metadata: run_metadata: 96 rows where experiment.library_layout = "PAIRED", experiment.library_selection = "size fractionation" and technology = "unknown"

96 rows where experiment.library_layout = "PAIRED", experiment.library_selection = "size fractionation" and technology = "unknown"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.description	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.spot_descriptor	experiment.study_ref	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
28490	28490	SRR26319601	SRX22027740	SRS19100857	SRP465070	PRJNA1025141	Danio rerio Raw sequence reads	PRJNA1025141	Other	Transcriptome sequencing of A. sinensis leaf tea treated on zebrafish sleep.		Treatment	CX3 for transcriptome 3	CX3	strain:AB\|cultivar:WT\|ecotype:China: Jiangsu\|age:7 dpf\|dev stage:Larvae\|collection date:2022 11\|geo loc name:China: Jiangsu suzhou\|sex:pooled male and female\|tissue:larvae\|lat lon:31.32 N 120.67 E\|treatment:Treatment Group\|BioSampleModel:Model organism or animal								ALST3 for transcriptome 3	CX3 for transcriptome 3	CX3 for transcriptome 3	CX3 for transcriptome 3			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	HiSeq X Ten		SRP465070		Unknown_AY803-03T0006_good_1.fq.gz Unknown_AY803-03T0006_good_2.fq.gz	fastq fastq	6255596356.0	20929531.0	Unknown AY803 03T0006 good 1.fq.gz	0:149.44 1:149.44	A:1657365560;C:1463722268;G:1467057724;T:1667269298;N:181506	149	149	1657365560	1463722268	1467057724	1667269298	181506	SRX22027740	SRS19100857	SRA1727563	Soochow University\|School of biology & basic medical sciences	Soochow University	2	0.89228	0.91654	0.09286	0.09714	0.6588	0.65604	0.4631	0.45773	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Unknown	2023-10-11	Larval	Larval	Whole Organism	All anatomical structures
28491	28491	SRR26319602	SRX22027739	SRS19100854	SRP465070	PRJNA1025141	Danio rerio Raw sequence reads	PRJNA1025141	Other	Transcriptome sequencing of A. sinensis leaf tea treated on zebrafish sleep.		Treatment	CX2 for transcriptome 2	CX2	strain:AB\|cultivar:WT\|ecotype:China: Jiangsu\|age:7 dpf\|dev stage:Larvae\|collection date:2022 11\|geo loc name:China: Jiangsu suzhou\|sex:pooled male and female\|tissue:larvae\|lat lon:31.32 N 120.66 E\|treatment:Treatment Group\|BioSampleModel:Model organism or animal								ALST2 for transcriptome 2	CX2 for transcriptome 2	CX2 for transcriptome 2	CX2 for transcriptome 2			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	HiSeq X Ten		SRP465070		Unknown_AY803-03T0005_good_1.fq.gz Unknown_AY803-03T0005_good_2.fq.gz	fastq fastq	6598066464.0	22061446.0	Unknown AY803 03T0005 good 1.fq.gz	0:149.54 1:149.54	A:1747291499;C:1543289262;G:1549193118;T:1758088368;N:204217	149	149	1747291499	1543289262	1549193118	1758088368	204217	SRX22027739	SRS19100854	SRA1727563	Soochow University\|School of biology & basic medical sciences	Soochow University	2	0.88949	0.92148	0.08893	0.0947	0.65596	0.65228	0.46045	0.47087	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Unknown	2023-10-11	Larval	Larval	Whole Organism	All anatomical structures
28492	28492	SRR26319603	SRX22027738	SRS19100853	SRP465070	PRJNA1025141	Danio rerio Raw sequence reads	PRJNA1025141	Other	Transcriptome sequencing of A. sinensis leaf tea treated on zebrafish sleep.		Treatment	CX1 for transcriptome 1	CX1	strain:AB\|cultivar:WT\|ecotype:China: Jiangsu\|age:7 dpf\|dev stage:Larvae\|collection date:2022 11\|geo loc name:China: Jiangsu suzhou\|sex:pooled male and female\|tissue:larvae\|lat lon:31.32 N 120.65 E\|treatment:Treatment Group\|BioSampleModel:Model organism or animal								ALST1 for transcriptome 1	CX1 for transcriptome 1	CX1 for transcriptome 1	CX1 for transcriptome 1			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	HiSeq X Ten		SRP465070		Unknown_AY803-03T0004_good_1.fq.gz Unknown_AY803-03T0004_good_2.fq.gz	fastq fastq	6478923586.0	21662443.0	Unknown AY803 03T0004 good 1.fq.gz	0:149.54 1:149.54	A:1712718473;C:1518937459;G:1523570227;T:1723510437;N:186990	149	149	1712718473	1518937459	1523570227	1723510437	186990	SRX22027738	SRS19100853	SRA1727563	Soochow University\|School of biology & basic medical sciences	Soochow University	2	0.89423	0.9176	0.08944	0.09254	0.6575	0.65458	0.4693	0.46842	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Unknown	2023-10-11	Larval	Larval	Whole Organism	All anatomical structures
28493	28493	SRR26319604	SRX22027737	SRS19100856	SRP465070	PRJNA1025141	Danio rerio Raw sequence reads	PRJNA1025141	Other	Transcriptome sequencing of A. sinensis leaf tea treated on zebrafish sleep.		Control	con3 for transcriptome 3	con3	strain:AB\|cultivar:Wild type\|ecotype:China: Jiangsu suzhou\|age:7 dpf\|dev stage:Larvae phase\|collection date:2022 11\|geo loc name:China: Jiangsu suzhou\|sex:pooled male and female\|tissue:larvae\|lat lon:31.32 N 120.64 E\|treatment:Control Group\|BioSampleModel:Model organism or animal								con3 for transcriptome 3	con3 for transcriptome 3	con3 for transcriptome 3	con3 for transcriptome 3			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	HiSeq X Ten		SRP465070		Unknown_AY803-03T0003_good_2.fq.gz Unknown_AY803-03T0003_good_1.fq.gz	fastq fastq	6341537566.0	21218597.0	Unknown AY803 03T0003 good 1.fq.gz	0:149.43 1:149.43	A:1679811754;C:1483631833;G:1489430825;T:1688482904;N:180250	149	149	1679811754	1483631833	1489430825	1688482904	180250	SRX22027737	SRS19100856	SRA1727563	Soochow University\|School of biology & basic medical sciences	Soochow University	2	0.88245	0.91856	0.09069	0.09654	0.66253	0.65817	0.46245	0.46336	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Unknown	2023-10-11	Larval	Larval	Whole Organism	All anatomical structures
28494	28494	SRR26319605	SRX22027736	SRS19100855	SRP465070	PRJNA1025141	Danio rerio Raw sequence reads	PRJNA1025141	Other	Transcriptome sequencing of A. sinensis leaf tea treated on zebrafish sleep.		Control	con2 for transcriptome 2	con2	strain:AB\|cultivar:Wild type\|ecotype:China: Jiangsu suzhou\|age:7 dpf\|dev stage:Larvae phase\|collection date:2022 11\|geo loc name:China: Jiangsu suzhou\|sex:pooled male and female\|tissue:larvae\|lat lon:31.32 N 120.63 E\|treatment:Control Group\|BioSampleModel:Model organism or animal								con2 for transcriptome 2	con2 for transcriptome 2	con2 for transcriptome 2	con2 for transcriptome 2			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	HiSeq X Ten		SRP465070		Unknown_AY803-03T0002_good_2.fq.gz Unknown_AY803-03T0002_good_1.fq.gz	fastq fastq	5709771178.0	19100144.0	Unknown AY803 03T0002 good 1.fq.gz	0:149.47 1:149.47	A:1505730979;C:1342843084;G:1346105868;T:1514941964;N:149283	149	149	1505730979	1342843084	1346105868	1514941964	149283	SRX22027736	SRS19100855	SRA1727563	Soochow University\|School of biology & basic medical sciences	Soochow University	2	0.8924	0.91903	0.09155	0.09604	0.65902	0.65593	0.4634	0.46028	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Unknown	2023-10-11	Larval	Larval	Whole Organism	All anatomical structures
28495	28495	SRR26319606	SRX22027735	SRS19100852	SRP465070	PRJNA1025141	Danio rerio Raw sequence reads	PRJNA1025141	Other	Transcriptome sequencing of A. sinensis leaf tea treated on zebrafish sleep.		Control	con1 for transcriptome 1	con1	strain:AB\|cultivar:Wild type\|ecotype:China: Jiangsu suzhou\|age:7 dpf\|dev stage:Larvae phase\|collection date:2022 11\|geo loc name:China: Jiangsu suzhou\|sex:pooled male and female\|tissue:larvae\|lat lon:31.32 N 120.62 E\|treatment:Control Group\|BioSampleModel:Model organism or animal								con1 for transcriptome 1	con1 for transcriptome 1	con1 for transcriptome 1	con1 for transcriptome 1			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	HiSeq X Ten		SRP465070		Unknown_AY803-03T0001_good_1.fq.gz Unknown_AY803-03T0001_good_2.fq.gz	fastq fastq	6544586118.0	21872265.0	Unknown AY803 03T0001 good 1.fq.gz	0:149.61 1:149.61	A:1731179229;C:1528367346;G:1541103688;T:1743735521;N:200334	149	149	1731179229	1528367346	1541103688	1743735521	200334	SRX22027735	SRS19100852	SRA1727563	Soochow University\|School of biology & basic medical sciences	Soochow University	2	0.87588	0.92739	0.08683	0.09494	0.65711	0.6504	0.46774	0.47072	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Unknown	2023-10-11	Larval	Larval	Whole Organism	All anatomical structures
29746	29746	SRR27467679	SRX23139227	SRS20090270	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other					ovary BS R2	strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:adult\|collection date:2022\|geo loc name:Austria\|sex:female\|tissue:ovary\|treatment:BS\|BioSampleModel:Model organism or animal								tRAM seq of zebrafish: ovary BS rep2	EV02003	EV02003	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	NextSeq 500		SRP482074		EV02003.R1.fastq.gz EV02003.R2.fastq.gz	fastq fastq	1031891720.0	3416860.0	EV02003.R1.fastq.gz	0:151 1:151	A:264464363;C:153440613;G:408557241;T:205367487;N:62016	151	151	264464363	153440613	408557241	205367487	62016	SRX23139227	SRS20090270	SRA1781872	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	2	0.0	0.00019	0.0	0.00015	1.0	0.99993		1.0	151	151	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-09	Adult	Adult	Gonad	Reproductive System
29755	29755	SRR27467688	SRX23139218	SRS20090261	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other					ovary DM R2	strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:adult\|collection date:2022\|geo loc name:Austria\|sex:female\|tissue:ovary\|treatment:DM\|BioSampleModel:Model organism or animal								tRAM seq of zebrafish: ovary DM rep2	EV02002	EV02002	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	NextSeq 500		SRP482074		EV02002.R1.fastq.gz EV02002.R2.fastq.gz	fastq fastq	861320308.0	2852054.0	EV02002.R1.fastq.gz	0:151 1:151	A:205625519;C:162178974;G:334206312;T:159256900;N:52603	151	151	205625519	162178974	334206312	159256900	52603	SRX23139218	SRS20090261	SRA1781872	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	2	2e-05	0.00049	0.0	0.00027	1.0	0.99947		0.44444	151	151	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-09	Adult	Adult	Gonad	Reproductive System
29756	29756	SRR27467689	SRX23139217	SRS20090260	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other					ovary mock R2	strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:adult\|collection date:2022\|geo loc name:Austria\|sex:female\|tissue:ovary\|treatment:mock\|BioSampleModel:Model organism or animal								tRAM seq of zebrafish: ovary mock rep2	EV02001	EV02001	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	NextSeq 500		SRP482074		EV02001.R1.fastq.gz EV02001.R2.fastq.gz	fastq fastq	520371066.0	1723083.0	EV02001.R1.fastq.gz	0:151 1:151	A:116107273;C:90896560;G:218652568;T:94682244;N:32421	151	151	116107273	90896560	218652568	94682244	32421	SRX23139217	SRS20090260	SRA1781872	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	2	2e-05	0.00086	0.0	0.00078	0.99995	0.99981	0.0	0.61538	151	151	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-09	Adult	Adult	Gonad	Reproductive System
31514	31514	SRR28435337	SRX24039257	SRS20832031	SRP497569	PRJNA1090643	Danio rerio Raw sequence reads	PRJNA1090643	Other	The transcriptome of WT and cry dash / mutant are tested at CT 4 and CT 16.		cry dash / group 2 at CT 16	Cryd CT16G2	Unknown BA023 04T0008.fq.gz	isolate:The second group of cry dash / fish collected at CT 16.\|age:120 hpf\|collection date:2023 06 10\|geo loc name:China:Suzhou\|sex:not determined\|tissue:larvae\|biomaterial provider:Han Wang\|birth date:2023 06 05\|genotype:cry dash / \|health state:Health\|BioSampleModel:Model organism or animal								RNA seq of Danio rerio: larvae	Unknown BA023 04T0008.fq.gz	Unknown BA023 04T0008.fq.gz	CT16 cry dash group2			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	HiSeq X Five		SRP497569		Unknown_BA023-04T0008_good_2.fq.gz Unknown_BA023-04T0008_good_1.fq.gz	fastq fastq	6928082472.0	23162452.0	Unknown BA023 04T0008 good 1.fq.gz	0:149.55 1:149.55	A:1783381005;C:1671764458;G:1686432861;T:1786331460;N:172688	149	149	1783381005	1671764458	1686432861	1786331460	172688	SRX24039257	SRS20832031	SRA1832685	Soochow University\|School of Biology & Basic Medical Sciences	Soochow University	2	0.96107	0.96048	0.06638	0.06578	0.68546	0.68582	0.46626	0.45803	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Unknown	2024-03-25	Larval	Larval	Undetermined	Undetermined
31515	31515	SRR28435338	SRX24039256	SRS20832030	SRP497569	PRJNA1090643	Danio rerio Raw sequence reads	PRJNA1090643	Other	The transcriptome of WT and cry dash / mutant are tested at CT 4 and CT 16.		cry dash / group 1 at CT 16	Cryd CT16G1	Unknown BA023 04T0007.fq.gz	isolate:The first group of cry dash / fish collected at CT 16.\|age:120 hpf\|collection date:2023 06 10\|geo loc name:China:Suzhou\|sex:not determined\|tissue:larvae\|biomaterial provider:Han Wang\|birth date:2023 06 05\|genotype:cry dash / \|health state:Health\|BioSampleModel:Model organism or animal								RNA seq of Danio rerio: larvae	Unknown BA023 04T0007.fq.gz	Unknown BA023 04T0007.fq.gz	CT16 cry dash group1			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	HiSeq X Five		SRP497569		Unknown_BA023-04T0007_good_2.fq.gz Unknown_BA023-04T0007_good_1.fq.gz	fastq fastq	7247045982.0	24239568.0	Unknown BA023 04T0007 good 1.fq.gz	0:149.49 1:149.49	A:1868252704;C:1747715656;G:1761213537;T:1869681292;N:182793	149	149	1868252704	1747715656	1761213537	1869681292	182793	SRX24039256	SRS20832030	SRA1832685	Soochow University\|School of Biology & Basic Medical Sciences	Soochow University	2	0.95954	0.95937	0.0624	0.06218	0.68809	0.68765	0.47347	0.47429	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Unknown	2024-03-25	Larval	Larval	Undetermined	Undetermined
31516	31516	SRR28435339	SRX24039255	SRS20832029	SRP497569	PRJNA1090643	Danio rerio Raw sequence reads	PRJNA1090643	Other	The transcriptome of WT and cry dash / mutant are tested at CT 4 and CT 16.		cry dash / group 2 at CT 4	Cryd CT4G2	Unknown BA023 04T0006.fq.gz	isolate:The second group of cry dash / fish collected at CT 4.\|age:120 hpf\|collection date:2023 06 10\|geo loc name:China:Suzhou\|sex:not determined\|tissue:larvae\|biomaterial provider:Han Wang\|birth date:2023 06 05\|genotype:cry dash / \|health state:Health\|BioSampleModel:Model organism or animal								RNA seq of Danio rerio: larvae	Unknown BA023 04T0006.fq.gz	Unknown BA023 04T0006.fq.gz	CT4 cry dash group2			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	HiSeq X Five		SRP497569		Unknown_BA023-04T0006_good_1.fq.gz Unknown_BA023-04T0006_good_2.fq.gz	fastq fastq	7467294282.0	24985127.0	Unknown BA023 04T0006 good 1.fq.gz	0:149.43 1:149.43	A:1940430660;C:1790773066;G:1798765445;T:1937139187;N:185924	149	149	1940430660	1790773066	1798765445	1937139187	185924	SRX24039255	SRS20832029	SRA1832685	Soochow University\|School of Biology & Basic Medical Sciences	Soochow University	2	0.95702	0.95753	0.08848	0.08877	0.6829	0.68199	0.49417	0.49443	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Unknown	2024-03-25	Larval	Larval	Undetermined	Undetermined
31517	31517	SRR28435340	SRX24039254	SRS20832028	SRP497569	PRJNA1090643	Danio rerio Raw sequence reads	PRJNA1090643	Other	The transcriptome of WT and cry dash / mutant are tested at CT 4 and CT 16.		cry dash / group 1 at CT 4	Cryd CT4G1	Unknown BA023 04T0005.fq.gz	isolate:The first group of cry dash / fish collected at CT 4.\|age:120 hpf\|collection date:2023 06 10\|geo loc name:China:Suzhou\|sex:not determined\|tissue:larvae\|biomaterial provider:Han Wang\|birth date:2023 06 05\|genotype:cry dash / \|health state:Health\|BioSampleModel:Model organism or animal								RNA seq of Danio rerio: larvae	Unknown BA023 04T0005.fq.gz	Unknown BA023 04T0005.fq.gz	CT4 cry dash group1			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	HiSeq X Five		SRP497569		Unknown_BA023-04T0005_good_1.fq.gz Unknown_BA023-04T0005_good_2.fq.gz	fastq fastq	6766310740.0	22646274.0	Unknown BA023 04T0005 good 1.fq.gz	0:149.39 1:149.39	A:1762324132;C:1615995203;G:1625767974;T:1762055354;N:168077	149	149	1762324132	1615995203	1625767974	1762055354	168077	SRX24039254	SRS20832028	SRA1832685	Soochow University\|School of Biology & Basic Medical Sciences	Soochow University	2	0.95588	0.95587	0.06663	0.06633	0.67911	0.67888	0.46701	0.47626	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Unknown	2024-03-25	Larval	Larval	Undetermined	Undetermined
31518	31518	SRR28435341	SRX24039253	SRS20832027	SRP497569	PRJNA1090643	Danio rerio Raw sequence reads	PRJNA1090643	Other	The transcriptome of WT and cry dash / mutant are tested at CT 4 and CT 16.		WT group 2 at CT 16	WT CT16G2	Unknown BA023 04T0004.fq.gz	isolate:The second group of WT fish collected at CT 16.\|age:120 hpf\|collection date:2023 06 10\|geo loc name:China:Suzhou\|sex:not determined\|tissue:larvae\|biomaterial provider:Han Wang\|birth date:2023 06 05\|genotype:wildtype\|health state:Health\|BioSampleModel:Model organism or animal								RNA seq of Danio rerio: larvae	Unknown BA023 04T0004.fq.gz	Unknown BA023 04T0004.fq.gz	CT6 WT group2			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	HiSeq X Five		SRP497569		Unknown_BA023-04T0004_good_2.fq.gz Unknown_BA023-04T0004_good_1.fq.gz	fastq fastq	6830283170.0	22847843.0	Unknown BA023 04T0004 good 1.fq.gz	0:149.47 1:149.47	A:1791839697;C:1618554485;G:1627518993;T:1792199298;N:170697	149	149	1791839697	1618554485	1627518993	1792199298	170697	SRX24039253	SRS20832027	SRA1832685	Soochow University\|School of Biology & Basic Medical Sciences	Soochow University	2	0.9515	0.94997	0.08493	0.08422	0.67178	0.67316	0.47915	0.48187	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Unknown	2024-03-25	Larval	Larval	Undetermined	Undetermined
31519	31519	SRR28435342	SRX24039252	SRS20832026	SRP497569	PRJNA1090643	Danio rerio Raw sequence reads	PRJNA1090643	Other	The transcriptome of WT and cry dash / mutant are tested at CT 4 and CT 16.		WT group 1 at CT 16	WT CT16G1	Unknown BA023 04T0003.fq.gz	isolate:The first group of WT fish collected at CT 16.\|age:120 hpf\|collection date:2023 06 10\|geo loc name:China:Suzhou\|sex:not determined\|tissue:larvae\|biomaterial provider:Han Wang\|birth date:2023 06 05\|genotype:wildtype\|health state:Health\|BioSampleModel:Model organism or animal								RNA seq of Danio rerio: larvae	Unknown BA023 04T0003.fq.gz	Unknown BA023 04T0003.fq.gz	CT6 WT group1			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	HiSeq X Five		SRP497569		Unknown_BA023-04T0003_good_1.fq.gz Unknown_BA023-04T0003_good_2.fq.gz	fastq fastq	6430546584.0	21512133.0	Unknown BA023 04T0003 good 1.fq.gz	0:149.46 1:149.46	A:1678015842;C:1530296350;G:1541505212;T:1680568743;N:160437	149	149	1678015842	1530296350	1541505212	1680568743	160437	SRX24039252	SRS20832026	SRA1832685	Soochow University\|School of Biology & Basic Medical Sciences	Soochow University	2	0.94974	0.95051	0.08145	0.0819	0.6775	0.67848	0.47999	0.47986	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Unknown	2024-03-25	Larval	Larval	Undetermined	Undetermined
31520	31520	SRR28435343	SRX24039251	SRS20832025	SRP497569	PRJNA1090643	Danio rerio Raw sequence reads	PRJNA1090643	Other	The transcriptome of WT and cry dash / mutant are tested at CT 4 and CT 16.		WT group 2 at CT 4	WT CT4G2	Unknown BA023 04T0002.fq.gz	isolate:The second group of WT fish collected at CT 4.\|age:120 hpf\|collection date:2023 06 10\|geo loc name:China:Suzhou\|sex:not determined\|tissue:larvae\|biomaterial provider:Han Wang\|birth date:2023 06 05\|genotype:wildtype\|health state:Health\|BioSampleModel:Model organism or animal								RNA seq of Danio rerio: larvae	Unknown BA023 04T0002.fq.gz	Unknown BA023 04T0002.fq.gz	CT4 WT group2			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	HiSeq X Five		SRP497569		Unknown_BA023-04T0002_good_1.fq.gz Unknown_BA023-04T0002_good_2.fq.gz	fastq fastq	7084078326.0	23701315.0	Unknown BA023 04T0002 good 1.fq.gz	0:149.44 1:149.44	A:1855453089;C:1679520129;G:1688607029;T:1860319577;N:178502	149	149	1855453089	1679520129	1688607029	1860319577	178502	SRX24039251	SRS20832025	SRA1832685	Soochow University\|School of Biology & Basic Medical Sciences	Soochow University	2	0.95393	0.95431	0.07799	0.07802	0.66728	0.66835	0.46237	0.47322	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Unknown	2024-03-25	Larval	Larval	Undetermined	Undetermined
31521	31521	SRR28435344	SRX24039250	SRS20832024	SRP497569	PRJNA1090643	Danio rerio Raw sequence reads	PRJNA1090643	Other	The transcriptome of WT and cry dash / mutant are tested at CT 4 and CT 16.		WT group 1 at CT 4	WT CT4G1	Unknown BA023 04T0001.fq.gz	isolate:The first group of WT fish collected at CT 4.\|age:120 hpf\|collection date:2023 06 10\|geo loc name:China:Suzhou\|sex:not determined\|tissue:larvae\|biomaterial provider:Han Wang\|birth date:2023 06 05\|genotype:wildtype\|health state:Health\|BioSampleModel:Model organism or animal								RNA seq of Danio rerio: larvae	Unknown BA023 04T0001.fq.gz	Unknown BA023 04T0001.fq.gz	CT4 WT group1			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	HiSeq X Five		SRP497569		Unknown_BA023-04T0001_good_2.fq.gz Unknown_BA023-04T0001_good_1.fq.gz	fastq fastq	7360015710.0	24625447.0	Unknown BA023 04T0001 good 1.fq.gz	0:149.44 1:149.44	A:1931324589;C:1743134275;G:1748699685;T:1936672740;N:184421	149	149	1931324589	1743134275	1748699685	1936672740	184421	SRX24039250	SRS20832024	SRA1832685	Soochow University\|School of Biology & Basic Medical Sciences	Soochow University	2	0.954	0.95301	0.08257	0.08182	0.66772	0.66906	0.47505	0.47577	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Unknown	2024-03-25	Larval	Larval	Undetermined	Undetermined
32923	32923	SRR29498567	SRX25008885	SRS21709104	SRP515416	PRJNA1127032	Zebrafish Tissue Mid Range RNA Sequencing	PRJNA1127032	Other	This project sequenced mid size ranged RNA from zebrafish liver brain and gut tissues using male and female parallel samples.				F2g	strain:AB\|age:adult\|dev stage:adult\|collection date:2020\|geo loc name:Hungary\|sex:female\|tissue:gut\|identifier:F2g\|BioSampleModel:Model organism or animal								midRNA seq Danio rerio	10	10	Total RNA was extracted from different zebrafish tissues using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. post size selection our samples were sequenced with Illumina technology.			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP515416		F2g_R2.fq.gz F2g_R1.fq.gz	fastq fastq	9101949000.0	30339830.0	F2g R1.fq.gz	0:150 1:150	A:2052853923;C:2394247721;G:2773304460;T:1881440199;N:102697	150	150	2052853923	2394247721	2773304460	1881440199	102697	SRX25008885	SRS21709104	SRA1905460	Eotvos Lorand University\|Genetics	Eotvos Lorand University	2	0.65449	0.37434	0.04313	0.12258	0.99519	0.99527	0.61425	0.56139	150	150	B	B	mate2-mate1 similar by mapping diff	illumina	novaseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Hungary	2024-06-22	Adult	Adult	Gut	Digestive System
32924	32924	SRR29498568	SRX25008884	SRS21709103	SRP515416	PRJNA1127032	Zebrafish Tissue Mid Range RNA Sequencing	PRJNA1127032	Other	This project sequenced mid size ranged RNA from zebrafish liver brain and gut tissues using male and female parallel samples.				F1g	strain:AB\|age:adult\|dev stage:adult\|collection date:2020\|geo loc name:Hungary\|sex:female\|tissue:gut\|identifier:F1g\|BioSampleModel:Model organism or animal								midRNA seq Danio rerio	09	09	Total RNA was extracted from different zebrafish tissues using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. post size selection our samples were sequenced with Illumina technology.			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP515416		F1g_R1.fq.gz F1g_R2.fq.gz	fastq fastq	8132653500.0	27108845.0	F1g R1.fq.gz	0:150 1:150	A:1811779602;C:2095863397;G:2529881799;T:1695036688;N:92014	150	150	1811779602	2095863397	2529881799	1695036688	92014	SRX25008884	SRS21709103	SRA1905460	Eotvos Lorand University\|Genetics	Eotvos Lorand University	2	0.53909	0.24181	0.01966	0.04797	0.99598	0.99624	0.59302	0.62038	150	150	B	B	mate2-mate1 similar by mapping diff	illumina	novaseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Hungary	2024-06-22	Adult	Adult	Gut	Digestive System
32925	32925	SRR29498569	SRX25008883	SRS21709102	SRP515416	PRJNA1127032	Zebrafish Tissue Mid Range RNA Sequencing	PRJNA1127032	Other	This project sequenced mid size ranged RNA from zebrafish liver brain and gut tissues using male and female parallel samples.				M2l	strain:AB\|age:adult\|dev stage:adult\|collection date:2020\|geo loc name:Hungary\|sex:male\|tissue:liver\|identifier:M2l\|BioSampleModel:Model organism or animal								midRNA seq Danio rerio	08	08	Total RNA was extracted from different zebrafish tissues using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. post size selection our samples were sequenced with Illumina technology.			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP515416		M2l_R1.fq.gz M2l_R2.fq.gz	fastq fastq	7733826600.0	25779422.0	M2l R1.fq.gz	0:150 1:150	A:1754773283;C:2022716836;G:2330439864;T:1625790112;N:106505	150	150	1754773283	2022716836	2330439864	1625790112	106505	SRX25008883	SRS21709102	SRA1905460	Eotvos Lorand University\|Genetics	Eotvos Lorand University	2	0.60941	0.31539	0.0377	0.09053	0.995	0.99478	0.50937	0.57123	150	150	B	B	mate2-mate1 similar by mapping diff	illumina	novaseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Hungary	2024-06-22	Adult	Adult	Liver	Liver and Biliary System
32926	32926	SRR29498570	SRX25008882	SRS21709101	SRP515416	PRJNA1127032	Zebrafish Tissue Mid Range RNA Sequencing	PRJNA1127032	Other	This project sequenced mid size ranged RNA from zebrafish liver brain and gut tissues using male and female parallel samples.				M2b	strain:AB\|age:adult\|dev stage:adult\|collection date:2020\|geo loc name:Hungary\|sex:male\|tissue:brain\|identifier:M2b\|BioSampleModel:Model organism or animal								midRNA seq Danio rerio	07	07	Total RNA was extracted from different zebrafish tissues using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. post size selection our samples were sequenced with Illumina technology.			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP515416		M2b_R1.fq.gz M2b_R2.fq.gz	fastq fastq	9324874800.0	31082916.0	M2b R1.fq.gz	0:150 1:150	A:2073617286;C:2382074775;G:2948687855;T:1920389281;N:105603	150	150	2073617286	2382074775	2948687855	1920389281	105603	SRX25008882	SRS21709101	SRA1905460	Eotvos Lorand University\|Genetics	Eotvos Lorand University	2	0.57388	0.29571	0.04187	0.10168	0.99506	0.99513	0.61677	0.60641	150	150	B	B	mate2-mate1 similar by mapping diff	illumina	novaseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Hungary	2024-06-22	Adult	Adult	Brain	Nervous System
32927	32927	SRR29498571	SRX25008881	SRS21709100	SRP515416	PRJNA1127032	Zebrafish Tissue Mid Range RNA Sequencing	PRJNA1127032	Other	This project sequenced mid size ranged RNA from zebrafish liver brain and gut tissues using male and female parallel samples.				M1l	strain:AB\|age:adult\|dev stage:adult\|collection date:2020\|geo loc name:Hungary\|sex:male\|tissue:liver\|identifier:M1l\|BioSampleModel:Model organism or animal								midRNA seq Danio rerio	06	06	Total RNA was extracted from different zebrafish tissues using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. post size selection our samples were sequenced with Illumina technology.			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP515416		M1l_R2.fq.gz M1l_R1.fq.gz	fastq fastq	8301268800.0	27670896.0	M1l R1.fq.gz	0:150 1:150	A:1856070257;C:2266693166;G:2413641098;T:1764769457;N:94822	150	150	1856070257	2266693166	2413641098	1764769457	94822	SRX25008881	SRS21709100	SRA1905460	Eotvos Lorand University\|Genetics	Eotvos Lorand University	2	0.8289	0.73852	0.21964	0.50932	0.99648	0.99701	0.57332	0.51129	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Hungary	2024-06-22	Adult	Adult	Liver	Liver and Biliary System
32928	32928	SRR29498572	SRX25008880	SRS21709099	SRP515416	PRJNA1127032	Zebrafish Tissue Mid Range RNA Sequencing	PRJNA1127032	Other	This project sequenced mid size ranged RNA from zebrafish liver brain and gut tissues using male and female parallel samples.				M1b	strain:AB\|age:adult\|dev stage:adult\|collection date:2020\|geo loc name:Hungary\|sex:male\|tissue:brain\|identifier:M1b\|BioSampleModel:Model organism or animal								midRNA seq Danio rerio	05	05	Total RNA was extracted from different zebrafish tissues using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. post size selection our samples were sequenced with Illumina technology.			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP515416		M1b_R1.fq.gz M1b_R2.fq.gz	fastq fastq	7947472800.0	26491576.0	M1b R1.fq.gz	0:150 1:150	A:1764190500;C:1937842699;G:2595509352;T:1649839967;N:90282	150	150	1764190500	1937842699	2595509352	1649839967	90282	SRX25008880	SRS21709099	SRA1905460	Eotvos Lorand University\|Genetics	Eotvos Lorand University	2	0.96542	0.21476	0.17288	0.05982	0.97289	0.99711	0.57845	0.611	150	150	B	T	mate2 technical by mapping diff	illumina	novaseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Hungary	2024-06-22	Adult	Adult	Brain	Nervous System
32929	32929	SRR29498573	SRX25008879	SRS21709098	SRP515416	PRJNA1127032	Zebrafish Tissue Mid Range RNA Sequencing	PRJNA1127032	Other	This project sequenced mid size ranged RNA from zebrafish liver brain and gut tissues using male and female parallel samples.				F2l	strain:AB\|age:adult\|dev stage:adult\|collection date:2020\|geo loc name:Hungary\|sex:female\|tissue:liver\|identifier:F2l\|BioSampleModel:Model organism or animal								midRNA seq Danio rerio	04	04	Total RNA was extracted from different zebrafish tissues using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. post size selection our samples were sequenced with Illumina technology.			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP515416		F2l_R1.fq.gz F2l_R2.fq.gz	fastq fastq	8701893900.0	29006313.0	F2l R1.fq.gz	0:150 1:150	A:1977580339;C:2299061131;G:2585058451;T:1840095650;N:98329	150	150	1977580339	2299061131	2585058451	1840095650	98329	SRX25008879	SRS21709098	SRA1905460	Eotvos Lorand University\|Genetics	Eotvos Lorand University	2	0.72425	0.57704	0.15111	0.37121	0.99744	0.99762	0.61161	0.55762	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Hungary	2024-06-22	Adult	Adult	Liver	Liver and Biliary System
32930	32930	SRR29498574	SRX25008878	SRS21709097	SRP515416	PRJNA1127032	Zebrafish Tissue Mid Range RNA Sequencing	PRJNA1127032	Other	This project sequenced mid size ranged RNA from zebrafish liver brain and gut tissues using male and female parallel samples.				F2b	strain:AB\|age:adult\|dev stage:adult\|collection date:2020\|geo loc name:Hungary\|sex:female\|tissue:brain\|identifier:F2b\|BioSampleModel:Model organism or animal								midRNA seq Danio rerio	03	03	Total RNA was extracted from different zebrafish tissues using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. post size selection our samples were sequenced with Illumina technology.			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP515416		F2b_R1.fq.gz F2b_R2.fq.gz	fastq fastq	9249410100.0	30831367.0	F2b R1.fq.gz	0:150 1:150	A:2101671138;C:2272479255;G:2931272789;T:1943881150;N:105768	150	150	2101671138	2272479255	2931272789	1943881150	105768	SRX25008878	SRS21709097	SRA1905460	Eotvos Lorand University\|Genetics	Eotvos Lorand University	2	0.96654	0.19343	0.23127	0.08081	0.95272	0.99326	0.63762	0.64901	150	150	B	T	mate2 technical by mapping diff	illumina	novaseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Hungary	2024-06-22	Adult	Adult	Brain	Nervous System
32931	32931	SRR29498575	SRX25008877	SRS21709096	SRP515416	PRJNA1127032	Zebrafish Tissue Mid Range RNA Sequencing	PRJNA1127032	Other	This project sequenced mid size ranged RNA from zebrafish liver brain and gut tissues using male and female parallel samples.				M2g	strain:AB\|age:adult\|dev stage:adult\|collection date:2020\|geo loc name:Hungary\|sex:male\|tissue:gut\|identifier:M2g\|BioSampleModel:Model organism or animal								midRNA seq Danio rerio	12	12	Total RNA was extracted from different zebrafish tissues using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. post size selection our samples were sequenced with Illumina technology.			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP515416		M2g_R1.fq.gz M2g_R2.fq.gz	fastq fastq	7106243100.0	23687477.0	M2g R1.fq.gz	0:150 1:150	A:1567154123;C:1866065312;G:2213286944;T:1459656676;N:80045	150	150	1567154123	1866065312	2213286944	1459656676	80045	SRX25008877	SRS21709096	SRA1905460	Eotvos Lorand University\|Genetics	Eotvos Lorand University	2	0.56476	0.25026	0.02259	0.04481	0.99667	0.99701	0.63277	0.65693	150	150	B	B	mate2-mate1 similar by mapping diff	illumina	novaseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Hungary	2024-06-22	Adult	Adult	Gut	Digestive System
32932	32932	SRR29498576	SRX25008876	SRS21709095	SRP515416	PRJNA1127032	Zebrafish Tissue Mid Range RNA Sequencing	PRJNA1127032	Other	This project sequenced mid size ranged RNA from zebrafish liver brain and gut tissues using male and female parallel samples.				M1g	strain:AB\|age:adult\|dev stage:adult\|collection date:2020\|geo loc name:Hungary\|sex:male\|tissue:gut\|identifier:M1g\|BioSampleModel:Model organism or animal								midRNA seq Danio rerio	11	11	Total RNA was extracted from different zebrafish tissues using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. post size selection our samples were sequenced with Illumina technology.			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP515416		M1g_R2.fq.gz M1g_R1.fq.gz	fastq fastq	7351182000.0	24503940.0	M1g R1.fq.gz	0:150 1:150	A:1623685246;C:1858847576;G:2315396486;T:1553169371;N:83321	150	150	1623685246	1858847576	2315396486	1553169371	83321	SRX25008876	SRS21709095	SRA1905460	Eotvos Lorand University\|Genetics	Eotvos Lorand University	2	0.96004	0.21521	0.16113	0.04578	0.92431	0.99143	0.61867	0.63432	150	150	B	T	mate2 technical by mapping diff	illumina	novaseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Hungary	2024-06-22	Adult	Adult	Gut	Digestive System
32933	32933	SRR29498577	SRX25008875	SRS21709094	SRP515416	PRJNA1127032	Zebrafish Tissue Mid Range RNA Sequencing	PRJNA1127032	Other	This project sequenced mid size ranged RNA from zebrafish liver brain and gut tissues using male and female parallel samples.				F1l	strain:AB\|age:adult\|dev stage:adult\|collection date:2020\|geo loc name:Hungary\|sex:female\|tissue:liver\|identifier:F1l\|BioSampleModel:Model organism or animal								midRNA seq Danio rerio	02	02	Total RNA was extracted from different zebrafish tissues using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. post size selection our samples were sequenced with Illumina technology.			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP515416		F1l_R2.fq.gz F1l_R1.fq.gz	fastq fastq	4647564000.0	15491880.0	F1l R1.fq.gz	0:150 1:150	A:993332389;C:862184908;G:1814249126;T:977710185;N:87392	150	150	993332389	862184908	1814249126	977710185	87392	SRX25008875	SRS21709094	SRA1905460	Eotvos Lorand University\|Genetics	Eotvos Lorand University	2	0.88683	0.14922	0.24654	0.08178	0.9583	0.99819	0.70978	0.20254	150	150	B	T	mate2 technical by mapping diff	illumina	novaseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Hungary	2024-06-22	Adult	Adult	Liver	Liver and Biliary System
32934	32934	SRR29498578	SRX25008874	SRS21709093	SRP515416	PRJNA1127032	Zebrafish Tissue Mid Range RNA Sequencing	PRJNA1127032	Other	This project sequenced mid size ranged RNA from zebrafish liver brain and gut tissues using male and female parallel samples.				F1b	strain:AB\|age:adult\|dev stage:adult\|collection date:2020\|geo loc name:Hungary\|sex:female\|tissue:brain\|identifier:F1b\|BioSampleModel:Model organism or animal								midRNA seq Danio rerio	01	01	Total RNA was extracted from different zebrafish tissues using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. post size selection our samples were sequenced with Illumina technology.			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP515416		F1b_R2.fq.gz F1b_R1.fq.gz	fastq fastq	7995852300.0	26652841.0	F1b R1.fq.gz	0:150 1:150	A:1744452113;C:2053788787;G:2580416325;T:1617104387;N:90688	150	150	1744452113	2053788787	2580416325	1617104387	90688	SRX25008874	SRS21709093	SRA1905460	Eotvos Lorand University\|Genetics	Eotvos Lorand University	2	0.96107	0.17798	0.16452	0.02921	0.96759	0.99677	0.66455	0.62672	150	150	B	T	mate2 technical by mapping diff	illumina	novaseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Hungary	2024-06-22	Adult	Adult	Brain	Nervous System
40707	40707	SRR3502888	SRX1760541	SRS1436386	SRP072296	PRJNA316313	Codon optimality and mRNA decay in zebrafish and Xenopus	PRJNA316313	Other	Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.			Zebrafish tRNA at 6hpf	tRNA AB 6h	strain:TUAB\|age:6hpf\|dev stage:Shield\|sex:pooled male and female\|tissue:Whole animal\|collected by:Ariel Bazzini\|genotype:WT\|BioSampleModel:Model organism or animal								Zebrafish tRNAs at 6hpf	tRNA 6hpf zebrafish	TGIRT tRNA Library	1			OTHER	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>152</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>77</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP072296		AB-tRNA_S9_R1_001.fastq.gz AB-tRNA_S9_R2_001.fastq.gz	fastq fastq	7860522000.0	26201740.0	tRNA zebrafish 6hpf	0:150 1:150	A:1945184302;C:2012637521;G:2171934357;T:1730625218;N:140602	150	150	1945184302	2012637521	2171934357	1730625218	140602	SRX1760541	SRS1436386	SRA395141	Yale University\|Giraldez Lab	Yale University	2	0.04186	0.04313	0.00633	0.00639	0.96834	0.96913	0.53967	0.5329	150	150	T	T	mates < 9% mapping rate	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	United States	2016-06-17	Gastrula	Embryo	Whole Organism	All anatomical structures
41348	41348	SRR4302022	SRX2194190	SRS1716514	SRP090540	PRJNA344550	Danio rerio strain:AB Raw sequence reads	PRJNA344550	Whole Genome Sequencing	Identification of circular RNAs in zebrafish	pubmed:27878987			Zebrafish circRNA	strain:AB\|age:Adult\|sex:pooled male and female\|tissue:brain eyes heart liver spleen kidney intestines skin muscle gill ovary testis\|BioSampleModel:Model organism or animal								Identification of circular RNAs in zebrafish	Zebrafish circRNAs	Key Lab of Agricultural Animal Genetics	1			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP090540		MIX_R1.fastq.gz MIX_R2.fastq.gz	fastq fastq	21319208400.0	71064028.0	Zebrafish circRNAs	0:150 1:150	A:4973737880;C:5734846860;G:5920594296;T:4689011877;N:1017487	150	150	4973737880	5734846860	5920594296	4689011877	1017487	SRX2194190	SRS1716514	SRA480645	Huazhong Agricultural University\|Key Lab of Agricultural Animal Genetics	Huazhong Agricultural University	2	0.89959	0.92292	0.28429	0.27588	0.87207	0.86866	0.65238	0.78485	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	China	2016-11-28	Adult	Adult	Multi-tissue	Multi-system
42495	42495	SRR5666979	SRX2902577	SRS2269173	SRP108989	PRJNA390119	HLX & Hematopoiesis	PRJNA390119	Other	HLX & Hematopoiesis		rnaseq and atacseq	hlx hematopoiesis	hlx	isolate:multiisolates\|age:N/A\|sex:pooled male and female\|tissue:heart\|BioSampleModel:Model organism or animal								kdrl GFP cells hlx1 MO rep2	3	kdrl GFP cells hlx1 MO rep2	SMART SEQ ultra low RNA seq kit Clonetech			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP108989	assembly:danRer10	flk_gfp_hlx_8ng_48hrs_2_R1.fastq.gz flk_gfp_hlx_8ng_48hrs_2_R2.fastq.gz	fastq fastq	1887289200.0	12581928.0	flk gfp hlx 8ng 48hrs 2 R1.fastq.gz	0:75 1:75	A:493825524;C:448630716;G:436118597;T:508410442;N:303921	75	75	493825524	448630716	436118597	508410442	303921	SRX2902577	SRS2269173	SRA573518	BRFAA\|Molecular Biology	BRFAA	2	0.9202	0.9216	0.09499	0.09558	0.73805	0.73878	0.48809	0.48787	75	75	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Greece	2017-06-13	Undetermined	Undetermined	Heart	Cardiovascular System
42496	42496	SRR5666980	SRX2902576	SRS2269173	SRP108989	PRJNA390119	HLX & Hematopoiesis	PRJNA390119	Other	HLX & Hematopoiesis		rnaseq and atacseq	hlx hematopoiesis	hlx	isolate:multiisolates\|age:N/A\|sex:pooled male and female\|tissue:heart\|BioSampleModel:Model organism or animal								kdrl GFP cells hlx1 MO rep1	2	kdrl GFP cells hlx1 MO rep1	SMART SEQ ultra low RNA seq kit Clonetech			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP108989	assembly:danRer10	flk_gfp_hlx_8ng_48hrs_1_R1.fastq.gz flk_gfp_hlx_8ng_48hrs_1_R2.fastq.gz	fastq fastq	1561083900.0	10407226.0	flk gfp hlx 8ng 48hrs 1 R2.fastq.gz	0:75 1:75	A:412744284;C:366776465;G:356834742;T:424473871;N:254538	75	75	412744284	366776465	356834742	424473871	254538	SRX2902576	SRS2269173	SRA573518	BRFAA\|Molecular Biology	BRFAA	2	0.9172	0.91824	0.09957	0.09961	0.73965	0.73975	0.48906	0.48977	75	75	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Greece	2017-06-13	Undetermined	Undetermined	Heart	Cardiovascular System
42497	42497	SRR5666981	SRX2902575	SRS2269173	SRP108989	PRJNA390119	HLX & Hematopoiesis	PRJNA390119	Other	HLX & Hematopoiesis		rnaseq and atacseq	hlx hematopoiesis	hlx	isolate:multiisolates\|age:N/A\|sex:pooled male and female\|tissue:heart\|BioSampleModel:Model organism or animal								kdrl GFP cells control 2	1	kdrl GFP cells control 2	SMART SEQ ultra low RNA seq kit Clonetech			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP108989	assembly:danRer10	flk_gfp_48hrs_con2_R1.fastq.gz flk_gfp_48hrs_con2_R2.fastq.gz	fastq fastq	2042164500.0	13614430.0	flk gfp 48hrs con2 R1.fastq.gz	0:75 1:75	A:537008617;C:483956616;G:465380092;T:555490621;N:328554	75	75	537008617	483956616	465380092	555490621	328554	SRX2902575	SRS2269173	SRA573518	BRFAA\|Molecular Biology	BRFAA	2	0.91492	0.91762	0.10575	0.10669	0.75519	0.75546	0.49482	0.49617	75	75	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Greece	2017-06-13	Undetermined	Undetermined	Heart	Cardiovascular System
42498	42498	SRR5666982	SRX2902574	SRS2269173	SRP108989	PRJNA390119	HLX & Hematopoiesis	PRJNA390119	Other	HLX & Hematopoiesis		rnaseq and atacseq	hlx hematopoiesis	hlx	isolate:multiisolates\|age:N/A\|sex:pooled male and female\|tissue:heart\|BioSampleModel:Model organism or animal								kdrl GFP cells control 1	0	kdrl GFP cells control 1	SMART SEQ ultra low RNA seq kit Clonetech			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP108989	assembly:danRer10	flk_gfp_48hrs_con1_R2.fastq.gz flk_gfp_48hrs_con1_R1.fastq.gz	fastq fastq	1678987200.0	11193248.0	flk gfp 48hrs con1 R2.fastq.gz	0:75 1:75	A:437283407;C:401234553;G:387947515;T:452257282;N:264443	75	75	437283407	401234553	387947515	452257282	264443	SRX2902574	SRS2269173	SRA573518	BRFAA\|Molecular Biology	BRFAA	2	0.91593	0.91737	0.08937	0.08988	0.75607	0.75696	0.50103	0.45539	75	75	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Greece	2017-06-13	Undetermined	Undetermined	Heart	Cardiovascular System
42499	42499	SRR5666985	SRX2902571	SRS2269173	SRP108989	PRJNA390119	HLX & Hematopoiesis	PRJNA390119	Other	HLX & Hematopoiesis		rnaseq and atacseq	hlx hematopoiesis	hlx	isolate:multiisolates\|age:N/A\|sex:pooled male and female\|tissue:heart\|BioSampleModel:Model organism or animal								fli GFP cells hHLXOE rep 2	5	fli GFP cells hHLXOE rep 2	SMART SEQ ultra low RNA seq kit Clonetech			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP108989	assembly:danRer10	fli_gal4_uas_hlx_endo_48h_s2_R2.fastq.gz fli_gal4_uas_hlx_endo_48h_s2_R1.fastq.gz	fastq fastq	4490898450.0	29939323.0	fli gal4 uas hlx endo 48h s2 R2.fastq.gz	0:75 1:75	A:870349076;C:1346136891;G:1401796534;T:869066463;N:3549486	75	75	870349076	1346136891	1401796534	869066463	3549486	SRX2902571	SRS2269173	SRA573518	BRFAA\|Molecular Biology	BRFAA	2	0.5714	0.57344	0.27957	0.28321	0.85102	0.85342	0.53304	0.53368	75	75	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Greece	2017-06-13	Undetermined	Undetermined	Heart	Cardiovascular System
42500	42500	SRR5666986	SRX2902570	SRS2269173	SRP108989	PRJNA390119	HLX & Hematopoiesis	PRJNA390119	Other	HLX & Hematopoiesis		rnaseq and atacseq	hlx hematopoiesis	hlx	isolate:multiisolates\|age:N/A\|sex:pooled male and female\|tissue:heart\|BioSampleModel:Model organism or animal								fli GFP cells hHLXOE rep 1	4	fli GFP cells hHLXOE rep 1	SMART SEQ ultra low RNA seq kit Clonetech			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP108989	assembly:danRer10	fli_gal4_uas_hlx_endo_48h_s1_R1.fastq.gz fli_gal4_uas_hlx_endo_48h_s1_R2.fastq.gz	fastq fastq	3459602100.0	23064014.0	fli gal4 uas hlx endo 48h s1 R1.fastq.gz	0:75 1:75	A:658343595;C:1050309687;G:1097759573;T:650443491;N:2745754	75	75	658343595	1050309687	1097759573	650443491	2745754	SRX2902570	SRS2269173	SRA573518	BRFAA\|Molecular Biology	BRFAA	2	0.57077	0.57481	0.2173	0.2185	0.79553	0.79762	0.50405	0.48708	75	75	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Greece	2017-06-13	Undetermined	Undetermined	Heart	Cardiovascular System
48625	48625	SRR7280652	SRX4184230	SRS3395609	SRP149913	PRJNA474911	Origin and Evolution of Neural Microexons	PRJNA474911	Other	Our study focuses on the origin of the neural microexon program.We discover that neural microexon programs are present in non vertebrate speciesand trace their origin to bilaterian ancestors through the emergenceof a previously uncharacterized "enhancer of microexon" eMIC protein domain			Telencephalon	Brain Telenc	strain:AB\|age:adult\|sex:pooled male and female\|tissue:Telencephalon\|BioSampleModel:Model organism or animal								RNA seq of Danio rerio: telencephalon	Brain Telenc	Brain Telenc	RNA from dissociated telencephalons of males and females			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina HiSeq 2500		SRP149913		Brain_Telenc_R1-125.fq.gz Brain_Telenc_R2-125.fq.gz	fastq fastq	71366993000.0	285467972.0	Brain Telenc R1 125.fq.gz	0:125 1:125	A:19965884492;C:15794543428;G:15865015134;T:19703234174;N:38315772	125	125	19965884492	15794543428	15865015134	19703234174	38315772	SRX4184230	SRS3395609	SRA717220	Centre for Genomic Regulation\|Systems Biology Department	Centre for Genomic Regulation	2	0.94146	0.94273	0.14194	0.14162	0.70167	0.70396	0.52125	0.51616	125	125	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Spain	2019-01-22	Adult	Adult	Brain	Nervous System
48626	48626	SRR7280653	SRX4184229	SRS3395610	SRP149913	PRJNA474911	Origin and Evolution of Neural Microexons	PRJNA474911	Other	Our study focuses on the origin of the neural microexon program.We discover that neural microexon programs are present in non vertebrate speciesand trace their origin to bilaterian ancestors through the emergenceof a previously uncharacterized "enhancer of microexon" eMIC protein domain			Cerebellum	Cerebellum	strain:AB\|age:adult\|sex:pooled male and female\|tissue:Cerebellum\|BioSampleModel:Model organism or animal								RNA seq of Danio rerio: cerebellum	Cerebellum	Cerebellum	RNA from dissociated cerebellum from males and females			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina HiSeq 2500		SRP149913		Cerebellum_R1-125.fq.gz Cerebellum_R2-125.fq.gz	fastq fastq	34135866750.0	136543467.0	Cerebellum R2 125.fq.gz	0:125 1:125	A:9659073468;C:7434102293;G:7478952142;T:9549216912;N:14521935	125	125	9659073468	7434102293	7478952142	9549216912	14521935	SRX4184229	SRS3395610	SRA717220	Centre for Genomic Regulation\|Systems Biology Department	Centre for Genomic Regulation	2	0.93517	0.93417	0.16496	0.16457	0.73695	0.73476	0.47363	0.48287	125	125	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Spain	2019-01-22	Adult	Adult	Brain	Nervous System
48627	48627	SRR7280654	SRX4184228	SRS3395608	SRP149913	PRJNA474911	Origin and Evolution of Neural Microexons	PRJNA474911	Other	Our study focuses on the origin of the neural microexon program.We discover that neural microexon programs are present in non vertebrate speciesand trace their origin to bilaterian ancestors through the emergenceof a previously uncharacterized "enhancer of microexon" eMIC protein domain		Pool of one hundred 2hpf embryos	2hpf embryos	Embr 2hpf	strain:AB\|dev stage:2hpf\|sex:pooled male and female\|tissue:whole body\|BioSampleModel:Model organism or animal								RNA seq of Danio rerio: 2hpf embryos	Embr 2hpf	Embr 2hpf	RNA extracted from a pool of one hundred embryos			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina HiSeq 2500		SRP149913		Embr_2hpf_R2-125.fq.gz Embr_2hpf_R1-125.fq.gz	fastq fastq	17109578000.0	68438312.0	Embr 2hpf R1 125.fq.gz	0:125 1:125	A:4536550134;C:4009266695;G:4076560218;T:4484964079;N:2236874	125	125	4536550134	4009266695	4076560218	4484964079	2236874	SRX4184228	SRS3395608	SRA717220	Centre for Genomic Regulation\|Systems Biology Department	Centre for Genomic Regulation	2	0.96221	0.96458	0.02765	0.02716	0.77116	0.77325	0.48649	0.4853	125	125	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Spain	2019-01-22	Cleavage	Embryo	Trunk	Surface Structure
48628	48628	SRR7280655	SRX4184227	SRS3395607	SRP149913	PRJNA474911	Origin and Evolution of Neural Microexons	PRJNA474911	Other	Our study focuses on the origin of the neural microexon program.We discover that neural microexon programs are present in non vertebrate speciesand trace their origin to bilaterian ancestors through the emergenceof a previously uncharacterized "enhancer of microexon" eMIC protein domain		Pool of one hundred 8hpf embryos	8hpf embryos	Embr 8hpf	strain:AB\|dev stage:8hpf\|sex:pooled male and female\|tissue:whole body\|BioSampleModel:Model organism or animal								RNA seq of Danio rerio: 8hpf embryos	Embr 8hpf	Embr 8hpf	RNA extracted from a pool of one hundred embryos			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina HiSeq 2500		SRP149913		Embr_8hpf_R1-125.fq.gz Embr_8hpf_R2-125.fq.gz	fastq fastq	20486524750.0	81946099.0	Embr 8hpf R2 125.fq.gz	0:125 1:125	A:5437735333;C:4808439456;G:4859422420;T:5377132981;N:3794560	125	125	5437735333	4808439456	4859422420	5377132981	3794560	SRX4184227	SRS3395607	SRA717220	Centre for Genomic Regulation\|Systems Biology Department	Centre for Genomic Regulation	2	0.96373	0.95763	0.07096	0.0702	0.75937	0.75866	0.48455	0.484	125	125	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Spain	2019-01-22	Gastrula	Embryo	Trunk	Surface Structure
48629	48629	SRR7280656	SRX4184226	SRS3395606	SRP149913	PRJNA474911	Origin and Evolution of Neural Microexons	PRJNA474911	Other	Our study focuses on the origin of the neural microexon program.We discover that neural microexon programs are present in non vertebrate speciesand trace their origin to bilaterian ancestors through the emergenceof a previously uncharacterized "enhancer of microexon" eMIC protein domain		Pool of one hundred 12hpf embryos	12hpf embryos	Embr 12hpf	strain:AB\|dev stage:12hpf\|sex:pooled male and female\|tissue:whole body\|BioSampleModel:Model organism or animal								RNA seq of Danio rerio: 12hpf embryos	Embr 12hpf	Embr 12hpf	RNA extracted from a pool of one hundred embryos			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina HiSeq 2500		SRP149913		Embr_12hpf_R2-125.fq.gz Embr_12hpf_R1-125.fq.gz	fastq fastq	22366284500.0	89465138.0	Embr 12hpf R1 125.fq.gz	0:125 1:125	A:5886492098;C:5284016845;G:5382041408;T:5809628253;N:4105896	125	125	5886492098	5284016845	5382041408	5809628253	4105896	SRX4184226	SRS3395606	SRA717220	Centre for Genomic Regulation\|Systems Biology Department	Centre for Genomic Regulation	2	0.96226	0.96763	0.06393	0.06451	0.74355	0.74472	0.48233	0.48387	125	125	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Spain	2019-01-22	Segmentation	Embryo	Trunk	Surface Structure
49091	49091	SRR7666344	SRX4527573	SRS3645455	SRP157045	PRJNA485433	Diurnal transcriptome of adult zebrafish eye	PRJNA485433	Other	Circadian rhythms orchestrate organism physiology to rhythmic changes in the environment with the daily day and night cycle being the most prominent cyclic change occurring. In this regard retina being a light responsive organ shows its vital physiological processes to be regulated by the clock. Here we report the diurnal transcriptome of zebrafish retina at Zt4day and Zt16night. We found 39% and 31% of the known genes to be expressed in retina at Zt4 and Zt16 respectively Reference genome Zv9. Also by applying stringent cutoff of 5FPKM we identified 123 transcripts to be expressed differentially between the two time points which contains few novel transcripts. In future this study will contribute to the understanding of organ and species specific regulation of circadian rhythms and will also provide novel genes involved in the circadian regulation of retina.				ZT4	strain:Assam wild type\|age:>3 month\|dev stage:adult\|sex:pooled male and female\|tissue:eye\|BioSampleModel:Model organism or animal								diurnal trancriptome of retina	ZT4 101nt	ZT4 101nt	total transcriptome with Truseq stranded library			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina HiSeq 2500		SRP157045		ZF_Eye_CT4_gt50_R1_P.fastq ZF_Eye_CT4_gt50_R2_P.fastq	fastq fastq	4550334348.0	22527137.0	ZF Eye CT4 gt50 R1 P.fastq	0:101.00 1:101.00	A:1196463938;C:1068045211;G:1064853438;T:1220233324;N:738437	101	101	1196463938	1068045211	1064853438	1220233324	738437	SRX4527573	SRS3645455	SRA756783	CSIR Insitute of Genomics and Integrative Biology\|Functional Genomics	CSIR Insitute of Genomics and Integrative Biology	2	0.92663	0.92909	0.33125	0.32333	0.70197	0.7013	0.55991	0.52684	101	101	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	India	2018-12-27	Adult	Adult	Eye	Sensory System
49092	49092	SRR7666345	SRX4527572	SRS3645456	SRP157045	PRJNA485433	Diurnal transcriptome of adult zebrafish eye	PRJNA485433	Other	Circadian rhythms orchestrate organism physiology to rhythmic changes in the environment with the daily day and night cycle being the most prominent cyclic change occurring. In this regard retina being a light responsive organ shows its vital physiological processes to be regulated by the clock. Here we report the diurnal transcriptome of zebrafish retina at Zt4day and Zt16night. We found 39% and 31% of the known genes to be expressed in retina at Zt4 and Zt16 respectively Reference genome Zv9. Also by applying stringent cutoff of 5FPKM we identified 123 transcripts to be expressed differentially between the two time points which contains few novel transcripts. In future this study will contribute to the understanding of organ and species specific regulation of circadian rhythms and will also provide novel genes involved in the circadian regulation of retina.				ZT16	strain:Assam wild type\|age:>3months\|dev stage:adult\|sex:pooled male and female\|tissue:eye\|BioSampleModel:Model organism or animal								diurnal transcriptome of retina	ZT16 101nt	ZT16 101nt	total transcriptome with Truseq stranded library			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina HiSeq 2500		SRP157045		ZF_Eye_CT016_gt50_R1_P.fastq ZF_Eye_CT016_gt50_R2_P.fastq	fastq fastq	14656436974.0	72560331.0	ZF Eye CT016 gt50 R1 P.fastq	0:100.99 1:100.99	A:3573626926;C:3724443056;G:3714836422;T:3641178568;N:2352002	100	100	3573626926	3724443056	3714836422	3641178568	2352002	SRX4527572	SRS3645456	SRA756783	CSIR Insitute of Genomics and Integrative Biology\|Functional Genomics	CSIR Insitute of Genomics and Integrative Biology	2	0.917	0.91899	0.27178	0.261	0.72135	0.72082	0.63885	0.63571	101	101	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	India	2018-08-10	Adult	Adult	Eye	Sensory System
49332	49332	SRR7888761	SRX4726390	SRS3810123	SRP162319	PRJNA492406	Profiles analysis reveals circRNAs involving zebrafish physiological development	GSE120289	Transcriptome Analysis	Recent studies have found that known functions of circRNAs include sequestration of microRNAs or proteins modulation of transcription and interference with splicing and even translation to produce poly peptides. The zebrafish model is also demonstrably similar to humans in many studies. In order to explore the changes in circRNAs during embryonic development further to research the mechanism of action of circRNAs in development related diseases. Zebrafish embryos at blastula period gastrula period segmentation period throat stage and incubation period were collected. Illumina deep sequencing technology and CIRI algorithm were used to detecting circRNAs. Totally we identified 1028 circRNAs junction reads = 5 and p < 0.05. Considering that circRNAs function is related to host genes then bioinformatics analysis revealed these differentially expressed host genes are involved in NOTCH signaling pathways cardiovascular system development retinal ganglion cell axon guidance and so on. Moreover circRNAs can participate in biological regulation through miRNA sponges function. TargetScan and miRanda were used to predict 73 miRNAs binding to circRNAs such as miR 19b miR 124 and so on some miRNAs play important roles in embryogenesis. The peak expression of circRNAs is distributed at different time points suggesting that it may be involved in embryogenesis at different stages. Our study provides a foundation for understanding the dynamic regulation of circRNA transcriptomes during embryogenesis and identifies novel key circRNAs that might control embryonic development in zebrafish model. Overall design: circRNAs of five periods blastula gastrula segmentation throat and incubation in zebrafish were detected by deep sequencing using Illumina HiSeq 2500.			72h	GSM3397729	source name:Embryo\|tissue:Embryo\|age:72 hpf\|developmental stage:incubation\|strain:Tubingenz\|genotype:WT	72h	Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to z10 whole genome using bwa 0.7.5a r405 with parameters "mem T 19". CircRNA prediction of sequencing results by CIRI algorithm v1.1. SRPBM Spliced Reads per Billion Mapped Reads=number of circular reads/number of mapped reads units in billion/read length used to normalize the expression of circRNAs. For differential expression analysis of circRNAs raw counts of reads that spanned a particular head to tail junction were analyzed using edgeR package version 3.12.1 with TMM normalization in generalized linear model. The Trimmed Mean of M values TMM normalization method was used to remove the size basis of sequencing libraries between samples. The following criteria were used to screen out significantly differentially expressed circRNAs: Fold change FC ≥2 and p< 0.05. Genome build: z10 Supplementary files format and content: tab delimited text files include SRPBM values and junction reads for each Sample.	Embryo	Zebrafish were reared at 28±1℃ in a water circulatory system that osmotic pressure stability UV disinfects and aerates the recycled water.The embryos were obtained post spontaneous mating from sexually mature wild type WT adult fish and cultivated at 28.5±0.5℃. Morphological features were used to judge the stage of embryonic development.	Total RNA was isolated using the standard TRIzol Invitrogen protocol Genomic DNA was removed by DNase treatment. Then the total RNA were subject to ribosomal RNA depletion according to the manufacturer’s protocol of RiboMinus kit Life Technology. The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bio analyzer. Strand specific libraries were constructed by following the manufacturer’s instructions Illumina	tissue:Embryo\|age:72 hpf\|developmental stage:incubation\|strain:Tubingenz\|genotype:WT	GSM3397729	GSM3397729: 72h; Danio rerio; ncRNA Seq	GSM3397729		1	Total RNA was isolated using the standard TRIzol Invitrogen protocol Genomic DNA was removed by DNase treatment. Then the total RNA were subject to ribosomal RNA depletion according to the manufacturer's protocol of RiboMinus kit Life Technology. The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bio analyzer. Strand specific libraries were constructed by following the manufacturer's instructions Illumina	GEO Accession:GSM3397729	ncRNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina HiSeq 2500		SRP162319		72h_1.fq.gz 72h_2.fq.gz	fastq fastq	12097159200.0	40323864.0	GSM3397729 r1	0:150 1:150	A:2809307023;C:3169515166;G:3184429517;T:2931448896;N:2458598	150	150	2809307023	3169515166	3184429517	2931448896	2458598	SRX4726390	SRS3810123	SRA781248	GEO	Department of Pediatrics, Nanjing Maternity and Child Health Care Hospital	2	0.90426	0.90717	0.27165	0.26439	0.70739	0.72397	0.60155	0.60561	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	China	2018-09-21	Larval	Larval	Embryo Imprecise	All anatomical structures
49333	49333	SRR7888760	SRX4726389	SRS3810122	SRP162319	PRJNA492406	Profiles analysis reveals circRNAs involving zebrafish physiological development	GSE120289	Transcriptome Analysis	Recent studies have found that known functions of circRNAs include sequestration of microRNAs or proteins modulation of transcription and interference with splicing and even translation to produce poly peptides. The zebrafish model is also demonstrably similar to humans in many studies. In order to explore the changes in circRNAs during embryonic development further to research the mechanism of action of circRNAs in development related diseases. Zebrafish embryos at blastula period gastrula period segmentation period throat stage and incubation period were collected. Illumina deep sequencing technology and CIRI algorithm were used to detecting circRNAs. Totally we identified 1028 circRNAs junction reads = 5 and p < 0.05. Considering that circRNAs function is related to host genes then bioinformatics analysis revealed these differentially expressed host genes are involved in NOTCH signaling pathways cardiovascular system development retinal ganglion cell axon guidance and so on. Moreover circRNAs can participate in biological regulation through miRNA sponges function. TargetScan and miRanda were used to predict 73 miRNAs binding to circRNAs such as miR 19b miR 124 and so on some miRNAs play important roles in embryogenesis. The peak expression of circRNAs is distributed at different time points suggesting that it may be involved in embryogenesis at different stages. Our study provides a foundation for understanding the dynamic regulation of circRNA transcriptomes during embryogenesis and identifies novel key circRNAs that might control embryonic development in zebrafish model. Overall design: circRNAs of five periods blastula gastrula segmentation throat and incubation in zebrafish were detected by deep sequencing using Illumina HiSeq 2500.			48h	GSM3397728	source name:Embryo\|tissue:Embryo\|age:48 hpf\|developmental stage:throat\|strain:Tubingenz\|genotype:WT	48h	Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to z10 whole genome using bwa 0.7.5a r405 with parameters "mem T 19". CircRNA prediction of sequencing results by CIRI algorithm v1.1. SRPBM Spliced Reads per Billion Mapped Reads=number of circular reads/number of mapped reads units in billion/read length used to normalize the expression of circRNAs. For differential expression analysis of circRNAs raw counts of reads that spanned a particular head to tail junction were analyzed using edgeR package version 3.12.1 with TMM normalization in generalized linear model. The Trimmed Mean of M values TMM normalization method was used to remove the size basis of sequencing libraries between samples. The following criteria were used to screen out significantly differentially expressed circRNAs: Fold change FC ≥2 and p< 0.05. Genome build: z10 Supplementary files format and content: tab delimited text files include SRPBM values and junction reads for each Sample.	Embryo	Zebrafish were reared at 28±1℃ in a water circulatory system that osmotic pressure stability UV disinfects and aerates the recycled water.The embryos were obtained post spontaneous mating from sexually mature wild type WT adult fish and cultivated at 28.5±0.5℃. Morphological features were used to judge the stage of embryonic development.	Total RNA was isolated using the standard TRIzol Invitrogen protocol Genomic DNA was removed by DNase treatment. Then the total RNA were subject to ribosomal RNA depletion according to the manufacturer’s protocol of RiboMinus kit Life Technology. The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bio analyzer. Strand specific libraries were constructed by following the manufacturer’s instructions Illumina	tissue:Embryo\|age:48 hpf\|developmental stage:throat\|strain:Tubingenz\|genotype:WT	GSM3397728	GSM3397728: 48h; Danio rerio; ncRNA Seq	GSM3397728		1	Total RNA was isolated using the standard TRIzol Invitrogen protocol Genomic DNA was removed by DNase treatment. Then the total RNA were subject to ribosomal RNA depletion according to the manufacturer's protocol of RiboMinus kit Life Technology. The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bio analyzer. Strand specific libraries were constructed by following the manufacturer's instructions Illumina	GEO Accession:GSM3397728	ncRNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina HiSeq 2500		SRP162319		48h_2.fq.gz 48h_1.fq.gz	fastq fastq	13525174500.0	45083915.0	GSM3397728 r1	0:150 1:150	A:2352542664;C:4312268007;G:4256218842;T:2601416951;N:2728036	150	150	2352542664	4312268007	4256218842	2601416951	2728036	SRX4726389	SRS3810122	SRA781248	GEO	Department of Pediatrics, Nanjing Maternity and Child Health Care Hospital	2	0.91614	0.91412	0.12891	0.12218	0.76751	0.77948	0.71008	0.73648	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	China	2018-09-21	Hatching	Embryo	Embryo Imprecise	All anatomical structures
49334	49334	SRR7888759	SRX4726388	SRS3810120	SRP162319	PRJNA492406	Profiles analysis reveals circRNAs involving zebrafish physiological development	GSE120289	Transcriptome Analysis	Recent studies have found that known functions of circRNAs include sequestration of microRNAs or proteins modulation of transcription and interference with splicing and even translation to produce poly peptides. The zebrafish model is also demonstrably similar to humans in many studies. In order to explore the changes in circRNAs during embryonic development further to research the mechanism of action of circRNAs in development related diseases. Zebrafish embryos at blastula period gastrula period segmentation period throat stage and incubation period were collected. Illumina deep sequencing technology and CIRI algorithm were used to detecting circRNAs. Totally we identified 1028 circRNAs junction reads = 5 and p < 0.05. Considering that circRNAs function is related to host genes then bioinformatics analysis revealed these differentially expressed host genes are involved in NOTCH signaling pathways cardiovascular system development retinal ganglion cell axon guidance and so on. Moreover circRNAs can participate in biological regulation through miRNA sponges function. TargetScan and miRanda were used to predict 73 miRNAs binding to circRNAs such as miR 19b miR 124 and so on some miRNAs play important roles in embryogenesis. The peak expression of circRNAs is distributed at different time points suggesting that it may be involved in embryogenesis at different stages. Our study provides a foundation for understanding the dynamic regulation of circRNA transcriptomes during embryogenesis and identifies novel key circRNAs that might control embryonic development in zebrafish model. Overall design: circRNAs of five periods blastula gastrula segmentation throat and incubation in zebrafish were detected by deep sequencing using Illumina HiSeq 2500.			24h	GSM3397727	source name:Embryo\|tissue:Embryo\|age:24 hpf\|developmental stage:segmentation\|strain:Tubingenz\|genotype:WT	24h	Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to z10 whole genome using bwa 0.7.5a r405 with parameters "mem T 19". CircRNA prediction of sequencing results by CIRI algorithm v1.1. SRPBM Spliced Reads per Billion Mapped Reads=number of circular reads/number of mapped reads units in billion/read length used to normalize the expression of circRNAs. For differential expression analysis of circRNAs raw counts of reads that spanned a particular head to tail junction were analyzed using edgeR package version 3.12.1 with TMM normalization in generalized linear model. The Trimmed Mean of M values TMM normalization method was used to remove the size basis of sequencing libraries between samples. The following criteria were used to screen out significantly differentially expressed circRNAs: Fold change FC ≥2 and p< 0.05. Genome build: z10 Supplementary files format and content: tab delimited text files include SRPBM values and junction reads for each Sample.	Embryo	Zebrafish were reared at 28±1℃ in a water circulatory system that osmotic pressure stability UV disinfects and aerates the recycled water.The embryos were obtained post spontaneous mating from sexually mature wild type WT adult fish and cultivated at 28.5±0.5℃. Morphological features were used to judge the stage of embryonic development.	Total RNA was isolated using the standard TRIzol Invitrogen protocol Genomic DNA was removed by DNase treatment. Then the total RNA were subject to ribosomal RNA depletion according to the manufacturer’s protocol of RiboMinus kit Life Technology. The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bio analyzer. Strand specific libraries were constructed by following the manufacturer’s instructions Illumina	tissue:Embryo\|age:24 hpf\|developmental stage:segmentation\|strain:Tubingenz\|genotype:WT	GSM3397727	GSM3397727: 24h; Danio rerio; ncRNA Seq	GSM3397727		1	Total RNA was isolated using the standard TRIzol Invitrogen protocol Genomic DNA was removed by DNase treatment. Then the total RNA were subject to ribosomal RNA depletion according to the manufacturer's protocol of RiboMinus kit Life Technology. The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bio analyzer. Strand specific libraries were constructed by following the manufacturer's instructions Illumina	GEO Accession:GSM3397727	ncRNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina HiSeq 2500		SRP162319		24h_1.fq.gz 24h_2.fq.gz	fastq fastq	14333175000.0	47777250.0	GSM3397727 r1	0:150 1:150	A:2728754113;C:4276840070;G:4344116037;T:2980570245;N:2894535	150	150	2728754113	4276840070	4344116037	2980570245	2894535	SRX4726388	SRS3810120	SRA781248	GEO	Department of Pediatrics, Nanjing Maternity and Child Health Care Hospital	2	0.89719	0.89478	0.18044	0.18119	0.76942	0.7876	0.75758	0.75366	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	China	2018-09-21	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
49335	49335	SRR7888758	SRX4726387	SRS3810121	SRP162319	PRJNA492406	Profiles analysis reveals circRNAs involving zebrafish physiological development	GSE120289	Transcriptome Analysis	Recent studies have found that known functions of circRNAs include sequestration of microRNAs or proteins modulation of transcription and interference with splicing and even translation to produce poly peptides. The zebrafish model is also demonstrably similar to humans in many studies. In order to explore the changes in circRNAs during embryonic development further to research the mechanism of action of circRNAs in development related diseases. Zebrafish embryos at blastula period gastrula period segmentation period throat stage and incubation period were collected. Illumina deep sequencing technology and CIRI algorithm were used to detecting circRNAs. Totally we identified 1028 circRNAs junction reads = 5 and p < 0.05. Considering that circRNAs function is related to host genes then bioinformatics analysis revealed these differentially expressed host genes are involved in NOTCH signaling pathways cardiovascular system development retinal ganglion cell axon guidance and so on. Moreover circRNAs can participate in biological regulation through miRNA sponges function. TargetScan and miRanda were used to predict 73 miRNAs binding to circRNAs such as miR 19b miR 124 and so on some miRNAs play important roles in embryogenesis. The peak expression of circRNAs is distributed at different time points suggesting that it may be involved in embryogenesis at different stages. Our study provides a foundation for understanding the dynamic regulation of circRNA transcriptomes during embryogenesis and identifies novel key circRNAs that might control embryonic development in zebrafish model. Overall design: circRNAs of five periods blastula gastrula segmentation throat and incubation in zebrafish were detected by deep sequencing using Illumina HiSeq 2500.			8h	GSM3397726	source name:Embryo\|tissue:Embryo\|age:8 hpf\|developmental stage:gastrula\|strain:Tubingenz\|genotype:WT	8h	Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to z10 whole genome using bwa 0.7.5a r405 with parameters "mem T 19". CircRNA prediction of sequencing results by CIRI algorithm v1.1. SRPBM Spliced Reads per Billion Mapped Reads=number of circular reads/number of mapped reads units in billion/read length used to normalize the expression of circRNAs. For differential expression analysis of circRNAs raw counts of reads that spanned a particular head to tail junction were analyzed using edgeR package version 3.12.1 with TMM normalization in generalized linear model. The Trimmed Mean of M values TMM normalization method was used to remove the size basis of sequencing libraries between samples. The following criteria were used to screen out significantly differentially expressed circRNAs: Fold change FC ≥2 and p< 0.05. Genome build: z10 Supplementary files format and content: tab delimited text files include SRPBM values and junction reads for each Sample.	Embryo	Zebrafish were reared at 28±1℃ in a water circulatory system that osmotic pressure stability UV disinfects and aerates the recycled water.The embryos were obtained post spontaneous mating from sexually mature wild type WT adult fish and cultivated at 28.5±0.5℃. Morphological features were used to judge the stage of embryonic development.	Total RNA was isolated using the standard TRIzol Invitrogen protocol Genomic DNA was removed by DNase treatment. Then the total RNA were subject to ribosomal RNA depletion according to the manufacturer’s protocol of RiboMinus kit Life Technology. The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bio analyzer. Strand specific libraries were constructed by following the manufacturer’s instructions Illumina	tissue:Embryo\|age:8 hpf\|developmental stage:gastrula\|strain:Tubingenz\|genotype:WT	GSM3397726	GSM3397726: 8h; Danio rerio; ncRNA Seq	GSM3397726		1	Total RNA was isolated using the standard TRIzol Invitrogen protocol Genomic DNA was removed by DNase treatment. Then the total RNA were subject to ribosomal RNA depletion according to the manufacturer's protocol of RiboMinus kit Life Technology. The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bio analyzer. Strand specific libraries were constructed by following the manufacturer's instructions Illumina	GEO Accession:GSM3397726	ncRNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina HiSeq 2500		SRP162319		8h_2.fq.gz 8h_1.fq.gz	fastq fastq	15434085600.0	51446952.0	GSM3397726 r1	0:150 1:150	A:2318158791;C:5134519748;G:5292209580;T:2686084369;N:3113112	150	150	2318158791	5134519748	5292209580	2686084369	3113112	SRX4726387	SRS3810121	SRA781248	GEO	Department of Pediatrics, Nanjing Maternity and Child Health Care Hospital	2	0.95788	0.95584	0.07233	0.07686	0.81889	0.82946	0.81383	0.80143	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	China	2018-09-21	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
49336	49336	SRR7888757	SRX4726386	SRS3810119	SRP162319	PRJNA492406	Profiles analysis reveals circRNAs involving zebrafish physiological development	GSE120289	Transcriptome Analysis	Recent studies have found that known functions of circRNAs include sequestration of microRNAs or proteins modulation of transcription and interference with splicing and even translation to produce poly peptides. The zebrafish model is also demonstrably similar to humans in many studies. In order to explore the changes in circRNAs during embryonic development further to research the mechanism of action of circRNAs in development related diseases. Zebrafish embryos at blastula period gastrula period segmentation period throat stage and incubation period were collected. Illumina deep sequencing technology and CIRI algorithm were used to detecting circRNAs. Totally we identified 1028 circRNAs junction reads = 5 and p < 0.05. Considering that circRNAs function is related to host genes then bioinformatics analysis revealed these differentially expressed host genes are involved in NOTCH signaling pathways cardiovascular system development retinal ganglion cell axon guidance and so on. Moreover circRNAs can participate in biological regulation through miRNA sponges function. TargetScan and miRanda were used to predict 73 miRNAs binding to circRNAs such as miR 19b miR 124 and so on some miRNAs play important roles in embryogenesis. The peak expression of circRNAs is distributed at different time points suggesting that it may be involved in embryogenesis at different stages. Our study provides a foundation for understanding the dynamic regulation of circRNA transcriptomes during embryogenesis and identifies novel key circRNAs that might control embryonic development in zebrafish model. Overall design: circRNAs of five periods blastula gastrula segmentation throat and incubation in zebrafish were detected by deep sequencing using Illumina HiSeq 2500.			4.5h	GSM3397725	source name:Embryo\|tissue:Embryo\|age:4.5 hpf\|developmental stage:blastula\|strain:Tubingenz\|genotype:WT	4.5h	Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to z10 whole genome using bwa 0.7.5a r405 with parameters "mem T 19". CircRNA prediction of sequencing results by CIRI algorithm v1.1. SRPBM Spliced Reads per Billion Mapped Reads=number of circular reads/number of mapped reads units in billion/read length used to normalize the expression of circRNAs. For differential expression analysis of circRNAs raw counts of reads that spanned a particular head to tail junction were analyzed using edgeR package version 3.12.1 with TMM normalization in generalized linear model. The Trimmed Mean of M values TMM normalization method was used to remove the size basis of sequencing libraries between samples. The following criteria were used to screen out significantly differentially expressed circRNAs: Fold change FC ≥2 and p< 0.05. Genome build: z10 Supplementary files format and content: tab delimited text files include SRPBM values and junction reads for each Sample.	Embryo	Zebrafish were reared at 28±1℃ in a water circulatory system that osmotic pressure stability UV disinfects and aerates the recycled water.The embryos were obtained post spontaneous mating from sexually mature wild type WT adult fish and cultivated at 28.5±0.5℃. Morphological features were used to judge the stage of embryonic development.	Total RNA was isolated using the standard TRIzol Invitrogen protocol Genomic DNA was removed by DNase treatment. Then the total RNA were subject to ribosomal RNA depletion according to the manufacturer’s protocol of RiboMinus kit Life Technology. The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bio analyzer. Strand specific libraries were constructed by following the manufacturer’s instructions Illumina	tissue:Embryo\|age:4.5 hpf\|developmental stage:blastula\|strain:Tubingenz\|genotype:WT	GSM3397725	GSM3397725: 4.5h; Danio rerio; ncRNA Seq	GSM3397725		1	Total RNA was isolated using the standard TRIzol Invitrogen protocol Genomic DNA was removed by DNase treatment. Then the total RNA were subject to ribosomal RNA depletion according to the manufacturer's protocol of RiboMinus kit Life Technology. The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bio analyzer. Strand specific libraries were constructed by following the manufacturer's instructions Illumina	GEO Accession:GSM3397725	ncRNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina HiSeq 2500		SRP162319		4_5h_2.fq.gz 4_5h_1.fq.gz	fastq fastq	12988242600.0	43294142.0	GSM3397725 r1	0:150 1:150	A:2232301074;C:3998769528;G:4233380689;T:2521224783;N:2566526	150	150	2232301074	3998769528	4233380689	2521224783	2566526	SRX4726386	SRS3810119	SRA781248	GEO	Department of Pediatrics, Nanjing Maternity and Child Health Care Hospital	2	0.96961	0.96817	0.05627	0.05463	0.77068	0.78198	0.74899	0.75759	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	China	2018-09-21	Blastula	Embryo	Embryo Imprecise	All anatomical structures
53507	53507	SRR9899207	SRX6651058	SRS5212730	SRP217299	PRJNA558506	Bmpr2b mutant zebrafish sequencing	PRJNA558506	Other	In order to explore the differential expression genes and related pathways caused by bmpr2b deletion in zebrafish. The comparative transcriptome analysis between wild and mutant samples was conducted.				zebrafish bmpr2b mutant	strain:AB zebrafish\|isolate:mutant\|breed:zebrafish\|cultivar:zebrafish\|ecotype:Wuhan China\|age:15 days\|dev stage:larval fish\|sex:unknown\|tissue:skeleton muscle\|BioSampleModel:Model organism or animal								RNA Seq of mutant fish	mutant1	mutant1	Total RNA was isolated from the 15 dpf dpf bmpr2b mutant larval fishes using RNAiso Plus Reagent TaKaRa China according to the manufacturers protocol. post RNA quality and quantity control the transcriptome equencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina NEB USA following manufacturers recommendations and index codes were added to attribute sequences to each sample.			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP217299		m1_1.fq.gz m1_2.fq.gz	fastq fastq	8332769700.0	27775899.0	m1 1.fq.gz	0:150 1:150	A:2157086519;C:2009631895;G:2036110721;T:2129846686;N:93879	150	150	2157086519	2009631895	2036110721	2129846686	93879	SRX6651058	SRS5212730	SRA932406	Huazhong Agricultural University\|College of Fisheries, Key Lab of Freshwater Animal	Huazhong Agricultural University	2	0.95476	0.95486	0.06414	0.06413	0.66115	0.66156	0.47619	0.47307	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	nebnext	bulk	unknown	unknown	China	2019-08-03	Larval	Larval	Muscle	Muscular System
53508	53508	SRR9899208	SRX6651057	SRS5212731	SRP217299	PRJNA558506	Bmpr2b mutant zebrafish sequencing	PRJNA558506	Other	In order to explore the differential expression genes and related pathways caused by bmpr2b deletion in zebrafish. The comparative transcriptome analysis between wild and mutant samples was conducted.				zebrafish wild	strain:AB zebrafish\|isolate:wild fish\|breed:zebrafish\|cultivar:zebrafish\|ecotype:Wuhan China\|age:15 days\|dev stage:larval fish\|sex:unknown\|tissue:skeleton muscle\|BioSampleModel:Model organism or animal								RNA Seq of wild fish	wild3	wild3	Total RNA was isolated from the 15 dpf dpf wild larval fishes using RNAiso Plus Reagent TaKaRa China according to the manufacturers protocol. post RNA quality and quantity control the transcriptome equencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina NEB USA following manufacturers recommendations and index codes were added to attribute sequences to each sample.			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP217299		w3_1.fq.gz w3_2.fq.gz	fastq fastq	8715170100.0	29050567.0	w3 1.fq.gz	0:150 1:150	A:2265881414;C:2090871457;G:2123814411;T:2234503490;N:99328	150	150	2265881414	2090871457	2123814411	2234503490	99328	SRX6651057	SRS5212731	SRA932406	Huazhong Agricultural University\|College of Fisheries, Key Lab of Freshwater Animal	Huazhong Agricultural University	2	0.95085	0.95146	0.06684	0.0667	0.65886	0.6588	0.47356	0.48005	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	nebnext	bulk	unknown	unknown	China	2019-08-03	Larval	Larval	Muscle	Muscular System
53509	53509	SRR9899209	SRX6651056	SRS5212731	SRP217299	PRJNA558506	Bmpr2b mutant zebrafish sequencing	PRJNA558506	Other	In order to explore the differential expression genes and related pathways caused by bmpr2b deletion in zebrafish. The comparative transcriptome analysis between wild and mutant samples was conducted.				zebrafish wild	strain:AB zebrafish\|isolate:wild fish\|breed:zebrafish\|cultivar:zebrafish\|ecotype:Wuhan China\|age:15 days\|dev stage:larval fish\|sex:unknown\|tissue:skeleton muscle\|BioSampleModel:Model organism or animal								RNA Seq of wild fish	wild2	wild2	Total RNA was isolated from the 15 dpf dpf wild larval fishes using RNAiso Plus Reagent TaKaRa China according to the manufacturers protocol. post RNA quality and quantity control the transcriptome equencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina NEB USA following manufacturers recommendations and index codes were added to attribute sequences to each sample.			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP217299		w2_1.fq.gz w2_2.fq.gz	fastq fastq	9346269600.0	31154232.0	w2 1.fq.gz	0:150 1:150	A:2421899244;C:2254190061;G:2283375277;T:2386698720;N:106298	150	150	2421899244	2254190061	2283375277	2386698720	106298	SRX6651056	SRS5212731	SRA932406	Huazhong Agricultural University\|College of Fisheries, Key Lab of Freshwater Animal	Huazhong Agricultural University	2	0.95445	0.95603	0.06361	0.06276	0.6616	0.66121	0.47635	0.47716	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	nebnext	bulk	unknown	unknown	China	2019-08-03	Larval	Larval	Muscle	Muscular System
53510	53510	SRR9899210	SRX6651055	SRS5212731	SRP217299	PRJNA558506	Bmpr2b mutant zebrafish sequencing	PRJNA558506	Other	In order to explore the differential expression genes and related pathways caused by bmpr2b deletion in zebrafish. The comparative transcriptome analysis between wild and mutant samples was conducted.				zebrafish wild	strain:AB zebrafish\|isolate:wild fish\|breed:zebrafish\|cultivar:zebrafish\|ecotype:Wuhan China\|age:15 days\|dev stage:larval fish\|sex:unknown\|tissue:skeleton muscle\|BioSampleModel:Model organism or animal								RNA Seq of wild fish	wild1	wild1	Total RNA was isolated from the 15 dpf dpf wild larval fishes using RNAiso Plus Reagent TaKaRa China according to the manufacturers protocol. post RNA quality and quantity control the transcriptome equencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina NEB USA following manufacturers recommendations and index codes were added to attribute sequences to each sample.			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP217299		w1_1.fq.gz w1_2.fq.gz	fastq fastq	8756101500.0	29187005.0	w1 1.fq.gz	0:150 1:150	A:2274557262;C:2102935324;G:2133197715;T:2245310628;N:100571	150	150	2274557262	2102935324	2133197715	2245310628	100571	SRX6651055	SRS5212731	SRA932406	Huazhong Agricultural University\|College of Fisheries, Key Lab of Freshwater Animal	Huazhong Agricultural University	2	0.95161	0.95225	0.06682	0.06678	0.65831	0.65993	0.47144	0.47166	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	nebnext	bulk	unknown	unknown	China	2019-08-03	Larval	Larval	Muscle	Muscular System
53511	53511	SRR9899211	SRX6651054	SRS5212730	SRP217299	PRJNA558506	Bmpr2b mutant zebrafish sequencing	PRJNA558506	Other	In order to explore the differential expression genes and related pathways caused by bmpr2b deletion in zebrafish. The comparative transcriptome analysis between wild and mutant samples was conducted.				zebrafish bmpr2b mutant	strain:AB zebrafish\|isolate:mutant\|breed:zebrafish\|cultivar:zebrafish\|ecotype:Wuhan China\|age:15 days\|dev stage:larval fish\|sex:unknown\|tissue:skeleton muscle\|BioSampleModel:Model organism or animal								RNA Seq of mutant fish	mutant3	mutant3	Total RNA was isolated from the 15 dpf dpf bmpr2b mutant larval fishes using RNAiso Plus Reagent TaKaRa China according to the manufacturers protocol. post RNA quality and quantity control the transcriptome equencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina NEB USA following manufacturers recommendations and index codes were added to attribute sequences to each sample.			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP217299		m3_1.fq.gz m3_2.fq.gz	fastq fastq	8385335400.0	27951118.0	m3 1.fq.gz	0:150 1:150	A:2179183324;C:2013493686;G:2044351918;T:2148211353;N:95119	150	150	2179183324	2013493686	2044351918	2148211353	95119	SRX6651054	SRS5212730	SRA932406	Huazhong Agricultural University\|College of Fisheries, Key Lab of Freshwater Animal	Huazhong Agricultural University	2	0.94884	0.94904	0.0643	0.06403	0.66145	0.66316	0.46951	0.4767	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	nebnext	bulk	unknown	unknown	China	2019-08-03	Larval	Larval	Muscle	Muscular System
53512	53512	SRR9899212	SRX6651053	SRS5212730	SRP217299	PRJNA558506	Bmpr2b mutant zebrafish sequencing	PRJNA558506	Other	In order to explore the differential expression genes and related pathways caused by bmpr2b deletion in zebrafish. The comparative transcriptome analysis between wild and mutant samples was conducted.				zebrafish bmpr2b mutant	strain:AB zebrafish\|isolate:mutant\|breed:zebrafish\|cultivar:zebrafish\|ecotype:Wuhan China\|age:15 days\|dev stage:larval fish\|sex:unknown\|tissue:skeleton muscle\|BioSampleModel:Model organism or animal								RNA Seq of mutant fish	mutant2	mutant2	Total RNA was isolated from the 15 dpf dpf bmpr2b mutant larval fishes using RNAiso Plus Reagent TaKaRa China according to the manufacturers protocol. post RNA quality and quantity control the transcriptome equencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina NEB USA following manufacturers recommendations and index codes were added to attribute sequences to each sample.			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP217299		m2_1.fq.gz m2_2.fq.gz	fastq fastq	8728240500.0	29094135.0	m2 1.fq.gz	0:150 1:150	A:2262292258;C:2101600854;G:2129980194;T:2234266968;N:100226	150	150	2262292258	2101600854	2129980194	2234266968	100226	SRX6651053	SRS5212730	SRA932406	Huazhong Agricultural University\|College of Fisheries, Key Lab of Freshwater Animal	Huazhong Agricultural University	2	0.95297	0.95358	0.06449	0.06417	0.65965	0.65918	0.47932	0.4645	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	nebnext	bulk	unknown	unknown	China	2019-08-03	Larval	Larval	Muscle	Muscular System
55379	55379	SRR10323881	SRX7034716	SRS5554730	SRP226614	PRJNA578896	Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence	PRJNA578896	Other	In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.				danRer10 raw data	strain:AB/tu\|age:not applicable\|sex:pooled male and female\|tissue:endothelial and hemogenic endothelial\|BioSampleModel:Model organism or animal								RNA seq control for lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2	10	10	NEBNext Low Input RNA Library Prep Kit			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina HiSeq 3000		SRP226614		RNA_seq control for lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R1.fastq.gz RNA_seq control for lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R2.fastq.gz	fastq fastq	3356658750.0	22377725.0	RNA seq control for lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2 R1.fastq.gz	0:75 1:75	A:875300673;C:782517555;G:796855605;T:901672776;N:312141	75	75	875300673	782517555	796855605	901672776	312141	SRX7034716	SRS5554730	SRA983011	Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany\|Department of Cellular and Molecular Immunology	Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany	2	0.68437	0.73326	0.04743	0.05194	0.80241	0.80517	0.51875	0.52196	75	75	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Germany	2019-10-24	Pharyngula	Embryo	Endothelium	Cardiovascular System
55380	55380	SRR10323882	SRX7034715	SRS5554730	SRP226614	PRJNA578896	Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence	PRJNA578896	Other	In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.				danRer10 raw data	strain:AB/tu\|age:not applicable\|sex:pooled male and female\|tissue:endothelial and hemogenic endothelial\|BioSampleModel:Model organism or animal								RNA seq control for lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1	9	9	NEBNext Low Input RNA Library Prep Kit			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina HiSeq 3000		SRP226614		RNA_seq control for lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R2.fastq.gz RNA_seq control for lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R1.fastq.gz	fastq fastq	3459242400.0	23061616.0	RNA seq control for lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1 R1.fastq.gz	0:75 1:75	A:924400584;C:762078140;G:779330250;T:993109509;N:323917	75	75	924400584	762078140	779330250	993109509	323917	SRX7034715	SRS5554730	SRA983011	Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany\|Department of Cellular and Molecular Immunology	Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany	2	0.67032	0.73764	0.07629	0.08303	0.80856	0.80748	0.52094	0.52695	75	75	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Germany	2019-10-24	Pharyngula	Embryo	Endothelium	Cardiovascular System
55381	55381	SRR10323883	SRX7034714	SRS5554730	SRP226614	PRJNA578896	Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence	PRJNA578896	Other	In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.				danRer10 raw data	strain:AB/tu\|age:not applicable\|sex:pooled male and female\|tissue:endothelial and hemogenic endothelial\|BioSampleModel:Model organism or animal								RNA seq mda5 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2	8	8	NEBNext Low Input RNA Library Prep Kit			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina HiSeq 3000		SRP226614		RNA_seq mda5 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R1.fastq.gz RNA_seq mda5 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R2.fastq.gz	fastq fastq	3238312500.0	21588750.0	RNA seq mda5 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2 R1.fastq.gz	0:75 1:75	A:881635390;C:656958401;G:673596788;T:1025824968;N:296953	75	75	881635390	656958401	673596788	1025824968	296953	SRX7034714	SRS5554730	SRA983011	Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany\|Department of Cellular and Molecular Immunology	Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany	2	0.59623	0.72377	0.07781	0.08944	0.80608	0.8016	0.53277	0.53095	75	75	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Germany	2019-10-24	Pharyngula	Embryo	Endothelium	Cardiovascular System
55382	55382	SRR10323884	SRX7034713	SRS5554730	SRP226614	PRJNA578896	Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence	PRJNA578896	Other	In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.				danRer10 raw data	strain:AB/tu\|age:not applicable\|sex:pooled male and female\|tissue:endothelial and hemogenic endothelial\|BioSampleModel:Model organism or animal								RNA seq mda5 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1	7	7	NEBNext Low Input RNA Library Prep Kit			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina HiSeq 3000		SRP226614		RNA_seq mda5 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R1.fastq.gz RNA_seq mda5 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R2.fastq.gz	fastq fastq	3255021150.0	21700141.0	RNA seq mda5 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1 R1.fastq.gz	0:75 1:75	A:858912760;C:733048670;G:750496371;T:912263495;N:299854	75	75	858912760	733048670	750496371	912263495	299854	SRX7034713	SRS5554730	SRA983011	Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany\|Department of Cellular and Molecular Immunology	Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany	2	0.65481	0.71883	0.05477	0.05995	0.7903	0.7921	0.51367	0.51188	75	75	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Germany	2019-10-24	Pharyngula	Embryo	Endothelium	Cardiovascular System
55383	55383	SRR10323885	SRX7034712	SRS5554730	SRP226614	PRJNA578896	Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence	PRJNA578896	Other	In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.				danRer10 raw data	strain:AB/tu\|age:not applicable\|sex:pooled male and female\|tissue:endothelial and hemogenic endothelial\|BioSampleModel:Model organism or animal								RNA seq control for mda5 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2	6	6	NEBNext Low Input RNA Library Prep Kit			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina HiSeq 3000		SRP226614		RNA_seq control for mda5 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R2.fastq.gz RNA_seq control for mda5 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R1.fastq.gz	fastq fastq	2413394850.0	16089299.0	RNA seq control for mda5 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2 R1.fastq.gz	0:75 1:75	A:660807483;C:490677840;G:505039519;T:756646234;N:223774	75	75	660807483	490677840	505039519	756646234	223774	SRX7034712	SRS5554730	SRA983011	Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany\|Department of Cellular and Molecular Immunology	Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany	2	0.60009	0.72319	0.09185	0.10528	0.82175	0.81815	0.5234	0.51725	75	75	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Germany	2019-10-24	Pharyngula	Embryo	Endothelium	Cardiovascular System
55384	55384	SRR10323886	SRX7034711	SRS5554730	SRP226614	PRJNA578896	Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence	PRJNA578896	Other	In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.				danRer10 raw data	strain:AB/tu\|age:not applicable\|sex:pooled male and female\|tissue:endothelial and hemogenic endothelial\|BioSampleModel:Model organism or animal								RNA seq control for mda5 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1	5	5	NEBNext Low Input RNA Library Prep Kit			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina HiSeq 3000		SRP226614		RNA_seq control for mda5 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R1.fastq.gz RNA_seq control for mda5 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R2.fastq.gz	fastq fastq	3124357200.0	20829048.0	RNA seq control for mda5 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1 R1.fastq.gz	0:75 1:75	A:844721216;C:673572690;G:689308705;T:916479849;N:274740	75	75	844721216	673572690	689308705	916479849	274740	SRX7034711	SRS5554730	SRA983011	Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany\|Department of Cellular and Molecular Immunology	Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany	2	0.66396	0.73861	0.09392	0.10351	0.80856	0.80797	0.53225	0.5369	75	75	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Germany	2019-10-24	Pharyngula	Embryo	Endothelium	Cardiovascular System
55385	55385	SRR10323891	SRX7034706	SRS5554730	SRP226614	PRJNA578896	Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence	PRJNA578896	Other	In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.				danRer10 raw data	strain:AB/tu\|age:not applicable\|sex:pooled male and female\|tissue:endothelial and hemogenic endothelial\|BioSampleModel:Model organism or animal								RNA seq rig 1 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2	4	4	NEBNext Low Input RNA Library Prep Kit			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina HiSeq 3000		SRP226614		RNA_seq rig_1 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R2.fastq.gz RNA_seq rig_1 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R1.fastq.gz	fastq fastq	2812593000.0	18750620.0	RNA seq rig 1 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2 R1.fastq.gz	0:75 1:75	A:759189725;C:611361876;G:625876145;T:815905469;N:259785	75	75	759189725	611361876	625876145	815905469	259785	SRX7034706	SRS5554730	SRA983011	Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany\|Department of Cellular and Molecular Immunology	Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany	2	0.63609	0.70403	0.08285	0.0932	0.79847	0.79959	0.52487	0.52941	75	75	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Germany	2019-10-24	Pharyngula	Embryo	Endothelium	Cardiovascular System
55386	55386	SRR10323898	SRX7034699	SRS5554730	SRP226614	PRJNA578896	Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence	PRJNA578896	Other	In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.				danRer10 raw data	strain:AB/tu\|age:not applicable\|sex:pooled male and female\|tissue:endothelial and hemogenic endothelial\|BioSampleModel:Model organism or animal								RNA seq decitabine treatment in hemogenic endothelial cell 26hpf replicate 2	24	24	NEBNext Low Input RNA Library Prep Kit			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina HiSeq 3000		SRP226614		RNA_seq decitabine treatment in hemogenic endothelial cell 26hpf replicate 2_R2.fastq.gz RNA_seq decitabine treatment in hemogenic endothelial cell 26hpf replicate 2_R1.fastq.gz	fastq fastq	5849571450.0	38997143.0	RNA seq decitabine treatment in hemogenic endothelial cell 26hpf replicate 2 R1.fastq.gz	0:75 1:75	A:1574421853;C:1316832574;G:1315527058;T:1642305644;N:484321	75	75	1574421853	1316832574	1315527058	1642305644	484321	SRX7034699	SRS5554730	SRA983011	Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany\|Department of Cellular and Molecular Immunology	Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany	2	0.78221	0.84034	0.0684	0.07089	0.76607	0.77025	0.50712	0.50772	75	75	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Germany	2019-10-24	Pharyngula	Embryo	Endothelium	Cardiovascular System
55387	55387	SRR10323899	SRX7034698	SRS5554730	SRP226614	PRJNA578896	Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence	PRJNA578896	Other	In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.				danRer10 raw data	strain:AB/tu\|age:not applicable\|sex:pooled male and female\|tissue:endothelial and hemogenic endothelial\|BioSampleModel:Model organism or animal								RNA seq decitabine treatment in hemogenic endothelial cell 26hpf replicate 1	23	23	NEBNext Low Input RNA Library Prep Kit			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina HiSeq 3000		SRP226614		RNA_seq decitabine treatment in hemogenic endothelial cell 26hpf replicate 1_R1.fastq.gz RNA_seq decitabine treatment in hemogenic endothelial cell 26hpf replicate 1_R2.fastq.gz	fastq fastq	5656815000.0	37712100.0	RNA seq decitabine treatment in hemogenic endothelial cell 26hpf replicate 1 R1.fastq.gz	0:75 1:75	A:1487198866;C:1332723090;G:1275197163;T:1514410765;N:47285116	75	75	1487198866	1332723090	1275197163	1514410765	47285116	SRX7034698	SRS5554730	SRA983011	Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany\|Department of Cellular and Molecular Immunology	Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany	2	0.86399	0.76012	0.0587	0.05779	0.76461	0.9105	0.49754	0.51037	75	75	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Germany	2019-10-24	Pharyngula	Embryo	Endothelium	Cardiovascular System
55388	55388	SRR10323900	SRX7034697	SRS5554730	SRP226614	PRJNA578896	Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence	PRJNA578896	Other	In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.				danRer10 raw data	strain:AB/tu\|age:not applicable\|sex:pooled male and female\|tissue:endothelial and hemogenic endothelial\|BioSampleModel:Model organism or animal								RNA seq VPA treatment in hemogenic endothelial cell 26hpf replicate 2	22	22	NEBNext Low Input RNA Library Prep Kit			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina HiSeq 3000		SRP226614		RNA_seq VPA treatment in hemogenic endothelial cell 26hpf replicate 2_R2.fastq.gz RNA_seq VPA treatment in hemogenic endothelial cell 26hpf replicate 2_R1.fastq.gz	fastq fastq	5978780250.0	39858535.0	RNA seq VPA treatment in hemogenic endothelial cell 26hpf replicate 2 R1.fastq.gz	0:75 1:75	A:1580804547;C:1404640964;G:1399714637;T:1593586843;N:33259	75	75	1580804547	1404640964	1399714637	1593586843	33259	SRX7034697	SRS5554730	SRA983011	Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany\|Department of Cellular and Molecular Immunology	Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany	2	0.92216	0.92477	0.04155	0.04126	0.74537	0.7512	0.48148	0.49049	75	75	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Germany	2019-10-24	Pharyngula	Embryo	Endothelium	Cardiovascular System
55389	55389	SRR10323901	SRX7034696	SRS5554730	SRP226614	PRJNA578896	Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence	PRJNA578896	Other	In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.				danRer10 raw data	strain:AB/tu\|age:not applicable\|sex:pooled male and female\|tissue:endothelial and hemogenic endothelial\|BioSampleModel:Model organism or animal								RNA seq VPA or decitabine treatment in hemogenic endothelial cell 26hpf replicate 1	21	21	NEBNext Low Input RNA Library Prep Kit			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina HiSeq 3000		SRP226614		RNA_seq VPA treatment in hemogenic endothelial cell 26hpf replicate 1_R1.fastq.gz RNA_seq VPA treatment in hemogenic endothelial cell 26hpf replicate 1_R2.fastq.gz	fastq fastq	8777730900.0	58518206.0	RNA seq VPA treatment in hemogenic endothelial cell 26hpf replicate 1 R1.fastq.gz	0:75 1:75	A:2331650285;C:2053244561;G:2042022053;T:2350762388;N:51613	75	75	2331650285	2053244561	2042022053	2350762388	51613	SRX7034696	SRS5554730	SRA983011	Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany\|Department of Cellular and Molecular Immunology	Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany	2	0.92143	0.92455	0.04604	0.04567	0.73361	0.73923	0.4802	0.48613	75	75	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Germany	2019-10-24	Pharyngula	Embryo	Endothelium	Cardiovascular System
55390	55390	SRR10323902	SRX7034695	SRS5554730	SRP226614	PRJNA578896	Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence	PRJNA578896	Other	In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.				danRer10 raw data	strain:AB/tu\|age:not applicable\|sex:pooled male and female\|tissue:endothelial and hemogenic endothelial\|BioSampleModel:Model organism or animal								RNA seq rig 1 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1	3	3	NEBNext Low Input RNA Library Prep Kit			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina HiSeq 3000		SRP226614		RNA_seq rig_1 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R1.fastq.gz RNA_seq rig_1 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R2.fastq.gz	fastq fastq	3613041150.0	24086941.0	RNA seq rig 1 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1 R1.fastq.gz	0:75 1:75	A:972417798;C:795483066;G:808300399;T:1036510724;N:329163	75	75	972417798	795483066	808300399	1036510724	329163	SRX7034695	SRS5554730	SRA983011	Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany\|Department of Cellular and Molecular Immunology	Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany	2	0.66853	0.7231	0.08329	0.0907	0.78953	0.79131	0.51481	0.52637	75	75	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Germany	2019-10-24	Pharyngula	Embryo	Endothelium	Cardiovascular System
55391	55391	SRR10323903	SRX7034694	SRS5554730	SRP226614	PRJNA578896	Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence	PRJNA578896	Other	In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.				danRer10 raw data	strain:AB/tu\|age:not applicable\|sex:pooled male and female\|tissue:endothelial and hemogenic endothelial\|BioSampleModel:Model organism or animal								RNA seq control for VPA or decitabine treatment in hemogenic endothelial cell 26hpf replicate 2	20	20	NEBNext Low Input RNA Library Prep Kit			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina HiSeq 3000		SRP226614		RNA_seq control for VPA_or_decitabine treatment in hemogenic endothelial cell 26hpf replicate 2_R1.fastq.gz RNA_seq control for VPA_or_decitabine treatment in hemogenic endothelial cell 26hpf replicate 2_R2.fastq.gz	fastq fastq	7211828100.0	48078854.0	RNA seq control for VPA or decitabine treatment in hemogenic endothelial cell 26hpf replicate 2 R1.fastq.gz	0:75 1:75	A:1904350731;C:1693709371;G:1687946675;T:1925778331;N:42992	75	75	1904350731	1693709371	1687946675	1925778331	42992	SRX7034694	SRS5554730	SRA983011	Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany\|Department of Cellular and Molecular Immunology	Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany	2	0.91819	0.92224	0.03958	0.03841	0.75584	0.76161	0.46923	0.46415	75	75	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Germany	2019-10-24	Pharyngula	Embryo	Endothelium	Cardiovascular System
55392	55392	SRR10323904	SRX7034693	SRS5554730	SRP226614	PRJNA578896	Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence	PRJNA578896	Other	In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.				danRer10 raw data	strain:AB/tu\|age:not applicable\|sex:pooled male and female\|tissue:endothelial and hemogenic endothelial\|BioSampleModel:Model organism or animal								RNA seq control for VPA treatment in hemogenic endothelial cell 26hpf replicate 1	19	19	NEBNext Low Input RNA Library Prep Kit			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina HiSeq 3000		SRP226614		RNA_seq control for VPA_or_decitabine treatment in hemogenic endothelial cell 26hpf replicate 1_R1.fastq.gz RNA_seq control for VPA_or_decitabine treatment in hemogenic endothelial cell 26hpf replicate 1_R2.fastq.gz	fastq fastq	8021297850.0	53475319.0	RNA seq control for VPA or decitabine treatment in hemogenic endothelial cell 26hpf replicate 1 R1.fastq.gz	0:75 1:75	A:2121666298;C:1880005094;G:1872358379;T:2147221627;N:46452	75	75	2121666298	1880005094	1872358379	2147221627	46452	SRX7034693	SRS5554730	SRA983011	Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany\|Department of Cellular and Molecular Immunology	Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany	2	0.91273	0.91897	0.0437	0.04345	0.75485	0.76037	0.46259	0.47199	75	75	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Germany	2019-10-24	Pharyngula	Embryo	Endothelium	Cardiovascular System
55393	55393	SRR10323905	SRX7034692	SRS5554730	SRP226614	PRJNA578896	Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence	PRJNA578896	Other	In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.				danRer10 raw data	strain:AB/tu\|age:not applicable\|sex:pooled male and female\|tissue:endothelial and hemogenic endothelial\|BioSampleModel:Model organism or animal								RNA seq mda5 lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2	18	18	TruSeq stranded mRNA			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina HiSeq 3000		SRP226614		RNA_seq mda5_lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R1.fastq.gz RNA_seq mda5_lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R2.fastq.gz	fastq fastq	4925792850.0	32838619.0	RNA seq mda5 lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2 R1.fastq.gz	0:75 1:75	A:1327496924;C:1143172265;G:1121827107;T:1332765205;N:531349	75	75	1327496924	1143172265	1121827107	1332765205	531349	SRX7034692	SRS5554730	SRA983011	Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany\|Department of Cellular and Molecular Immunology	Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany	2	0.9235	0.923	0.07189	0.07157	0.74576	0.7486	0.46424	0.46997	75	75	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	Germany	2019-10-24	Pharyngula	Embryo	Endothelium	Cardiovascular System
55394	55394	SRR10323906	SRX7034691	SRS5554730	SRP226614	PRJNA578896	Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence	PRJNA578896	Other	In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.				danRer10 raw data	strain:AB/tu\|age:not applicable\|sex:pooled male and female\|tissue:endothelial and hemogenic endothelial\|BioSampleModel:Model organism or animal								RNA seq mda5 lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1	17	17	TruSeq stranded mRNA			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina HiSeq 3000		SRP226614		RNA_seq mda5_lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R1.fastq.gz RNA_seq mda5_lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R2.fastq.gz	fastq fastq	4481194200.0	29874628.0	RNA seq mda5 lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1 R1.fastq.gz	0:75 1:75	A:1207561849;C:1040055195;G:1022613796;T:1210492037;N:471323	75	75	1207561849	1040055195	1022613796	1210492037	471323	SRX7034691	SRS5554730	SRA983011	Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany\|Department of Cellular and Molecular Immunology	Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany	2	0.92094	0.92157	0.07292	0.07281	0.74704	0.75067	0.47205	0.47416	75	75	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	Germany	2019-10-24	Pharyngula	Embryo	Endothelium	Cardiovascular System
55395	55395	SRR10323907	SRX7034690	SRS5554730	SRP226614	PRJNA578896	Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence	PRJNA578896	Other	In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.				danRer10 raw data	strain:AB/tu\|age:not applicable\|sex:pooled male and female\|tissue:endothelial and hemogenic endothelial\|BioSampleModel:Model organism or animal								RNA seq rig 1 lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2	16	16	TruSeq stranded mRNA			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina HiSeq 3000		SRP226614		RNA_seq rig_1_lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R2.fastq.gz RNA_seq rig_1_lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R1.fastq.gz	fastq fastq	2071385250.0	13809235.0	RNA seq rig 1 lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2 R1.fastq.gz	0:75 1:75	A:497024628;C:535934066;G:538798491;T:499539772;N:88293	75	75	497024628	535934066	538798491	499539772	88293	SRX7034690	SRS5554730	SRA983011	Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany\|Department of Cellular and Molecular Immunology	Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany	2	0.92507	0.92563	0.0745	0.07106	0.74148	0.74186	0.5137	0.52923	75	75	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	Germany	2019-10-24	Pharyngula	Embryo	Endothelium	Cardiovascular System
55396	55396	SRR10323908	SRX7034689	SRS5554730	SRP226614	PRJNA578896	Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence	PRJNA578896	Other	In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.				danRer10 raw data	strain:AB/tu\|age:not applicable\|sex:pooled male and female\|tissue:endothelial and hemogenic endothelial\|BioSampleModel:Model organism or animal								RNA seq rig 1 lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1	15	15	TruSeq stranded mRNA			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina HiSeq 3000		SRP226614		RNA_seq rig_1_lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R1.fastq.gz RNA_seq rig_1_lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R2.fastq.gz	fastq fastq	1708336800.0	11388912.0	RNA seq rig 1 lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1 R1.fastq.gz	0:75 1:75	A:413739883;C:438115098;G:440441368;T:415968029;N:72422	75	75	413739883	438115098	440441368	415968029	72422	SRX7034689	SRS5554730	SRA983011	Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany\|Department of Cellular and Molecular Immunology	Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany	2	0.92948	0.93123	0.08112	0.07757	0.7472	0.74921	0.49384	0.502	75	75	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	Germany	2019-10-24	Pharyngula	Embryo	Endothelium	Cardiovascular System
55397	55397	SRR10323909	SRX7034688	SRS5554730	SRP226614	PRJNA578896	Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence	PRJNA578896	Other	In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.				danRer10 raw data	strain:AB/tu\|age:not applicable\|sex:pooled male and female\|tissue:endothelial and hemogenic endothelial\|BioSampleModel:Model organism or animal								RNA seq control for double morphants endothelial hemogenic endothelial cell 26hpf replicate 2	14	14	TruSeq stranded mRNA			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina HiSeq 3000		SRP226614		RNA_seq control for double morphants endothelial_hemogenic endothelial cell 26hpf replicate 2_R1.fastq.gz RNA_seq control for double morphants endothelial_hemogenic endothelial cell 26hpf replicate 2_R2.fastq.gz	fastq fastq	2742841800.0	18285612.0	RNA seq control for double morphants endothelial hemogenic endothelial cell 26hpf replicate 2 R1.fastq.gz	0:75 1:75	A:771268784;C:600759252;G:605972112;T:764554978;N:286674	75	75	771268784	600759252	605972112	764554978	286674	SRX7034688	SRS5554730	SRA983011	Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany\|Department of Cellular and Molecular Immunology	Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany	2	0.91195	0.91276	0.15552	0.15531	0.7191	0.7247	0.487	0.47379	75	75	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	Germany	2019-10-24	Pharyngula	Embryo	Endothelium	Cardiovascular System
55398	55398	SRR10323910	SRX7034687	SRS5554730	SRP226614	PRJNA578896	Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence	PRJNA578896	Other	In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.				danRer10 raw data	strain:AB/tu\|age:not applicable\|sex:pooled male and female\|tissue:endothelial and hemogenic endothelial\|BioSampleModel:Model organism or animal								RNA seq control for double morphants endothelial hemogenic endothelial cell 26hpf replicate 1	13	13	TruSeq stranded mRNA			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina HiSeq 3000		SRP226614		RNA_seq control for double morphants endothelial_hemogenic endothelial cell 26hpf replicate 1_R1.fastq.gz RNA_seq control for double morphants endothelial_hemogenic endothelial cell 26hpf replicate 1_R2.fastq.gz	fastq fastq	1909021350.0	12726809.0	RNA seq control for double morphants endothelial hemogenic endothelial cell 26hpf replicate 1 R1.fastq.gz	0:75 1:75	A:536542827;C:420010389;G:423642042;T:528630203;N:195889	75	75	536542827	420010389	423642042	528630203	195889	SRX7034687	SRS5554730	SRA983011	Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany\|Department of Cellular and Molecular Immunology	Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany	2	0.91535	0.91534	0.11578	0.11457	0.73705	0.74373	0.47609	0.47115	75	75	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	Germany	2019-10-24	Pharyngula	Embryo	Endothelium	Cardiovascular System
55399	55399	SRR10323911	SRX7034686	SRS5554730	SRP226614	PRJNA578896	Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence	PRJNA578896	Other	In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.				danRer10 raw data	strain:AB/tu\|age:not applicable\|sex:pooled male and female\|tissue:endothelial and hemogenic endothelial\|BioSampleModel:Model organism or animal								RNA seq lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2	12	12	NEBNext Low Input RNA Library Prep Kit			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina HiSeq 3000		SRP226614		RNA_seq lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R1.fastq.gz RNA_seq lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R2.fastq.gz	fastq fastq	5135290500.0	34235270.0	RNA seq lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2 R1.fastq.gz	0:75 1:75	A:1339180940;C:1202946694;G:1230552771;T:1362120185;N:489910	75	75	1339180940	1202946694	1230552771	1362120185	489910	SRX7034686	SRS5554730	SRA983011	Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany\|Department of Cellular and Molecular Immunology	Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany	2	0.66031	0.70687	0.04575	0.04896	0.81075	0.81195	0.50951	0.47552	75	75	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Germany	2019-10-24	Pharyngula	Embryo	Endothelium	Cardiovascular System
55400	55400	SRR10323912	SRX7034685	SRS5554730	SRP226614	PRJNA578896	Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence	PRJNA578896	Other	In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.				danRer10 raw data	strain:AB/tu\|age:not applicable\|sex:pooled male and female\|tissue:endothelial and hemogenic endothelial\|BioSampleModel:Model organism or animal								RNA seq lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1	11	11	NEBNext Low Input RNA Library Prep Kit			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina HiSeq 3000		SRP226614		RNA_seq lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R1.fastq.gz RNA_seq lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R2.fastq.gz	fastq fastq	3890046300.0	25933642.0	RNA seq lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1 R1.fastq.gz	0:75 1:75	A:1020376762;C:903218301;G:916043426;T:1050047618;N:360193	75	75	1020376762	903218301	916043426	1050047618	360193	SRX7034685	SRS5554730	SRA983011	Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany\|Department of Cellular and Molecular Immunology	Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany	2	0.70733	0.75223	0.05929	0.06271	0.80807	0.81071	0.48475	0.49323	75	75	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Germany	2019-10-24	Pharyngula	Embryo	Endothelium	Cardiovascular System
55401	55401	SRR10323913	SRX7034684	SRS5554730	SRP226614	PRJNA578896	Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence	PRJNA578896	Other	In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.				danRer10 raw data	strain:AB/tu\|age:not applicable\|sex:pooled male and female\|tissue:endothelial and hemogenic endothelial\|BioSampleModel:Model organism or animal								RNA seq control for rig 1 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2	2	2	NEBNext Low Input RNA Library Prep Kit			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina HiSeq 3000		SRP226614		RNA_seq control for rig_1 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R1.fastq.gz RNA_seq control for rig_1 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R2.fastq.gz	fastq fastq	2547796350.0	16985309.0	RNA seq control for rig 1 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2 R1.fastq.gz	0:75 1:75	A:686259539;C:560800822;G:567842650;T:732652800;N:240539	75	75	686259539	560800822	567842650	732652800	240539	SRX7034684	SRS5554730	SRA983011	Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany\|Department of Cellular and Molecular Immunology	Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany	2	0.70188	0.75886	0.08072	0.08833	0.8034	0.80649	0.51507	0.5194	75	75	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Germany	2019-10-24	Pharyngula	Embryo	Endothelium	Cardiovascular System
55402	55402	SRR10323914	SRX7034683	SRS5554730	SRP226614	PRJNA578896	Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence	PRJNA578896	Other	In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.				danRer10 raw data	strain:AB/tu\|age:not applicable\|sex:pooled male and female\|tissue:endothelial and hemogenic endothelial\|BioSampleModel:Model organism or animal								RNA seq control for rig 1 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1	1	1	NEBNext Low Input RNA Library Prep Kit			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina HiSeq 3000		SRP226614		RNA_seq control for rig_1 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R1.fastq.gz RNA_seq control for rig_1 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R2.fastq.gz	fastq fastq	2438070600.0	16253804.0	RNA seq control for rig 1 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1 R1.fastq.gz	0:75 1:75	A:654282012;C:534555119;G:543878428;T:705130425;N:224616	75	75	654282012	534555119	543878428	705130425	224616	SRX7034683	SRS5554730	SRA983011	Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany\|Department of Cellular and Molecular Immunology	Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany	2	0.69336	0.75626	0.09168	0.09896	0.80166	0.80253	0.51795	0.52538	75	75	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Germany	2019-10-24	Pharyngula	Embryo	Endothelium	Cardiovascular System
67823	67823	SRR17335719	SRX13511115	SRS11405356	SRP352585	PRJNA792582	circRNA based biomarker candidates for acute cypermethrin and chlorpyrisfos toxication in the brain of Zebrafish Danio rerio	GSE192669	Transcriptome Analysis	Cypermethrin CYP and chlorpyrifos CPF are pesticides which are frequently used in agricultural areas around the world. These chemicals have been shown to cause serious toxicological damage in the brain of fish which is non target organisms. However circRNAs associated with acute brain toxicity caused by cypermethrin and chlorpyrifos have not been studied yet. In this study circRNAs were identified and characterized using RNA seq in Zebrafish brains exposed to acute cypermethrin and chlorpyrifos toxicity. A total of 10375 circRNAs were detected. It was determined that 6 circRNAs were up regulated 10 circRNAs were down regulated in CYP brain samples compared to controls . In addition it was found that 57 circRNAs are up regulated and 3 circRNAs down regulated in CPF brain samples compared to controls. Moreover 62 circRNAs were down regulated in the CYP samples when CYP and CPF samples were compared. However up regulated circRNA could not be detected. It was revealed that the detected circRNAs specifically regulated the MAPK signaling pathway endocytosis mechanism apoptosis and p53 signaling pathway. This study which was conducted for the first time in terms of the subject of the study could bring a different perspective especially to pesticide toxicity studies. Overall design: Examination of circRNA related to acute cypermethrin and chlopyrifos toxication in brain of zebrafish	pubmed:35304207		CPF3	GSM5754470	source name:Brain tissue\|tissue:Brain\|treatment:CPF toxication\|geo loc name:missing\|collection date:missing	CPF3	Raw data raw reads of FASTQ format were firstly processed through in house scripts. In this step clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time Q20 Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.An upgraded computational pipeline CIRCexplorer2 is applied to detect circRNAs and identify alternative back splicing in back spliced circular RNAs circRNAs The expression of circRNAs is usually represented by the fragments that are mapped to the back spliced exon–exon junction sites. In addition to the raw fragment numbers normalized RNA seq fragments that are mapped to a specific back spliced exon–exon junction by total mapped fragments is used to quantitate circRNA expression. With FPM Fragments mapped to back spliced junction Per Million mapped fragments circRNAs from different samples with distinct sequencing depths can be directly compared. The input data for differential gene expression analysis is read counts from gene expression level analysis. For DESeq2 with biological replicates Differential expression analysis between two conditions/groups three biological replicates per condition was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate FDR. Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed. A common way for searching shared functions among genes is to incorporate the biological knowledge provided by biological ontologies. Gene Ontology GO annotates genes to biological processes molecular functions and cellular components in a directed acyclic graph structure and Kyoto Encyclopedia of Genes and Genomes …	Brain tissue		Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols	tissue:Brain\|treatment:CPF toxication	GSM5754470	GSM5754470: CPF3; Danio rerio; ncRNA Seq	GSM5754470 r1	GSM5754470	1	Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols		ncRNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina HiSeq 4000		SRP352585	loader:fastq load.py	CPF3_1.fq.gz CPF3_2.fq.gz	fastq fastq	12726241500.0	42420805.0	GSM5754470 r1	0:150 1:150	A:3447613023;C:2896153797;G:2922038320;T:3459698412;N:737948	150	150	3447613023	2896153797	2922038320	3459698412	737948	SRX13511115	SRS11405356	SRA1349262	Atatürk University	Atatürk University	2	0.89399	0.89612	0.38172	0.37657	0.66628	0.66799	0.53056	0.53213	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Turkey	2021-12-27	Undetermined	Undetermined	Brain	Nervous System
67824	67824	SRR17335720	SRX13511114	SRS11405355	SRP352585	PRJNA792582	circRNA based biomarker candidates for acute cypermethrin and chlorpyrisfos toxication in the brain of Zebrafish Danio rerio	GSE192669	Transcriptome Analysis	Cypermethrin CYP and chlorpyrifos CPF are pesticides which are frequently used in agricultural areas around the world. These chemicals have been shown to cause serious toxicological damage in the brain of fish which is non target organisms. However circRNAs associated with acute brain toxicity caused by cypermethrin and chlorpyrifos have not been studied yet. In this study circRNAs were identified and characterized using RNA seq in Zebrafish brains exposed to acute cypermethrin and chlorpyrifos toxicity. A total of 10375 circRNAs were detected. It was determined that 6 circRNAs were up regulated 10 circRNAs were down regulated in CYP brain samples compared to controls . In addition it was found that 57 circRNAs are up regulated and 3 circRNAs down regulated in CPF brain samples compared to controls. Moreover 62 circRNAs were down regulated in the CYP samples when CYP and CPF samples were compared. However up regulated circRNA could not be detected. It was revealed that the detected circRNAs specifically regulated the MAPK signaling pathway endocytosis mechanism apoptosis and p53 signaling pathway. This study which was conducted for the first time in terms of the subject of the study could bring a different perspective especially to pesticide toxicity studies. Overall design: Examination of circRNA related to acute cypermethrin and chlopyrifos toxication in brain of zebrafish	pubmed:35304207		CPF2	GSM5754469	source name:Brain tissue\|tissue:Brain\|treatment:CPF toxication\|geo loc name:missing\|collection date:missing	CPF2	Raw data raw reads of FASTQ format were firstly processed through in house scripts. In this step clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time Q20 Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.An upgraded computational pipeline CIRCexplorer2 is applied to detect circRNAs and identify alternative back splicing in back spliced circular RNAs circRNAs The expression of circRNAs is usually represented by the fragments that are mapped to the back spliced exon–exon junction sites. In addition to the raw fragment numbers normalized RNA seq fragments that are mapped to a specific back spliced exon–exon junction by total mapped fragments is used to quantitate circRNA expression. With FPM Fragments mapped to back spliced junction Per Million mapped fragments circRNAs from different samples with distinct sequencing depths can be directly compared. The input data for differential gene expression analysis is read counts from gene expression level analysis. For DESeq2 with biological replicates Differential expression analysis between two conditions/groups three biological replicates per condition was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate FDR. Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed. A common way for searching shared functions among genes is to incorporate the biological knowledge provided by biological ontologies. Gene Ontology GO annotates genes to biological processes molecular functions and cellular components in a directed acyclic graph structure and Kyoto Encyclopedia of Genes and Genomes …	Brain tissue		Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols	tissue:Brain\|treatment:CPF toxication	GSM5754469	GSM5754469: CPF2; Danio rerio; ncRNA Seq	GSM5754469 r1	GSM5754469	1	Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols		ncRNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina HiSeq 4000		SRP352585	loader:fastq load.py	CPF2_1.fq.gz CPF2_2.fq.gz	fastq fastq	14881715100.0	49605717.0	GSM5754469 r1	0:150 1:150	A:4214905088;C:3201163283;G:3225795074;T:4239665352;N:186303	150	150	4214905088	3201163283	3225795074	4239665352	186303	SRX13511114	SRS11405355	SRA1349262	Atatürk University	Atatürk University	2	0.87491	0.87638	0.40844	0.40479	0.67123	0.67018	0.49174	0.48952	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Turkey	2021-12-27	Undetermined	Undetermined	Brain	Nervous System
67825	67825	SRR17335721	SRX13511113	SRS11405354	SRP352585	PRJNA792582	circRNA based biomarker candidates for acute cypermethrin and chlorpyrisfos toxication in the brain of Zebrafish Danio rerio	GSE192669	Transcriptome Analysis	Cypermethrin CYP and chlorpyrifos CPF are pesticides which are frequently used in agricultural areas around the world. These chemicals have been shown to cause serious toxicological damage in the brain of fish which is non target organisms. However circRNAs associated with acute brain toxicity caused by cypermethrin and chlorpyrifos have not been studied yet. In this study circRNAs were identified and characterized using RNA seq in Zebrafish brains exposed to acute cypermethrin and chlorpyrifos toxicity. A total of 10375 circRNAs were detected. It was determined that 6 circRNAs were up regulated 10 circRNAs were down regulated in CYP brain samples compared to controls . In addition it was found that 57 circRNAs are up regulated and 3 circRNAs down regulated in CPF brain samples compared to controls. Moreover 62 circRNAs were down regulated in the CYP samples when CYP and CPF samples were compared. However up regulated circRNA could not be detected. It was revealed that the detected circRNAs specifically regulated the MAPK signaling pathway endocytosis mechanism apoptosis and p53 signaling pathway. This study which was conducted for the first time in terms of the subject of the study could bring a different perspective especially to pesticide toxicity studies. Overall design: Examination of circRNA related to acute cypermethrin and chlopyrifos toxication in brain of zebrafish	pubmed:35304207		CPF1	GSM5754468	source name:Brain tissue\|tissue:Brain\|treatment:CPF toxication\|geo loc name:missing\|collection date:missing	CPF1	Raw data raw reads of FASTQ format were firstly processed through in house scripts. In this step clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time Q20 Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.An upgraded computational pipeline CIRCexplorer2 is applied to detect circRNAs and identify alternative back splicing in back spliced circular RNAs circRNAs The expression of circRNAs is usually represented by the fragments that are mapped to the back spliced exon–exon junction sites. In addition to the raw fragment numbers normalized RNA seq fragments that are mapped to a specific back spliced exon–exon junction by total mapped fragments is used to quantitate circRNA expression. With FPM Fragments mapped to back spliced junction Per Million mapped fragments circRNAs from different samples with distinct sequencing depths can be directly compared. The input data for differential gene expression analysis is read counts from gene expression level analysis. For DESeq2 with biological replicates Differential expression analysis between two conditions/groups three biological replicates per condition was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate FDR. Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed. A common way for searching shared functions among genes is to incorporate the biological knowledge provided by biological ontologies. Gene Ontology GO annotates genes to biological processes molecular functions and cellular components in a directed acyclic graph structure and Kyoto Encyclopedia of Genes and Genomes …	Brain tissue		Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols	tissue:Brain\|treatment:CPF toxication	GSM5754468	GSM5754468: CPF1; Danio rerio; ncRNA Seq	GSM5754468 r1	GSM5754468	1	Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols		ncRNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina HiSeq 4000		SRP352585	loader:fastq load.py	CPF1_1.fq.gz CPF1_2.fq.gz	fastq fastq	16447798800.0	54825996.0	GSM5754468 r1	0:150 1:150	A:4454573413;C:3748270411;G:3776995203;T:4467442717;N:517056	150	150	4454573413	3748270411	3776995203	4467442717	517056	SRX13511113	SRS11405354	SRA1349262	Atatürk University	Atatürk University	2	0.89313	0.8947	0.35381	0.35194	0.64954	0.64831	0.51962	0.52475	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Turkey	2021-12-27	Undetermined	Undetermined	Brain	Nervous System
67826	67826	SRR17335722	SRX13511112	SRS11405353	SRP352585	PRJNA792582	circRNA based biomarker candidates for acute cypermethrin and chlorpyrisfos toxication in the brain of Zebrafish Danio rerio	GSE192669	Transcriptome Analysis	Cypermethrin CYP and chlorpyrifos CPF are pesticides which are frequently used in agricultural areas around the world. These chemicals have been shown to cause serious toxicological damage in the brain of fish which is non target organisms. However circRNAs associated with acute brain toxicity caused by cypermethrin and chlorpyrifos have not been studied yet. In this study circRNAs were identified and characterized using RNA seq in Zebrafish brains exposed to acute cypermethrin and chlorpyrifos toxicity. A total of 10375 circRNAs were detected. It was determined that 6 circRNAs were up regulated 10 circRNAs were down regulated in CYP brain samples compared to controls . In addition it was found that 57 circRNAs are up regulated and 3 circRNAs down regulated in CPF brain samples compared to controls. Moreover 62 circRNAs were down regulated in the CYP samples when CYP and CPF samples were compared. However up regulated circRNA could not be detected. It was revealed that the detected circRNAs specifically regulated the MAPK signaling pathway endocytosis mechanism apoptosis and p53 signaling pathway. This study which was conducted for the first time in terms of the subject of the study could bring a different perspective especially to pesticide toxicity studies. Overall design: Examination of circRNA related to acute cypermethrin and chlopyrifos toxication in brain of zebrafish	pubmed:35304207		CYP3	GSM5754467	source name:Brain tissue\|tissue:Brain\|treatment:CYP toxication\|geo loc name:missing\|collection date:missing	CYP3	Raw data raw reads of FASTQ format were firstly processed through in house scripts. In this step clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time Q20 Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.An upgraded computational pipeline CIRCexplorer2 is applied to detect circRNAs and identify alternative back splicing in back spliced circular RNAs circRNAs The expression of circRNAs is usually represented by the fragments that are mapped to the back spliced exon–exon junction sites. In addition to the raw fragment numbers normalized RNA seq fragments that are mapped to a specific back spliced exon–exon junction by total mapped fragments is used to quantitate circRNA expression. With FPM Fragments mapped to back spliced junction Per Million mapped fragments circRNAs from different samples with distinct sequencing depths can be directly compared. The input data for differential gene expression analysis is read counts from gene expression level analysis. For DESeq2 with biological replicates Differential expression analysis between two conditions/groups three biological replicates per condition was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate FDR. Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed. A common way for searching shared functions among genes is to incorporate the biological knowledge provided by biological ontologies. Gene Ontology GO annotates genes to biological processes molecular functions and cellular components in a directed acyclic graph structure and Kyoto Encyclopedia of Genes and Genomes …	Brain tissue		Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols	tissue:Brain\|treatment:CYP toxication	GSM5754467	GSM5754467: CYP3; Danio rerio; ncRNA Seq	GSM5754467 r1	GSM5754467	1	Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols		ncRNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina HiSeq 4000		SRP352585	loader:fastq load.py	CYP3_1.fq.gz CYP3_2.fq.gz	fastq fastq	13417868100.0	44726227.0	GSM5754467 r1	0:150 1:150	A:3645134270;C:3041754103;G:3084809543;T:3645750889;N:419295	150	150	3645134270	3041754103	3084809543	3645750889	419295	SRX13511112	SRS11405353	SRA1349262	Atatürk University	Atatürk University	2	0.86122	0.8638	0.4112	0.40785	0.68738	0.68519	0.54768	0.44856	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Turkey	2021-12-27	Undetermined	Undetermined	Brain	Nervous System
67827	67827	SRR17335723	SRX13511111	SRS11405352	SRP352585	PRJNA792582	circRNA based biomarker candidates for acute cypermethrin and chlorpyrisfos toxication in the brain of Zebrafish Danio rerio	GSE192669	Transcriptome Analysis	Cypermethrin CYP and chlorpyrifos CPF are pesticides which are frequently used in agricultural areas around the world. These chemicals have been shown to cause serious toxicological damage in the brain of fish which is non target organisms. However circRNAs associated with acute brain toxicity caused by cypermethrin and chlorpyrifos have not been studied yet. In this study circRNAs were identified and characterized using RNA seq in Zebrafish brains exposed to acute cypermethrin and chlorpyrifos toxicity. A total of 10375 circRNAs were detected. It was determined that 6 circRNAs were up regulated 10 circRNAs were down regulated in CYP brain samples compared to controls . In addition it was found that 57 circRNAs are up regulated and 3 circRNAs down regulated in CPF brain samples compared to controls. Moreover 62 circRNAs were down regulated in the CYP samples when CYP and CPF samples were compared. However up regulated circRNA could not be detected. It was revealed that the detected circRNAs specifically regulated the MAPK signaling pathway endocytosis mechanism apoptosis and p53 signaling pathway. This study which was conducted for the first time in terms of the subject of the study could bring a different perspective especially to pesticide toxicity studies. Overall design: Examination of circRNA related to acute cypermethrin and chlopyrifos toxication in brain of zebrafish	pubmed:35304207		CYP2	GSM5754466	source name:Brain tissue\|tissue:Brain\|treatment:CYP toxication\|geo loc name:missing\|collection date:missing	CYP2	Raw data raw reads of FASTQ format were firstly processed through in house scripts. In this step clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time Q20 Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.An upgraded computational pipeline CIRCexplorer2 is applied to detect circRNAs and identify alternative back splicing in back spliced circular RNAs circRNAs The expression of circRNAs is usually represented by the fragments that are mapped to the back spliced exon–exon junction sites. In addition to the raw fragment numbers normalized RNA seq fragments that are mapped to a specific back spliced exon–exon junction by total mapped fragments is used to quantitate circRNA expression. With FPM Fragments mapped to back spliced junction Per Million mapped fragments circRNAs from different samples with distinct sequencing depths can be directly compared. The input data for differential gene expression analysis is read counts from gene expression level analysis. For DESeq2 with biological replicates Differential expression analysis between two conditions/groups three biological replicates per condition was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate FDR. Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed. A common way for searching shared functions among genes is to incorporate the biological knowledge provided by biological ontologies. Gene Ontology GO annotates genes to biological processes molecular functions and cellular components in a directed acyclic graph structure and Kyoto Encyclopedia of Genes and Genomes …	Brain tissue		Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols	tissue:Brain\|treatment:CYP toxication	GSM5754466	GSM5754466: CYP2; Danio rerio; ncRNA Seq	GSM5754466 r1	GSM5754466	1	Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols		ncRNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina HiSeq 4000		SRP352585	loader:fastq load.py	CYP2_1.fq.gz CYP2_2.fq.gz	fastq fastq	13096007700.0	43653359.0	GSM5754466 r1	0:150 1:150	A:3638241155;C:2892284693;G:2925857490;T:3639296449;N:327913	150	150	3638241155	2892284693	2925857490	3639296449	327913	SRX13511111	SRS11405352	SRA1349262	Atatürk University	Atatürk University	2	0.85953	0.86247	0.41975	0.41734	0.68174	0.67862	0.52504	0.5324	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Turkey	2021-12-27	Undetermined	Undetermined	Brain	Nervous System
67828	67828	SRR17335724	SRX13511110	SRS11405351	SRP352585	PRJNA792582	circRNA based biomarker candidates for acute cypermethrin and chlorpyrisfos toxication in the brain of Zebrafish Danio rerio	GSE192669	Transcriptome Analysis	Cypermethrin CYP and chlorpyrifos CPF are pesticides which are frequently used in agricultural areas around the world. These chemicals have been shown to cause serious toxicological damage in the brain of fish which is non target organisms. However circRNAs associated with acute brain toxicity caused by cypermethrin and chlorpyrifos have not been studied yet. In this study circRNAs were identified and characterized using RNA seq in Zebrafish brains exposed to acute cypermethrin and chlorpyrifos toxicity. A total of 10375 circRNAs were detected. It was determined that 6 circRNAs were up regulated 10 circRNAs were down regulated in CYP brain samples compared to controls . In addition it was found that 57 circRNAs are up regulated and 3 circRNAs down regulated in CPF brain samples compared to controls. Moreover 62 circRNAs were down regulated in the CYP samples when CYP and CPF samples were compared. However up regulated circRNA could not be detected. It was revealed that the detected circRNAs specifically regulated the MAPK signaling pathway endocytosis mechanism apoptosis and p53 signaling pathway. This study which was conducted for the first time in terms of the subject of the study could bring a different perspective especially to pesticide toxicity studies. Overall design: Examination of circRNA related to acute cypermethrin and chlopyrifos toxication in brain of zebrafish	pubmed:35304207		CYP1	GSM5754465	source name:Brain tissue\|tissue:Brain\|treatment:CYP toxication\|geo loc name:missing\|collection date:missing	CYP1	Raw data raw reads of FASTQ format were firstly processed through in house scripts. In this step clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time Q20 Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.An upgraded computational pipeline CIRCexplorer2 is applied to detect circRNAs and identify alternative back splicing in back spliced circular RNAs circRNAs The expression of circRNAs is usually represented by the fragments that are mapped to the back spliced exon–exon junction sites. In addition to the raw fragment numbers normalized RNA seq fragments that are mapped to a specific back spliced exon–exon junction by total mapped fragments is used to quantitate circRNA expression. With FPM Fragments mapped to back spliced junction Per Million mapped fragments circRNAs from different samples with distinct sequencing depths can be directly compared. The input data for differential gene expression analysis is read counts from gene expression level analysis. For DESeq2 with biological replicates Differential expression analysis between two conditions/groups three biological replicates per condition was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate FDR. Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed. A common way for searching shared functions among genes is to incorporate the biological knowledge provided by biological ontologies. Gene Ontology GO annotates genes to biological processes molecular functions and cellular components in a directed acyclic graph structure and Kyoto Encyclopedia of Genes and Genomes …	Brain tissue		Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols	tissue:Brain\|treatment:CYP toxication	GSM5754465	GSM5754465: CYP1; Danio rerio; ncRNA Seq	GSM5754465 r1	GSM5754465	1	Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols		ncRNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina HiSeq 4000		SRP352585	loader:fastq load.py	CYP1_1.fq.gz CYP1_2.fq.gz	fastq fastq	16372872000.0	54576240.0	GSM5754465 r1	0:150 1:150	A:4747286217;C:3417115980;G:3453793026;T:4754530080;N:146697	150	150	4747286217	3417115980	3453793026	4754530080	146697	SRX13511110	SRS11405351	SRA1349262	Atatürk University	Atatürk University	2	0.85322	0.85414	0.46298	0.45901	0.68016	0.67866	0.47694	0.47897	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Turkey	2021-12-27	Undetermined	Undetermined	Brain	Nervous System
67829	67829	SRR17335725	SRX13511109	SRS11405350	SRP352585	PRJNA792582	circRNA based biomarker candidates for acute cypermethrin and chlorpyrisfos toxication in the brain of Zebrafish Danio rerio	GSE192669	Transcriptome Analysis	Cypermethrin CYP and chlorpyrifos CPF are pesticides which are frequently used in agricultural areas around the world. These chemicals have been shown to cause serious toxicological damage in the brain of fish which is non target organisms. However circRNAs associated with acute brain toxicity caused by cypermethrin and chlorpyrifos have not been studied yet. In this study circRNAs were identified and characterized using RNA seq in Zebrafish brains exposed to acute cypermethrin and chlorpyrifos toxicity. A total of 10375 circRNAs were detected. It was determined that 6 circRNAs were up regulated 10 circRNAs were down regulated in CYP brain samples compared to controls . In addition it was found that 57 circRNAs are up regulated and 3 circRNAs down regulated in CPF brain samples compared to controls. Moreover 62 circRNAs were down regulated in the CYP samples when CYP and CPF samples were compared. However up regulated circRNA could not be detected. It was revealed that the detected circRNAs specifically regulated the MAPK signaling pathway endocytosis mechanism apoptosis and p53 signaling pathway. This study which was conducted for the first time in terms of the subject of the study could bring a different perspective especially to pesticide toxicity studies. Overall design: Examination of circRNA related to acute cypermethrin and chlopyrifos toxication in brain of zebrafish	pubmed:35304207		Cont3	GSM5754464	source name:Brain tissue\|tissue:Brain\|treatment:No toxication\|geo loc name:missing\|collection date:missing	Cont3	Raw data raw reads of FASTQ format were firstly processed through in house scripts. In this step clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time Q20 Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.An upgraded computational pipeline CIRCexplorer2 is applied to detect circRNAs and identify alternative back splicing in back spliced circular RNAs circRNAs The expression of circRNAs is usually represented by the fragments that are mapped to the back spliced exon–exon junction sites. In addition to the raw fragment numbers normalized RNA seq fragments that are mapped to a specific back spliced exon–exon junction by total mapped fragments is used to quantitate circRNA expression. With FPM Fragments mapped to back spliced junction Per Million mapped fragments circRNAs from different samples with distinct sequencing depths can be directly compared. The input data for differential gene expression analysis is read counts from gene expression level analysis. For DESeq2 with biological replicates Differential expression analysis between two conditions/groups three biological replicates per condition was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate FDR. Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed. A common way for searching shared functions among genes is to incorporate the biological knowledge provided by biological ontologies. Gene Ontology GO annotates genes to biological processes molecular functions and cellular components in a directed acyclic graph structure and Kyoto Encyclopedia of Genes and Genomes …	Brain tissue		Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols	tissue:Brain\|treatment:No toxication	GSM5754464	GSM5754464: Cont3; Danio rerio; ncRNA Seq	GSM5754464 r1	GSM5754464	1	Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols		ncRNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina HiSeq 4000		SRP352585	loader:fastq load.py	Cont3_1.fq.gz Cont3_2.fq.gz	fastq fastq	15202443900.0	50674813.0	GSM5754464 r1	0:150 1:150	A:4400470018;C:3173803928;G:3218623722;T:4409335756;N:210476	150	150	4400470018	3173803928	3218623722	4409335756	210476	SRX13511109	SRS11405350	SRA1349262	Atatürk University	Atatürk University	2	0.86129	0.84677	0.45657	0.44799	0.67884	0.68083	0.48291	0.4763	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Turkey	2021-12-27	Undetermined	Undetermined	Brain	Nervous System
67830	67830	SRR17335726	SRX13511108	SRS11405349	SRP352585	PRJNA792582	circRNA based biomarker candidates for acute cypermethrin and chlorpyrisfos toxication in the brain of Zebrafish Danio rerio	GSE192669	Transcriptome Analysis	Cypermethrin CYP and chlorpyrifos CPF are pesticides which are frequently used in agricultural areas around the world. These chemicals have been shown to cause serious toxicological damage in the brain of fish which is non target organisms. However circRNAs associated with acute brain toxicity caused by cypermethrin and chlorpyrifos have not been studied yet. In this study circRNAs were identified and characterized using RNA seq in Zebrafish brains exposed to acute cypermethrin and chlorpyrifos toxicity. A total of 10375 circRNAs were detected. It was determined that 6 circRNAs were up regulated 10 circRNAs were down regulated in CYP brain samples compared to controls . In addition it was found that 57 circRNAs are up regulated and 3 circRNAs down regulated in CPF brain samples compared to controls. Moreover 62 circRNAs were down regulated in the CYP samples when CYP and CPF samples were compared. However up regulated circRNA could not be detected. It was revealed that the detected circRNAs specifically regulated the MAPK signaling pathway endocytosis mechanism apoptosis and p53 signaling pathway. This study which was conducted for the first time in terms of the subject of the study could bring a different perspective especially to pesticide toxicity studies. Overall design: Examination of circRNA related to acute cypermethrin and chlopyrifos toxication in brain of zebrafish	pubmed:35304207		Cont2	GSM5754463	source name:Brain tissue\|tissue:Brain\|treatment:No toxication\|geo loc name:missing\|collection date:missing	Cont2	Raw data raw reads of FASTQ format were firstly processed through in house scripts. In this step clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time Q20 Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.An upgraded computational pipeline CIRCexplorer2 is applied to detect circRNAs and identify alternative back splicing in back spliced circular RNAs circRNAs The expression of circRNAs is usually represented by the fragments that are mapped to the back spliced exon–exon junction sites. In addition to the raw fragment numbers normalized RNA seq fragments that are mapped to a specific back spliced exon–exon junction by total mapped fragments is used to quantitate circRNA expression. With FPM Fragments mapped to back spliced junction Per Million mapped fragments circRNAs from different samples with distinct sequencing depths can be directly compared. The input data for differential gene expression analysis is read counts from gene expression level analysis. For DESeq2 with biological replicates Differential expression analysis between two conditions/groups three biological replicates per condition was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate FDR. Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed. A common way for searching shared functions among genes is to incorporate the biological knowledge provided by biological ontologies. Gene Ontology GO annotates genes to biological processes molecular functions and cellular components in a directed acyclic graph structure and Kyoto Encyclopedia of Genes and Genomes …	Brain tissue		Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols	tissue:Brain\|treatment:No toxication	GSM5754463	GSM5754463: Cont2; Danio rerio; ncRNA Seq	GSM5754463 r1	GSM5754463	1	Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols		ncRNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina HiSeq 4000		SRP352585	loader:fastq load.py	Cont2_1.fq.gz Cont2_2.fq.gz	fastq fastq	12927267600.0	43090892.0	GSM5754463 r1	0:150 1:150	A:3474574877;C:2959326086;G:3006553706;T:3486600752;N:212179	150	150	3474574877	2959326086	3006553706	3486600752	212179	SRX13511108	SRS11405349	SRA1349262	Atatürk University	Atatürk University	2	0.87695	0.87907	0.41673	0.41416	0.69266	0.69266	0.53339	0.58145	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Turkey	2021-12-27	Undetermined	Undetermined	Brain	Nervous System
67831	67831	SRR17335727	SRX13511107	SRS11405348	SRP352585	PRJNA792582	circRNA based biomarker candidates for acute cypermethrin and chlorpyrisfos toxication in the brain of Zebrafish Danio rerio	GSE192669	Transcriptome Analysis	Cypermethrin CYP and chlorpyrifos CPF are pesticides which are frequently used in agricultural areas around the world. These chemicals have been shown to cause serious toxicological damage in the brain of fish which is non target organisms. However circRNAs associated with acute brain toxicity caused by cypermethrin and chlorpyrifos have not been studied yet. In this study circRNAs were identified and characterized using RNA seq in Zebrafish brains exposed to acute cypermethrin and chlorpyrifos toxicity. A total of 10375 circRNAs were detected. It was determined that 6 circRNAs were up regulated 10 circRNAs were down regulated in CYP brain samples compared to controls . In addition it was found that 57 circRNAs are up regulated and 3 circRNAs down regulated in CPF brain samples compared to controls. Moreover 62 circRNAs were down regulated in the CYP samples when CYP and CPF samples were compared. However up regulated circRNA could not be detected. It was revealed that the detected circRNAs specifically regulated the MAPK signaling pathway endocytosis mechanism apoptosis and p53 signaling pathway. This study which was conducted for the first time in terms of the subject of the study could bring a different perspective especially to pesticide toxicity studies. Overall design: Examination of circRNA related to acute cypermethrin and chlopyrifos toxication in brain of zebrafish	pubmed:35304207		Cont1	GSM5754462	source name:Brain tissue\|tissue:Brain\|treatment:No toxication\|geo loc name:missing\|collection date:missing	Cont1	Raw data raw reads of FASTQ format were firstly processed through in house scripts. In this step clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time Q20 Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.An upgraded computational pipeline CIRCexplorer2 is applied to detect circRNAs and identify alternative back splicing in back spliced circular RNAs circRNAs The expression of circRNAs is usually represented by the fragments that are mapped to the back spliced exon–exon junction sites. In addition to the raw fragment numbers normalized RNA seq fragments that are mapped to a specific back spliced exon–exon junction by total mapped fragments is used to quantitate circRNA expression. With FPM Fragments mapped to back spliced junction Per Million mapped fragments circRNAs from different samples with distinct sequencing depths can be directly compared. The input data for differential gene expression analysis is read counts from gene expression level analysis. For DESeq2 with biological replicates Differential expression analysis between two conditions/groups three biological replicates per condition was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate FDR. Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed. A common way for searching shared functions among genes is to incorporate the biological knowledge provided by biological ontologies. Gene Ontology GO annotates genes to biological processes molecular functions and cellular components in a directed acyclic graph structure and Kyoto Encyclopedia of Genes and Genomes …	Brain tissue		Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols	tissue:Brain\|treatment:No toxication	GSM5754462	GSM5754462: Cont1; Danio rerio; ncRNA Seq	GSM5754462 r1	GSM5754462	1	Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols		ncRNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	Illumina HiSeq 4000		SRP352585	loader:fastq load.py	Cont1_1.fq.gz Cont1_2.fq.gz	fastq fastq	18395362500.0	61317875.0	GSM5754462 r1	0:150 1:150	A:5379624768;C:3792463355;G:3842313235;T:5380702187;N:258955	150	150	5379624768	3792463355	3842313235	5380702187	258955	SRX13511107	SRS11405348	SRA1349262	Atatürk University	Atatürk University	2	0.83439	0.83446	0.45703	0.44894	0.68828	0.68578	0.4957	0.49639	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Turkey	2021-12-27	Undetermined	Undetermined	Brain	Nervous System
75414	75414	SRR24517729	SRX20302027	SRS17627883	SRP437283	PRJNA971676	zebrafish kiss genes knockouts deep sequencing	PRJNA971676	Other	Mammals possess only one Kisspeptin gene but in teleost like zebrafish there are two copies. While knockout of Kiss1 results in infertility in mammals knockout of both kiss1 and kiss2 barely affects zebrafish reproduction. The functions and their functional divergence of zebrafish kiss genes are still not fully elucidated. Deep sequencing results will reveal the different downstream pathways affected by the two kiss genes and will help to understand their functions and functional divergence.			RNA seq of zebrafish:5dpf larvae kiss1kiss2DKO Replicate2	zebrafish AO149 01T0008	strain:AB\|age:5dpf\|dev stage:larvae\|sex:not determined\|tissue:whole organism\|collection date:2020\|genotype:kiss1 and kiss2 double knockout\|geo loc name:China: Suzhou\|sample type:whole organism\|Replicate:2\|BioSampleModel:Model organism or animal								RNA Seq of zebrafish: larvae	RNA Seq for zebrafish kiss1kiss2DKO larvae 2	RNA Seq for zebrafish kiss1kiss2DKO larvae 2	RNA Seq zebrafish kiss1kiss2DKO larvae 2			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	HiSeq X Five		SRP437283		Unknown_AO149-01T0008_good_1.fq.gz Unknown_AO149-01T0008_good_2.fq.gz	fastq fastq	6912158300.0	23173882.0	Unknown AO149 01T0008 good 1.fq.gz	0:149.14 1:149.14	A:1796529490;C:1649628994;G:1669079817;T:1796880198;N:39801	149	149	1796529490	1649628994	1669079817	1796880198	39801	SRX20302027	SRS17627883	SRA1636880	Soochow University\|Medical College	Soochow University	2	0.95632	0.95592	0.06085	0.06019	0.66515	0.66563	0.47686	0.47575	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Unknown	2023-05-11	Larval	Larval	Whole Organism	All anatomical structures
75415	75415	SRR24517730	SRX20302026	SRS17627882	SRP437283	PRJNA971676	zebrafish kiss genes knockouts deep sequencing	PRJNA971676	Other	Mammals possess only one Kisspeptin gene but in teleost like zebrafish there are two copies. While knockout of Kiss1 results in infertility in mammals knockout of both kiss1 and kiss2 barely affects zebrafish reproduction. The functions and their functional divergence of zebrafish kiss genes are still not fully elucidated. Deep sequencing results will reveal the different downstream pathways affected by the two kiss genes and will help to understand their functions and functional divergence.			RNA seq of zebrafish:5dpf larvae kiss1kiss2DKO Replicate1	zebrafish AO149 01T0007	strain:AB\|age:5dpf\|dev stage:larvae\|sex:not determined\|tissue:whole organism\|collection date:2020\|genotype:kiss1 and kiss2 double knockout\|geo loc name:China: Suzhou\|sample type:whole organism\|Replicate:1\|BioSampleModel:Model organism or animal								RNA Seq of zebrafish: larvae	RNA Seq for zebrafish kiss1kiss2DKO larvae 1	RNA Seq for zebrafish kiss1kiss2DKO larvae 1	RNA Seq zebrafish kiss1kiss2DKO larvae 1			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	HiSeq X Five		SRP437283		Unknown_AO149-01T0007_good_1.fq.gz Unknown_AO149-01T0007_good_2.fq.gz	fastq fastq	8005311792.0	26909041.0	Unknown AO149 01T0007 good 1.fq.gz	0:148.75 1:148.75	A:2077441584;C:1913582326;G:1934120275;T:2080121870;N:45737	148	148	2077441584	1913582326	1934120275	2080121870	45737	SRX20302026	SRS17627882	SRA1636880	Soochow University\|Medical College	Soochow University	2	0.9522	0.95194	0.06345	0.06296	0.65691	0.65744	0.48074	0.48185	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Unknown	2023-05-11	Larval	Larval	Whole Organism	All anatomical structures
75416	75416	SRR24517731	SRX20302025	SRS17627881	SRP437283	PRJNA971676	zebrafish kiss genes knockouts deep sequencing	PRJNA971676	Other	Mammals possess only one Kisspeptin gene but in teleost like zebrafish there are two copies. While knockout of Kiss1 results in infertility in mammals knockout of both kiss1 and kiss2 barely affects zebrafish reproduction. The functions and their functional divergence of zebrafish kiss genes are still not fully elucidated. Deep sequencing results will reveal the different downstream pathways affected by the two kiss genes and will help to understand their functions and functional divergence.			RNA seq of zebrafish:5dpf larvae kiss2KO Replicate2	zebrafish AO149 01T0006	strain:AB\|age:5dpf\|dev stage:larvae\|sex:not determined\|tissue:whole organism\|collection date:2020\|genotype:kiss2 knockout\|geo loc name:China: Suzhou\|sample type:whole organism\|Replicate:2\|BioSampleModel:Model organism or animal								RNA Seq of zebrafish: larvae	RNA Seq for zebrafish kiss2KO larvae 2	RNA Seq for zebrafish kiss2KO larvae 2	RNA Seq zebrafish kiss2KO larvae 2			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	HiSeq X Five		SRP437283		Unknown_AO149-01T0006_good_1.fq.gz Unknown_AO149-01T0006_good_2.fq.gz	fastq fastq	7638089446.0	25894588.0	Unknown AO149 01T0006 good 1.fq.gz	0:147.48 1:147.48	A:2051138070;C:1759130157;G:1773591862;T:2054190526;N:38831	147	147	2051138070	1759130157	1773591862	2054190526	38831	SRX20302025	SRS17627881	SRA1636880	Soochow University\|Medical College	Soochow University	2	0.94967	0.94887	0.08556	0.08576	0.64898	0.64954	0.47984	0.48067	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Unknown	2023-05-11	Larval	Larval	Whole Organism	All anatomical structures
75417	75417	SRR24517732	SRX20302024	SRS17627879	SRP437283	PRJNA971676	zebrafish kiss genes knockouts deep sequencing	PRJNA971676	Other	Mammals possess only one Kisspeptin gene but in teleost like zebrafish there are two copies. While knockout of Kiss1 results in infertility in mammals knockout of both kiss1 and kiss2 barely affects zebrafish reproduction. The functions and their functional divergence of zebrafish kiss genes are still not fully elucidated. Deep sequencing results will reveal the different downstream pathways affected by the two kiss genes and will help to understand their functions and functional divergence.			RNA seq of zebrafish:5dpf larvae kiss2KO Replicate1	zebrafish AO149 01T0005	strain:AB\|age:5dpf\|dev stage:larvae\|sex:not determined\|tissue:whole organism\|collection date:2020\|genotype:kiss2 knockout\|geo loc name:China: Suzhou\|sample type:whole organism\|Replicate:1\|BioSampleModel:Model organism or animal								RNA Seq of zebrafish: larvae	RNA Seq for zebrafish kiss2KO larvae 1	RNA Seq for zebrafish kiss2KO larvae 1	RNA Seq zebrafish kiss2KO larvae 1			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	HiSeq X Five		SRP437283		Unknown_AO149-01T0005_good_1.fq.gz Unknown_AO149-01T0005_good_2.fq.gz	fastq fastq	7054134954.0	23687508.0	Unknown AO149 01T0005 good 1.fq.gz	0:148.90 1:148.90	A:1848389593;C:1667928954;G:1687707295;T:1850068763;N:40349	148	148	1848389593	1667928954	1687707295	1850068763	40349	SRX20302024	SRS17627879	SRA1636880	Soochow University\|Medical College	Soochow University	2	0.94976	0.95007	0.07472	0.07458	0.65299	0.65324	0.48045	0.47909	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Unknown	2023-05-11	Larval	Larval	Whole Organism	All anatomical structures
75418	75418	SRR24517733	SRX20302023	SRS17627880	SRP437283	PRJNA971676	zebrafish kiss genes knockouts deep sequencing	PRJNA971676	Other	Mammals possess only one Kisspeptin gene but in teleost like zebrafish there are two copies. While knockout of Kiss1 results in infertility in mammals knockout of both kiss1 and kiss2 barely affects zebrafish reproduction. The functions and their functional divergence of zebrafish kiss genes are still not fully elucidated. Deep sequencing results will reveal the different downstream pathways affected by the two kiss genes and will help to understand their functions and functional divergence.			RNA seq of zebrafish:5dpf larvae kiss1KO Replicate2	zebrafish AO149 01T0004	strain:AB\|age:5dpf\|dev stage:larvae\|sex:not determined\|tissue:whole organism\|collection date:2020\|genotype:kiss1 knockout\|geo loc name:China: Suzhou\|sample type:whole organism\|Replicate:2\|BioSampleModel:Model organism or animal								RNA Seq of zebrafish: larvae	RNA Seq for zebrafish kiss1KO larvae 2	RNA Seq for zebrafish kiss1KO larvae 2	RNA Seq zebrafish kiss1KO larvae 2			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	HiSeq X Five		SRP437283		Unknown_AO149-01T0004_good_1.fq.gz Unknown_AO149-01T0004_good_2.fq.gz	fastq fastq	5814495346.0	19499621.0	Unknown AO149 01T0004 good 1.fq.gz	0:149.09 1:149.09	A:1528388873;C:1369910846;G:1386794007;T:1529368087;N:33533	149	149	1528388873	1369910846	1386794007	1529368087	33533	SRX20302023	SRS17627880	SRA1636880	Soochow University\|Medical College	Soochow University	2	0.94765	0.94711	0.07972	0.07979	0.65283	0.65397	0.48362	0.48203	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Unknown	2023-05-11	Larval	Larval	Whole Organism	All anatomical structures
75419	75419	SRR24517734	SRX20302022	SRS17627877	SRP437283	PRJNA971676	zebrafish kiss genes knockouts deep sequencing	PRJNA971676	Other	Mammals possess only one Kisspeptin gene but in teleost like zebrafish there are two copies. While knockout of Kiss1 results in infertility in mammals knockout of both kiss1 and kiss2 barely affects zebrafish reproduction. The functions and their functional divergence of zebrafish kiss genes are still not fully elucidated. Deep sequencing results will reveal the different downstream pathways affected by the two kiss genes and will help to understand their functions and functional divergence.			RNA seq of zebrafish:5dpf larvae kiss1KO Replicate1	zebrafish AO149 01T0003	strain:AB\|age:5dpf\|dev stage:larvae\|sex:not determined\|tissue:whole organism\|collection date:2020\|genotype:kiss1 knockout\|geo loc name:China: Suzhou\|sample type:whole organism\|Replicate:1\|BioSampleModel:Model organism or animal								RNA Seq of zebrafish: larvae	RNA Seq for zebrafish kiss1KO larvae 1	RNA Seq for zebrafish kiss1KO larvae 1	RNA Seq zebrafish kiss1KO larvae 1			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	HiSeq X Five		SRP437283		Unknown_AO149-01T0003_good_1.fq.gz Unknown_AO149-01T0003_good_2.fq.gz	fastq fastq	6174484352.0	20748774.0	Unknown AO149 01T0003 good 1.fq.gz	0:148.79 1:148.79	A:1629263285;C:1446858897;G:1467609266;T:1630717493;N:35411	148	148	1629263285	1446858897	1467609266	1630717493	35411	SRX20302022	SRS17627877	SRA1636880	Soochow University\|Medical College	Soochow University	2	0.94831	0.94853	0.07898	0.07866	0.65295	0.65419	0.47605	0.47682	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Unknown	2023-05-11	Larval	Larval	Whole Organism	All anatomical structures
75420	75420	SRR24517735	SRX20302021	SRS17627878	SRP437283	PRJNA971676	zebrafish kiss genes knockouts deep sequencing	PRJNA971676	Other	Mammals possess only one Kisspeptin gene but in teleost like zebrafish there are two copies. While knockout of Kiss1 results in infertility in mammals knockout of both kiss1 and kiss2 barely affects zebrafish reproduction. The functions and their functional divergence of zebrafish kiss genes are still not fully elucidated. Deep sequencing results will reveal the different downstream pathways affected by the two kiss genes and will help to understand their functions and functional divergence.			RNA seq of zebrafish:5dpf larvae wt Replicate2	zebrafish AO149 01T0002	strain:AB\|age:5dpf\|dev stage:larvae\|sex:not determined\|tissue:whole organism\|collection date:2020\|genotype:WT\|geo loc name:China: Suzhou\|sample type:whole organism\|Replicate:2\|BioSampleModel:Model organism or animal								RNA Seq of zebrafish: larvae	RNA Seq for zebrafish WT larvae 2	RNA Seq for zebrafish WT larvae 2	RNA Seq zebrafish WT larvae 2			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	HiSeq X Five		SRP437283		Unknown_AO149-01T0002_good_1.fq.gz Unknown_AO149-01T0002_good_2.fq.gz	fastq fastq	6059983436.0	20361363.0	Unknown AO149 01T0002 good 1.fq.gz	0:148.81 1:148.81	A:1608075382;C:1408291949;G:1433236990;T:1610344312;N:34803	148	148	1608075382	1408291949	1433236990	1610344312	34803	SRX20302021	SRS17627878	SRA1636880	Soochow University\|Medical College	Soochow University	2	0.9529	0.95334	0.07296	0.07315	0.65435	0.65247	0.49743	0.47334	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Unknown	2023-05-11	Larval	Larval	Whole Organism	All anatomical structures
75421	75421	SRR24517736	SRX20302020	SRS17627876	SRP437283	PRJNA971676	zebrafish kiss genes knockouts deep sequencing	PRJNA971676	Other	Mammals possess only one Kisspeptin gene but in teleost like zebrafish there are two copies. While knockout of Kiss1 results in infertility in mammals knockout of both kiss1 and kiss2 barely affects zebrafish reproduction. The functions and their functional divergence of zebrafish kiss genes are still not fully elucidated. Deep sequencing results will reveal the different downstream pathways affected by the two kiss genes and will help to understand their functions and functional divergence.			RNA seq of zebrafish:5dpf larvae wt Replicate1	zebrafish AO149 01T0001	strain:AB\|age:5dpf\|dev stage:larvae\|sex:not determined\|tissue:whole organism\|collection date:2020\|genotype:WT\|geo loc name:China: Suzhou\|sample type:whole organism\|Replicate:1\|BioSampleModel:Model organism or animal								RNA Seq of zebrafish: larvae	RNA Seq for zebrafish WT larvae 1	RNA Seq for zebrafish WT larvae 1	RNA Seq zebrafish WT larvae 1			RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	HiSeq X Five		SRP437283		Unknown_AO149-01T0001_good_1.fq.gz Unknown_AO149-01T0001_good_2.fq.gz	fastq fastq	6809997812.0	22853255.0	Unknown AO149 01T0001 good 1.fq.gz	0:148.99 1:148.99	A:1813360438;C:1582845212;G:1601287701;T:1812465242;N:39219	148	148	1813360438	1582845212	1601287701	1812465242	39219	SRX20302020	SRS17627876	SRA1636880	Soochow University\|Medical College	Soochow University	2	0.94825	0.94824	0.087	0.08724	0.64695	0.64715	0.49206	0.493	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Unknown	2023-05-11	Larval	Larval	Whole Organism	All anatomical structures

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