008001	NextSeq 2000 sequencing of SAMD00422595				3148691934.0	31307464.0	DRR334975	0:100.57 1:0	A:785000734;C:791315678;G:766594599;T:805780465;N:458	100	0	785000734	791315678	766594599	805780465	458	DRX323971	DRS217311	DRA013226	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	1	0.37139	0.09061	0.94065	0.74047	101	B	usable mapping rate	illumina	nextseq_v2	unknown	random_priming	nebnext	bulk	unknown	unknown	Taiwan	2021-12-23	Adult	Adult	Undetermined	Undetermined
17	17	DRR334974	DRX323970	DRS217310	DRP008001	PRJDB12578	Allometric scaling of RNA abundance from genes to communities	DRP008001	Other	The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole body RNA content in organisms. However testing RNA allometric scaling with next generation sequencing is yet to be done. Here we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling while the assumed temperature dependence appeared to be weak. Lastly allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.		totalRNA metatranscriptomic sequences from mock communities consist of five model species	rRNA mock community at 19 degrees rep 3	SAMD00422594		sample name:rRNA mock community 19 degrees rep 3\|biological replicate:2\|collection date:2021 01 15\|dev stage:Adult\|technical replicate:3\|temp:19\|treatment:rRNA	NextSeq 2000 sequencing of SAMD00422594	DRX323970	t19 3 tRNA.fastq	1	NEBNext Kit for Illumina		RNA-Seq	METATRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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>	DRP008001	NextSeq 2000 sequencing of SAMD00422594				2856186273.0	28400524.0	DRR334974	0:100.57 1:0	A:695685787;C:733754277;G:715270279;T:711475544;N:386	100	0	695685787	733754277	715270279	711475544	386	DRX323970	DRS217310	DRA013226	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	1	0.48152	0.10933	0.87105	0.7287	101	B	usable mapping rate	illumina	nextseq_v2	unknown	random_priming	nebnext	bulk	unknown	unknown	Taiwan	2021-12-23	Adult	Adult	Undetermined	Undetermined
18	18	DRR334973	DRX323969	DRS217309	DRP008001	PRJDB12578	Allometric scaling of RNA abundance from genes to communities	DRP008001	Other	The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole body RNA content in organisms. However testing RNA allometric scaling with next generation sequencing is yet to be done. Here we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling while the assumed temperature dependence appeared to be weak. Lastly allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.		totalRNA metatranscriptomic sequences from mock communities consist of five model species	rRNA mock community at 19 degrees rep 2	SAMD00422593		sample name:rRNA mock community 19 degrees rep 2\|biological replicate:2\|collection date:2021 01 15\|dev stage:Adult\|technical replicate:2\|temp:19\|treatment:rRNA	NextSeq 2000 sequencing of SAMD00422593	DRX323969	t19 2 tRNA.fastq	1	NEBNext Kit for Illumina		RNA-Seq	METATRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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>	DRP008001	NextSeq 2000 sequencing of SAMD00422593				3199929804.0	31816971.0	DRR334973	0:100.57 1:0	A:777149590;C:825478743;G:804835148;T:792466124;N:199	100	0	777149590	825478743	804835148	792466124	199	DRX323969	DRS217309	DRA013226	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	1	0.4418	0.10282	0.89706	0.74667	101	B	usable mapping rate	illumina	nextseq_v2	unknown	random_priming	nebnext	bulk	unknown	unknown	Taiwan	2021-12-23	Adult	Adult	Undetermined	Undetermined
19	19	DRR334972	DRX323968	DRS217308	DRP008001	PRJDB12578	Allometric scaling of RNA abundance from genes to communities	DRP008001	Other	The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole body RNA content in organisms. However testing RNA allometric scaling with next generation sequencing is yet to be done. Here we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling while the assumed temperature dependence appeared to be weak. Lastly allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.		totalRNA metatranscriptomic sequences from mock communities consist of five model species	rRNA mock community at 19 degrees rep 1	SAMD00422592		sample name:rRNA mock community 19 degrees rep 1\|biological replicate:2\|collection date:2021 01 15\|dev stage:Adult\|technical replicate:1\|temp:19\|treatment:rRNA	NextSeq 2000 sequencing of SAMD00422592	DRX323968	t19 1 tRNA.fastq	1	NEBNext Kit for Illumina		RNA-Seq	METATRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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>	DRP008001	NextSeq 2000 sequencing of SAMD00422592				3658675391.0	36374718.0	DRR334972	0:100.58 1:0	A:879342063;C:954687406;G:929537615;T:895107890;N:417	100	0	879342063	954687406	929537615	895107890	417	DRX323968	DRS217308	DRA013226	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	1	0.49439	0.11691	0.88239	0.73925	101	B	usable mapping rate	illumina	nextseq_v2	unknown	random_priming	nebnext	bulk	unknown	unknown	Taiwan	2021-12-23	Adult	Adult	Undetermined	Undetermined
20	20	DRR334971	DRX323967	DRS217307	DRP008001	PRJDB12578	Allometric scaling of RNA abundance from genes to communities	DRP008001	Other	The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole body RNA content in organisms. However testing RNA allometric scaling with next generation sequencing is yet to be done. Here we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling while the assumed temperature dependence appeared to be weak. Lastly allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.		totalRNA metatranscriptomic sequences from mock communities consist of five model species	rRNA mock community at 10 degrees rep 3	SAMD00422591		sample name:rRNA mock community 10 degrees rep 3\|biological replicate:1\|collection date:2021 01 15\|dev stage:Adult\|technical replicate:3\|temp:10\|treatment:rRNA	NextSeq 2000 sequencing of SAMD00422591	DRX323967	t10 3 tRNA.fastq	1	NEBNext Kit for Illumina		RNA-Seq	METATRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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>	DRP008001	NextSeq 2000 sequencing of SAMD00422591				3017524690.0	30006334.0	DRR334971	0:100.56 1:0	A:771967717;C:738814269;G:712866126;T:793876235;N:343	100	0	771967717	738814269	712866126	793876235	343	DRX323967	DRS217307	DRA013226	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	1	0.33157	0.07363	0.9093	0.73422	100	B	usable mapping rate	illumina	nextseq_v2	unknown	random_priming	nebnext	bulk	unknown	unknown	Taiwan	2021-12-23	Adult	Adult	Undetermined	Undetermined
21	21	DRR334970	DRX323966	DRS217306	DRP008001	PRJDB12578	Allometric scaling of RNA abundance from genes to communities	DRP008001	Other	The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole body RNA content in organisms. However testing RNA allometric scaling with next generation sequencing is yet to be done. Here we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling while the assumed temperature dependence appeared to be weak. Lastly allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.		totalRNA metatranscriptomic sequences from mock communities consist of five model species	rRNA mock community at 10 degrees rep 2	SAMD00422590		sample name:rRNA mock community 10 degrees rep 2\|biological replicate:1\|collection date:2021 01 15\|dev stage:Adult\|technical replicate:2\|temp:10\|treatment:rRNA	NextSeq 2000 sequencing of SAMD00422590	DRX323966	t10 2 tRNA.fastq	1	NEBNext Kit for Illumina		RNA-Seq	METATRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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>	DRP008001	NextSeq 2000 sequencing of SAMD00422590				3115915184.0	30982336.0	DRR334970	0:100.57 1:0	A:765727966;C:794741415;G:771082024;T:784363609;N:170	100	0	765727966	794741415	771082024	784363609	170	DRX323966	DRS217306	DRA013226	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	1	0.45458	0.10504	0.89357	0.749	100	B	usable mapping rate	illumina	nextseq_v2	unknown	random_priming	nebnext	bulk	unknown	unknown	Taiwan	2021-12-23	Adult	Adult	Undetermined	Undetermined
22	22	DRR334969	DRX323965	DRS217305	DRP008001	PRJDB12578	Allometric scaling of RNA abundance from genes to communities	DRP008001	Other	The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole body RNA content in organisms. However testing RNA allometric scaling with next generation sequencing is yet to be done. Here we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling while the assumed temperature dependence appeared to be weak. Lastly allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.		totalRNA metatranscriptomic sequences from mock communities consist of five model species	rRNA mock community at 10 degrees rep 1	SAMD00422589		sample name:rRNA mock community 10 degrees rep 1\|biological replicate:1\|collection date:2021 01 15\|dev stage:Adult\|technical replicate:1\|temp:10\|treatment:rRNA	NextSeq 2000 sequencing of SAMD00422589	DRX323965	t10 1 tRNA.fastq	1	NEBNext Kit for Illumina		RNA-Seq	METATRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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>	DRP008001	NextSeq 2000 sequencing of SAMD00422589				3206657309.0	31883532.0	DRR334969	0:100.57 1:0	A:792874386;C:814578518;G:787469614;T:811734581;N:210	100	0	792874386	814578518	787469614	811734581	210	DRX323965	DRS217305	DRA013226	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	1	0.40156	0.09664	0.92898	0.74114	101	B	usable mapping rate	illumina	nextseq_v2	unknown	random_priming	nebnext	bulk	unknown	unknown	Taiwan	2021-12-23	Adult	Adult	Undetermined	Undetermined
50	50	DRR029944	DRX026962	DRS086502	DRP004756	PRJDB3475	Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish	DRP004756	Other	To identify ovulation inducing genes RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.		ovulation duirng natural paring	zebrafish ovary isolated from adult fish at ovulation duirng natural paring. [RNAseq]	SAMD00025434		sample name:6 Ovu\|strain:roy\|tissue type:ovary\|dev stage:adult	Illumina HiSeq 2500 sequencing of SAMD00025434	DRX026962	6 Ovu	1	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</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>	DRP004756	Illumina HiSeq 2500 sequencing of SAMD00025434				351766656.0	9771296.0	DRR029944	0:36	A:79811727;C:85391142;G:90185809;T:96371771;N:6207	36		79811727	85391142	90185809	96371771	6207	DRX026962	DRS086502	DRA003031	SHIZUOKA\|Shizuoka University	Shizuoka University	1	0.91956	0.01686	0.76637	0.45997	36	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Japan	2019-01-23	Adult	Adult	Gonad	Reproductive System
51	51	DRR029943	DRX026961	DRS086501	DRP004756	PRJDB3475	Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish	DRP004756	Other	To identify ovulation inducing genes RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.		oocyte maturation duirng natural paring	zebrafish ovary isolated from adult fish at oocyte maturation duirng natural paring. [RNAseq]	SAMD00025433		sample name:5 OM\|strain:roy\|tissue type:ovary\|dev stage:adult	Illumina HiSeq 2500 sequencing of SAMD00025433	DRX026961	5 OM	1	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</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>	DRP004756	Illumina HiSeq 2500 sequencing of SAMD00025433				573617016.0	15933806.0	DRR029943	0:36	A:130606804;C:141376330;G:145891720;T:155734276;N:7886	36		130606804	141376330	145891720	155734276	7886	DRX026961	DRS086501	DRA003031	SHIZUOKA\|Shizuoka University	Shizuoka University	1	0.91108	0.0173	0.76205	0.46319	36	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Japan	2019-01-23	Adult	Adult	Multi-tissue	Multi-system
52	52	DRR029942	DRX026960	DRS086500	DRP004756	PRJDB3475	Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish	DRP004756	Other	To identify ovulation inducing genes RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.		in vivo testosterone treatment	zebrafish ovary isolated from adult fish in vivo testoster1 treatment. [RNAseq replicate]	SAMD00025432		sample name:4 Tes rep\|strain:roy\|tissue type:ovary\|dev stage:adult	Illumina HiSeq 2500 sequencing of SAMD00025432	DRX026960	4 Tes rep	1	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</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>	DRP004756	Illumina HiSeq 2500 sequencing of SAMD00025432				366042528.0	10167848.0	DRR029942	0:36	A:84988522;C:88640326;G:93559022;T:98847003;N:7655	36		84988522	88640326	93559022	98847003	7655	DRX026960	DRS086500	DRA003031	SHIZUOKA\|Shizuoka University	Shizuoka University	1	0.91602	0.01846	0.76015	0.46475	36	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Japan	2019-01-23	Adult	Adult	Gonad	Reproductive System
53	53	DRR029941	DRX026959	DRS086499	DRP004756	PRJDB3475	Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish	DRP004756	Other	To identify ovulation inducing genes RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.		in vivo testosterone treatment	zebrafish ovary isolated from adult fish in vivo testoster1 treatment. [RNAseq]	SAMD00025431		sample name:4 Tes\|strain:roy\|tissue type:ovary\|dev stage:adult	Illumina HiSeq 2500 sequencing of SAMD00025431	DRX026959	4 Tes	1	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</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>	DRP004756	Illumina HiSeq 2500 sequencing of SAMD00025431				1269835992.0	35273222.0	DRR029941	0:36	A:275250658;C:323605136;G:316729009;T:354204170;N:47019	36		275250658	323605136	316729009	354204170	47019	DRX026959	DRS086499	DRA003031	SHIZUOKA\|Shizuoka University	Shizuoka University	1	0.91467	0.02353	0.75962	0.46861	36	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Japan	2019-01-23	Adult	Adult	Gonad	Reproductive System
54	54	DRR029940	DRX026958	DRS086498	DRP004756	PRJDB3475	Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish	DRP004756	Other	To identify ovulation inducing genes RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.		in vivo diethylstilbestrol DES treatment	zebrafish ovary isolated from adult fish in vivo diethylstilbestrol DES treatment. [RNAseq replicate]	SAMD00025430		sample name:3 DES rep\|strain:roy\|tissue type:ovary\|dev stage:adult	Illumina HiSeq 2500 sequencing of SAMD00025430	DRX026958	3 DES rep	1	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</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>	DRP004756	Illumina HiSeq 2500 sequencing of SAMD00025430				658651536.0	18295876.0	DRR029940										DRX026958	DRS086498	DRA003031	SHIZUOKA\|Shizuoka University	Shizuoka University	1	0.89964	0.01785	0.76451	0.45872	36	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Japan	2019-01-23	Adult	Adult	Gonad	Reproductive System
55	55	DRR029939	DRX026957	DRS086497	DRP004756	PRJDB3475	Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish	DRP004756	Other	To identify ovulation inducing genes RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.		in vivo diethylstilbestrol DES treatment	zebrafish ovary isolated from adult fish in vivo diethylstilbestrol DES treatment. [RNAseq]	SAMD00025429		sample name:3 DES\|strain:roy\|tissue type:ovary\|dev stage:adult	Illumina HiSeq 2500 sequencing of SAMD00025429	DRX026957	3 DES	1	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</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>	DRP004756	Illumina HiSeq 2500 sequencing of SAMD00025429				1202024016.0	33389556.0	DRR029939	0:36	A:263319430;C:305852921;G:298798093;T:334008544;N:45028	36		263319430	305852921	298798093	334008544	45028	DRX026957	DRS086497	DRA003031	SHIZUOKA\|Shizuoka University	Shizuoka University	1	0.90643	0.02337	0.75008	0.47587	36	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Japan	2019-01-23	Adult	Adult	Gonad	Reproductive System
56	56	DRR029938	DRX026956	DRS086496	DRP004756	PRJDB3475	Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish	DRP004756	Other	To identify ovulation inducing genes RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.		in vivo maturation inducing hormone DHP treatment	zebrafish ovary isolated from adult fish in vivo maturation inducing horm1 DHP treatment. [RNAseq replicate]	SAMD00025428		sample name:2 DHP rep\|strain:roy\|tissue type:ovary\|dev stage:adult	Illumina HiSeq 2500 sequencing of SAMD00025428	DRX026956	2 DHP rep	1	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</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>	DRP004756	Illumina HiSeq 2500 sequencing of SAMD00025428				434243088.0	12062308.0	DRR029938	0:36	A:99859342;C:105890785;G:110526688;T:117957580;N:8693	36		99859342	105890785	110526688	117957580	8693	DRX026956	DRS086496	DRA003031	SHIZUOKA\|Shizuoka University	Shizuoka University	1	0.91529	0.02061	0.7595	0.45809	36	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Japan	2019-01-23	Adult	Adult	Gonad	Reproductive System
57	57	DRR029937	DRX026955	DRS086495	DRP004756	PRJDB3475	Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish	DRP004756	Other	To identify ovulation inducing genes RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.		in vivo maturation inducing hormone DHP treatment	zebrafish ovary isolated from adult fish in vivo maturation inducing horm1 DHP treatment. [RNAseq]	SAMD00025427		sample name:2 DHP\|strain:roy\|tissue type:ovary\|dev stage:adult	Illumina HiSeq 2500 sequencing of SAMD00025427	DRX026955	2 DHP	1	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</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>	DRP004756	Illumina HiSeq 2500 sequencing of SAMD00025427				1463868972.0	40663027.0	DRR029937	0:36	A:316060780;C:369221844;G:372845502;T:405685804;N:55042	36		316060780	369221844	372845502	405685804	55042	DRX026955	DRS086495	DRA003031	SHIZUOKA\|Shizuoka University	Shizuoka University	1	0.91556	0.01967	0.76621	0.46541	36	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Japan	2019-01-23	Adult	Adult	Gonad	Reproductive System
58	58	DRR029936	DRX026954	DRS086494	DRP004756	PRJDB3475	Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish	DRP004756	Other	To identify ovulation inducing genes RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.		in vivo ethanol treatment	zebrafish ovary isolated from adult fish in vivo ethanol treatment. [RNAseq replicate]	SAMD00025426		sample name:1 EtOH rep\|strain:roy\|tissue type:ovary\|dev stage:adult	Illumina HiSeq 2500 sequencing of SAMD00025426	DRX026954	1 EtOH rep	1	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</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>	DRP004756	Illumina HiSeq 2500 sequencing of SAMD00025426				438020208.0	12167228.0	DRR029936	0:36	A:101672612;C:105602774;G:110120652;T:120615069;N:9101	36		101672612	105602774	110120652	120615069	9101	DRX026954	DRS086494	DRA003031	SHIZUOKA\|Shizuoka University	Shizuoka University	1	0.90777	0.01929	0.7652	0.45988	36	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Japan	2019-01-23	Adult	Adult	Gonad	Reproductive System
59	59	DRR029935	DRX026953	DRS086493	DRP004756	PRJDB3475	Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish	DRP004756	Other	To identify ovulation inducing genes RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.		in vivo ethanol treatment	zebrafish ovary isolated from adult fish in vivo ethanol treatment. [RNAseq]	SAMD00025425		sample name:1 EtOH\|strain:roy\|tissue type:ovary\|dev stage:adult	Illumina HiSeq 2500 sequencing of SAMD00025425	DRX026953	1 EtOH	1	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</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>	DRP004756	Illumina HiSeq 2500 sequencing of SAMD00025425				1365603372.0	37933427.0	DRR029935	0:36	A:299786286;C:345487829;G:342408447;T:377870789;N:50021	36		299786286	345487829	342408447	377870789	50021	DRX026953	DRS086493	DRA003031	SHIZUOKA\|Shizuoka University	Shizuoka University	1	0.91103	0.02142	0.75402	0.46574	36	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Japan	2019-01-23	Adult	Adult	Gonad	Reproductive System
95	95	DRR050167	DRX045209	DRS025834	DRP003043	PRJDB4416	Transcriptome analysis in ES1 expressing rods of zebrafish	DRP003043	Transcriptome Analysis	Transcriptome analysis using next generation sequencing system for isolated rods from zebrafish of wild type T?bingen long fin TL line. Transgenic zebrafish expressing ES1 and/or EGFP in rods were used.		Zebrafish rods expressing ES1 and EGFP	ES1 3	SAMD00044057		sample name:ES1 EGFP rod 003\|strain:Tubingen long fin\|cell type:rod	Ion Torrent PGM sequencing of SAMD00044057	DRX045209	1	1	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent PGM	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>105</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>	DRP003043	Ion Torrent PGM sequencing of SAMD00044057				371748120.0	3469843.0	DRR050167	0:107.14	A:107190409;C:79475572;G:83520360;T:101561779;N:0	107		107190409	79475572	83520360	101561779	0	DRX045209	DRS025834	DRA004229	OSAKA_FB\|Kawamura lab., Frontier Biology, Osaka univ.	Osaka university	1	0.81026	0.26715	0.86953	0.52321	51	B	usable mapping rate	ion_torrent	ion_torrent	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Japan	2016-03-09	Undetermined	Undetermined	Fin	Surface Structure
96	96	DRR050166	DRX045208	DRS025833	DRP003043	PRJDB4416	Transcriptome analysis in ES1 expressing rods of zebrafish	DRP003043	Transcriptome Analysis	Transcriptome analysis using next generation sequencing system for isolated rods from zebrafish of wild type T?bingen long fin TL line. Transgenic zebrafish expressing ES1 and/or EGFP in rods were used.		Zebrafish rods expressing ES1 and EGFP	ES1 2	SAMD00044056		sample name:ES1 EGFP rod 002\|strain:Tubingen long fin\|cell type:rod	Ion Torrent PGM sequencing of SAMD00044056	DRX045208	1	1	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent PGM	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>128</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>	DRP003043	Ion Torrent PGM sequencing of SAMD00044056				425549011.0	3275261.0	DRR050166	0:129.93	A:126640704;C:86415371;G:90822163;T:121670773;N:0	129		126640704	86415371	90822163	121670773	0	DRX045208	DRS025833	DRA004229	OSAKA_FB\|Kawamura lab., Frontier Biology, Osaka univ.	Osaka university	1	0.80223	0.31429	0.85861	0.5272	57	B	usable mapping rate	ion_torrent	ion_torrent	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Japan	2016-03-09	Undetermined	Undetermined	Fin	Surface Structure
97	97	DRR050165	DRX045207	DRS025832	DRP003043	PRJDB4416	Transcriptome analysis in ES1 expressing rods of zebrafish	DRP003043	Transcriptome Analysis	Transcriptome analysis using next generation sequencing system for isolated rods from zebrafish of wild type T?bingen long fin TL line. Transgenic zebrafish expressing ES1 and/or EGFP in rods were used.		Zebrafish rods expressing ES1 and EGFP	ES1 1	SAMD00044055		sample name:ES1 EGFP rod 001\|strain:Tubingen long fin\|cell type:rod	Ion Torrent PGM sequencing of SAMD00044055	DRX045207	1	1	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent PGM	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>147</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>	DRP003043	Ion Torrent PGM sequencing of SAMD00044055				584599765.0	3941083.0	DRR050165	0:148.33	A:164329030;C:129885620;G:136727379;T:153657736;N:0	148		164329030	129885620	136727379	153657736	0	DRX045207	DRS025832	DRA004229	OSAKA_FB\|Kawamura lab., Frontier Biology, Osaka univ.	Osaka university	1	0.83769	0.25395	0.83116	0.52784	185	B	usable mapping rate	ion_torrent	ion_torrent	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Japan	2016-03-09	Undetermined	Undetermined	Fin	Surface Structure
98	98	DRR050164	DRX045206	DRS025831	DRP003043	PRJDB4416	Transcriptome analysis in ES1 expressing rods of zebrafish	DRP003043	Transcriptome Analysis	Transcriptome analysis using next generation sequencing system for isolated rods from zebrafish of wild type T?bingen long fin TL line. Transgenic zebrafish expressing ES1 and/or EGFP in rods were used.		Zebrafish rods expressing EGFP	EGFP 3	SAMD00044054		sample name:EGFP rod 003\|strain:Tubingen long fin\|cell type:rod	Ion Torrent PGM sequencing of SAMD00044054	DRX045206	1	1	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent PGM	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>88</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>	DRP003043	Ion Torrent PGM sequencing of SAMD00044054				343014114.0	3827762.0	DRR050164	0:89.61	A:99421434;C:73070267;G:77738821;T:92783592;N:0	89		99421434	73070267	77738821	92783592	0	DRX045206	DRS025831	DRA004229	OSAKA_FB\|Kawamura lab., Frontier Biology, Osaka univ.	Osaka university	1	0.78953	0.25529	0.87367	0.52148	24	B	usable mapping rate	ion_torrent	ion_torrent	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Japan	2016-03-09	Undetermined	Undetermined	Fin	Surface Structure
99	99	DRR050163	DRX045205	DRS025830	DRP003043	PRJDB4416	Transcriptome analysis in ES1 expressing rods of zebrafish	DRP003043	Transcriptome Analysis	Transcriptome analysis using next generation sequencing system for isolated rods from zebrafish of wild type T?bingen long fin TL line. Transgenic zebrafish expressing ES1 and/or EGFP in rods were used.		Zebrafish rods expressing EGFP	EGFP 2	SAMD00044053		sample name:EGFP rod 002\|strain:Tubingen long fin\|cell type:rod	Ion Torrent PGM sequencing of SAMD00044053	DRX045205	1	1	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent PGM	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>137</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>	DRP003043	Ion Torrent PGM sequencing of SAMD00044053				533069427.0	3824140.0	DRR050163	0:139.40	A:152608173;C:113928273;G:120051739;T:146481242;N:0	139		152608173	113928273	120051739	146481242	0	DRX045205	DRS025830	DRA004229	OSAKA_FB\|Kawamura lab., Frontier Biology, Osaka univ.	Osaka university	1	0.80412	0.26768	0.85338	0.52255	245	B	usable mapping rate	ion_torrent	ion_torrent	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Japan	2016-03-09	Undetermined	Undetermined	Fin	Surface Structure
100	100	DRR050162	DRX045204	DRS025829	DRP003043	PRJDB4416	Transcriptome analysis in ES1 expressing rods of zebrafish	DRP003043	Transcriptome Analysis	Transcriptome analysis using next generation sequencing system for isolated rods from zebrafish of wild type T?bingen long fin TL line. Transgenic zebrafish expressing ES1 and/or EGFP in rods were used.		Zebrafish rods expressing EGFP	EGFP 1	SAMD00044052		sample name:EGFP rod 001\|strain:Tubingen long fin\|cell type:rod	Ion Torrent PGM sequencing of SAMD00044052	DRX045204	1	1	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent PGM	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>113</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>	DRP003043	Ion Torrent PGM sequencing of SAMD00044052				478262965.0	4224064.0	DRR050162	0:113.22	A:136348264;C:104872341;G:113114502;T:123927858;N:0	113		136348264	104872341	113114502	123927858	0	DRX045204	DRS025829	DRA004229	OSAKA_FB\|Kawamura lab., Frontier Biology, Osaka univ.	Osaka university	1	0.86947	0.29839	0.83317	0.51453	80	B	usable mapping rate	ion_torrent	ion_torrent	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Japan	2016-03-09	Undetermined	Undetermined	Fin	Surface Structure
168	168	DRR075402	DRX069316	DRS075497	DRP004473	PRJDB5226	Effects of local gut tumor on whole organismal gene expressions in zebrafish	DRP004473	Other	How tumors affects whole organismal physiology remains largely unknown. To address this we established the novel gut tumor model in zebrafish Danio rerio. This model develops tumor at an early stage of juvenile development when zebrafish larvae are small <4mm enabling us to perform whole organismal RNA seq experiments. Control or tumor bearing zebrafish were dissected into the three parts under microscope: the liver the gut/gut tumor and others. Tissues from >10 individuals were pooled and RNA extracted. Analyses on these RNA seq samples identified a set of host genes affected by the gut tumor contributing to discovering novel tumor organ interactions and their mediators in zebrafish.		The liver of tumor fish 7dpf	Tumor liver	SAMD00065416		sample name:6 Tumor liver 150701 Hiseq3A l3 022\|tissue type:Liver	Illumina HiSeq 2500 sequencing of SAMD00065416	DRX069316	Tumor liver	1	Agilent SureSelect Strand Specific RNA Prep Kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</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>	DRP004473	Illumina HiSeq 2500 sequencing of SAMD00065416				1091167236.0	30310201.0	DRR075402	0:36	A:272216839;C:257523620;G:259746158;T:301642763;N:37856	36		272216839	257523620	259746158	301642763	37856	DRX069316	DRS075497	DRA005199	ATR\|The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International	The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International	1	0.90443	0.08935	0.71863	0.51145	36	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Japan	2018-09-19	Larval	Larval	Multi-tissue	Multi-system
169	169	DRR075401	DRX069315	DRS075496	DRP004473	PRJDB5226	Effects of local gut tumor on whole organismal gene expressions in zebrafish	DRP004473	Other	How tumors affects whole organismal physiology remains largely unknown. To address this we established the novel gut tumor model in zebrafish Danio rerio. This model develops tumor at an early stage of juvenile development when zebrafish larvae are small <4mm enabling us to perform whole organismal RNA seq experiments. Control or tumor bearing zebrafish were dissected into the three parts under microscope: the liver the gut/gut tumor and others. Tissues from >10 individuals were pooled and RNA extracted. Analyses on these RNA seq samples identified a set of host genes affected by the gut tumor contributing to discovering novel tumor organ interactions and their mediators in zebrafish.		The gut of tumor fish 7dpf	Tumor gut	SAMD00065415		sample name:5 Tumor gut 150701 Hiseq3A l3 021\|tissue type:Gut	Illumina HiSeq 2500 sequencing of SAMD00065415	DRX069315	Tumor gut	1	Agilent SureSelect Strand Specific RNA Prep Kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</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>	DRP004473	Illumina HiSeq 2500 sequencing of SAMD00065415				1423792872.0	39549802.0	DRR075401	0:36	A:342328685;C:346616167;G:341519547;T:393278536;N:49937	36		342328685	346616167	341519547	393278536	49937	DRX069315	DRS075496	DRA005199	ATR\|The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International	The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International	1	0.91303	0.0869	0.70494	0.44332	36	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Japan	2018-09-19	Larval	Larval	Multi-tissue	Multi-system
170	170	DRR075400	DRX069314	DRS075495	DRP004473	PRJDB5226	Effects of local gut tumor on whole organismal gene expressions in zebrafish	DRP004473	Other	How tumors affects whole organismal physiology remains largely unknown. To address this we established the novel gut tumor model in zebrafish Danio rerio. This model develops tumor at an early stage of juvenile development when zebrafish larvae are small <4mm enabling us to perform whole organismal RNA seq experiments. Control or tumor bearing zebrafish were dissected into the three parts under microscope: the liver the gut/gut tumor and others. Tissues from >10 individuals were pooled and RNA extracted. Analyses on these RNA seq samples identified a set of host genes affected by the gut tumor contributing to discovering novel tumor organ interactions and their mediators in zebrafish.		The remaining part of body of tumor fish 7dpf	Tumor body	SAMD00065414		sample name:4 Tumor body 150701 Hiseq3A l3 020\|tissue type:Body	Illumina HiSeq 2500 sequencing of SAMD00065414	DRX069314	Tumor body	1	Agilent SureSelect Strand Specific RNA Prep Kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</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>	DRP004473	Illumina HiSeq 2500 sequencing of SAMD00065414				1168514964.0	32458749.0	DRR075400	0:36	A:286579925;C:275496498;G:278133055;T:328265078;N:40408	36		286579925	275496498	278133055	328265078	40408	DRX069314	DRS075495	DRA005199	ATR\|The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International	The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International	1	0.89927	0.15051	0.66714	0.47579	36	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Japan	2018-09-19	Larval	Larval	Multi-tissue	Multi-system
171	171	DRR075399	DRX069313	DRS075494	DRP004473	PRJDB5226	Effects of local gut tumor on whole organismal gene expressions in zebrafish	DRP004473	Other	How tumors affects whole organismal physiology remains largely unknown. To address this we established the novel gut tumor model in zebrafish Danio rerio. This model develops tumor at an early stage of juvenile development when zebrafish larvae are small <4mm enabling us to perform whole organismal RNA seq experiments. Control or tumor bearing zebrafish were dissected into the three parts under microscope: the liver the gut/gut tumor and others. Tissues from >10 individuals were pooled and RNA extracted. Analyses on these RNA seq samples identified a set of host genes affected by the gut tumor contributing to discovering novel tumor organ interactions and their mediators in zebrafish.		The liver of control fish 7dpf	Control liver	SAMD00065413		sample name:3 control liver 150701 Hiseq3A l3 019\|tissue type:Liver	Illumina HiSeq 2500 sequencing of SAMD00065413	DRX069313	Control liver	1	Agilent SureSelect Strand Specific RNA Prep Kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</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>	DRP004473	Illumina HiSeq 2500 sequencing of SAMD00065413				951579036.0	26432751.0	DRR075399	0:36	A:231570583;C:228182815;G:227223430;T:264569214;N:32994	36		231570583	228182815	227223430	264569214	32994	DRX069313	DRS075494	DRA005199	ATR\|The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International	The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International	1	0.8903	0.08667	0.7236	0.51557	36	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Japan	2018-09-19	Larval	Larval	Liver	Liver and Biliary System
172	172	DRR075398	DRX069312	DRS075493	DRP004473	PRJDB5226	Effects of local gut tumor on whole organismal gene expressions in zebrafish	DRP004473	Other	How tumors affects whole organismal physiology remains largely unknown. To address this we established the novel gut tumor model in zebrafish Danio rerio. This model develops tumor at an early stage of juvenile development when zebrafish larvae are small <4mm enabling us to perform whole organismal RNA seq experiments. Control or tumor bearing zebrafish were dissected into the three parts under microscope: the liver the gut/gut tumor and others. Tissues from >10 individuals were pooled and RNA extracted. Analyses on these RNA seq samples identified a set of host genes affected by the gut tumor contributing to discovering novel tumor organ interactions and their mediators in zebrafish.		The gut of control fish 7dpf	Control gut	SAMD00065412		sample name:2 control gut 150701 Hiseq3A l3 018\|tissue type:Gut	Illumina HiSeq 2500 sequencing of SAMD00065412	DRX069312	Control gut	1	Agilent SureSelect Strand Specific RNA Prep Kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</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>	DRP004473	Illumina HiSeq 2500 sequencing of SAMD00065412				1008093492.0	28002597.0	DRR075398	0:36	A:230431417;C:251640901;G:244174255;T:281811580;N:35339	36		230431417	251640901	244174255	281811580	35339	DRX069312	DRS075493	DRA005199	ATR\|The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International	The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International	1	0.9173	0.07181	0.72017	0.45193	36	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Japan	2018-09-19	Larval	Larval	Gut	Digestive System
173	173	DRR075397	DRX069311	DRS075492	DRP004473	PRJDB5226	Effects of local gut tumor on whole organismal gene expressions in zebrafish	DRP004473	Other	How tumors affects whole organismal physiology remains largely unknown. To address this we established the novel gut tumor model in zebrafish Danio rerio. This model develops tumor at an early stage of juvenile development when zebrafish larvae are small <4mm enabling us to perform whole organismal RNA seq experiments. Control or tumor bearing zebrafish were dissected into the three parts under microscope: the liver the gut/gut tumor and others. Tissues from >10 individuals were pooled and RNA extracted. Analyses on these RNA seq samples identified a set of host genes affected by the gut tumor contributing to discovering novel tumor organ interactions and their mediators in zebrafish.		The remaining part of body of control fish 7dpf	Control body	SAMD00065411		sample name:1 control body 150701 Hiseq3A l3 017\|tissue type:Body	Illumina HiSeq 2500 sequencing of SAMD00065411	DRX069311	Control body	1	Agilent SureSelect Strand Specific RNA Prep Kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</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>	DRP004473	Illumina HiSeq 2500 sequencing of SAMD00065411				2653100352.0	73697232.0	DRR075397	0:36	A:656791658;C:620507513;G:625038612;T:750671135;N:91434	36		656791658	620507513	625038612	750671135	91434	DRX069311	DRS075492	DRA005199	ATR\|The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International	The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International	1	0.89666	0.15749	0.67048	0.47755	36	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Japan	2018-09-19	Larval	Larval	Trunk	Surface Structure
3015	3015	ERR1396841	ERX1468100	ERS1051448	ERP013615	PRJEB12173	Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts	Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011	Transcriptome Analysis	Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos.	ArrayExpress:E ERAD 449		zmp ph230 dgcr8 C7	SAMEA3864314	Wellcome Sanger Institute	ArrayExpress DevelopmentalStage:ZFS:0000037\|ArrayExpress Species:Danio rerio\|ENA first public:2016 05 03\|ENA last update:2016 02 03\|External Id:SAMEA3864314\|INSDC center alias:SC\|INSDC center name:Wellcome Sanger Institute\|INSDC first public:2016 05 03T14:21:56Z\|INSDC last update:2016 02 03T09:48:35Z\|INSDC status:public\|Submitter Id:2a85d100 99a3 11e5 bdcf 3c4a9275d6c6\|common name:zebrafish\|sample description:Sample wild type for dgcr8 allele sa223. Total RNA from a 5 dpf zebrafish embryo treated with DNase.\|sample name:2a85d100 99a3 11e5 bdcf 3c4a9275d6c6\|strain:mixed	Illumina HiSeq 2500 sequencing	SC EXP 18732 2#24	15616955	Illumina sequencing of library 15616955 constructed from sample accession ERS1051448 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence ATTCCT.	Small RNA miRNA		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		ERP013615	Illumina HiSeq 2500 sequencing	ENA FIRST PUBLIC:2016 05 03\|ENA LAST UPDATE:2018 11 16	18732_2#24.cram	cram	252742350.0	5054847.0	SC RUN 18732 2#24	0:50	A:72444190;C:64568625;G:62796637;T:52911792;N:21106	50		72444190	64568625	62796637	52911792	21106	ERX1468100	ERS1051448	ERA612385	European Nucleotide Archive	Wellcome Sanger Institute	1	0.61824	0.09608	0.8842	0.56978	50	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United Kingdom	2016-02-03	Larval	Larval	Embryo Imprecise	All anatomical structures
3016	3016	ERR1396840	ERX1468099	ERS1051447	ERP013615	PRJEB12173	Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts	Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011	Transcriptome Analysis	Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos.	ArrayExpress:E ERAD 449		zmp ph230 dgcr8 B12	SAMEA3864313	Wellcome Sanger Institute	ArrayExpress DevelopmentalStage:ZFS:0000037\|ArrayExpress OrganismPart:Whole embryo\|ArrayExpress Species:Danio rerio\|ENA first public:2016 05 03\|ENA last update:2016 02 03\|External Id:SAMEA3864313\|INSDC center alias:SC\|INSDC center name:Wellcome Sanger Institute\|INSDC first public:2016 05 03T14:21:56Z\|INSDC last update:2016 02 03T09:48:35Z\|INSDC status:public\|Submitter Id:2a7dbab0 99a3 11e5 bdcf 3c4a9275d6c6\|common name:zebrafish\|sample description:Sample wild type for dgcr8 allele sa223. Total RNA from a 5 dpf zebrafish embryo treated with DNase.\|sample name:2a7dbab0 99a3 11e5 bdcf 3c4a9275d6c6\|strain:mixed	Illumina HiSeq 2500 sequencing	SC EXP 18732 2#23	15616943	Illumina sequencing of library 15616943 constructed from sample accession ERS1051447 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence ACTGAT.	Small RNA miRNA		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		ERP013615	Illumina HiSeq 2500 sequencing	ENA FIRST PUBLIC:2016 05 03\|ENA LAST UPDATE:2018 11 16	18732_2#23.cram	cram	911394150.0	18227883.0	SC RUN 18732 2#23	0:50	A:264591252;C:227216187;G:236072241;T:183438530;N:75940	50		264591252	227216187	236072241	183438530	75940	ERX1468099	ERS1051447	ERA612385	European Nucleotide Archive	Wellcome Sanger Institute	1	0.58273	0.09754	0.87448	0.55833	50	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United Kingdom	2016-02-03	Larval	Larval	Whole Organism	All anatomical structures
3017	3017	ERR1396839	ERX1468098	ERS1051446	ERP013615	PRJEB12173	Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts	Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011	Transcriptome Analysis	Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos.	ArrayExpress:E ERAD 449		zmp ph230 dgcr8 B10	SAMEA3864312	Wellcome Sanger Institute	ArrayExpress DevelopmentalStage:ZFS:0000037\|ArrayExpress OrganismPart:Whole embryo\|ArrayExpress Species:Danio rerio\|ENA first public:2016 05 03\|ENA last update:2016 02 03\|External Id:SAMEA3864312\|INSDC center alias:SC\|INSDC center name:Wellcome Sanger Institute\|INSDC first public:2016 05 03T14:21:56Z\|INSDC last update:2016 02 03T09:48:34Z\|INSDC status:public\|Submitter Id:2a70e970 99a3 11e5 bdcf 3c4a9275d6c6\|common name:zebrafish\|sample description:Sample wild type for dgcr8 allele sa223. Total RNA from a 5 dpf zebrafish embryo treated with DNase.\|sample name:2a70e970 99a3 11e5 bdcf 3c4a9275d6c6\|strain:mixed	Illumina HiSeq 2500 sequencing	SC EXP 18732 2#22	15616931	Illumina sequencing of library 15616931 constructed from sample accession ERS1051446 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence GAGTGG.	Small RNA miRNA		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		ERP013615	Illumina HiSeq 2500 sequencing	ENA FIRST PUBLIC:2016 05 03\|ENA LAST UPDATE:2018 11 16	18732_2#22.cram	cram	242466400.0	4849328.0	SC RUN 18732 2#22	0:50	A:69326734;C:60104801;G:65507097;T:47507301;N:20467	50		69326734	60104801	65507097	47507301	20467	ERX1468098	ERS1051446	ERA612385	European Nucleotide Archive	Wellcome Sanger Institute	1	0.60819	0.09544	0.87864	0.58472	50	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United Kingdom	2016-02-03	Larval	Larval	Whole Organism	All anatomical structures
3018	3018	ERR1396838	ERX1468097	ERS1051445	ERP013615	PRJEB12173	Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts	Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011	Transcriptome Analysis	Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos.	ArrayExpress:E ERAD 449		zmp ph230 dgcr8 B3	SAMEA3864311	Wellcome Sanger Institute	ArrayExpress DevelopmentalStage:ZFS:0000037\|ArrayExpress OrganismPart:Whole embryo\|ArrayExpress Species:Danio rerio\|ENA first public:2016 05 03\|ENA last update:2016 02 03\|External Id:SAMEA3864311\|INSDC center alias:SC\|INSDC center name:Wellcome Sanger Institute\|INSDC first public:2016 05 03T14:21:56Z\|INSDC last update:2016 02 03T09:48:34Z\|INSDC status:public\|Submitter Id:2a6aa7e0 99a3 11e5 bdcf 3c4a9275d6c6\|common name:zebrafish\|sample description:Sample wild type for dgcr8 allele sa223. Total RNA from a 5 dpf zebrafish embryo treated with DNase.\|sample name:2a6aa7e0 99a3 11e5 bdcf 3c4a9275d6c6\|strain:mixed	Illumina HiSeq 2500 sequencing	SC EXP 18732 2#21	15616919	Illumina sequencing of library 15616919 constructed from sample accession ERS1051445 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence CGTACG.	Small RNA miRNA		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		ERP013615	Illumina HiSeq 2500 sequencing	ENA FIRST PUBLIC:2016 05 03\|ENA LAST UPDATE:2018 11 16	18732_2#21.cram	cram	630737800.0	12614756.0	SC RUN 18732 2#21	0:50	A:180007611;C:161281943;G:164376347;T:125019243;N:52656	50		180007611	161281943	164376347	125019243	52656	ERX1468097	ERS1051445	ERA612385	European Nucleotide Archive	Wellcome Sanger Institute	1	0.62407	0.10189	0.87825	0.57526	50	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United Kingdom	2016-02-03	Larval	Larval	Whole Organism	All anatomical structures
3019	3019	ERR1396837	ERX1468096	ERS1051444	ERP013615	PRJEB12173	Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts	Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011	Transcriptome Analysis	Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos.	ArrayExpress:E ERAD 449		zmp ph230 dgcr8 A4	SAMEA3864310	Wellcome Sanger Institute	ArrayExpress DevelopmentalStage:ZFS:0000037\|ArrayExpress OrganismPart:Whole embryo\|ArrayExpress Species:Danio rerio\|ENA first public:2016 05 03\|ENA last update:2016 02 03\|External Id:SAMEA3864310\|INSDC center alias:SC\|INSDC center name:Wellcome Sanger Institute\|INSDC first public:2016 05 03T14:21:56Z\|INSDC last update:2016 02 03T09:48:33Z\|INSDC status:public\|Submitter Id:2a61a730 99a3 11e5 bdcf 3c4a9275d6c6\|common name:zebrafish\|sample description:Sample homozygous for dgcr8 allele sa223. Total RNA from a 5 dpf zebrafish embryo treated with DNase.\|sample name:2a61a730 99a3 11e5 bdcf 3c4a9275d6c6\|strain:mixed	Illumina HiSeq 2500 sequencing	SC EXP 18732 2#20	15616907	Illumina sequencing of library 15616907 constructed from sample accession ERS1051444 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence GTTTCG.	Small RNA miRNA		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		ERP013615	Illumina HiSeq 2500 sequencing	ENA FIRST PUBLIC:2016 05 03\|ENA LAST UPDATE:2018 11 16	18732_2#20.cram	cram	488336450.0	9766729.0	SC RUN 18732 2#20	0:50	A:137910201;C:123586221;G:128373512;T:98425645;N:40871	50		137910201	123586221	128373512	98425645	40871	ERX1468096	ERS1051444	ERA612385	European Nucleotide Archive	Wellcome Sanger Institute	1	0.5453	0.11361	0.86594	0.58106	50	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United Kingdom	2016-02-03	Larval	Larval	Whole Organism	All anatomical structures
3020	3020	ERR1396836	ERX1468095	ERS1051443	ERP013615	PRJEB12173	Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts	Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011	Transcriptome Analysis	Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos.	ArrayExpress:E ERAD 449		zmp ph230 dgcr8 A3	SAMEA3864309	Wellcome Sanger Institute	ArrayExpress DevelopmentalStage:ZFS:0000037\|ArrayExpress OrganismPart:Whole embryo\|ArrayExpress Species:Danio rerio\|ENA first public:2016 05 03\|ENA last update:2016 02 03\|External Id:SAMEA3864309\|INSDC center alias:SC\|INSDC center name:Wellcome Sanger Institute\|INSDC first public:2016 05 03T14:21:56Z\|INSDC last update:2016 02 03T09:48:32Z\|INSDC status:public\|Submitter Id:2a5a0610 99a3 11e5 bdcf 3c4a9275d6c6\|common name:zebrafish\|sample description:Sample homozygous for dgcr8 allele sa223. Total RNA from a 5 dpf zebrafish embryo treated with DNase.\|sample name:2a5a0610 99a3 11e5 bdcf 3c4a9275d6c6\|strain:mixed	Illumina HiSeq 2500 sequencing	SC EXP 18732 2#19	15616895	Illumina sequencing of library 15616895 constructed from sample accession ERS1051443 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence GTGGCC.	Small RNA miRNA		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		ERP013615	Illumina HiSeq 2500 sequencing	ENA FIRST PUBLIC:2016 05 03\|ENA LAST UPDATE:2018 11 16	18732_2#19.cram	cram	502748050.0	10054961.0	SC RUN 18732 2#19	0:50	A:140684190;C:129525504;G:133998850;T:98497819;N:41687	50		140684190	129525504	133998850	98497819	41687	ERX1468095	ERS1051443	ERA612385	European Nucleotide Archive	Wellcome Sanger Institute	1	0.55085	0.11739	0.87077	0.6012	50	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United Kingdom	2016-02-03	Larval	Larval	Whole Organism	All anatomical structures
3021	3021	ERR1396835	ERX1468094	ERS1051442	ERP013615	PRJEB12173	Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts	Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011	Transcriptome Analysis	Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos.	ArrayExpress:E ERAD 449		zmp ph230 dgcr8 A2	SAMEA3864308	Wellcome Sanger Institute	ArrayExpress DevelopmentalStage:ZFS:0000037\|ArrayExpress OrganismPart:Whole embryo\|ArrayExpress Species:Danio rerio\|ENA first public:2016 05 03\|ENA last update:2016 02 03\|External Id:SAMEA3864308\|INSDC center alias:SC\|INSDC center name:Wellcome Sanger Institute\|INSDC first public:2016 05 03T14:21:56Z\|INSDC last update:2016 02 03T09:48:32Z\|INSDC status:public\|Submitter Id:2a537660 99a3 11e5 bdcf 3c4a9275d6c6\|common name:zebrafish\|sample description:Sample homozygous for dgcr8 allele sa223. Total RNA from a 5 dpf zebrafish embryo treated with DNase.\|sample name:2a537660 99a3 11e5 bdcf 3c4a9275d6c6\|strain:mixed	Illumina HiSeq 2500 sequencing	SC EXP 18732 2#18	15616883	Illumina sequencing of library 15616883 constructed from sample accession ERS1051442 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence GTGAAA.	Small RNA miRNA		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		ERP013615	Illumina HiSeq 2500 sequencing	ENA FIRST PUBLIC:2016 05 03\|ENA LAST UPDATE:2018 11 16	18732_2#18.cram	cram	512343000.0	10246860.0	SC RUN 18732 2#18	0:50	A:149660992;C:130013834;G:134888430;T:97736324;N:43420	50		149660992	130013834	134888430	97736324	43420	ERX1468094	ERS1051442	ERA612385	European Nucleotide Archive	Wellcome Sanger Institute	1	0.54809	0.11505	0.88254	0.5985	50	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United Kingdom	2016-02-03	Larval	Larval	Whole Organism	All anatomical structures
3022	3022	ERR1396834	ERX1468093	ERS1051441	ERP013615	PRJEB12173	Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts	Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011	Transcriptome Analysis	Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos.	ArrayExpress:E ERAD 449		zmp ph230 dgcr8 A1	SAMEA3864307	Wellcome Sanger Institute	ArrayExpress DevelopmentalStage:ZFS:0000037\|ArrayExpress OrganismPart:Whole embryo\|ArrayExpress Species:Danio rerio\|ENA first public:2016 05 03\|ENA last update:2016 02 03\|External Id:SAMEA3864307\|INSDC center alias:SC\|INSDC center name:Wellcome Sanger Institute\|INSDC first public:2016 05 03T14:21:56Z\|INSDC last update:2016 02 03T09:48:31Z\|INSDC status:public\|Submitter Id:2a4c4a70 99a3 11e5 bdcf 3c4a9275d6c6\|common name:zebrafish\|sample description:Sample homozygous for dgcr8 allele sa223. Total RNA from a 5 dpf zebrafish embryo treated with DNase.\|sample name:2a4c4a70 99a3 11e5 bdcf 3c4a9275d6c6\|strain:mixed	Illumina HiSeq 2500 sequencing	SC EXP 18732 2#17	15616871	Illumina sequencing of library 15616871 constructed from sample accession ERS1051441 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence GTCCGC.	Small RNA miRNA		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		ERP013615	Illumina HiSeq 2500 sequencing	ENA FIRST PUBLIC:2016 05 03\|ENA LAST UPDATE:2018 11 16	18732_2#17.cram	cram	296362850.0	5927257.0	SC RUN 18732 2#17	0:50	A:84251830;C:79653531;G:76748992;T:55683722;N:24775	50		84251830	79653531	76748992	55683722	24775	ERX1468093	ERS1051441	ERA612385	European Nucleotide Archive	Wellcome Sanger Institute	1	0.50115	0.10395	0.90185	0.6019	50	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United Kingdom	2016-02-03	Larval	Larval	Whole Organism	All anatomical structures
3023	3023	ERR1396833	ERX1468092	ERS1051440	ERP013615	PRJEB12173	Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts	Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011	Transcriptome Analysis	Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos.	ArrayExpress:E ERAD 449		zmp ph229 dicer C3	SAMEA3864306	Wellcome Sanger Institute	ArrayExpress DevelopmentalStage:ZFS:0000037\|ArrayExpress OrganismPart:Whole embryo\|ArrayExpress Species:Danio rerio\|ENA first public:2016 05 03\|ENA last update:2016 02 03\|External Id:SAMEA3864306\|INSDC center alias:SC\|INSDC center name:Wellcome Sanger Institute\|INSDC first public:2016 05 03T14:21:56Z\|INSDC last update:2016 02 03T09:48:31Z\|INSDC status:public\|Submitter Id:2a3ba8a0 99a3 11e5 bdcf 3c4a9275d6c6\|common name:zebrafish\|sample description:Sample wild type for dicer allele sa9205. Total RNA from a 5 dpf zebrafish embryo treated with DNase.\|sample name:2a3ba8a0 99a3 11e5 bdcf 3c4a9275d6c6\|strain:mixed	Illumina HiSeq 2500 sequencing	SC EXP 18732 2#16	15616954	Illumina sequencing of library 15616954 constructed from sample accession ERS1051440 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence CCGTCC.	Small RNA miRNA		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		ERP013615	Illumina HiSeq 2500 sequencing	ENA FIRST PUBLIC:2016 05 03\|ENA LAST UPDATE:2018 11 16	18732_2#16.cram	cram	247427250.0	4948545.0	SC RUN 18732 2#16	0:50	A:69477894;C:64165990;G:64753499;T:49009156;N:20711	50		69477894	64165990	64753499	49009156	20711	ERX1468092	ERS1051440	ERA612385	European Nucleotide Archive	Wellcome Sanger Institute	1	0.66601	0.10439	0.88156	0.5519	50	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United Kingdom	2016-02-03	Larval	Larval	Whole Organism	All anatomical structures
3024	3024	ERR1396832	ERX1468091	ERS1051439	ERP013615	PRJEB12173	Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts	Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011	Transcriptome Analysis	Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos.	ArrayExpress:E ERAD 449		zmp ph229 dicer B4	SAMEA3864305	Wellcome Sanger Institute	ArrayExpress DevelopmentalStage:ZFS:0000037\|ArrayExpress OrganismPart:Whole embryo\|ArrayExpress Species:Danio rerio\|ENA first public:2016 05 03\|ENA last update:2016 02 03\|External Id:SAMEA3864305\|INSDC center alias:SC\|INSDC center name:Wellcome Sanger Institute\|INSDC first public:2016 05 03T14:21:56Z\|INSDC last update:2016 02 03T09:48:30Z\|INSDC status:public\|Submitter Id:2a319680 99a3 11e5 bdcf 3c4a9275d6c6\|common name:zebrafish\|sample description:Sample wild type for dicer allele sa9205. Total RNA from a 5 dpf zebrafish embryo treated with DNase.\|sample name:2a319680 99a3 11e5 bdcf 3c4a9275d6c6\|strain:mixed	Illumina HiSeq 2500 sequencing	SC EXP 18732 2#15	15616942	Illumina sequencing of library 15616942 constructed from sample accession ERS1051439 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence ATGTCA.	Small RNA miRNA		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		ERP013615	Illumina HiSeq 2500 sequencing	ENA FIRST PUBLIC:2016 05 03\|ENA LAST UPDATE:2018 11 16	18732_2#15.cram	cram	268495550.0	5369911.0	SC RUN 18732 2#15	0:50	A:78316008;C:67311837;G:69086954;T:53758238;N:22513	50		78316008	67311837	69086954	53758238	22513	ERX1468091	ERS1051439	ERA612385	European Nucleotide Archive	Wellcome Sanger Institute	1	0.61927	0.0935	0.89745	0.55698	50	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United Kingdom	2016-02-03	Larval	Larval	Whole Organism	All anatomical structures
3025	3025	ERR1396831	ERX1468090	ERS1051438	ERP013615	PRJEB12173	Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts	Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011	Transcriptome Analysis	Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos.	ArrayExpress:E ERAD 449		zmp ph229 dicer A7	SAMEA3864304	Wellcome Sanger Institute	ArrayExpress DevelopmentalStage:ZFS:0000037\|ArrayExpress OrganismPart:Whole embryo\|ArrayExpress Species:Danio rerio\|ENA first public:2016 05 03\|ENA last update:2016 02 03\|External Id:SAMEA3864304\|INSDC center alias:SC\|INSDC center name:Wellcome Sanger Institute\|INSDC first public:2016 05 03T14:21:56Z\|INSDC last update:2016 02 03T09:48:29Z\|INSDC status:public\|Submitter Id:2a2a6a90 99a3 11e5 bdcf 3c4a9275d6c6\|common name:zebrafish\|sample description:Sample wild type for dicer allele sa9205. Total RNA from a 5 dpf zebrafish embryo treated with DNase.\|sample name:2a2a6a90 99a3 11e5 bdcf 3c4a9275d6c6\|strain:mixed	Illumina HiSeq 2500 sequencing	SC EXP 18732 2#14	15616930	Illumina sequencing of library 15616930 constructed from sample accession ERS1051438 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence AGTTCC.	Small RNA miRNA		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		ERP013615	Illumina HiSeq 2500 sequencing	ENA FIRST PUBLIC:2016 05 03\|ENA LAST UPDATE:2018 11 16	18732_2#14.cram	cram	457637200.0	9152744.0	SC RUN 18732 2#14	0:50	A:131304805;C:115755054;G:118778813;T:91760838;N:37690	50		131304805	115755054	118778813	91760838	37690	ERX1468090	ERS1051438	ERA612385	European Nucleotide Archive	Wellcome Sanger Institute	1	0.64717	0.09607	0.89832	0.56732	50	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United Kingdom	2016-02-03	Larval	Larval	Whole Organism	All anatomical structures
3026	3026	ERR1396830	ERX1468089	ERS1051437	ERP013615	PRJEB12173	Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts	Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011	Transcriptome Analysis	Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos.	ArrayExpress:E ERAD 449		zmp ph229 dicer A1	SAMEA3864303	Wellcome Sanger Institute	ArrayExpress DevelopmentalStage:ZFS:0000037\|ArrayExpress OrganismPart:Whole embryo\|ArrayExpress Species:Danio rerio\|ENA first public:2016 05 03\|ENA last update:2016 02 03\|External Id:SAMEA3864303\|INSDC center alias:SC\|INSDC center name:Wellcome Sanger Institute\|INSDC first public:2016 05 03T14:21:56Z\|INSDC last update:2016 02 03T09:48:29Z\|INSDC status:public\|Submitter Id:2a238cc0 99a3 11e5 bdcf 3c4a9275d6c6\|common name:zebrafish\|sample description:Sample wild type for dicer allele sa9205. Total RNA from a 5 dpf zebrafish embryo treated with DNase.\|sample name:2a238cc0 99a3 11e5 bdcf 3c4a9275d6c6\|strain:mixed	Illumina HiSeq 2500 sequencing	SC EXP 18732 2#13	15616918	Illumina sequencing of library 15616918 constructed from sample accession ERS1051437 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence AGTCAA.	Small RNA miRNA		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		ERP013615	Illumina HiSeq 2500 sequencing	ENA FIRST PUBLIC:2016 05 03\|ENA LAST UPDATE:2018 11 16	18732_2#13.cram	cram	156613950.0	3132279.0	SC RUN 18732 2#13	0:50	A:45659102;C:39445557;G:40495414;T:31000827;N:13050	50		45659102	39445557	40495414	31000827	13050	ERX1468089	ERS1051437	ERA612385	European Nucleotide Archive	Wellcome Sanger Institute	1	0.65923	0.09289	0.90096	0.52171	50	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United Kingdom	2016-02-03	Larval	Larval	Whole Organism	All anatomical structures
3027	3027	ERR1396829	ERX1468088	ERS1051436	ERP013615	PRJEB12173	Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts	Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011	Transcriptome Analysis	Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos.	ArrayExpress:E ERAD 449		zmp ph229 dicer C1	SAMEA3864302	Wellcome Sanger Institute	ArrayExpress DevelopmentalStage:ZFS:0000037\|ArrayExpress OrganismPart:Whole embryo\|ArrayExpress Species:Danio rerio\|ENA first public:2016 05 03\|ENA last update:2016 02 03\|External Id:SAMEA3864302\|INSDC center alias:SC\|INSDC center name:Wellcome Sanger Institute\|INSDC first public:2016 05 03T14:21:56Z\|INSDC last update:2016 02 03T09:48:28Z\|INSDC status:public\|Submitter Id:2a1b9d80 99a3 11e5 bdcf 3c4a9275d6c6\|common name:zebrafish\|sample description:Sample homozygous for dicer allele sa9205. Total RNA from a 5 dpf zebrafish embryo treated with DNase.\|sample name:2a1b9d80 99a3 11e5 bdcf 3c4a9275d6c6\|strain:mixed	Illumina HiSeq 2500 sequencing	SC EXP 18732 2#12	15616906	Illumina sequencing of library 15616906 constructed from sample accession ERS1051436 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence CTTGTA.	Small RNA miRNA		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		ERP013615	Illumina HiSeq 2500 sequencing	ENA FIRST PUBLIC:2016 05 03\|ENA LAST UPDATE:2018 11 16	18732_2#12.cram	cram	370496150.0	7409923.0	SC RUN 18732 2#12	0:50	A:104657486;C:92274677;G:97465315;T:76068240;N:30432	50		104657486	92274677	97465315	76068240	30432	ERX1468088	ERS1051436	ERA612385	European Nucleotide Archive	Wellcome Sanger Institute	1	0.64244	0.11811	0.86578	0.55798	50	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United Kingdom	2016-02-03	Larval	Larval	Whole Organism	All anatomical structures
3028	3028	ERR1396828	ERX1468087	ERS1051435	ERP013615	PRJEB12173	Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts	Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011	Transcriptome Analysis	Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos.	ArrayExpress:E ERAD 449		zmp ph229 dicer B3	SAMEA3864301	Wellcome Sanger Institute	ArrayExpress DevelopmentalStage:ZFS:0000037\|ArrayExpress OrganismPart:Whole embryo\|ArrayExpress Species:Danio rerio\|ENA first public:2016 05 03\|ENA last update:2016 02 03\|External Id:SAMEA3864301\|INSDC center alias:SC\|INSDC center name:Wellcome Sanger Institute\|INSDC first public:2016 05 03T14:21:55Z\|INSDC last update:2016 02 03T09:48:28Z\|INSDC status:public\|Submitter Id:2a0d93c0 99a3 11e5 bdcf 3c4a9275d6c6\|common name:zebrafish\|sample description:Sample homozygous for dicer allele sa9205. Total RNA from a 5 dpf zebrafish embryo treated with DNase.\|sample name:2a0d93c0 99a3 11e5 bdcf 3c4a9275d6c6\|strain:mixed	Illumina HiSeq 2500 sequencing	SC EXP 18732 2#11	15616894	Illumina sequencing of library 15616894 constructed from sample accession ERS1051435 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence GGCTAC.	Small RNA miRNA		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		ERP013615	Illumina HiSeq 2500 sequencing	ENA FIRST PUBLIC:2016 05 03\|ENA LAST UPDATE:2018 11 16	18732_2#11.cram	cram	136326100.0	2726522.0	SC RUN 18732 2#11	0:50	A:38914874;C:34737645;G:36229387;T:26432631;N:11563	50		38914874	34737645	36229387	26432631	11563	ERX1468087	ERS1051435	ERA612385	European Nucleotide Archive	Wellcome Sanger Institute	1	0.60295	0.10315	0.89092	0.58169	50	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United Kingdom	2016-02-03	Larval	Larval	Whole Organism	All anatomical structures
3029	3029	ERR1396827	ERX1468086	ERS1051434	ERP013615	PRJEB12173	Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts	Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011	Transcriptome Analysis	Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos.	ArrayExpress:E ERAD 449		zmp ph229 dicer A12	SAMEA3864300	Wellcome Sanger Institute	ArrayExpress DevelopmentalStage:ZFS:0000037\|ArrayExpress OrganismPart:Whole embryo\|ArrayExpress Species:Danio rerio\|ENA first public:2016 05 03\|ENA last update:2016 02 03\|External Id:SAMEA3864300\|INSDC center alias:SC\|INSDC center name:Wellcome Sanger Institute\|INSDC first public:2016 05 03T14:21:56Z\|INSDC last update:2016 02 03T09:48:27Z\|INSDC status:public\|Submitter Id:2a075230 99a3 11e5 bdcf 3c4a9275d6c6\|common name:zebrafish\|sample description:Sample homozygous for dicer allele sa9205. Total RNA from a 5 dpf zebrafish embryo treated with DNase.\|sample name:2a075230 99a3 11e5 bdcf 3c4a9275d6c6\|strain:mixed	Illumina HiSeq 2500 sequencing	SC EXP 18732 2#10	15616882	Illumina sequencing of library 15616882 constructed from sample accession ERS1051434 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence TAGCTT.	Small RNA miRNA		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		ERP013615	Illumina HiSeq 2500 sequencing	ENA FIRST PUBLIC:2016 05 03\|ENA LAST UPDATE:2018 11 16	18732_2#10.cram	cram	257740250.0	5154805.0	SC RUN 18732 2#10	0:50	A:73736881;C:64681440;G:67096497;T:52203988;N:21444	50		73736881	64681440	67096497	52203988	21444	ERX1468086	ERS1051434	ERA612385	European Nucleotide Archive	Wellcome Sanger Institute	1	0.62041	0.10196	0.89706	0.55474	50	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United Kingdom	2016-02-03	Larval	Larval	Whole Organism	All anatomical structures
3030	3030	ERR1396826	ERX1468085	ERS1051433	ERP013615	PRJEB12173	Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts	Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011	Transcriptome Analysis	Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos.	ArrayExpress:E ERAD 449		zmp ph229 dicer A10	SAMEA3864299	Wellcome Sanger Institute	ArrayExpress DevelopmentalStage:ZFS:0000037\|ArrayExpress OrganismPart:Whole embryo\|ArrayExpress Species:Danio rerio\|ENA first public:2016 05 03\|ENA last update:2016 02 03\|External Id:SAMEA3864299\|INSDC center alias:SC\|INSDC center name:Wellcome Sanger Institute\|INSDC first public:2016 05 03T14:21:56Z\|INSDC last update:2016 02 03T09:48:26Z\|INSDC status:public\|Submitter Id:29ffff30 99a3 11e5 bdcf 3c4a9275d6c6\|common name:zebrafish\|sample description:Sample homozygous for dicer allele sa9205. Total RNA from a 5 dpf zebrafish embryo treated with DNase.\|sample name:29ffff30 99a3 11e5 bdcf 3c4a9275d6c6\|strain:mixed	Illumina HiSeq 2500 sequencing	SC EXP 18732 2#9	15616870	Illumina sequencing of library 15616870 constructed from sample accession ERS1051433 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence GATCAG.	Small RNA miRNA		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		ERP013615	Illumina HiSeq 2500 sequencing	ENA FIRST PUBLIC:2016 05 03\|ENA LAST UPDATE:2018 11 16	18732_2#9.cram	cram	7356000.0	147120.0	SC RUN 18732 2#9	0:50	A:2152284;C:1844982;G:1920243;T:1437897;N:594	50		2152284	1844982	1920243	1437897	594	ERX1468085	ERS1051433	ERA612385	European Nucleotide Archive	Wellcome Sanger Institute	1	0.60239	0.10502	0.91084	0.55869	50	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United Kingdom	2016-02-03	Larval	Larval	Whole Organism	All anatomical structures
3031	3031	ERR1396825	ERX1468084	ERS1051432	ERP013615	PRJEB12173	Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts	Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011	Transcriptome Analysis	Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos.	ArrayExpress:E ERAD 449		zmp ph228 drosha C1	SAMEA3864298	Wellcome Sanger Institute	ArrayExpress DevelopmentalStage:ZFS:0000037\|ArrayExpress OrganismPart:Whole embryo\|ArrayExpress Species:Danio rerio\|ENA first public:2016 05 03\|ENA last update:2016 02 03\|External Id:SAMEA3864298\|INSDC center alias:SC\|INSDC center name:Wellcome Sanger Institute\|INSDC first public:2016 05 03T14:21:56Z\|INSDC last update:2016 02 03T09:48:26Z\|INSDC status:public\|Submitter Id:29f306e0 99a3 11e5 bdcf 3c4a9275d6c6\|common name:zebrafish\|sample description:Sample wild type for drosha allele sa191. Total RNA from a 5 dpf zebrafish embryo treated with DNase.\|sample name:29f306e0 99a3 11e5 bdcf 3c4a9275d6c6\|strain:mixed	Illumina HiSeq 2500 sequencing	SC EXP 18732 2#8	15616953	Illumina sequencing of library 15616953 constructed from sample accession ERS1051432 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence ACTTGA.	Small RNA miRNA		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		ERP013615	Illumina HiSeq 2500 sequencing	ENA FIRST PUBLIC:2016 05 03\|ENA LAST UPDATE:2018 11 16	18732_2#8.cram	cram	454519900.0	9090398.0	SC RUN 18732 2#8	0:50	A:133717355;C:117574792;G:114940340;T:88249706;N:37707	50		133717355	117574792	114940340	88249706	37707	ERX1468084	ERS1051432	ERA612385	European Nucleotide Archive	Wellcome Sanger Institute	1	0.51063	0.10053	0.88572	0.60434	50	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United Kingdom	2016-02-03	Larval	Larval	Whole Organism	All anatomical structures
3032	3032	ERR1396824	ERX1468083	ERS1051431	ERP013615	PRJEB12173	Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts	Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011	Transcriptome Analysis	Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos.	ArrayExpress:E ERAD 449		zmp ph228 drosha A9	SAMEA3864297	Wellcome Sanger Institute	ArrayExpress DevelopmentalStage:ZFS:0000037\|ArrayExpress OrganismPart:Whole embryo\|ArrayExpress Species:Danio rerio\|ENA first public:2016 05 03\|ENA last update:2016 02 03\|External Id:SAMEA3864297\|INSDC center alias:SC\|INSDC center name:Wellcome Sanger Institute\|INSDC first public:2016 05 03T14:21:56Z\|INSDC last update:2016 02 03T09:48:25Z\|INSDC status:public\|Submitter Id:29e942e0 99a3 11e5 bdcf 3c4a9275d6c6\|common name:zebrafish\|sample description:Sample wild type for drosha allele sa191. Total RNA from a 5 dpf zebrafish embryo treated with DNase.\|sample name:29e942e0 99a3 11e5 bdcf 3c4a9275d6c6\|strain:mixed	Illumina HiSeq 2500 sequencing	SC EXP 18732 2#7	15616941	Illumina sequencing of library 15616941 constructed from sample accession ERS1051431 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence CAGATC.	Small RNA miRNA		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		ERP013615	Illumina HiSeq 2500 sequencing	ENA FIRST PUBLIC:2016 05 03\|ENA LAST UPDATE:2018 11 16	18732_2#7.cram	cram	288165650.0	5763313.0	SC RUN 18732 2#7	0:50	A:83874531;C:74578491;G:74739497;T:54949008;N:24123	50		83874531	74578491	74739497	54949008	24123	ERX1468083	ERS1051431	ERA612385	European Nucleotide Archive	Wellcome Sanger Institute	1	0.56561	0.10234	0.88278	0.59066	50	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United Kingdom	2016-02-03	Larval	Larval	Whole Organism	All anatomical structures
3033	3033	ERR1396823	ERX1468082	ERS1051430	ERP013615	PRJEB12173	Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts	Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011	Transcriptome Analysis	Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos.	ArrayExpress:E ERAD 449		zmp ph228 drosha A6	SAMEA3864296	Wellcome Sanger Institute	ArrayExpress DevelopmentalStage:ZFS:0000037\|ArrayExpress OrganismPart:Whole embryo\|ArrayExpress Species:Danio rerio\|ENA first public:2016 05 03\|ENA last update:2016 02 03\|External Id:SAMEA3864296\|INSDC center alias:SC\|INSDC center name:Wellcome Sanger Institute\|INSDC first public:2016 05 03T14:21:56Z\|INSDC last update:2016 02 03T09:48:25Z\|INSDC status:public\|Submitter Id:29e06940 99a3 11e5 bdcf 3c4a9275d6c6\|common name:zebrafish\|sample description:Sample wild type for drosha allele sa191. Total RNA from a 5 dpf zebrafish embryo treated with DNase.\|sample name:29e06940 99a3 11e5 bdcf 3c4a9275d6c6\|strain:mixed	Illumina HiSeq 2500 sequencing	SC EXP 18732 2#6	15616929	Illumina sequencing of library 15616929 constructed from sample accession ERS1051430 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence GCCAAT.	Small RNA miRNA		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		ERP013615	Illumina HiSeq 2500 sequencing	ENA FIRST PUBLIC:2016 05 03\|ENA LAST UPDATE:2018 11 16	18732_2#6.cram	cram	234507600.0	4690152.0	SC RUN 18732 2#6	0:50	A:67284766;C:59565829;G:61407599;T:46229970;N:19436	50		67284766	59565829	61407599	46229970	19436	ERX1468082	ERS1051430	ERA612385	European Nucleotide Archive	Wellcome Sanger Institute	1	0.64334	0.10252	0.88905	0.5695	50	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United Kingdom	2016-02-03	Larval	Larval	Whole Organism	All anatomical structures
3034	3034	ERR1396822	ERX1468081	ERS1051429	ERP013615	PRJEB12173	Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts	Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011	Transcriptome Analysis	Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos.	ArrayExpress:E ERAD 449		zmp ph228 drosha A1	SAMEA3864295	Wellcome Sanger Institute	ArrayExpress DevelopmentalStage:ZFS:0000037\|ArrayExpress OrganismPart:Whole embryo\|ArrayExpress Species:Danio rerio\|ENA first public:2016 05 03\|ENA last update:2016 02 03\|External Id:SAMEA3864295\|INSDC center alias:SC\|INSDC center name:Wellcome Sanger Institute\|INSDC first public:2016 05 03T14:21:56Z\|INSDC last update:2016 02 03T09:48:24Z\|INSDC status:public\|Submitter Id:29d74180 99a3 11e5 bdcf 3c4a9275d6c6\|common name:zebrafish\|sample description:Sample wild type for drosha allele sa191. Total RNA from a 5 dpf zebrafish embryo treated with DNase.\|sample name:29d74180 99a3 11e5 bdcf 3c4a9275d6c6\|strain:mixed	Illumina HiSeq 2500 sequencing	SC EXP 18732 2#5	15616917	Illumina sequencing of library 15616917 constructed from sample accession ERS1051429 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence ACAGTG.	Small RNA miRNA		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		ERP013615	Illumina HiSeq 2500 sequencing	ENA FIRST PUBLIC:2016 05 03\|ENA LAST UPDATE:2018 11 16	18732_2#5.cram	cram	161797350.0	3235947.0	SC RUN 18732 2#5	0:50	A:46711991;C:40739475;G:42456048;T:31876390;N:13446	50		46711991	40739475	42456048	31876390	13446	ERX1468081	ERS1051429	ERA612385	European Nucleotide Archive	Wellcome Sanger Institute	1	0.64666	0.09851	0.90508	0.56607	50	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United Kingdom	2016-02-03	Larval	Larval	Whole Organism	All anatomical structures
3035	3035	ERR1396821	ERX1468080	ERS1051428	ERP013615	PRJEB12173	Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts	Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011	Transcriptome Analysis	Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos.	ArrayExpress:E ERAD 449		zmp ph228 drosha B12	SAMEA3864294	Wellcome Sanger Institute	ArrayExpress DevelopmentalStage:ZFS:0000037\|ArrayExpress OrganismPart:Whole embryo\|ArrayExpress Species:Danio rerio\|ENA first public:2016 05 03\|ENA last update:2016 02 03\|External Id:SAMEA3864294\|INSDC center alias:SC\|INSDC center name:Wellcome Sanger Institute\|INSDC first public:2016 05 03T14:21:56Z\|INSDC last update:2016 02 03T09:48:23Z\|INSDC status:public\|Submitter Id:29cf7950 99a3 11e5 bdcf 3c4a9275d6c6\|common name:zebrafish\|sample description:Sample homozygous for drosha allele sa191. Total RNA from a 5 dpf zebrafish embryo treated with DNase.\|sample name:29cf7950 99a3 11e5 bdcf 3c4a9275d6c6\|strain:mixed	Illumina HiSeq 2500 sequencing	SC EXP 18732 2#4	15616905	Illumina sequencing of library 15616905 constructed from sample accession ERS1051428 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence TGACCA.	Small RNA miRNA		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		ERP013615	Illumina HiSeq 2500 sequencing	ENA FIRST PUBLIC:2016 05 03\|ENA LAST UPDATE:2018 11 16	18732_2#4.cram	cram	393377600.0	7867552.0	SC RUN 18732 2#4	0:50	A:115292812;C:103803007;G:98535312;T:75713409;N:33060	50		115292812	103803007	98535312	75713409	33060	ERX1468080	ERS1051428	ERA612385	European Nucleotide Archive	Wellcome Sanger Institute	1	0.51888	0.1037	0.89948	0.59445	50	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United Kingdom	2016-02-03	Larval	Larval	Whole Organism	All anatomical structures
3036	3036	ERR1396820	ERX1468079	ERS1051427	ERP013615	PRJEB12173	Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts	Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011	Transcriptome Analysis	Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos.	ArrayExpress:E ERAD 449		zmp ph228 drosha B10	SAMEA3864293	Wellcome Sanger Institute	ArrayExpress DevelopmentalStage:ZFS:0000037\|ArrayExpress OrganismPart:Whole embryo\|ArrayExpress Species:Danio rerio\|ENA first public:2016 05 03\|ENA last update:2016 02 03\|External Id:SAMEA3864293\|INSDC center alias:SC\|INSDC center name:Wellcome Sanger Institute\|INSDC first public:2016 05 03T14:21:56Z\|INSDC last update:2016 02 03T09:48:22Z\|INSDC status:public\|Submitter Id:29c84d60 99a3 11e5 bdcf 3c4a9275d6c6\|common name:zebrafish\|sample description:Sample homozygous for drosha allele sa191. Total RNA from a 5 dpf zebrafish embryo treated with DNase.\|sample name:29c84d60 99a3 11e5 bdcf 3c4a9275d6c6\|strain:mixed	Illumina HiSeq 2500 sequencing	SC EXP 18732 2#3	15616893	Illumina sequencing of library 15616893 constructed from sample accession ERS1051427 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence TTAGGC.	Small RNA miRNA		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		ERP013615	Illumina HiSeq 2500 sequencing	ENA FIRST PUBLIC:2016 05 03\|ENA LAST UPDATE:2018 11 16	18732_2#3.cram	cram	211138300.0	4222766.0	SC RUN 18732 2#3	0:50	A:60487130;C:53019786;G:55472125;T:42141858;N:17401	50		60487130	53019786	55472125	42141858	17401	ERX1468079	ERS1051427	ERA612385	European Nucleotide Archive	Wellcome Sanger Institute	1	0.57434	0.11571	0.88633	0.6058	50	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United Kingdom	2016-02-03	Larval	Larval	Whole Organism	All anatomical structures
3037	3037	ERR1396819	ERX1468078	ERS1051426	ERP013615	PRJEB12173	Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts	Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011	Transcriptome Analysis	Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos.	ArrayExpress:E ERAD 449		zmp ph228 drosha B7	SAMEA3864292	Wellcome Sanger Institute	ArrayExpress DevelopmentalStage:ZFS:0000037\|ArrayExpress OrganismPart:Whole embryo\|ArrayExpress Species:Danio rerio\|ENA first public:2016 05 03\|ENA last update:2016 02 03\|External Id:SAMEA3864292\|INSDC center alias:SC\|INSDC center name:Wellcome Sanger Institute\|INSDC first public:2016 05 03T14:21:56Z\|INSDC last update:2016 02 03T09:48:22Z\|INSDC status:public\|Submitter Id:29b1df30 99a3 11e5 bdcf 3c4a9275d6c6\|common name:zebrafish\|sample description:Sample homozygous for drosha allele sa191. Total RNA from a 5 dpf zebrafish embryo treated with DNase.\|sample name:29b1df30 99a3 11e5 bdcf 3c4a9275d6c6\|strain:mixed	Illumina HiSeq 2500 sequencing	SC EXP 18732 2#2	15616881	Illumina sequencing of library 15616881 constructed from sample accession ERS1051426 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence CGATGT.	Small RNA miRNA		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		ERP013615	Illumina HiSeq 2500 sequencing	ENA FIRST PUBLIC:2016 05 03\|ENA LAST UPDATE:2018 11 16	18732_2#2.cram	cram	318903600.0	6378072.0	SC RUN 18732 2#2	0:50	A:91235181;C:80984947;G:84861359;T:61795663;N:26450	50		91235181	80984947	84861359	61795663	26450	ERX1468078	ERS1051426	ERA612385	European Nucleotide Archive	Wellcome Sanger Institute	1	0.57408	0.11398	0.87629	0.60954	50	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United Kingdom	2016-02-03	Larval	Larval	Whole Organism	All anatomical structures
3038	3038	ERR1396818	ERX1468077	ERS1051425	ERP013615	PRJEB12173	Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts	Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011	Transcriptome Analysis	Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos.	ArrayExpress:E ERAD 449		zmp ph228 drosha B1	SAMEA3864291	Wellcome Sanger Institute	ArrayExpress DevelopmentalStage:ZFS:0000037\|ArrayExpress OrganismPart:Whole embryo\|ArrayExpress Species:Danio rerio\|ENA first public:2016 05 03\|ENA last update:2016 02 03\|External Id:SAMEA3864291\|INSDC center alias:SC\|INSDC center name:Wellcome Sanger Institute\|INSDC first public:2016 05 03T14:21:55Z\|INSDC last update:2016 02 03T09:48:20Z\|INSDC status:public\|Submitter Id:29904d70 99a3 11e5 bdcf 3c4a9275d6c6\|common name:zebrafish\|sample description:Sample homozygous for drosha allele sa191. Total RNA from a 5 dpf zebrafish embryo treated with DNase.\|sample name:29904d70 99a3 11e5 bdcf 3c4a9275d6c6\|strain:mixed	Illumina HiSeq 2500 sequencing	SC EXP 18732 2#1	15616869	Illumina sequencing of library 15616869 constructed from sample accession ERS1051425 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence ATCACG.	Small RNA miRNA		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		ERP013615	Illumina HiSeq 2500 sequencing	ENA FIRST PUBLIC:2016 05 03\|ENA LAST UPDATE:2018 11 16	18732_2#1.cram	cram	411180300.0	8223606.0	SC RUN 18732 2#1	0:50	A:118946374;C:103897659;G:107565667;T:80736319;N:34281	50		118946374	103897659	107565667	80736319	34281	ERX1468077	ERS1051425	ERA612385	European Nucleotide Archive	Wellcome Sanger Institute	1	0.60674	0.11483	0.90258	0.54833	50	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United Kingdom	2016-02-03	Larval	Larval	Whole Organism	All anatomical structures
3039	3039	ERR1396817	ERX1468076	ERS1051448	ERP013615	PRJEB12173	Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts	Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011	Transcriptome Analysis	Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos.	ArrayExpress:E ERAD 449		zmp ph230 dgcr8 C7	SAMEA3864314	Wellcome Sanger Institute	ArrayExpress DevelopmentalStage:ZFS:0000037\|ArrayExpress Species:Danio rerio\|ENA first public:2016 05 03\|ENA last update:2016 02 03\|External Id:SAMEA3864314\|INSDC center alias:SC\|INSDC center name:Wellcome Sanger Institute\|INSDC first public:2016 05 03T14:21:56Z\|INSDC last update:2016 02 03T09:48:35Z\|INSDC status:public\|Submitter Id:2a85d100 99a3 11e5 bdcf 3c4a9275d6c6\|common name:zebrafish\|sample description:Sample wild type for dgcr8 allele sa223. Total RNA from a 5 dpf zebrafish embryo treated with DNase.\|sample name:2a85d100 99a3 11e5 bdcf 3c4a9275d6c6\|strain:mixed	Illumina HiSeq 2500 sequencing	SC EXP 18732 1#24	15616955	Illumina sequencing of library 15616955 constructed from sample accession ERS1051448 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence ATTCCT.	Small RNA miRNA		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		ERP013615	Illumina HiSeq 2500 sequencing	ENA FIRST PUBLIC:2016 05 03\|ENA LAST UPDATE:2018 11 16	18732_1#24.cram	cram	258624300.0	5172486.0	SC RUN 18732 1#24	0:50	A:74123846;C:66047722;G:64286422;T:54141623;N:24687	50		74123846	66047722	64286422	54141623	24687	ERX1468076	ERS1051448	ERA612385	European Nucleotide Archive	Wellcome Sanger Institute	1	0.62009	0.09612	0.88434	0.55718	50	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United Kingdom	2016-02-03	Larval	Larval	Embryo Imprecise	All anatomical structures
3040	3040	ERR1396816	ERX1468075	ERS1051447	ERP013615	PRJEB12173	Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts	Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011	Transcriptome Analysis	Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos.	ArrayExpress:E ERAD 449		zmp ph230 dgcr8 B12	SAMEA3864313	Wellcome Sanger Institute	ArrayExpress DevelopmentalStage:ZFS:0000037\|ArrayExpress OrganismPart:Whole embryo\|ArrayExpress Species:Danio rerio\|ENA first public:2016 05 03\|ENA last update:2016 02 03\|External Id:SAMEA3864313\|INSDC center alias:SC\|INSDC center name:Wellcome Sanger Institute\|INSDC first public:2016 05 03T14:21:56Z\|INSDC last update:2016 02 03T09:48:35Z\|INSDC status:public\|Submitter Id:2a7dbab0 99a3 11e5 bdcf 3c4a9275d6c6\|common name:zebrafish\|sample description:Sample wild type for dgcr8 allele sa223. Total RNA from a 5 dpf zebrafish embryo treated with DNase.\|sample name:2a7dbab0 99a3 11e5 bdcf 3c4a9275d6c6\|strain:mixed	Illumina HiSeq 2500 sequencing	SC EXP 18732 1#23	15616943	Illumina sequencing of library 15616943 constructed from sample accession ERS1051447 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence ACTGAT.	Small RNA miRNA		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		ERP013615	Illumina HiSeq 2500 sequencing	ENA FIRST PUBLIC:2016 05 03\|ENA LAST UPDATE:2018 11 16	18732_1#23.cram	cram	932669450.0	18653389.0	SC RUN 18732 1#23	0:50	A:270743929;C:232449590;G:241669732;T:187716399;N:89800	50		270743929	232449590	241669732	187716399	89800	ERX1468075	ERS1051447	ERA612385	European Nucleotide Archive	Wellcome Sanger Institute	1	0.58314	0.09813	0.87373	0.55534	50	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United Kingdom	2016-02-03	Larval	Larval	Whole Organism	All anatomical structures
3041	3041	ERR1396815	ERX1468074	ERS1051446	ERP013615	PRJEB12173	Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts	Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011	Transcriptome Analysis	Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos.	ArrayExpress:E ERAD 449		zmp ph230 dgcr8 B10	SAMEA3864312	Wellcome Sanger Institute	ArrayExpress DevelopmentalStage:ZFS:0000037\|ArrayExpress OrganismPart:Whole embryo\|ArrayExpress Species:Danio rerio\|ENA first public:2016 05 03\|ENA last update:2016 02 03\|External Id:SAMEA3864312\|INSDC center alias:SC\|INSDC center name:Wellcome Sanger Institute\|INSDC first public:2016 05 03T14:21:56Z\|INSDC last update:2016 02 03T09:48:34Z\|INSDC status:public\|Submitter Id:2a70e970 99a3 11e5 bdcf 3c4a9275d6c6\|common name:zebrafish\|sample description:Sample wild type for dgcr8 allele sa223. Total RNA from a 5 dpf zebrafish embryo treated with DNase.\|sample name:2a70e970 99a3 11e5 bdcf 3c4a9275d6c6\|strain:mixed	Illumina HiSeq 2500 sequencing	SC EXP 18732 1#22	15616931	Illumina sequencing of library 15616931 constructed from sample accession ERS1051446 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence GAGTGG.	Small RNA miRNA		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		ERP013615	Illumina HiSeq 2500 sequencing	ENA FIRST PUBLIC:2016 05 03\|ENA LAST UPDATE:2018 11 16	18732_1#22.cram	cram	247740600.0	4954812.0	SC RUN 18732 1#22	0:50	A:70832472;C:61402287;G:66930146;T:48552217;N:23478	50		70832472	61402287	66930146	48552217	23478	ERX1468074	ERS1051446	ERA612385	European Nucleotide Archive	Wellcome Sanger Institute	1	0.60866	0.09645	0.87842	0.56581	50	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United Kingdom	2016-02-03	Larval	Larval	Whole Organism	All anatomical structures
3042	3042	ERR1396814	ERX1468073	ERS1051445	ERP013615	PRJEB12173	Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts	Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011	Transcriptome Analysis	Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos.	ArrayExpress:E ERAD 449		zmp ph230 dgcr8 B3	SAMEA3864311	Wellcome Sanger Institute	ArrayExpress DevelopmentalStage:ZFS:0000037\|ArrayExpress OrganismPart:Whole embryo\|ArrayExpress Species:Danio rerio\|ENA first public:2016 05 03\|ENA last update:2016 02 03\|External Id:SAMEA3864311\|INSDC center alias:SC\|INSDC center name:Wellcome Sanger Institute\|INSDC first public:2016 05 03T14:21:56Z\|INSDC last update:2016 02 03T09:48:34Z\|INSDC status:public\|Submitter Id:2a6aa7e0 99a3 11e5 bdcf 3c4a9275d6c6\|common name:zebrafish\|sample description:Sample wild type for dgcr8 allele sa223. Total RNA from a 5 dpf zebrafish embryo treated with DNase.\|sample name:2a6aa7e0 99a3 11e5 bdcf 3c4a9275d6c6\|strain:mixed	Illumina HiSeq 2500 sequencing	SC EXP 18732 1#21	15616919	Illumina sequencing of library 15616919 constructed from sample accession ERS1051445 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence CGTACG.	Small RNA miRNA		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		ERP013615	Illumina HiSeq 2500 sequencing	ENA FIRST PUBLIC:2016 05 03\|ENA LAST UPDATE:2018 11 16	18732_1#21.cram	cram	644730800.0	12894616.0	SC RUN 18732 1#21	0:50	A:183986486;C:164794735;G:168072875;T:127815308;N:61396	50		183986486	164794735	168072875	127815308	61396	ERX1468073	ERS1051445	ERA612385	European Nucleotide Archive	Wellcome Sanger Institute	1	0.62529	0.10255	0.87673	0.58496	50	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United Kingdom	2016-02-03	Larval	Larval	Whole Organism	All anatomical structures
3043	3043	ERR1396813	ERX1468072	ERS1051444	ERP013615	PRJEB12173	Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts	Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011	Transcriptome Analysis	Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos.	ArrayExpress:E ERAD 449		zmp ph230 dgcr8 A4	SAMEA3864310	Wellcome Sanger Institute	ArrayExpress DevelopmentalStage:ZFS:0000037\|ArrayExpress OrganismPart:Whole embryo\|ArrayExpress Species:Danio rerio\|ENA first public:2016 05 03\|ENA last update:2016 02 03\|External Id:SAMEA3864310\|INSDC center alias:SC\|INSDC center name:Wellcome Sanger Institute\|INSDC first public:2016 05 03T14:21:56Z\|INSDC last update:2016 02 03T09:48:33Z\|INSDC status:public\|Submitter Id:2a61a730 99a3 11e5 bdcf 3c4a9275d6c6\|common name:zebrafish\|sample description:Sample homozygous for dgcr8 allele sa223. Total RNA from a 5 dpf zebrafish embryo treated with DNase.\|sample name:2a61a730 99a3 11e5 bdcf 3c4a9275d6c6\|strain:mixed	Illumina HiSeq 2500 sequencing	SC EXP 18732 1#20	15616907	Illumina sequencing of library 15616907 constructed from sample accession ERS1051444 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence GTTTCG.	Small RNA miRNA		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		ERP013615	Illumina HiSeq 2500 sequencing	ENA FIRST PUBLIC:2016 05 03\|ENA LAST UPDATE:2018 11 16	18732_1#20.cram	cram	498997400.0	9979948.0	SC RUN 18732 1#20	0:50	A:140918075;C:126256924;G:131206962;T:100567098;N:48341	50		140918075	126256924	131206962	100567098	48341	ERX1468072	ERS1051444	ERA612385	European Nucleotide Archive	Wellcome Sanger Institute	1	0.54672	0.11372	0.8659	0.58386	50	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United Kingdom	2016-02-03	Larval	Larval	Whole Organism	All anatomical structures
3044	3044	ERR1396812	ERX1468071	ERS1051443	ERP013615	PRJEB12173	Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts	Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011	Transcriptome Analysis	Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos.	ArrayExpress:E ERAD 449		zmp ph230 dgcr8 A3	SAMEA3864309	Wellcome Sanger Institute	ArrayExpress DevelopmentalStage:ZFS:0000037\|ArrayExpress OrganismPart:Whole embryo\|ArrayExpress Species:Danio rerio\|ENA first public:2016 05 03\|ENA last update:2016 02 03\|External Id:SAMEA3864309\|INSDC center alias:SC\|INSDC center name:Wellcome Sanger Institute\|INSDC first public:2016 05 03T14:21:56Z\|INSDC last update:2016 02 03T09:48:32Z\|INSDC status:public\|Submitter Id:2a5a0610 99a3 11e5 bdcf 3c4a9275d6c6\|common name:zebrafish\|sample description:Sample homozygous for dgcr8 allele sa223. Total RNA from a 5 dpf zebrafish embryo treated with DNase.\|sample name:2a5a0610 99a3 11e5 bdcf 3c4a9275d6c6\|strain:mixed	Illumina HiSeq 2500 sequencing	SC EXP 18732 1#19	15616895	Illumina sequencing of library 15616895 constructed from sample accession ERS1051443 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence GTGGCC.	Small RNA miRNA		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		ERP013615	Illumina HiSeq 2500 sequencing	ENA FIRST PUBLIC:2016 05 03\|ENA LAST UPDATE:2018 11 16	18732_1#19.cram	cram	513060400.0	10261208.0	SC RUN 18732 1#19	0:50	A:143572990;C:132143361;G:136785883;T:100508957;N:49209	50		143572990	132143361	136785883	100508957	49209	ERX1468071	ERS1051443	ERA612385	European Nucleotide Archive	Wellcome Sanger Institute	1	0.55168	0.11683	0.86868	0.59303	50	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United Kingdom	2016-02-03	Larval	Larval	Whole Organism	All anatomical structures
3045	3045	ERR1396811	ERX1468070	ERS1051442	ERP013615	PRJEB12173	Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts	Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011	Transcriptome Analysis	Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos.	ArrayExpress:E ERAD 449		zmp ph230 dgcr8 A2	SAMEA3864308	Wellcome Sanger Institute	ArrayExpress DevelopmentalStage:ZFS:0000037\|ArrayExpress OrganismPart:Whole embryo\|ArrayExpress Species:Danio rerio\|ENA first public:2016 05 03\|ENA last update:2016 02 03\|External Id:SAMEA3864308\|INSDC center alias:SC\|INSDC center name:Wellcome Sanger Institute\|INSDC first public:2016 05 03T14:21:56Z\|INSDC last update:2016 02 03T09:48:32Z\|INSDC status:public\|Submitter Id:2a537660 99a3 11e5 bdcf 3c4a9275d6c6\|common name:zebrafish\|sample description:Sample homozygous for dgcr8 allele sa223. Total RNA from a 5 dpf zebrafish embryo treated with DNase.\|sample name:2a537660 99a3 11e5 bdcf 3c4a9275d6c6\|strain:mixed	Illumina HiSeq 2500 sequencing	SC EXP 18732 1#18	15616883	Illumina sequencing of library 15616883 constructed from sample accession ERS1051442 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence GTGAAA.	Small RNA miRNA		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		ERP013615	Illumina HiSeq 2500 sequencing	ENA FIRST PUBLIC:2016 05 03\|ENA LAST UPDATE:2018 11 16	18732_1#18.cram	cram	522864750.0	10457295.0	SC RUN 18732 1#18	0:50	A:152695334;C:132665110;G:137681171;T:99772629;N:50506	50		152695334	132665110	137681171	99772629	50506	ERX1468070	ERS1051442	ERA612385	European Nucleotide Archive	Wellcome Sanger Institute	1	0.54885	0.11528	0.88176	0.60373	50	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United Kingdom	2016-02-03	Larval	Larval	Whole Organism	All anatomical structures
3046	3046	ERR1396810	ERX1468069	ERS1051441	ERP013615	PRJEB12173	Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts	Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011	Transcriptome Analysis	Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos.	ArrayExpress:E ERAD 449		zmp ph230 dgcr8 A1	SAMEA3864307	Wellcome Sanger Institute	ArrayExpress DevelopmentalStage:ZFS:0000037\|ArrayExpress OrganismPart:Whole embryo\|ArrayExpress Species:Danio rerio\|ENA first public:2016 05 03\|ENA last update:2016 02 03\|External Id:SAMEA3864307\|INSDC center alias:SC\|INSDC center name:Wellcome Sanger Institute\|INSDC first public:2016 05 03T14:21:56Z\|INSDC last update:2016 02 03T09:48:31Z\|INSDC status:public\|Submitter Id:2a4c4a70 99a3 11e5 bdcf 3c4a9275d6c6\|common name:zebrafish\|sample description:Sample homozygous for dgcr8 allele sa223. Total RNA from a 5 dpf zebrafish embryo treated with DNase.\|sample name:2a4c4a70 99a3 11e5 bdcf 3c4a9275d6c6\|strain:mixed	Illumina HiSeq 2500 sequencing	SC EXP 18732 1#17	15616871	Illumina sequencing of library 15616871 constructed from sample accession ERS1051441 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence GTCCGC.	Small RNA miRNA		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		ERP013615	Illumina HiSeq 2500 sequencing	ENA FIRST PUBLIC:2016 05 03\|ENA LAST UPDATE:2018 11 16	18732_1#17.cram	cram	302165250.0	6043305.0	SC RUN 18732 1#17	0:50	A:85905345;C:81184773;G:78275206;T:56770744;N:29182	50		85905345	81184773	78275206	56770744	29182	ERX1468069	ERS1051441	ERA612385	European Nucleotide Archive	Wellcome Sanger Institute	1	0.50199	0.10346	0.90118	0.59572	50	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United Kingdom	2016-02-03	Larval	Larval	Whole Organism	All anatomical structures
3047	3047	ERR1396809	ERX1468068	ERS1051440	ERP013615	PRJEB12173	Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts	Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011	Transcriptome Analysis	Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos.	ArrayExpress:E ERAD 449		zmp ph229 dicer C3	SAMEA3864306	Wellcome Sanger Institute	ArrayExpress DevelopmentalStage:ZFS:0000037\|ArrayExpress OrganismPart:Whole embryo\|ArrayExpress Species:Danio rerio\|ENA first public:2016 05 03\|ENA last update:2016 02 03\|External Id:SAMEA3864306\|INSDC center alias:SC\|INSDC center name:Wellcome Sanger Institute\|INSDC first public:2016 05 03T14:21:56Z\|INSDC last update:2016 02 03T09:48:31Z\|INSDC status:public\|Submitter Id:2a3ba8a0 99a3 11e5 bdcf 3c4a9275d6c6\|common name:zebrafish\|sample description:Sample wild type for dicer allele sa9205. Total RNA from a 5 dpf zebrafish embryo treated with DNase.\|sample name:2a3ba8a0 99a3 11e5 bdcf 3c4a9275d6c6\|strain:mixed	Illumina HiSeq 2500 sequencing	SC EXP 18732 1#16	15616954	Illumina sequencing of library 15616954 constructed from sample accession ERS1051440 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence CCGTCC.	Small RNA miRNA		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		ERP013615	Illumina HiSeq 2500 sequencing	ENA FIRST PUBLIC:2016 05 03\|ENA LAST UPDATE:2018 11 16	18732_1#16.cram	cram	252866050.0	5057321.0	SC RUN 18732 1#16	0:50	A:71001103;C:65550329;G:66199420;T:50091388;N:23810	50		71001103	65550329	66199420	50091388	23810	ERX1468068	ERS1051440	ERA612385	European Nucleotide Archive	Wellcome Sanger Institute	1	0.66563	0.10454	0.88239	0.53964	50	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United Kingdom	2016-02-03	Larval	Larval	Whole Organism	All anatomical structures
3048	3048	ERR1396808	ERX1468067	ERS1051439	ERP013615	PRJEB12173	Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts	Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011	Transcriptome Analysis	Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos.	ArrayExpress:E ERAD 449		zmp ph229 dicer B4	SAMEA3864305	Wellcome Sanger Institute	ArrayExpress DevelopmentalStage:ZFS:0000037\|ArrayExpress OrganismPart:Whole embryo\|ArrayExpress Species:Danio rerio\|ENA first public:2016 05 03\|ENA last update:2016 02 03\|External Id:SAMEA3864305\|INSDC center alias:SC\|INSDC center name:Wellcome Sanger Institute\|INSDC first public:2016 05 03T14:21:56Z\|INSDC last update:2016 02 03T09:48:30Z\|INSDC status:public\|Submitter Id:2a319680 99a3 11e5 bdcf 3c4a9275d6c6\|common name:zebrafish\|sample description:Sample wild type for dicer allele sa9205. Total RNA from a 5 dpf zebrafish embryo treated with DNase.\|sample name:2a319680 99a3 11e5 bdcf 3c4a9275d6c6\|strain:mixed	Illumina HiSeq 2500 sequencing	SC EXP 18732 1#15	15616942	Illumina sequencing of library 15616942 constructed from sample accession ERS1051439 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence ATGTCA.	Small RNA miRNA		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		ERP013615	Illumina HiSeq 2500 sequencing	ENA FIRST PUBLIC:2016 05 03\|ENA LAST UPDATE:2018 11 16	18732_1#15.cram	cram	274471250.0	5489425.0	SC RUN 18732 1#15	0:50	A:80060226;C:68799356;G:70635515;T:54950129;N:26024	50		80060226	68799356	70635515	54950129	26024	ERX1468067	ERS1051439	ERA612385	European Nucleotide Archive	Wellcome Sanger Institute	1	0.61964	0.09406	0.89402	0.55473	50	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United Kingdom	2016-02-03	Larval	Larval	Whole Organism	All anatomical structures
3049	3049	ERR1396807	ERX1468066	ERS1051438	ERP013615	PRJEB12173	Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts	Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011	Transcriptome Analysis	Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos.	ArrayExpress:E ERAD 449		zmp ph229 dicer A7	SAMEA3864304	Wellcome Sanger Institute	ArrayExpress DevelopmentalStage:ZFS:0000037\|ArrayExpress OrganismPart:Whole embryo\|ArrayExpress Species:Danio rerio\|ENA first public:2016 05 03\|ENA last update:2016 02 03\|External Id:SAMEA3864304\|INSDC center alias:SC\|INSDC center name:Wellcome Sanger Institute\|INSDC first public:2016 05 03T14:21:56Z\|INSDC last update:2016 02 03T09:48:29Z\|INSDC status:public\|Submitter Id:2a2a6a90 99a3 11e5 bdcf 3c4a9275d6c6\|common name:zebrafish\|sample description:Sample wild type for dicer allele sa9205. Total RNA from a 5 dpf zebrafish embryo treated with DNase.\|sample name:2a2a6a90 99a3 11e5 bdcf 3c4a9275d6c6\|strain:mixed	Illumina HiSeq 2500 sequencing	SC EXP 18732 1#14	15616930	Illumina sequencing of library 15616930 constructed from sample accession ERS1051438 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence AGTTCC.	Small RNA miRNA		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		ERP013615	Illumina HiSeq 2500 sequencing	ENA FIRST PUBLIC:2016 05 03\|ENA LAST UPDATE:2018 11 16	18732_1#14.cram	cram	467847600.0	9356952.0	SC RUN 18732 1#14	0:50	A:134225837;C:118320475;G:121443773;T:93812243;N:45272	50		134225837	118320475	121443773	93812243	45272	ERX1468066	ERS1051438	ERA612385	European Nucleotide Archive	Wellcome Sanger Institute	1	0.64705	0.096	0.8983	0.56022	50	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United Kingdom	2016-02-03	Larval	Larval	Whole Organism	All anatomical structures
3050	3050	ERR1396806	ERX1468065	ERS1051437	ERP013615	PRJEB12173	Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts	Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011	Transcriptome Analysis	Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos.	ArrayExpress:E ERAD 449		zmp ph229 dicer A1	SAMEA3864303	Wellcome Sanger Institute	ArrayExpress DevelopmentalStage:ZFS:0000037\|ArrayExpress OrganismPart:Whole embryo\|ArrayExpress Species:Danio rerio\|ENA first public:2016 05 03\|ENA last update:2016 02 03\|External Id:SAMEA3864303\|INSDC center alias:SC\|INSDC center name:Wellcome Sanger Institute\|INSDC first public:2016 05 03T14:21:56Z\|INSDC last update:2016 02 03T09:48:29Z\|INSDC status:public\|Submitter Id:2a238cc0 99a3 11e5 bdcf 3c4a9275d6c6\|common name:zebrafish\|sample description:Sample wild type for dicer allele sa9205. Total RNA from a 5 dpf zebrafish embryo treated with DNase.\|sample name:2a238cc0 99a3 11e5 bdcf 3c4a9275d6c6\|strain:mixed	Illumina HiSeq 2500 sequencing	SC EXP 18732 1#13	15616918	Illumina sequencing of library 15616918 constructed from sample accession ERS1051437 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence AGTCAA.	Small RNA miRNA		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		ERP013615	Illumina HiSeq 2500 sequencing	ENA FIRST PUBLIC:2016 05 03\|ENA LAST UPDATE:2018 11 16	18732_1#13.cram	cram	160243100.0	3204862.0	SC RUN 18732 1#13	0:50	A:46708835;C:40347424;G:41434539;T:31737029;N:15273	50		46708835	40347424	41434539	31737029	15273	ERX1468065	ERS1051437	ERA612385	European Nucleotide Archive	Wellcome Sanger Institute	1	0.65975	0.09405	0.90065	0.54178	50	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United Kingdom	2016-02-03	Larval	Larval	Whole Organism	All anatomical structures
3051	3051	ERR1396805	ERX1468064	ERS1051436	ERP013615	PRJEB12173	Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts	Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011	Transcriptome Analysis	Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos.	ArrayExpress:E ERAD 449		zmp ph229 dicer C1	SAMEA3864302	Wellcome Sanger Institute	ArrayExpress DevelopmentalStage:ZFS:0000037\|ArrayExpress OrganismPart:Whole embryo\|ArrayExpress Species:Danio rerio\|ENA first public:2016 05 03\|ENA last update:2016 02 03\|External Id:SAMEA3864302\|INSDC center alias:SC\|INSDC center name:Wellcome Sanger Institute\|INSDC first public:2016 05 03T14:21:56Z\|INSDC last update:2016 02 03T09:48:28Z\|INSDC status:public\|Submitter Id:2a1b9d80 99a3 11e5 bdcf 3c4a9275d6c6\|common name:zebrafish\|sample description:Sample homozygous for dicer allele sa9205. Total RNA from a 5 dpf zebrafish embryo treated with DNase.\|sample name:2a1b9d80 99a3 11e5 bdcf 3c4a9275d6c6\|strain:mixed	Illumina HiSeq 2500 sequencing	SC EXP 18732 1#12	15616906	Illumina sequencing of library 15616906 constructed from sample accession ERS1051436 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence CTTGTA.	Small RNA miRNA		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		ERP013615	Illumina HiSeq 2500 sequencing	ENA FIRST PUBLIC:2016 05 03\|ENA LAST UPDATE:2018 11 16	18732_1#12.cram	cram	378715650.0	7574313.0	SC RUN 18732 1#12	0:50	A:106991982;C:94292878;G:99663404;T:77730801;N:36585	50		106991982	94292878	99663404	77730801	36585	ERX1468064	ERS1051436	ERA612385	European Nucleotide Archive	Wellcome Sanger Institute	1	0.64513	0.11804	0.86525	0.55346	50	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United Kingdom	2016-02-03	Larval	Larval	Whole Organism	All anatomical structures
3052	3052	ERR1396804	ERX1468063	ERS1051435	ERP013615	PRJEB12173	Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts	Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011	Transcriptome Analysis	Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos.	ArrayExpress:E ERAD 449		zmp ph229 dicer B3	SAMEA3864301	Wellcome Sanger Institute	ArrayExpress DevelopmentalStage:ZFS:0000037\|ArrayExpress OrganismPart:Whole embryo\|ArrayExpress Species:Danio rerio\|ENA first public:2016 05 03\|ENA last update:2016 02 03\|External Id:SAMEA3864301\|INSDC center alias:SC\|INSDC center name:Wellcome Sanger Institute\|INSDC first public:2016 05 03T14:21:55Z\|INSDC last update:2016 02 03T09:48:28Z\|INSDC status:public\|Submitter Id:2a0d93c0 99a3 11e5 bdcf 3c4a9275d6c6\|common name:zebrafish\|sample description:Sample homozygous for dicer allele sa9205. Total RNA from a 5 dpf zebrafish embryo treated with DNase.\|sample name:2a0d93c0 99a3 11e5 bdcf 3c4a9275d6c6\|strain:mixed	Illumina HiSeq 2500 sequencing	SC EXP 18732 1#11	15616894	Illumina sequencing of library 15616894 constructed from sample accession ERS1051435 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence GGCTAC.	Small RNA miRNA		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		ERP013615	Illumina HiSeq 2500 sequencing	ENA FIRST PUBLIC:2016 05 03\|ENA LAST UPDATE:2018 11 16	18732_1#11.cram	cram	139094000.0	2781880.0	SC RUN 18732 1#11	0:50	A:39702275;C:35436377;G:36969525;T:26972594;N:13229	50		39702275	35436377	36969525	26972594	13229	ERX1468063	ERS1051435	ERA612385	European Nucleotide Archive	Wellcome Sanger Institute	1	0.60357	0.10386	0.88872	0.5774	50	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United Kingdom	2016-02-03	Larval	Larval	Whole Organism	All anatomical structures
3053	3053	ERR1396803	ERX1468062	ERS1051434	ERP013615	PRJEB12173	Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts	Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011	Transcriptome Analysis	Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos.	ArrayExpress:E ERAD 449		zmp ph229 dicer A12	SAMEA3864300	Wellcome Sanger Institute	ArrayExpress DevelopmentalStage:ZFS:0000037\|ArrayExpress OrganismPart:Whole embryo\|ArrayExpress Species:Danio rerio\|ENA first public:2016 05 03\|ENA last update:2016 02 03\|External Id:SAMEA3864300\|INSDC center alias:SC\|INSDC center name:Wellcome Sanger Institute\|INSDC first public:2016 05 03T14:21:56Z\|INSDC last update:2016 02 03T09:48:27Z\|INSDC status:public\|Submitter Id:2a075230 99a3 11e5 bdcf 3c4a9275d6c6\|common name:zebrafish\|sample description:Sample homozygous for dicer allele sa9205. Total RNA from a 5 dpf zebrafish embryo treated with DNase.\|sample name:2a075230 99a3 11e5 bdcf 3c4a9275d6c6\|strain:mixed	Illumina HiSeq 2500 sequencing	SC EXP 18732 1#10	15616882	Illumina sequencing of library 15616882 constructed from sample accession ERS1051434 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence TAGCTT.	Small RNA miRNA		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		ERP013615	Illumina HiSeq 2500 sequencing	ENA FIRST PUBLIC:2016 05 03\|ENA LAST UPDATE:2018 11 16	18732_1#10.cram	cram	263295150.0	5265903.0	SC RUN 18732 1#10	0:50	A:75332297;C:66059671;G:68562462;T:53315439;N:25281	50		75332297	66059671	68562462	53315439	25281	ERX1468062	ERS1051434	ERA612385	European Nucleotide Archive	Wellcome Sanger Institute	1	0.61939	0.10112	0.89613	0.55542	50	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United Kingdom	2016-02-03	Larval	Larval	Whole Organism	All anatomical structures
3054	3054	ERR1396802	ERX1468061	ERS1051433	ERP013615	PRJEB12173	Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts	Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011	Transcriptome Analysis	Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos.	ArrayExpress:E ERAD 449		zmp ph229 dicer A10	SAMEA3864299	Wellcome Sanger Institute	ArrayExpress DevelopmentalStage:ZFS:0000037\|ArrayExpress OrganismPart:Whole embryo\|ArrayExpress Species:Danio rerio\|ENA first public:2016 05 03\|ENA last update:2016 02 03\|External Id:SAMEA3864299\|INSDC center alias:SC\|INSDC center name:Wellcome Sanger Institute\|INSDC first public:2016 05 03T14:21:56Z\|INSDC last update:2016 02 03T09:48:26Z\|INSDC status:public\|Submitter Id:29ffff30 99a3 11e5 bdcf 3c4a9275d6c6\|common name:zebrafish\|sample description:Sample homozygous for dicer allele sa9205. Total RNA from a 5 dpf zebrafish embryo treated with DNase.\|sample name:29ffff30 99a3 11e5 bdcf 3c4a9275d6c6\|strain:mixed	Illumina HiSeq 2500 sequencing	SC EXP 18732 1#9	15616870	Illumina sequencing of library 15616870 constructed from sample accession ERS1051433 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence GATCAG.	Small RNA miRNA		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		ERP013615	Illumina HiSeq 2500 sequencing	ENA FIRST PUBLIC:2016 05 03\|ENA LAST UPDATE:2018 11 16	18732_1#9.cram	cram	7506900.0	150138.0	SC RUN 18732 1#9	0:50	A:2194276;C:1883363;G:1959471;T:1468994;N:796	50		2194276	1883363	1959471	1468994	796	ERX1468061	ERS1051433	ERA612385	European Nucleotide Archive	Wellcome Sanger Institute	1	0.60026	0.10518	0.91106	0.55508	50	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United Kingdom	2016-02-03	Larval	Larval	Whole Organism	All anatomical structures
3055	3055	ERR1396801	ERX1468060	ERS1051432	ERP013615	PRJEB12173	Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts	Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011	Transcriptome Analysis	Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos.	ArrayExpress:E ERAD 449		zmp ph228 drosha C1	SAMEA3864298	Wellcome Sanger Institute	ArrayExpress DevelopmentalStage:ZFS:0000037\|ArrayExpress OrganismPart:Whole embryo\|ArrayExpress Species:Danio rerio\|ENA first public:2016 05 03\|ENA last update:2016 02 03\|External Id:SAMEA3864298\|INSDC center alias:SC\|INSDC center name:Wellcome Sanger Institute\|INSDC first public:2016 05 03T14:21:56Z\|INSDC last update:2016 02 03T09:48:26Z\|INSDC status:public\|Submitter Id:29f306e0 99a3 11e5 bdcf 3c4a9275d6c6\|common name:zebrafish\|sample description:Sample wild type for drosha allele sa191. Total RNA from a 5 dpf zebrafish embryo treated with DNase.\|sample name:29f306e0 99a3 11e5 bdcf 3c4a9275d6c6\|strain:mixed	Illumina HiSeq 2500 sequencing	SC EXP 18732 1#8	15616953	Illumina sequencing of library 15616953 constructed from sample accession ERS1051432 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence ACTTGA.	Small RNA miRNA		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		ERP013615	Illumina HiSeq 2500 sequencing	ENA FIRST PUBLIC:2016 05 03\|ENA LAST UPDATE:2018 11 16	18732_1#8.cram	cram	464447300.0	9288946.0	SC RUN 18732 1#8	0:50	A:136629424;C:120103988;G:117495447;T:90173901;N:44540	50		136629424	120103988	117495447	90173901	44540	ERX1468060	ERS1051432	ERA612385	European Nucleotide Archive	Wellcome Sanger Institute	1	0.51298	0.10188	0.88434	0.6034	50	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United Kingdom	2016-02-03	Larval	Larval	Whole Organism	All anatomical structures
3056	3056	ERR1396800	ERX1468059	ERS1051431	ERP013615	PRJEB12173	Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts	Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011	Transcriptome Analysis	Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos.	ArrayExpress:E ERAD 449		zmp ph228 drosha A9	SAMEA3864297	Wellcome Sanger Institute	ArrayExpress DevelopmentalStage:ZFS:0000037\|ArrayExpress OrganismPart:Whole embryo\|ArrayExpress Species:Danio rerio\|ENA first public:2016 05 03\|ENA last update:2016 02 03\|External Id:SAMEA3864297\|INSDC center alias:SC\|INSDC center name:Wellcome Sanger Institute\|INSDC first public:2016 05 03T14:21:56Z\|INSDC last update:2016 02 03T09:48:25Z\|INSDC status:public\|Submitter Id:29e942e0 99a3 11e5 bdcf 3c4a9275d6c6\|common name:zebrafish\|sample description:Sample wild type for drosha allele sa191. Total RNA from a 5 dpf zebrafish embryo treated with DNase.\|sample name:29e942e0 99a3 11e5 bdcf 3c4a9275d6c6\|strain:mixed	Illumina HiSeq 2500 sequencing	SC EXP 18732 1#7	15616941	Illumina sequencing of library 15616941 constructed from sample accession ERS1051431 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence CAGATC.	Small RNA miRNA		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		ERP013615	Illumina HiSeq 2500 sequencing	ENA FIRST PUBLIC:2016 05 03\|ENA LAST UPDATE:2018 11 16	18732_1#7.cram	cram	294666500.0	5893330.0	SC RUN 18732 1#7	0:50	A:85765921;C:76239559;G:76452231;T:56180868;N:27921	50		85765921	76239559	76452231	56180868	27921	ERX1468059	ERS1051431	ERA612385	European Nucleotide Archive	Wellcome Sanger Institute	1	0.56455	0.10217	0.88286	0.60374	50	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United Kingdom	2016-02-03	Larval	Larval	Whole Organism	All anatomical structures
3057	3057	ERR1396799	ERX1468058	ERS1051430	ERP013615	PRJEB12173	Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts	Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011	Transcriptome Analysis	Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos.	ArrayExpress:E ERAD 449		zmp ph228 drosha A6	SAMEA3864296	Wellcome Sanger Institute	ArrayExpress DevelopmentalStage:ZFS:0000037\|ArrayExpress OrganismPart:Whole embryo\|ArrayExpress Species:Danio rerio\|ENA first public:2016 05 03\|ENA last update:2016 02 03\|External Id:SAMEA3864296\|INSDC center alias:SC\|INSDC center name:Wellcome Sanger Institute\|INSDC first public:2016 05 03T14:21:56Z\|INSDC last update:2016 02 03T09:48:25Z\|INSDC status:public\|Submitter Id:29e06940 99a3 11e5 bdcf 3c4a9275d6c6\|common name:zebrafish\|sample description:Sample wild type for drosha allele sa191. Total RNA from a 5 dpf zebrafish embryo treated with DNase.\|sample name:29e06940 99a3 11e5 bdcf 3c4a9275d6c6\|strain:mixed	Illumina HiSeq 2500 sequencing	SC EXP 18732 1#6	15616929	Illumina sequencing of library 15616929 constructed from sample accession ERS1051430 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence GCCAAT.	Small RNA miRNA		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		ERP013615	Illumina HiSeq 2500 sequencing	ENA FIRST PUBLIC:2016 05 03\|ENA LAST UPDATE:2018 11 16	18732_1#6.cram	cram	239549350.0	4790987.0	SC RUN 18732 1#6	0:50	A:68726161;C:60828350;G:62739441;T:47232484;N:22914	50		68726161	60828350	62739441	47232484	22914	ERX1468058	ERS1051430	ERA612385	European Nucleotide Archive	Wellcome Sanger Institute	1	0.64469	0.1021	0.88878	0.58044	50	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United Kingdom	2016-02-03	Larval	Larval	Whole Organism	All anatomical structures
3058	3058	ERR1396798	ERX1468057	ERS1051429	ERP013615	PRJEB12173	Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts	Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011	Transcriptome Analysis	Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos.	ArrayExpress:E ERAD 449		zmp ph228 drosha A1	SAMEA3864295	Wellcome Sanger Institute	ArrayExpress DevelopmentalStage:ZFS:0000037\|ArrayExpress OrganismPart:Whole embryo\|ArrayExpress Species:Danio rerio\|ENA first public:2016 05 03\|ENA last update:2016 02 03\|External Id:SAMEA3864295\|INSDC center alias:SC\|INSDC center name:Wellcome Sanger Institute\|INSDC first public:2016 05 03T14:21:56Z\|INSDC last update:2016 02 03T09:48:24Z\|INSDC status:public\|Submitter Id:29d74180 99a3 11e5 bdcf 3c4a9275d6c6\|common name:zebrafish\|sample description:Sample wild type for drosha allele sa191. Total RNA from a 5 dpf zebrafish embryo treated with DNase.\|sample name:29d74180 99a3 11e5 bdcf 3c4a9275d6c6\|strain:mixed	Illumina HiSeq 2500 sequencing	SC EXP 18732 1#5	15616917	Illumina sequencing of library 15616917 constructed from sample accession ERS1051429 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence ACAGTG.	Small RNA miRNA		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		ERP013615	Illumina HiSeq 2500 sequencing	ENA FIRST PUBLIC:2016 05 03\|ENA LAST UPDATE:2018 11 16	18732_1#5.cram	cram	165341300.0	3306826.0	SC RUN 18732 1#5	0:50	A:47735538;C:41622088;G:43392205;T:32575765;N:15704	50		47735538	41622088	43392205	32575765	15704	ERX1468057	ERS1051429	ERA612385	European Nucleotide Archive	Wellcome Sanger Institute	1	0.64704	0.09836	0.90534	0.56172	50	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United Kingdom	2016-02-03	Larval	Larval	Whole Organism	All anatomical structures
3059	3059	ERR1396797	ERX1468056	ERS1051428	ERP013615	PRJEB12173	Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts	Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011	Transcriptome Analysis	Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos.	ArrayExpress:E ERAD 449		zmp ph228 drosha B12	SAMEA3864294	Wellcome Sanger Institute	ArrayExpress DevelopmentalStage:ZFS:0000037\|ArrayExpress OrganismPart:Whole embryo\|ArrayExpress Species:Danio rerio\|ENA first public:2016 05 03\|ENA last update:2016 02 03\|External Id:SAMEA3864294\|INSDC center alias:SC\|INSDC center name:Wellcome Sanger Institute\|INSDC first public:2016 05 03T14:21:56Z\|INSDC last update:2016 02 03T09:48:23Z\|INSDC status:public\|Submitter Id:29cf7950 99a3 11e5 bdcf 3c4a9275d6c6\|common name:zebrafish\|sample description:Sample homozygous for drosha allele sa191. Total RNA from a 5 dpf zebrafish embryo treated with DNase.\|sample name:29cf7950 99a3 11e5 bdcf 3c4a9275d6c6\|strain:mixed	Illumina HiSeq 2500 sequencing	SC EXP 18732 1#4	15616905	Illumina sequencing of library 15616905 constructed from sample accession ERS1051428 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence TGACCA.	Small RNA miRNA		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		ERP013615	Illumina HiSeq 2500 sequencing	ENA FIRST PUBLIC:2016 05 03\|ENA LAST UPDATE:2018 11 16	18732_1#4.cram	cram	401336200.0	8026724.0	SC RUN 18732 1#4	0:50	A:117609087;C:105872656;G:100576681;T:77238881;N:38895	50		117609087	105872656	100576681	77238881	38895	ERX1468056	ERS1051428	ERA612385	European Nucleotide Archive	Wellcome Sanger Institute	1	0.51741	0.10352	0.89749	0.58497	50	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United Kingdom	2016-02-03	Larval	Larval	Whole Organism	All anatomical structures
3060	3060	ERR1396796	ERX1468055	ERS1051427	ERP013615	PRJEB12173	Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts	Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011	Transcriptome Analysis	Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos.	ArrayExpress:E ERAD 449		zmp ph228 drosha B10	SAMEA3864293	Wellcome Sanger Institute	ArrayExpress DevelopmentalStage:ZFS:0000037\|ArrayExpress OrganismPart:Whole embryo\|ArrayExpress Species:Danio rerio\|ENA first public:2016 05 03\|ENA last update:2016 02 03\|External Id:SAMEA3864293\|INSDC center alias:SC\|INSDC center name:Wellcome Sanger Institute\|INSDC first public:2016 05 03T14:21:56Z\|INSDC last update:2016 02 03T09:48:22Z\|INSDC status:public\|Submitter Id:29c84d60 99a3 11e5 bdcf 3c4a9275d6c6\|common name:zebrafish\|sample description:Sample homozygous for drosha allele sa191. Total RNA from a 5 dpf zebrafish embryo treated with DNase.\|sample name:29c84d60 99a3 11e5 bdcf 3c4a9275d6c6\|strain:mixed	Illumina HiSeq 2500 sequencing	SC EXP 18732 1#3	15616893	Illumina sequencing of library 15616893 constructed from sample accession ERS1051427 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence TTAGGC.	Small RNA miRNA		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		ERP013615	Illumina HiSeq 2500 sequencing	ENA FIRST PUBLIC:2016 05 03\|ENA LAST UPDATE:2018 11 16	18732_1#3.cram	cram	214767600.0	4295352.0	SC RUN 18732 1#3	0:50	A:61527319;C:53911904;G:56445139;T:42862938;N:20300	50		61527319	53911904	56445139	42862938	20300	ERX1468055	ERS1051427	ERA612385	European Nucleotide Archive	Wellcome Sanger Institute	1	0.57363	0.11614	0.88487	0.61011	50	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United Kingdom	2016-02-03	Larval	Larval	Whole Organism	All anatomical structures
3061	3061	ERR1396795	ERX1468054	ERS1051426	ERP013615	PRJEB12173	Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts	Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011	Transcriptome Analysis	Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos.	ArrayExpress:E ERAD 449		zmp ph228 drosha B7	SAMEA3864292	Wellcome Sanger Institute	ArrayExpress DevelopmentalStage:ZFS:0000037\|ArrayExpress OrganismPart:Whole embryo\|ArrayExpress Species:Danio rerio\|ENA first public:2016 05 03\|ENA last update:2016 02 03\|External Id:SAMEA3864292\|INSDC center alias:SC\|INSDC center name:Wellcome Sanger Institute\|INSDC first public:2016 05 03T14:21:56Z\|INSDC last update:2016 02 03T09:48:22Z\|INSDC status:public\|Submitter Id:29b1df30 99a3 11e5 bdcf 3c4a9275d6c6\|common name:zebrafish\|sample description:Sample homozygous for drosha allele sa191. Total RNA from a 5 dpf zebrafish embryo treated with DNase.\|sample name:29b1df30 99a3 11e5 bdcf 3c4a9275d6c6\|strain:mixed	Illumina HiSeq 2500 sequencing	SC EXP 18732 1#2	15616881	Illumina sequencing of library 15616881 constructed from sample accession ERS1051426 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence CGATGT.	Small RNA miRNA		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		ERP013615	Illumina HiSeq 2500 sequencing	ENA FIRST PUBLIC:2016 05 03\|ENA LAST UPDATE:2018 11 16	18732_1#2.cram	cram	326025150.0	6520503.0	SC RUN 18732 1#2	0:50	A:93261648;C:82767834;G:86798075;T:63166259;N:31334	50		93261648	82767834	86798075	63166259	31334	ERX1468054	ERS1051426	ERA612385	European Nucleotide Archive	Wellcome Sanger Institute	1	0.57333	0.11365	0.87422	0.60838	50	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United Kingdom	2016-02-03	Larval	Larval	Whole Organism	All anatomical structures
3062	3062	ERR1396794	ERX1468053	ERS1051425	ERP013615	PRJEB12173	Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts	Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011	Transcriptome Analysis	Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos.	ArrayExpress:E ERAD 449		zmp ph228 drosha B1	SAMEA3864291	Wellcome Sanger Institute	ArrayExpress DevelopmentalStage:ZFS:0000037\|ArrayExpress OrganismPart:Whole embryo\|ArrayExpress Species:Danio rerio\|ENA first public:2016 05 03\|ENA last update:2016 02 03\|External Id:SAMEA3864291\|INSDC center alias:SC\|INSDC center name:Wellcome Sanger Institute\|INSDC first public:2016 05 03T14:21:55Z\|INSDC last update:2016 02 03T09:48:20Z\|INSDC status:public\|Submitter Id:29904d70 99a3 11e5 bdcf 3c4a9275d6c6\|common name:zebrafish\|sample description:Sample homozygous for drosha allele sa191. Total RNA from a 5 dpf zebrafish embryo treated with DNase.\|sample name:29904d70 99a3 11e5 bdcf 3c4a9275d6c6\|strain:mixed	Illumina HiSeq 2500 sequencing	SC EXP 18732 1#1	15616869	Illumina sequencing of library 15616869 constructed from sample accession ERS1051425 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence ATCACG.	Small RNA miRNA		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		ERP013615	Illumina HiSeq 2500 sequencing	ENA FIRST PUBLIC:2016 05 03\|ENA LAST UPDATE:2018 11 16	18732_1#1.cram	cram	419669000.0	8393380.0	SC RUN 18732 1#1	0:50	A:121378853;C:106010609;G:109826454;T:82412717;N:40367	50		121378853	106010609	109826454	82412717	40367	ERX1468053	ERS1051425	ERA612385	European Nucleotide Archive	Wellcome Sanger Institute	1	0.60815	0.11567	0.90289	0.5657	50	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	United Kingdom	2016-02-03	Larval	Larval	Whole Organism	All anatomical structures
8104	8104	ERR2455366	ERX2474426	ERS2327331	ERP107743	PRJEB25789	RNA seq of zebrafish larvae fed with different diets	E-MTAB-6636	Transcriptome Analysis	We aim to establish NAFLD model of Zebrafish. Zebrafish larvae fed with high cholesterol diet high fructose diet and overfeed diet to induce liver steatosis. RNA seq was employed to analyze the effects of different diets on NAFLD development.	ENA FIRST PUBLIC:2018 12 01\|ENA LAST UPDATE:2018 03 29	Protocols: Total RNAs were extracted from liver tissues of zebrafish larvae. A total amount of 1.5μg RNA per sample was used as input material for the RNA sample preparations. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample.	Sample 4	SAMEA104725948	Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College	ENA FIRST PUBLIC:2018 12 01T17:02:09Z\|ENA LAST UPDATE:2018 03 29T12:32:24Z\|External Id:SAMEA104725948\|INSDC center name:Institute of Medicinal Biotechnology Chinese Academy of Medical Sciences and Peking Union Medical College\|INSDC first public:2018 12 01T17:02:09Z\|INSDC last update:2018 03 29T12:32:24Z\|INSDC status:public\|Submitter Id:E MTAB 6636:Sample 4\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larval stage\|diet:overfeeding\|organism part:liver\|sample name:E MTAB 6636:Sample 4\|scientific name:Danio rerio	Illumina HiSeq 4000 sequencing; RNA seq of zebrafish larvae fed with different diets	E MTAB 6636:Sample 4 s	Sample 4 s	RNA seq of zebrafish larvae fed with different diets	Total RNAs were extracted from liver tissues of zebrafish larvae. A total amount of 1.5μg RNA per sample was used as input material for the RNA sample preparations. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample.	Experimental Factor: diet:overfeeding	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000		ERP107743	Illumina HiSeq 4000 sequencing; RNA seq of zebrafish larvae fed with different diets	ENA FIRST PUBLIC:2018 12 01\|ENA LAST UPDATE:2018 11 16	OF-4_H7MWNALXX_L6_1.fq.gz	fastq	4961276550.0	33075177.0	E MTAB 6636:Sample 4	0:150 1:0	A:1349413168;C:1135314970;G:1137935563;T:1338034716;N:578133	150	0	1349413168	1135314970	1137935563	1338034716	578133	ERX2474426	ERS2327331	ERA1259907	Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College\|European Nucleotide Archive	Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College\|European Nucleotide Archive	1	0.90787	0.11999	0.66123	0.49072	150	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	China	2018-03-29	Larval	Larval	Liver	Liver and Biliary System
8105	8105	ERR2455365	ERX2474425	ERS2327330	ERP107743	PRJEB25789	RNA seq of zebrafish larvae fed with different diets	E-MTAB-6636	Transcriptome Analysis	We aim to establish NAFLD model of Zebrafish. Zebrafish larvae fed with high cholesterol diet high fructose diet and overfeed diet to induce liver steatosis. RNA seq was employed to analyze the effects of different diets on NAFLD development.	ENA FIRST PUBLIC:2018 12 01\|ENA LAST UPDATE:2018 03 29	Protocols: Total RNAs were extracted from liver tissues of zebrafish larvae. A total amount of 1.5μg RNA per sample was used as input material for the RNA sample preparations. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample.	Sample 3	SAMEA104725947	Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College	ENA FIRST PUBLIC:2018 12 01T17:02:09Z\|ENA LAST UPDATE:2018 03 29T12:32:24Z\|External Id:SAMEA104725947\|INSDC center name:Institute of Medicinal Biotechnology Chinese Academy of Medical Sciences and Peking Union Medical College\|INSDC first public:2018 12 01T17:02:09Z\|INSDC last update:2018 03 29T12:32:24Z\|INSDC status:public\|Submitter Id:E MTAB 6636:Sample 3\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larval stage\|diet:fructose\|organism part:liver\|sample name:E MTAB 6636:Sample 3\|scientific name:Danio rerio	Illumina HiSeq 4000 sequencing; RNA seq of zebrafish larvae fed with different diets	E MTAB 6636:Sample 3 s	Sample 3 s	RNA seq of zebrafish larvae fed with different diets	Total RNAs were extracted from liver tissues of zebrafish larvae. A total amount of 1.5μg RNA per sample was used as input material for the RNA sample preparations. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample.	Experimental Factor: diet:fructose	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000		ERP107743	Illumina HiSeq 4000 sequencing; RNA seq of zebrafish larvae fed with different diets	ENA FIRST PUBLIC:2018 12 01\|ENA LAST UPDATE:2018 11 16	Fru-3_H7MWNALXX_L5_1.fq.gz	fastq	5858273250.0	39055155.0	E MTAB 6636:Sample 3	0:150 1:0	A:1580150663;C:1353221682;G:1355865524;T:1568428138;N:607243	150	0	1580150663	1353221682	1355865524	1568428138	607243	ERX2474425	ERS2327330	ERA1259907	Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College\|European Nucleotide Archive	Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College\|European Nucleotide Archive	1	0.91505	0.11036	0.65985	0.48443	150	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	China	2018-03-29	Larval	Larval	Liver	Liver and Biliary System
8106	8106	ERR2455364	ERX2474424	ERS2327329	ERP107743	PRJEB25789	RNA seq of zebrafish larvae fed with different diets	E-MTAB-6636	Transcriptome Analysis	We aim to establish NAFLD model of Zebrafish. Zebrafish larvae fed with high cholesterol diet high fructose diet and overfeed diet to induce liver steatosis. RNA seq was employed to analyze the effects of different diets on NAFLD development.	ENA FIRST PUBLIC:2018 12 01\|ENA LAST UPDATE:2018 03 29	Protocols: Total RNAs were extracted from liver tissues of zebrafish larvae. A total amount of 1.5μg RNA per sample was used as input material for the RNA sample preparations. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample.	Sample 2	SAMEA104725946	Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College	ENA FIRST PUBLIC:2018 12 01T17:02:09Z\|ENA LAST UPDATE:2018 03 29T12:32:24Z\|External Id:SAMEA104725946\|INSDC center name:Institute of Medicinal Biotechnology Chinese Academy of Medical Sciences and Peking Union Medical College\|INSDC first public:2018 12 01T17:02:09Z\|INSDC last update:2018 03 29T12:32:24Z\|INSDC status:public\|Submitter Id:E MTAB 6636:Sample 2\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larval stage\|diet:cholesterol\|organism part:liver\|sample name:E MTAB 6636:Sample 2\|scientific name:Danio rerio	Illumina HiSeq 4000 sequencing; RNA seq of zebrafish larvae fed with different diets	E MTAB 6636:Sample 2 s	Sample 2 s	RNA seq of zebrafish larvae fed with different diets	Total RNAs were extracted from liver tissues of zebrafish larvae. A total amount of 1.5μg RNA per sample was used as input material for the RNA sample preparations. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample.	Experimental Factor: diet:cholesterol	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000		ERP107743	Illumina HiSeq 4000 sequencing; RNA seq of zebrafish larvae fed with different diets	ENA FIRST PUBLIC:2018 12 01\|ENA LAST UPDATE:2018 11 16	Cho-2_H7MWNALXX_L5_1.fq.gz	fastq	5636304900.0	37575366.0	E MTAB 6636:Sample 2	0:150 1:0	A:1526862069;C:1295343770;G:1298751994;T:1514766898;N:580169	150	0	1526862069	1295343770	1298751994	1514766898	580169	ERX2474424	ERS2327329	ERA1259907	Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College\|European Nucleotide Archive	Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College\|European Nucleotide Archive	1	0.91032	0.11644	0.66649	0.47766	150	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	China	2018-03-29	Larval	Larval	Liver	Liver and Biliary System
8107	8107	ERR2455363	ERX2474423	ERS2327328	ERP107743	PRJEB25789	RNA seq of zebrafish larvae fed with different diets	E-MTAB-6636	Transcriptome Analysis	We aim to establish NAFLD model of Zebrafish. Zebrafish larvae fed with high cholesterol diet high fructose diet and overfeed diet to induce liver steatosis. RNA seq was employed to analyze the effects of different diets on NAFLD development.	ENA FIRST PUBLIC:2018 12 01\|ENA LAST UPDATE:2018 03 29	Protocols: Total RNAs were extracted from liver tissues of zebrafish larvae. A total amount of 1.5μg RNA per sample was used as input material for the RNA sample preparations. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample.	Sample 1	SAMEA104725945	Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College	ENA FIRST PUBLIC:2018 12 01T17:02:09Z\|ENA LAST UPDATE:2018 03 29T12:32:24Z\|External Id:SAMEA104725945\|INSDC center name:Institute of Medicinal Biotechnology Chinese Academy of Medical Sciences and Peking Union Medical College\|INSDC first public:2018 12 01T17:02:09Z\|INSDC last update:2018 03 29T12:32:24Z\|INSDC status:public\|Submitter Id:E MTAB 6636:Sample 1\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larval stage\|diet:control\|organism part:liver\|sample name:E MTAB 6636:Sample 1\|scientific name:Danio rerio	Illumina HiSeq 4000 sequencing; RNA seq of zebrafish larvae fed with different diets	E MTAB 6636:Sample 1 s	Sample 1 s	RNA seq of zebrafish larvae fed with different diets	Total RNAs were extracted from liver tissues of zebrafish larvae. A total amount of 1.5μg RNA per sample was used as input material for the RNA sample preparations. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample.	Experimental Factor: diet:control	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000		ERP107743	Illumina HiSeq 4000 sequencing; RNA seq of zebrafish larvae fed with different diets	ENA FIRST PUBLIC:2018 12 01\|ENA LAST UPDATE:2018 11 16	ND-1_H7MWNALXX_L5_1.fq.gz	fastq	5197165350.0	34647769.0	E MTAB 6636:Sample 1	0:150 1:0	A:1430911816;C:1174811274;G:1175616551;T:1415284019;N:541690	150	0	1430911816	1174811274	1175616551	1415284019	541690	ERX2474423	ERS2327328	ERA1259907	Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College\|European Nucleotide Archive	Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College\|European Nucleotide Archive	1	0.89838	0.13883	0.66129	0.48467	150	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	China	2018-03-29	Larval	Larval	Liver	Liver and Biliary System
9764	9764	ERR3454281	ERX3476201	ERS360451	ERP116513	PRJEB33700	Regulation of Dot Icm effectors translocation by T4SS GGDEF EAL proteins in Legionella pneumophila	ena-STUDY-CIRI-Inserm-U1111-26-07-2019-08:05:36:132-1961	Other	Legionella pneumophila is a waterborne bacterium that can replicate in a variety of host cells from environmental amoebae to human macrophages. Its virulence traits are subject to complex regulation that involves some signaling pathways dependent on cyclic di GMP. Cyclic di GMP is a second messenger that can result in transcriptional translational or post translational control of targets including secretion systems. We are particularly interested in the c di GMP metabolizing enzyme Lpl0780/Lpp0809 needed for the early steps of intracellular cycle and the appropriate translocation of bacterial effectors by Dot/Icm T4SS. Comparative transcriptomic analysis was performed from the RNA seq data of the Lens Wild Type strain and the ?lpl0780 mutant using DESeq2 package on normalized gene read counts. The results showed that only 12 genes among 2966 were significantly differentially expressed P < 0.01 and log2 fold change of >1 or < 1 between ?lpl0780 strain and the WT Lens strain. However the fold changes remain quite weak and moreover none of these genes can be connected to T4SS or effectors. These results suggest that Lpl0780/Lpp0809 acts at a post transcriptional level on the translocation of effectors.	ENA FIRST PUBLIC:2019 09 25\|ENA LAST UPDATE:2019 07 26			SAMEA2224102	SC	ArrayExpress DevelopmentalStage:Hatching long pec pec fin ZFS:0000033 ZFS:0000034\|ArrayExpress OrganismPart:Whole Embryo\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2014 03 04T09:16:47Z\|ENA LAST UPDATE:2018 03 08T16:47:37Z\|External Id:SAMEA2224102\|INSDC center name:SC\|INSDC first public:2014 03 04T09:16:47Z\|INSDC last update:2018 03 08T16:47:37Z\|INSDC status:public\|Submitter Id:ZMP phenotype 32 4 sibling sc 2013 10 17T10:16:28Z 1727409\|common name:zebrafish\|sample description:3 prime end enriched mRNA from morphologically normal embryos from ZMP phenotype 32 clutch 4. A 5 base indexing sequence CAAGA is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph32\|sample name:ZMP phenotype 32 4 sibling sc 2013 10 17T10:16:28Z 1727409\|scientific name:Danio rerio\|strain:mixed	Illumina HiSeq 2500 sequencing	ena EXPERIMENT CIRI Inserm U1111 26 07 2019 18:33:36:193 6	unspecified	1			RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		ERP116513	Illumina HiSeq 2500 sequencing	ENA FIRST PUBLIC:2019 09 25\|ENA LAST UPDATE:2019 07 26			659815100.0	13196302.0	ena RUN CIRI Inserm U1111 26 07 2019 18:33:36:193 6	0:50	A:163494131;C:142490716;G:153472608;T:200319869;N:37776	50		163494131	142490716	153472608	200319869	37776	ERX3476201	ERS360451	ERA2051096	CIRI-Inserm-U1111\|European Nucleotide Archive	CIRI-Inserm-U1111	1	0.00278	0.00206	0.99922	0.24031	50	T	under 1.2% mapping rate	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	France	2014-03-04	Hatching	Embryo	Whole Organism	All anatomical structures
9765	9765	ERR3454280	ERX3476200	ERS360450	ERP116513	PRJEB33700	Regulation of Dot Icm effectors translocation by T4SS GGDEF EAL proteins in Legionella pneumophila	ena-STUDY-CIRI-Inserm-U1111-26-07-2019-08:05:36:132-1961	Other	Legionella pneumophila is a waterborne bacterium that can replicate in a variety of host cells from environmental amoebae to human macrophages. Its virulence traits are subject to complex regulation that involves some signaling pathways dependent on cyclic di GMP. Cyclic di GMP is a second messenger that can result in transcriptional translational or post translational control of targets including secretion systems. We are particularly interested in the c di GMP metabolizing enzyme Lpl0780/Lpp0809 needed for the early steps of intracellular cycle and the appropriate translocation of bacterial effectors by Dot/Icm T4SS. Comparative transcriptomic analysis was performed from the RNA seq data of the Lens Wild Type strain and the ?lpl0780 mutant using DESeq2 package on normalized gene read counts. The results showed that only 12 genes among 2966 were significantly differentially expressed P < 0.01 and log2 fold change of >1 or < 1 between ?lpl0780 strain and the WT Lens strain. However the fold changes remain quite weak and moreover none of these genes can be connected to T4SS or effectors. These results suggest that Lpl0780/Lpp0809 acts at a post transcriptional level on the translocation of effectors.	ENA FIRST PUBLIC:2019 09 25\|ENA LAST UPDATE:2019 07 26			SAMEA2224101	SC	ArrayExpress DevelopmentalStage:Hatching long pec pec fin ZFS:0000033 ZFS:0000034\|ArrayExpress OrganismPart:Whole Embryo\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2014 03 04T09:16:47Z\|ENA LAST UPDATE:2018 03 08T16:50:06Z\|External Id:SAMEA2224101\|INSDC center name:SC\|INSDC first public:2014 03 04T09:16:47Z\|INSDC last update:2018 03 08T16:50:06Z\|INSDC status:public\|Submitter Id:ZMP phenotype 32 4 mutant sc 2013 10 17T10:16:27Z 1727408\|common name:zebrafish\|sample description:3 prime end enriched mRNA from morphologically abnormal embryos from ZMP phenotype32 clutch 4. A 5 base indexing sequence CGCAA is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph32\|sample name:ZMP phenotype 32 4 mutant sc 2013 10 17T10:16:27Z 1727408\|scientific name:Danio rerio\|strain:mixed	Illumina HiSeq 2500 sequencing	ena EXPERIMENT CIRI Inserm U1111 26 07 2019 18:33:36:193 5	unspecified	1			RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		ERP116513	Illumina HiSeq 2500 sequencing	ENA FIRST PUBLIC:2019 09 25\|ENA LAST UPDATE:2019 07 26			1031629900.0	20632598.0	ena RUN CIRI Inserm U1111 26 07 2019 18:33:36:193 5	0:50	A:266496533;C:234318648;G:214719546;T:316013013;N:82160	50		266496533	234318648	214719546	316013013	82160	ERX3476200	ERS360450	ERA2051096	CIRI-Inserm-U1111\|European Nucleotide Archive	CIRI-Inserm-U1111	1	0.003	0.00187	0.99902	0.27272	50	T	under 1.2% mapping rate	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	France	2014-03-04	Hatching	Embryo	Whole Organism	All anatomical structures
9766	9766	ERR3454279	ERX3476199	ERS360449	ERP116513	PRJEB33700	Regulation of Dot Icm effectors translocation by T4SS GGDEF EAL proteins in Legionella pneumophila	ena-STUDY-CIRI-Inserm-U1111-26-07-2019-08:05:36:132-1961	Other	Legionella pneumophila is a waterborne bacterium that can replicate in a variety of host cells from environmental amoebae to human macrophages. Its virulence traits are subject to complex regulation that involves some signaling pathways dependent on cyclic di GMP. Cyclic di GMP is a second messenger that can result in transcriptional translational or post translational control of targets including secretion systems. We are particularly interested in the c di GMP metabolizing enzyme Lpl0780/Lpp0809 needed for the early steps of intracellular cycle and the appropriate translocation of bacterial effectors by Dot/Icm T4SS. Comparative transcriptomic analysis was performed from the RNA seq data of the Lens Wild Type strain and the ?lpl0780 mutant using DESeq2 package on normalized gene read counts. The results showed that only 12 genes among 2966 were significantly differentially expressed P < 0.01 and log2 fold change of >1 or < 1 between ?lpl0780 strain and the WT Lens strain. However the fold changes remain quite weak and moreover none of these genes can be connected to T4SS or effectors. These results suggest that Lpl0780/Lpp0809 acts at a post transcriptional level on the translocation of effectors.	ENA FIRST PUBLIC:2019 09 25\|ENA LAST UPDATE:2019 07 26			SAMEA2224100	SC	ArrayExpress DevelopmentalStage:Hatching long pec pec fin ZFS:0000033 ZFS:0000034\|ArrayExpress OrganismPart:Whole Embryo\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2014 03 04T09:16:47Z\|ENA LAST UPDATE:2018 03 08T16:49:06Z\|External Id:SAMEA2224100\|INSDC center name:SC\|INSDC first public:2014 03 04T09:16:47Z\|INSDC last update:2018 03 08T16:49:06Z\|INSDC status:public\|Submitter Id:ZMP phenotype 32 3 sibling sc 2013 10 17T10:16:26Z 1727407\|common name:zebrafish\|sample description:3 prime end enriched mRNA from morphologically normal embryos from ZMP phenotype 32 clutch 3. A 5 base indexing sequence GCACG is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph32\|sample name:ZMP phenotype 32 3 sibling sc 2013 10 17T10:16:26Z 1727407\|scientific name:Danio rerio\|strain:mixed	Illumina HiSeq 2500 sequencing	ena EXPERIMENT CIRI Inserm U1111 26 07 2019 18:33:36:193 4	unspecified	1			RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		ERP116513	Illumina HiSeq 2500 sequencing	ENA FIRST PUBLIC:2019 09 25\|ENA LAST UPDATE:2019 07 26			547730200.0	10954604.0	ena RUN CIRI Inserm U1111 26 07 2019 18:33:36:193 4	0:50	A:142048050;C:118592881;G:112867934;T:174179317;N:42018	50		142048050	118592881	112867934	174179317	42018	ERX3476199	ERS360449	ERA2051096	CIRI-Inserm-U1111\|European Nucleotide Archive	CIRI-Inserm-U1111	1	0.00355	0.00226	0.99902	0.30487	50	T	under 1.2% mapping rate	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	France	2014-03-04	Hatching	Embryo	Whole Organism	All anatomical structures
9767	9767	ERR3454278	ERX3476198	ERS360448	ERP116513	PRJEB33700	Regulation of Dot Icm effectors translocation by T4SS GGDEF EAL proteins in Legionella pneumophila	ena-STUDY-CIRI-Inserm-U1111-26-07-2019-08:05:36:132-1961	Other	Legionella pneumophila is a waterborne bacterium that can replicate in a variety of host cells from environmental amoebae to human macrophages. Its virulence traits are subject to complex regulation that involves some signaling pathways dependent on cyclic di GMP. Cyclic di GMP is a second messenger that can result in transcriptional translational or post translational control of targets including secretion systems. We are particularly interested in the c di GMP metabolizing enzyme Lpl0780/Lpp0809 needed for the early steps of intracellular cycle and the appropriate translocation of bacterial effectors by Dot/Icm T4SS. Comparative transcriptomic analysis was performed from the RNA seq data of the Lens Wild Type strain and the ?lpl0780 mutant using DESeq2 package on normalized gene read counts. The results showed that only 12 genes among 2966 were significantly differentially expressed P < 0.01 and log2 fold change of >1 or < 1 between ?lpl0780 strain and the WT Lens strain. However the fold changes remain quite weak and moreover none of these genes can be connected to T4SS or effectors. These results suggest that Lpl0780/Lpp0809 acts at a post transcriptional level on the translocation of effectors.	ENA FIRST PUBLIC:2019 09 25\|ENA LAST UPDATE:2019 07 26			SAMEA2224099	SC	ArrayExpress DevelopmentalStage:Hatching long pec pec fin ZFS:0000033 ZFS:0000034\|ArrayExpress OrganismPart:Whole Embryo\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2014 03 04T09:16:47Z\|ENA LAST UPDATE:2018 03 08T16:47:37Z\|External Id:SAMEA2224099\|INSDC center name:SC\|INSDC first public:2014 03 04T09:16:47Z\|INSDC last update:2018 03 08T16:47:37Z\|INSDC status:public\|Submitter Id:ZMP phenotype 32 3 mutant sc 2013 10 17T10:16:24Z 1727406\|common name:zebrafish\|sample description:3 prime end enriched mRNA from morphologically abnormal embryos from ZMP phenotype 32 clutch 3. A 5 base indexing sequence CAGAG is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph32\|sample name:ZMP phenotype 32 3 mutant sc 2013 10 17T10:16:24Z 1727406\|scientific name:Danio rerio\|strain:mixed	Illumina HiSeq 2500 sequencing	ena EXPERIMENT CIRI Inserm U1111 26 07 2019 18:33:36:193 3	unspecified	1			RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		ERP116513	Illumina HiSeq 2500 sequencing	ENA FIRST PUBLIC:2019 09 25\|ENA LAST UPDATE:2019 07 26			844323050.0	16886461.0	ena RUN CIRI Inserm U1111 26 07 2019 18:33:36:193 3	0:50	A:219263127;C:181661743;G:173433057;T:269898556;N:66567	50		219263127	181661743	173433057	269898556	66567	ERX3476198	ERS360448	ERA2051096	CIRI-Inserm-U1111\|European Nucleotide Archive	CIRI-Inserm-U1111	1	0.00523	0.00319	0.99892	0.2637	50	T	under 1.2% mapping rate	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	France	2014-03-04	Hatching	Embryo	Whole Organism	All anatomical structures
9768	9768	ERR3454277	ERX3476197	ERS360447	ERP116513	PRJEB33700	Regulation of Dot Icm effectors translocation by T4SS GGDEF EAL proteins in Legionella pneumophila	ena-STUDY-CIRI-Inserm-U1111-26-07-2019-08:05:36:132-1961	Other	Legionella pneumophila is a waterborne bacterium that can replicate in a variety of host cells from environmental amoebae to human macrophages. Its virulence traits are subject to complex regulation that involves some signaling pathways dependent on cyclic di GMP. Cyclic di GMP is a second messenger that can result in transcriptional translational or post translational control of targets including secretion systems. We are particularly interested in the c di GMP metabolizing enzyme Lpl0780/Lpp0809 needed for the early steps of intracellular cycle and the appropriate translocation of bacterial effectors by Dot/Icm T4SS. Comparative transcriptomic analysis was performed from the RNA seq data of the Lens Wild Type strain and the ?lpl0780 mutant using DESeq2 package on normalized gene read counts. The results showed that only 12 genes among 2966 were significantly differentially expressed P < 0.01 and log2 fold change of >1 or < 1 between ?lpl0780 strain and the WT Lens strain. However the fold changes remain quite weak and moreover none of these genes can be connected to T4SS or effectors. These results suggest that Lpl0780/Lpp0809 acts at a post transcriptional level on the translocation of effectors.	ENA FIRST PUBLIC:2019 09 25\|ENA LAST UPDATE:2019 07 26			SAMEA2224098	SC	ArrayExpress DevelopmentalStage:Hatching long pec pec fin ZFS:0000033 ZFS:0000034\|ArrayExpress OrganismPart:Whole Embryo\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2014 03 04T09:16:47Z\|ENA LAST UPDATE:2018 03 08T16:50:06Z\|External Id:SAMEA2224098\|INSDC center name:SC\|INSDC first public:2014 03 04T09:16:47Z\|INSDC last update:2018 03 08T16:50:06Z\|INSDC status:public\|Submitter Id:ZMP phenotype 32 2 sibling sc 2013 10 17T10:16:23Z 1727405\|common name:zebrafish\|sample description:3 prime end enriched mRNA from morphologically normal embryos from ZMP phenotype 32 clutch 2. A 5 base indexing sequence AGAAG is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph32\|sample name:ZMP phenotype 32 2 sibling sc 2013 10 17T10:16:23Z 1727405\|scientific name:Danio rerio\|strain:mixed	Illumina HiSeq 2500 sequencing	ena EXPERIMENT CIRI Inserm U1111 26 07 2019 18:33:36:193 2	unspecified	1			RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		ERP116513	Illumina HiSeq 2500 sequencing	ENA FIRST PUBLIC:2019 09 25\|ENA LAST UPDATE:2019 07 26			600000000.0	12000000.0	ena RUN CIRI Inserm U1111 26 07 2019 18:33:36:193 2	0:50	A:153130383;C:136248892;G:127363796;T:183213089;N:43840	50		153130383	136248892	127363796	183213089	43840	ERX3476197	ERS360447	ERA2051096	CIRI-Inserm-U1111\|European Nucleotide Archive	CIRI-Inserm-U1111	1	0.00372	0.00211	0.99888	0.31649	50	T	under 1.2% mapping rate	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	France	2014-03-04	Hatching	Embryo	Whole Organism	All anatomical structures
9769	9769	ERR3454276	ERX3476196	ERS360446	ERP116513	PRJEB33700	Regulation of Dot Icm effectors translocation by T4SS GGDEF EAL proteins in Legionella pneumophila	ena-STUDY-CIRI-Inserm-U1111-26-07-2019-08:05:36:132-1961	Other	Legionella pneumophila is a waterborne bacterium that can replicate in a variety of host cells from environmental amoebae to human macrophages. Its virulence traits are subject to complex regulation that involves some signaling pathways dependent on cyclic di GMP. Cyclic di GMP is a second messenger that can result in transcriptional translational or post translational control of targets including secretion systems. We are particularly interested in the c di GMP metabolizing enzyme Lpl0780/Lpp0809 needed for the early steps of intracellular cycle and the appropriate translocation of bacterial effectors by Dot/Icm T4SS. Comparative transcriptomic analysis was performed from the RNA seq data of the Lens Wild Type strain and the ?lpl0780 mutant using DESeq2 package on normalized gene read counts. The results showed that only 12 genes among 2966 were significantly differentially expressed P < 0.01 and log2 fold change of >1 or < 1 between ?lpl0780 strain and the WT Lens strain. However the fold changes remain quite weak and moreover none of these genes can be connected to T4SS or effectors. These results suggest that Lpl0780/Lpp0809 acts at a post transcriptional level on the translocation of effectors.	ENA FIRST PUBLIC:2019 09 25\|ENA LAST UPDATE:2019 07 26			SAMEA2224097	SC	ArrayExpress DevelopmentalStage:Hatching long pec pec fin ZFS:0000033 ZFS:0000034\|ArrayExpress OrganismPart:Whole Embryo\|ArrayExpress Species:Danio rerio\|ENA FIRST PUBLIC:2014 03 04T09:16:47Z\|ENA LAST UPDATE:2018 03 08T16:49:06Z\|External Id:SAMEA2224097\|INSDC center name:SC\|INSDC first public:2014 03 04T09:16:47Z\|INSDC last update:2018 03 08T16:49:06Z\|INSDC status:public\|Submitter Id:ZMP phenotype 32 2 mutant sc 2013 10 17T10:16:20Z 1727404\|common name:zebrafish\|sample description:3 prime end enriched mRNA from morphologically abnormal embryos from ZMP phenotype 32 clutch 2. A 5 base indexing sequence GAGGC is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph32\|sample name:ZMP phenotype 32 2 mutant sc 2013 10 17T10:16:20Z 1727404\|scientific name:Danio rerio\|strain:mixed	Illumina HiSeq 2500 sequencing	ena EXPERIMENT CIRI Inserm U1111 26 07 2019 18:33:36:193 1	unspecified	1			RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		ERP116513	Illumina HiSeq 2500 sequencing	ENA FIRST PUBLIC:2019 09 25\|ENA LAST UPDATE:2019 07 26			600000000.0	12000000.0	ena RUN CIRI Inserm U1111 26 07 2019 18:33:36:193 1	0:50	A:153852410;C:135392627;G:125428239;T:185280608;N:46116	50		153852410	135392627	125428239	185280608	46116	ERX3476196	ERS360446	ERA2051096	CIRI-Inserm-U1111\|European Nucleotide Archive	CIRI-Inserm-U1111	1	0.00545	0.00291	0.9988	0.31681	50	T	under 1.2% mapping rate	illumina	hiseq_era	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	France	2014-03-04	Hatching	Embryo	Whole Organism	All anatomical structures
10000	10000	ERR6806877	ERX6430470	ERS5060067	ERP123913	PRJEB40292	Multidimensional chromatin profiling of zebrafish and human pancreas to uncover and validate disease related enhancers	ena-STUDY-I3S-10-09-2020-08:12:35:299-4	Other	The pancreas is a central organ for human diseases. Most disease associated alleles overlap with non coding cis regulatory elements of DNA suggesting that alterations in regulatory sequences contribute to pancreatic diseases. However the interspecies identification of equivalent cis regulatory elements required for in vivo testing face fundamental challenges including lack of sequence conservation. In this work we performed a combined analysis of ATAC seq ChIP seq 4C seq and HiChIP seq data from zebrafish and human pancreatic cells to identify interspecies functionally equivalent cis regulatory elements regardless of sequence conservation. To link cis regulation with the expression of target genes in the pancreas we additionally integrated in our analysis own and public RNA seq data from zebrafish pancreatic cell types. Among several disease associated sequences we identified a zebrafish ptf1a distal enhancer whose deletion generates pancreatic agenesis demonstrating the causality of this condition in humans. Our results further demonstrate that this phenotype is a consequence of loss of pancreas progenitor cells. Overall we show that chromatin profiling can uncover interspecies functional equivalency of cis regulatory elements contributing to the prediction of new disease causative enhancers and their role in human disease.	ChIP seq ATAC seq HiChIP seq 4C seq RNA seq\|chromatin accessibility\|cis regulatory mutations\|pancreas and pancreatic diseases\|transcriptional enhancers\|ENA FIRST PUBLIC:2020 09 11\|ENA LAST UPDATE:2021 09 22	Adult zebrafish muscle RNA seq replicate2 raw reads	Zebrafish Muscle RNA seq replicate2	SAMEA7301508	I3S	ENA first public:2021 09 23\|ENA last update:2021 09 23\|External Id:SAMEA7301508\|INSDC center alias:I3S\|INSDC center name:I3S\|INSDC first public:2021 09 23T20:37:00Z\|INSDC last update:2021 09 23T20:37:00Z\|INSDC status:public\|Submitter Id:Zebrafish Muscle RNA seq replicate2\|common name:zebrafish\|sample name:Zebrafish Muscle RNA seq replicate2\|tissue type:muscle	Illumina HiSeq 2000 sequencing	ena EXPERIMENT I3S 23 09 2021 16:43:09:330 8	Muscle2	1	Total RNA extracted with TRIZOL from zebrafish muscle and preprared for sequencing with the TruSeq kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000		ERP123913	Illumina HiSeq 2000 sequencing	ENA FIRST PUBLIC:2021 09 23\|ENA LAST UPDATE:2021 09 23	Muscle_Old_1.fastq.gz	fastq	1886870950.0	37737419.0	ena RUN I3S 23 09 2021 16:43:09:330 8	0:50 1:0	A:479832533;C:470338808;G:443061655;T:493513324;N:124630	50	0	479832533	470338808	443061655	493513324	124630	ERX6430470	ERS5060067	ERA6385885	I3S\|European Nucleotide Archive	I3S	1	0.95119	0.04224	0.79251	0.52332	50	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Portugal	2020-09-11	Adult	Adult	Muscle	Muscular System
10001	10001	ERR6806876	ERX6430469	ERS5060066	ERP123913	PRJEB40292	Multidimensional chromatin profiling of zebrafish and human pancreas to uncover and validate disease related enhancers	ena-STUDY-I3S-10-09-2020-08:12:35:299-4	Other	The pancreas is a central organ for human diseases. Most disease associated alleles overlap with non coding cis regulatory elements of DNA suggesting that alterations in regulatory sequences contribute to pancreatic diseases. However the interspecies identification of equivalent cis regulatory elements required for in vivo testing face fundamental challenges including lack of sequence conservation. In this work we performed a combined analysis of ATAC seq ChIP seq 4C seq and HiChIP seq data from zebrafish and human pancreatic cells to identify interspecies functionally equivalent cis regulatory elements regardless of sequence conservation. To link cis regulation with the expression of target genes in the pancreas we additionally integrated in our analysis own and public RNA seq data from zebrafish pancreatic cell types. Among several disease associated sequences we identified a zebrafish ptf1a distal enhancer whose deletion generates pancreatic agenesis demonstrating the causality of this condition in humans. Our results further demonstrate that this phenotype is a consequence of loss of pancreas progenitor cells. Overall we show that chromatin profiling can uncover interspecies functional equivalency of cis regulatory elements contributing to the prediction of new disease causative enhancers and their role in human disease.	ChIP seq ATAC seq HiChIP seq 4C seq RNA seq\|chromatin accessibility\|cis regulatory mutations\|pancreas and pancreatic diseases\|transcriptional enhancers\|ENA FIRST PUBLIC:2020 09 11\|ENA LAST UPDATE:2021 09 22	Adult zebrafish muscle RNA seq replicate1 raw reads	Zebrafish Muscle RNA seq replicate1	SAMEA7301507	I3S	ENA first public:2021 09 23\|ENA last update:2021 09 23\|External Id:SAMEA7301507\|INSDC center alias:I3S\|INSDC center name:I3S\|INSDC first public:2021 09 23T20:37:00Z\|INSDC last update:2021 09 23T20:37:00Z\|INSDC status:public\|Submitter Id:Zebrafish Muscle RNA seq replicate1\|common name:zebrafish\|sample name:Zebrafish Muscle RNA seq replicate1\|tissue type:muscle	Illumina HiSeq 2000 sequencing	ena EXPERIMENT I3S 23 09 2021 16:43:09:330 7	Muscle1	1	Total RNA extracted with TRIZOL from zebrafish muscle and preprared for sequencing with the TruSeq kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000		ERP123913	Illumina HiSeq 2000 sequencing	ENA FIRST PUBLIC:2021 09 23\|ENA LAST UPDATE:2021 09 23	Muscle_Young_1.fastq.gz	fastq	1795352850.0	35907057.0	ena RUN I3S 23 09 2021 16:43:09:330 7	0:50 1:0	A:451489686;C:453210606;G:425250111;T:465282474;N:119973	50	0	451489686	453210606	425250111	465282474	119973	ERX6430469	ERS5060066	ERA6385885	I3S\|European Nucleotide Archive	I3S	1	0.95698	0.02942	0.82126	0.56075	50	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Portugal	2020-09-11	Adult	Adult	Muscle	Muscular System
10002	10002	ERR6806875	ERX6430468	ERS5060069	ERP123913	PRJEB40292	Multidimensional chromatin profiling of zebrafish and human pancreas to uncover and validate disease related enhancers	ena-STUDY-I3S-10-09-2020-08:12:35:299-4	Other	The pancreas is a central organ for human diseases. Most disease associated alleles overlap with non coding cis regulatory elements of DNA suggesting that alterations in regulatory sequences contribute to pancreatic diseases. However the interspecies identification of equivalent cis regulatory elements required for in vivo testing face fundamental challenges including lack of sequence conservation. In this work we performed a combined analysis of ATAC seq ChIP seq 4C seq and HiChIP seq data from zebrafish and human pancreatic cells to identify interspecies functionally equivalent cis regulatory elements regardless of sequence conservation. To link cis regulation with the expression of target genes in the pancreas we additionally integrated in our analysis own and public RNA seq data from zebrafish pancreatic cell types. Among several disease associated sequences we identified a zebrafish ptf1a distal enhancer whose deletion generates pancreatic agenesis demonstrating the causality of this condition in humans. Our results further demonstrate that this phenotype is a consequence of loss of pancreas progenitor cells. Overall we show that chromatin profiling can uncover interspecies functional equivalency of cis regulatory elements contributing to the prediction of new disease causative enhancers and their role in human disease.	ChIP seq ATAC seq HiChIP seq 4C seq RNA seq\|chromatin accessibility\|cis regulatory mutations\|pancreas and pancreatic diseases\|transcriptional enhancers\|ENA FIRST PUBLIC:2020 09 11\|ENA LAST UPDATE:2021 09 22	Adult zebrafish whole pancreas RNA seq replicate2 raw reads	Zebrafish Whole Pancreas RNA seq replicate2	SAMEA7301510	I3S	ENA first public:2021 09 23\|ENA last update:2021 09 23\|External Id:SAMEA7301510\|INSDC center alias:I3S\|INSDC center name:I3S\|INSDC first public:2021 09 23T20:37:00Z\|INSDC last update:2021 09 23T20:37:00Z\|INSDC status:public\|Submitter Id:Zebrafish Whole Pancreas RNA seq replicate2\|common name:zebrafish\|sample name:Zebrafish Whole Pancreas RNA seq replicate2\|tissue type:whole pancreas	Illumina HiSeq 2000 sequencing	ena EXPERIMENT I3S 23 09 2021 16:43:09:330 6	Exocrine2	1	Total RNA extracted with TRIZOL from zebrafish whole pancreas and preprared for sequencing with the TruSeq kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000		ERP123913	Illumina HiSeq 2000 sequencing	ENA FIRST PUBLIC:2021 09 23\|ENA LAST UPDATE:2021 09 23	Exocrine_Old_1.fastq.gz	fastq	1715678250.0	34313565.0	ena RUN I3S 23 09 2021 16:43:09:330 6	0:50 1:0	A:423211245;C:429948631;G:413857387;T:448546996;N:113991	50	0	423211245	429948631	413857387	448546996	113991	ERX6430468	ERS5060069	ERA6385885	I3S\|European Nucleotide Archive	I3S	1	0.94581	0.03181	0.80026	0.48102	50	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Portugal	2020-09-11	Adult	Adult	Pancreas	Endocrine System
10003	10003	ERR6806874	ERX6430467	ERS5060068	ERP123913	PRJEB40292	Multidimensional chromatin profiling of zebrafish and human pancreas to uncover and validate disease related enhancers	ena-STUDY-I3S-10-09-2020-08:12:35:299-4	Other	The pancreas is a central organ for human diseases. Most disease associated alleles overlap with non coding cis regulatory elements of DNA suggesting that alterations in regulatory sequences contribute to pancreatic diseases. However the interspecies identification of equivalent cis regulatory elements required for in vivo testing face fundamental challenges including lack of sequence conservation. In this work we performed a combined analysis of ATAC seq ChIP seq 4C seq and HiChIP seq data from zebrafish and human pancreatic cells to identify interspecies functionally equivalent cis regulatory elements regardless of sequence conservation. To link cis regulation with the expression of target genes in the pancreas we additionally integrated in our analysis own and public RNA seq data from zebrafish pancreatic cell types. Among several disease associated sequences we identified a zebrafish ptf1a distal enhancer whose deletion generates pancreatic agenesis demonstrating the causality of this condition in humans. Our results further demonstrate that this phenotype is a consequence of loss of pancreas progenitor cells. Overall we show that chromatin profiling can uncover interspecies functional equivalency of cis regulatory elements contributing to the prediction of new disease causative enhancers and their role in human disease.	ChIP seq ATAC seq HiChIP seq 4C seq RNA seq\|chromatin accessibility\|cis regulatory mutations\|pancreas and pancreatic diseases\|transcriptional enhancers\|ENA FIRST PUBLIC:2020 09 11\|ENA LAST UPDATE:2021 09 22	Adult zebrafish whole pancreas RNA seq replicate1 raw reads	Zebrafish Whole Pancreas RNA seq replicate1	SAMEA7301509	I3S	ENA first public:2021 09 23\|ENA last update:2021 09 23\|External Id:SAMEA7301509\|INSDC center alias:I3S\|INSDC center name:I3S\|INSDC first public:2021 09 23T20:37:00Z\|INSDC last update:2021 09 23T20:37:00Z\|INSDC status:public\|Submitter Id:Zebrafish Whole Pancreas RNA seq replicate1\|common name:zebrafish\|sample name:Zebrafish Whole Pancreas RNA seq replicate1\|tissue type:whole pancreas	Illumina HiSeq 2000 sequencing	ena EXPERIMENT I3S 23 09 2021 16:43:09:330 5	Exocrine1	1	Total RNA extracted with TRIZOL from zebrafish whole pancreas and preprared for sequencing with the TruSeq kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000		ERP123913	Illumina HiSeq 2000 sequencing	ENA FIRST PUBLIC:2021 09 23\|ENA LAST UPDATE:2021 09 23	Exocrine_Young_1.fastq.gz	fastq	1751070500.0	35021410.0	ena RUN I3S 23 09 2021 16:43:09:330 5	0:50 1:0	A:412303526;C:454121976;G:438481251;T:446048184;N:115563	50	0	412303526	454121976	438481251	446048184	115563	ERX6430467	ERS5060068	ERA6385885	I3S\|European Nucleotide Archive	I3S	1	0.93968	0.02618	0.8003	0.58539	50	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Portugal	2020-09-11	Adult	Adult	Pancreas	Endocrine System
10004	10004	ERR6806873	ERX6430466	ERS5060036	ERP123913	PRJEB40292	Multidimensional chromatin profiling of zebrafish and human pancreas to uncover and validate disease related enhancers	ena-STUDY-I3S-10-09-2020-08:12:35:299-4	Other	The pancreas is a central organ for human diseases. Most disease associated alleles overlap with non coding cis regulatory elements of DNA suggesting that alterations in regulatory sequences contribute to pancreatic diseases. However the interspecies identification of equivalent cis regulatory elements required for in vivo testing face fundamental challenges including lack of sequence conservation. In this work we performed a combined analysis of ATAC seq ChIP seq 4C seq and HiChIP seq data from zebrafish and human pancreatic cells to identify interspecies functionally equivalent cis regulatory elements regardless of sequence conservation. To link cis regulation with the expression of target genes in the pancreas we additionally integrated in our analysis own and public RNA seq data from zebrafish pancreatic cell types. Among several disease associated sequences we identified a zebrafish ptf1a distal enhancer whose deletion generates pancreatic agenesis demonstrating the causality of this condition in humans. Our results further demonstrate that this phenotype is a consequence of loss of pancreas progenitor cells. Overall we show that chromatin profiling can uncover interspecies functional equivalency of cis regulatory elements contributing to the prediction of new disease causative enhancers and their role in human disease.	ChIP seq ATAC seq HiChIP seq 4C seq RNA seq\|chromatin accessibility\|cis regulatory mutations\|pancreas and pancreatic diseases\|transcriptional enhancers\|ENA FIRST PUBLIC:2020 09 11\|ENA LAST UPDATE:2021 09 22	Adult zebrafish endocrine pancreas RNA seq replicate4 raw reads	Zebrafish Endocrine Pancreas RNA seq replicate4	SAMEA7301477	I3S	ENA first public:2021 09 23\|ENA last update:2021 09 23\|External Id:SAMEA7301477\|INSDC center alias:I3S\|INSDC center name:I3S\|INSDC first public:2021 09 23T20:37:00Z\|INSDC last update:2021 09 23T20:37:00Z\|INSDC status:public\|Submitter Id:Zebrafish Endocrine Pancreas RNA seq replicate4\|common name:zebrafish\|sample name:Zebrafish Endocrine Pancreas RNA seq replicate4\|tissue type:endocrine pancreas principal islet	Illumina HiSeq 2000 sequencing	ena EXPERIMENT I3S 23 09 2021 16:43:09:330 4	Endocrine4	1	Total RNA extracted with TRIZOL from zebrafish primary pancreatic islet and preprared for sequencing with the TruSeq kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000		ERP123913	Illumina HiSeq 2000 sequencing	ENA FIRST PUBLIC:2021 09 23\|ENA LAST UPDATE:2021 09 23	Endocrine_Old_2.fastq.gz	fastq	1710560600.0	34211212.0	ena RUN I3S 23 09 2021 16:43:09:330 4	0:50 1:0	A:441527784;C:412091003;G:396100295;T:460728135;N:113383	50	0	441527784	412091003	396100295	460728135	113383	ERX6430466	ERS5060036	ERA6385885	I3S\|European Nucleotide Archive	I3S	1	0.95616	0.04334	0.84585	0.17182	50	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Portugal	2020-09-11	Adult	Adult	Pancreas	Endocrine System
10005	10005	ERR6806872	ERX6430465	ERS5060035	ERP123913	PRJEB40292	Multidimensional chromatin profiling of zebrafish and human pancreas to uncover and validate disease related enhancers	ena-STUDY-I3S-10-09-2020-08:12:35:299-4	Other	The pancreas is a central organ for human diseases. Most disease associated alleles overlap with non coding cis regulatory elements of DNA suggesting that alterations in regulatory sequences contribute to pancreatic diseases. However the interspecies identification of equivalent cis regulatory elements required for in vivo testing face fundamental challenges including lack of sequence conservation. In this work we performed a combined analysis of ATAC seq ChIP seq 4C seq and HiChIP seq data from zebrafish and human pancreatic cells to identify interspecies functionally equivalent cis regulatory elements regardless of sequence conservation. To link cis regulation with the expression of target genes in the pancreas we additionally integrated in our analysis own and public RNA seq data from zebrafish pancreatic cell types. Among several disease associated sequences we identified a zebrafish ptf1a distal enhancer whose deletion generates pancreatic agenesis demonstrating the causality of this condition in humans. Our results further demonstrate that this phenotype is a consequence of loss of pancreas progenitor cells. Overall we show that chromatin profiling can uncover interspecies functional equivalency of cis regulatory elements contributing to the prediction of new disease causative enhancers and their role in human disease.	ChIP seq ATAC seq HiChIP seq 4C seq RNA seq\|chromatin accessibility\|cis regulatory mutations\|pancreas and pancreatic diseases\|transcriptional enhancers\|ENA FIRST PUBLIC:2020 09 11\|ENA LAST UPDATE:2021 09 22	Adult zebrafish endocrine pancreas RNA seq replicate3 raw reads	Zebrafish Endocrine Pancreas RNA seq replicate3	SAMEA7301476	I3S	ENA first public:2021 09 23\|ENA last update:2021 09 23\|External Id:SAMEA7301476\|INSDC center alias:I3S\|INSDC center name:I3S\|INSDC first public:2021 09 23T20:37:00Z\|INSDC last update:2021 09 23T20:37:00Z\|INSDC status:public\|Submitter Id:Zebrafish Endocrine Pancreas RNA seq replicate3\|common name:zebrafish\|sample name:Zebrafish Endocrine Pancreas RNA seq replicate3\|tissue type:endocrine pancreas principal islet	Illumina HiSeq 2000 sequencing	ena EXPERIMENT I3S 23 09 2021 16:43:09:330 3	Endocrine3	1	Total RNA extracted with TRIZOL from zebrafish primary pancreatic islet and preprared for sequencing with the TruSeq kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000		ERP123913	Illumina HiSeq 2000 sequencing	ENA FIRST PUBLIC:2021 09 23\|ENA LAST UPDATE:2021 09 23	Endocrine_Old_1.fastq.gz	fastq	1979582750.0	39591655.0	ena RUN I3S 23 09 2021 16:43:09:330 3	0:50 1:0	A:483713055;C:499972514;G:479484600;T:516281513;N:131068	50	0	483713055	499972514	479484600	516281513	131068	ERX6430465	ERS5060035	ERA6385885	I3S\|European Nucleotide Archive	I3S	1	0.93722	0.04096	0.7559	0.52069	50	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Portugal	2020-09-11	Adult	Adult	Pancreas	Endocrine System
10006	10006	ERR6806871	ERX6430464	ERS5060034	ERP123913	PRJEB40292	Multidimensional chromatin profiling of zebrafish and human pancreas to uncover and validate disease related enhancers	ena-STUDY-I3S-10-09-2020-08:12:35:299-4	Other	The pancreas is a central organ for human diseases. Most disease associated alleles overlap with non coding cis regulatory elements of DNA suggesting that alterations in regulatory sequences contribute to pancreatic diseases. However the interspecies identification of equivalent cis regulatory elements required for in vivo testing face fundamental challenges including lack of sequence conservation. In this work we performed a combined analysis of ATAC seq ChIP seq 4C seq and HiChIP seq data from zebrafish and human pancreatic cells to identify interspecies functionally equivalent cis regulatory elements regardless of sequence conservation. To link cis regulation with the expression of target genes in the pancreas we additionally integrated in our analysis own and public RNA seq data from zebrafish pancreatic cell types. Among several disease associated sequences we identified a zebrafish ptf1a distal enhancer whose deletion generates pancreatic agenesis demonstrating the causality of this condition in humans. Our results further demonstrate that this phenotype is a consequence of loss of pancreas progenitor cells. Overall we show that chromatin profiling can uncover interspecies functional equivalency of cis regulatory elements contributing to the prediction of new disease causative enhancers and their role in human disease.	ChIP seq ATAC seq HiChIP seq 4C seq RNA seq\|chromatin accessibility\|cis regulatory mutations\|pancreas and pancreatic diseases\|transcriptional enhancers\|ENA FIRST PUBLIC:2020 09 11\|ENA LAST UPDATE:2021 09 22	Adult zebrafish endocrine pancreas principal islet RNA seq raw reads replicate2	Zebrafish Endocrine Pancreas RNA seq replicate2	SAMEA7301475	I3S	ENA first public:2021 09 23\|ENA last update:2021 09 23\|External Id:SAMEA7301475\|INSDC center alias:I3S\|INSDC center name:I3S\|INSDC first public:2021 09 23T20:37:00Z\|INSDC last update:2021 09 23T20:37:00Z\|INSDC status:public\|Submitter Id:Zebrafish Endocrine Pancreas RNA seq replicate2\|common name:zebrafish\|sample name:Zebrafish Endocrine Pancreas RNA seq replicate2\|tissue type:endocrine pancreas principal islet	Illumina HiSeq 2000 sequencing	ena EXPERIMENT I3S 23 09 2021 16:43:09:329 2	Endocrine2	1	Total RNA extracted with TRIZOL from zebrafish primary pancreatic islet and preprared for sequencing with the TruSeq kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000		ERP123913	Illumina HiSeq 2000 sequencing	ENA FIRST PUBLIC:2021 09 23\|ENA LAST UPDATE:2021 09 23	Endocrine_Young_2.fastq.gz	fastq	1846315600.0	36926312.0	ena RUN I3S 23 09 2021 16:43:09:329 2	0:50 1:0	A:466245839;C:453675875;G:433502059;T:492768958;N:122869	50	0	466245839	453675875	433502059	492768958	122869	ERX6430464	ERS5060034	ERA6385885	I3S\|European Nucleotide Archive	I3S	1	0.93566	0.06945	0.74065	0.47497	50	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Portugal	2020-09-11	Adult	Adult	Pancreas	Endocrine System
10007	10007	ERR6806870	ERX6430463	ERS5060033	ERP123913	PRJEB40292	Multidimensional chromatin profiling of zebrafish and human pancreas to uncover and validate disease related enhancers	ena-STUDY-I3S-10-09-2020-08:12:35:299-4	Other	The pancreas is a central organ for human diseases. Most disease associated alleles overlap with non coding cis regulatory elements of DNA suggesting that alterations in regulatory sequences contribute to pancreatic diseases. However the interspecies identification of equivalent cis regulatory elements required for in vivo testing face fundamental challenges including lack of sequence conservation. In this work we performed a combined analysis of ATAC seq ChIP seq 4C seq and HiChIP seq data from zebrafish and human pancreatic cells to identify interspecies functionally equivalent cis regulatory elements regardless of sequence conservation. To link cis regulation with the expression of target genes in the pancreas we additionally integrated in our analysis own and public RNA seq data from zebrafish pancreatic cell types. Among several disease associated sequences we identified a zebrafish ptf1a distal enhancer whose deletion generates pancreatic agenesis demonstrating the causality of this condition in humans. Our results further demonstrate that this phenotype is a consequence of loss of pancreas progenitor cells. Overall we show that chromatin profiling can uncover interspecies functional equivalency of cis regulatory elements contributing to the prediction of new disease causative enhancers and their role in human disease.	ChIP seq ATAC seq HiChIP seq 4C seq RNA seq\|chromatin accessibility\|cis regulatory mutations\|pancreas and pancreatic diseases\|transcriptional enhancers\|ENA FIRST PUBLIC:2020 09 11\|ENA LAST UPDATE:2021 09 22	Adult zebrafish endocrine pancreas principal islet RNA seq raw reads replicate1	Zebrafish Endocrine Pancreas RNA seq replicate1	SAMEA7301474	I3S	ENA first public:2021 09 23\|ENA last update:2021 09 23\|External Id:SAMEA7301474\|INSDC center alias:I3S\|INSDC center name:I3S\|INSDC first public:2021 09 23T20:37:00Z\|INSDC last update:2021 09 23T20:37:00Z\|INSDC status:public\|Submitter Id:Zebrafish Endocrine Pancreas RNA seq replicate1\|common name:zebrafish\|sample name:Zebrafish Endocrine Pancreas RNA seq replicate1\|tissue type:endocrine pancreas principal islet	Illumina HiSeq 2000 sequencing	ena EXPERIMENT I3S 23 09 2021 16:43:09:329 1	Endocrine1	1	Total RNA extracted with TRIZOL from zebrafish primary pancreatic islet and preprared for sequencing with the TruSeq kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000		ERP123913	Illumina HiSeq 2000 sequencing	ENA FIRST PUBLIC:2021 09 23\|ENA LAST UPDATE:2021 09 23	Endocrine_Young_1.fastq.gz	fastq	1331184450.0	26623689.0	ena RUN I3S 23 09 2021 16:43:09:329 1	0:50 1:0	A:336761837;C:326693218;G:311881921;T:355763246;N:84228	50	0	336761837	326693218	311881921	355763246	84228	ERX6430463	ERS5060033	ERA6385885	I3S\|European Nucleotide Archive	I3S	1	0.93154	0.07422	0.73064	0.53917	50	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Portugal	2020-09-11	Adult	Adult	Pancreas	Endocrine System
10451	10451	ERR9267483	ERX8809906	ERS10996035	ERP136287	PRJEB51640	CS2 UHEI DART 96 120h raw data EUT080	S-TOXR1835	Transcriptome Analysis		ENA FIRST PUBLIC:2024 03 15\|ENA LAST UPDATE:2024 03 15			SAMEA13393544	University of Heidelberg	Compound:Acetamiprid\|Concentration:100.0 µM\|ENA first public:2024 03 15\|Exposure time:120 hpf Id:SAMEA13393544\|Gender:null\|INSDC center name:University of Heidelberg\|INSDC last update:2022 03 15T10:42:02Z\|INSDC status:public\|Submitter Id:S TOXR1835:S ACE 100 1\|Treatment:repeated dose\|Treatment scheme:daily\|broker name:EU ToxRisk DCC\|cell line:null\|common name:zebrafish\|sample name:S TOXR1835:S ACE 100 1\|scientific name:Danio rerio	Illumina HiSeq 2500 sequencing	S TOXR1835:S ACE 100 1 e		TempO Seq library			RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		ERP136287	Illumina HiSeq 2500 sequencing	ENA FIRST PUBLIC:2024 03 15\|ENA LAST UPDATE:2024 03 15	S_ACE_100_1.fastq.gz	fastq	75873650.0	1517473.0	S TOXR1835:S ACE 100 1 r	0:50	A:15822311;C:19986026;G:18697821;T:21366861;N:631	50		15822311	19986026	18697821	21366861	631	ERX8809906	ERS10996035	ERA10091655	EMBL EBI	EMBL EBI							B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2022-03-15	Larval	Larval	Cell Line	Cell Line
10452	10452	ERR9267591	ERX8810014	ERS10996143	ERP136287	PRJEB51640	CS2 UHEI DART 96 120h raw data EUT080	S-TOXR1835	Transcriptome Analysis		ENA FIRST PUBLIC:2024 03 15\|ENA LAST UPDATE:2024 03 15			SAMEA13393652	University of Heidelberg	Compound:2 Mhex\|Concentration:110.5 µM\|ENA first public:2024 03 15\|Exposure time:48 hpf Id:SAMEA13393652\|Gender:null\|INSDC center name:University of Heidelberg\|INSDC last update:2022 03 15T10:42:06Z\|INSDC status:public\|Submitter Id:S TOXR1835:S 2 Mhex EC10 48h run4 C09\|Treatment:repeated dose\|Treatment scheme:daily\|broker name:EU ToxRisk DCC\|cell line:null\|common name:zebrafish\|sample name:S TOXR1835:S 2 Mhex EC10 48h run4 C09\|scientific name:Danio rerio	Illumina HiSeq 2500 sequencing	S TOXR1835:S 2 Mhex EC10 48h run4 C09 e		TempO Seq library			RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		ERP136287	Illumina HiSeq 2500 sequencing	ENA FIRST PUBLIC:2024 03 15\|ENA LAST UPDATE:2024 03 15	S_2-Mhex_EC10_48h_run4_C09.fastq.gz	fastq	73547800.0	1470956.0	S TOXR1835:S 2 Mhex EC10 48h run4 C09 r	0:50	A:15203281;C:19662939;G:18154185;T:20526838;N:557	50		15203281	19662939	18154185	20526838	557	ERX8810014	ERS10996143	ERA10091655	EMBL EBI	EMBL EBI							B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2022-03-15	Hatching	Embryo	Cell Line	Cell Line
10453	10453	ERR9267471	ERX8809894	ERS10996023	ERP136287	PRJEB51640	CS2 UHEI DART 96 120h raw data EUT080	S-TOXR1835	Transcriptome Analysis		ENA FIRST PUBLIC:2024 03 15\|ENA LAST UPDATE:2024 03 15			SAMEA13393532	University of Heidelberg	Compound:Imidacloprid\|Concentration:25.0 µM\|ENA first public:2024 03 15\|Exposure time:120 hpf Id:SAMEA13393532\|Gender:null\|INSDC center name:University of Heidelberg\|INSDC last update:2022 03 15T10:42:02Z\|INSDC status:public\|Submitter Id:S TOXR1835:S IMI 25 2\|Treatment:repeated dose\|Treatment scheme:daily\|broker name:EU ToxRisk DCC\|cell line:null\|common name:zebrafish\|sample name:S TOXR1835:S IMI 25 2\|scientific name:Danio rerio	Illumina HiSeq 2500 sequencing	S TOXR1835:S IMI 25 2 e		TempO Seq library			RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		ERP136287	Illumina HiSeq 2500 sequencing	ENA FIRST PUBLIC:2024 03 15\|ENA LAST UPDATE:2024 03 15	S_IMI_25_2.fastq.gz	fastq	67764800.0	1355296.0	S TOXR1835:S IMI 25 2 r	0:50	A:14102811;C:17769500;G:16248227;T:19643740;N:522	50		14102811	17769500	16248227	19643740	522	ERX8809894	ERS10996023	ERA10091655	EMBL EBI	EMBL EBI							B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United Kingdom	2022-03-15	Larval	Larval	Cell Line	Cell Line

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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");;