metadata: run_metadata: 17 rows where experiment.library_layout = "PAIRED", experiment.library_selection = "RT-PCR" and tissue

17 rows where experiment.library_layout = "PAIRED", experiment.library_selection = "RT-PCR" and tissue_curation = "Brain"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	sample.title	sample.alias	sample.attributes	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.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
34100	34100	SRR31179089	SRX26561802	SRS23067260	SRP542312	PRJNA1180208	RNA Sequencing of NPs in zebrafish brain	PRJNA1180208	Other		L21	L1EIC0700904 T L2.R1	strain:AB\|age:Adult\|collection date:not applicable\|geo loc name:Hong Kong\|sex:not applicable\|tissue:Brain\|Tmp:9\|BioSampleModel:Model organism or animal	RNA Seq of zebrafish brain	L21	L21	Adult zebrafish brain	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina HiSeq 3000	SRP542312	L1EIC0700904-T_L2.R1.raw.fastq.gz L1EIC0700904-T_L2.R2.raw.fastq.gz	fastq fastq	6755197306.0	22368203.0	L1EIC0700904 T L2.R1.raw.fastq.gz	0:151 1:151	A:1778527472;C:1586407415;G:1611223994;T:1770639781;N:8398644	151	151	1778527472	1586407415	1611223994	1770639781	8398644	SRX26561802	SRS23067260	SRA2001903	City University of Hong Kong\|School of Energy and Environmental	City University of Hong Kong												B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-10-31	Adult	Adult	Brain	Nervous System
34101	34101	SRR31179090	SRX26561801	SRS23067261	SRP542312	PRJNA1180208	RNA Sequencing of NPs in zebrafish brain	PRJNA1180208	Other		L11	L1EIC0700903 T L1.R1	strain:AB\|age:Adult\|collection date:not applicable\|geo loc name:Hong Kong\|sex:not applicable\|tissue:Brain\|Tmp:7\|BioSampleModel:Model organism or animal	RNA Seq of zebrafish brain	L11	L11	Adult zebrafish brain	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina HiSeq 3000	SRP542312	L1EIC0700903-T_L1.R1.raw.fastq.gz L1EIC0700903-T_L1.R2.raw.fastq.gz	fastq fastq	7262619518.0	24048409.0	L1EIC0700903 T L1.R1.raw.fastq.gz	0:151 1:151	A:1897564712;C:1719515913;G:1744510723;T:1891980402;N:9047768	151	151	1897564712	1719515913	1744510723	1891980402	9047768	SRX26561801	SRS23067261	SRA2001903	City University of Hong Kong\|School of Energy and Environmental	City University of Hong Kong												B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-10-31	Adult	Adult	Brain	Nervous System
34102	34102	SRR31179091	SRX26561800	SRS23067257	SRP542312	PRJNA1180208	RNA Sequencing of NPs in zebrafish brain	PRJNA1180208	Other		C31	L1EIC0700902 T C3.R1	strain:AB\|age:Adult\|collection date:not applicable\|geo loc name:Hong Kong\|sex:not applicable\|tissue:Brain\|Tmp:5\|BioSampleModel:Model organism or animal	RNA Seq of zebrafish brain	C31	C31	Adult zebrafish brain	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina HiSeq 3000	SRP542312	L1EIC0700902-T_C3.R1.raw.fastq.gz L1EIC0700902-T_C3.R2.raw.fastq.gz	fastq fastq	6986250560.0	23133280.0	L1EIC0700902 T C3.R1.raw.fastq.gz	0:151 1:151	A:1814714141;C:1667167814;G:1686637674;T:1809014055;N:8716876	151	151	1814714141	1667167814	1686637674	1809014055	8716876	SRX26561800	SRS23067257	SRA2001903	City University of Hong Kong\|School of Energy and Environmental	City University of Hong Kong												B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-10-31	Adult	Adult	Brain	Nervous System
34103	34103	SRR31179092	SRX26561799	SRS23067259	SRP542312	PRJNA1180208	RNA Sequencing of NPs in zebrafish brain	PRJNA1180208	Other		C21	L1EIC0700901 T C2.R1	strain:AB\|age:Adult\|collection date:not applicable\|geo loc name:Hong Kong\|sex:not applicable\|tissue:Brain\|Tmp:3\|BioSampleModel:Model organism or animal	RNA Seq of zebrafish brain	C21	C21	Adult zebrafish brain	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina HiSeq 3000	SRP542312	L1EIC0700901-T_C2.R1.raw.fastq.gz L1EIC0700901-T_C2.R2.raw.fastq.gz	fastq fastq	7084353146.0	23458123.0	L1EIC0700901 T C2.R1.raw.fastq.gz	0:151 1:151	A:1860686893;C:1670094870;G:1691858523;T:1852823738;N:8889122	151	151	1860686893	1670094870	1691858523	1852823738	8889122	SRX26561799	SRS23067259	SRA2001903	City University of Hong Kong\|School of Energy and Environmental	City University of Hong Kong												B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-10-31	Adult	Adult	Brain	Nervous System
34104	34104	SRR31179093	SRX26561798	SRS23067255	SRP542312	PRJNA1180208	RNA Sequencing of NPs in zebrafish brain	PRJNA1180208	Other		S31	L1EIC0700908 T S3.R1	strain:AB\|age:Adult\|collection date:not applicable\|geo loc name:Hong Kong\|sex:not applicable\|tissue:Brain\|Tmp:17\|BioSampleModel:Model organism or animal	RNA Seq of zebrafish brain	S31	S31	Adult zebrafish brain	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina HiSeq 3000	SRP542312	L1EIC0700908-T_S3.R1.raw.fastq.gz L1EIC0700908-T_S3.R2.raw.fastq.gz	fastq fastq	6992611888.0	23154344.0	L1EIC0700908 T S3.R1.raw.fastq.gz	0:151 1:151	A:1891265867;C:1594515809;G:1615494569;T:1882648469;N:8687174	151	151	1891265867	1594515809	1615494569	1882648469	8687174	SRX26561798	SRS23067255	SRA2001903	City University of Hong Kong\|School of Energy and Environmental	City University of Hong Kong												B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-10-31	Adult	Adult	Brain	Nervous System
34105	34105	SRR31179094	SRX26561797	SRS23067258	SRP542312	PRJNA1180208	RNA Sequencing of NPs in zebrafish brain	PRJNA1180208	Other		S21	L1EIC0700907 T S2.R1	strain:AB\|age:Adult\|collection date:not applicable\|geo loc name:Hong Kong\|sex:not applicable\|tissue:Brain\|Tmp:15\|BioSampleModel:Model organism or animal	RNA Seq of zebrafish brain	S21	S21	Adult zebrafish brain	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina HiSeq 3000	SRP542312	L1EIC0700907-T_S2.R1.raw.fastq.gz L1EIC0700907-T_S2.R2.raw.fastq.gz	fastq fastq	6223201958.0	20606629.0	L1EIC0700907 T S2.R1.raw.fastq.gz	0:151 1:151	A:1635455481;C:1467707544;G:1484789988;T:1627505187;N:7743758	151	151	1635455481	1467707544	1484789988	1627505187	7743758	SRX26561797	SRS23067258	SRA2001903	City University of Hong Kong\|School of Energy and Environmental	City University of Hong Kong												B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-10-31	Adult	Adult	Brain	Nervous System
34106	34106	SRR31179095	SRX26561796	SRS23067256	SRP542312	PRJNA1180208	RNA Sequencing of NPs in zebrafish brain	PRJNA1180208	Other		S11	L1EIC0700906 T S1.R1	strain:AB\|age:Adult\|collection date:not applicable\|geo loc name:Hong Kong\|sex:not applicable\|tissue:Brain\|Tmp:13\|BioSampleModel:Model organism or animal	RNA Seq of zebrafish brain	S11	S11	Adult zebrafish brain	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina HiSeq 3000	SRP542312	L1EIC0700906-T_S1.R1.raw.fastq.gz L1EIC0700906-T_S1.R2.raw.fastq.gz	fastq fastq	6882679660.0	22790330.0	L1EIC0700906 T S1.R1.raw.fastq.gz	0:151 1:151	A:1805328115;C:1625761692;G:1646060059;T:1796837143;N:8692651	151	151	1805328115	1625761692	1646060059	1796837143	8692651	SRX26561796	SRS23067256	SRA2001903	City University of Hong Kong\|School of Energy and Environmental	City University of Hong Kong												B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-10-31	Adult	Adult	Brain	Nervous System
34107	34107	SRR31179096	SRX26561795	SRS23067254	SRP542312	PRJNA1180208	RNA Sequencing of NPs in zebrafish brain	PRJNA1180208	Other		L31	L1EIC0700905 T L3.R1	strain:AB\|age:Adult\|collection date:not applicable\|geo loc name:Hong Kong\|sex:not applicable\|tissue:Brain\|Tmp:11\|BioSampleModel:Model organism or animal	RNA Seq of zebrafish brain	L31	L31	Adult zebrafish brain	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina HiSeq 3000	SRP542312	L1EIC0700905-T_L3.R1.raw.fastq.gz L1EIC0700905-T_L3.R2.raw.fastq.gz	fastq fastq	6901039146.0	22851123.0	L1EIC0700905 T L3.R1.raw.fastq.gz	0:151 1:151	A:1796093025;C:1641065561;G:1664159837;T:1791078184;N:8642539	151	151	1796093025	1641065561	1664159837	1791078184	8642539	SRX26561795	SRS23067254	SRA2001903	City University of Hong Kong\|School of Energy and Environmental	City University of Hong Kong												B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-10-31	Adult	Adult	Brain	Nervous System
34108	34108	SRR31179097	SRX26561794	SRS23067253	SRP542312	PRJNA1180208	RNA Sequencing of NPs in zebrafish brain	PRJNA1180208	Other		C11	L1EIC0700900 T C1.R1	strain:AB\|age:Adult\|collection date:not applicable\|geo loc name:Hong Kong\|sex:not applicable\|tissue:Brain\|Tmp:1\|BioSampleModel:Model organism or animal	RNA Seq of zebrafish brain	C11	C11	Adult zebrafish brain	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina HiSeq 3000	SRP542312	L1EIC0700900-T_C1.R1.raw.fastq.gz L1EIC0700900-T_C1.R2.raw.fastq.gz	fastq fastq	10565913034.0	34986467.0	L1EIC0700900 T C1.R1.raw.fastq.gz	0:151 1:151	A:2737543425;C:2523674862;G:2563177427;T:2728317948;N:13199372	151	151	2737543425	2523674862	2563177427	2728317948	13199372	SRX26561794	SRS23067253	SRA2001903	City University of Hong Kong\|School of Energy and Environmental	City University of Hong Kong												B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-10-31	Adult	Adult	Brain	Nervous System
66831	66831	SRR16674680	SRX12875367	SRS10818487	SRP343978	PRJNA776712	RNA seq analysis of nde1 mutant zebrafish	PRJNA776712	Other	We perform RNA sequencing to detect defferential expressed genes of nde1 deficiency mutant zebrafish brains compared to wild type.		brain nde1KO	strain:nde1KO\|dev stage:2mpf\|sex:male\|tissue:brain\|BioSampleModel:Model organism or animal	RNA seq of nde1 ko Danio rerio brain	B8	B8	RNA seq transcriptome librariy was prepared following TruSeqTM RNA sample preparation Kit from Illumina San Diego CA using 5g of total RNA. Shortly messenger RNA was isolated according to polyA selection method by oligodT beads and then fragmented by fragmentation buffer firstly. Secondly double stranded cDNA was synthesized using a SuperScript double stranded cDNA synthesis kit Invitrogen CA with random hexamer primers Illumina. Then the synthesized cDNA was subjected to end repair phosphorylation and A base addition according to Illuminas library construction protocol. Libraries were size selected for cDNA target fragments of 200300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. post quantified by TBS380 paired end RNA seq sequencing library was sequenced with the Illumina HiSeq 4000 2 150bp read length.	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP343978	B8.R1.fastq.gz B8.R2.fastq.gz	fastq fastq	6730442668.0	22286234.0	B8.R1.fastq.gz	0:151 1:151	A:1861252434;C:1503025278;G:1520846977;T:1845259260;N:58719	151	151	1861252434	1503025278	1520846977	1845259260	58719	SRX12875367	SRS10818487			Children's Hospital of Fudan University	2	0.94017	0.93241	0.13042	0.12914	0.68958	0.69132	0.48508	0.48284	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	China	2021-11-01	Juvenile	Juvenile	Brain	Nervous System
66832	66832	SRR16674681	SRX12875366	SRS10818487	SRP343978	PRJNA776712	RNA seq analysis of nde1 mutant zebrafish	PRJNA776712	Other	We perform RNA sequencing to detect defferential expressed genes of nde1 deficiency mutant zebrafish brains compared to wild type.		brain nde1KO	strain:nde1KO\|dev stage:2mpf\|sex:male\|tissue:brain\|BioSampleModel:Model organism or animal	RNA seq of nde1 ko Danio rerio brain	B5	B5	RNA seq transcriptome librariy was prepared following TruSeqTM RNA sample preparation Kit from Illumina San Diego CA using 5g of total RNA. Shortly messenger RNA was isolated according to polyA selection method by oligodT beads and then fragmented by fragmentation buffer firstly. Secondly double stranded cDNA was synthesized using a SuperScript double stranded cDNA synthesis kit Invitrogen CA with random hexamer primers Illumina. Then the synthesized cDNA was subjected to end repair phosphorylation and A base addition according to Illuminas library construction protocol. Libraries were size selected for cDNA target fragments of 200300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. post quantified by TBS380 paired end RNA seq sequencing library was sequenced with the Illumina HiSeq 4000 2 150bp read length.	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP343978	B5.R1.fastq.gz B5.R2.fastq.gz	fastq fastq	7110747040.0	23545520.0	B5.R1.fastq.gz	0:151 1:151	A:1977355863;C:1580608625;G:1601936422;T:1950785340;N:60790	151	151	1977355863	1580608625	1601936422	1950785340	60790	SRX12875366	SRS10818487			Children's Hospital of Fudan University	2	0.93839	0.92891	0.1351	0.13386	0.69175	0.69424	0.49143	0.49249	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	China	2021-11-01	Juvenile	Juvenile	Brain	Nervous System
66833	66833	SRR16674682	SRX12875365	SRS10818487	SRP343978	PRJNA776712	RNA seq analysis of nde1 mutant zebrafish	PRJNA776712	Other	We perform RNA sequencing to detect defferential expressed genes of nde1 deficiency mutant zebrafish brains compared to wild type.		brain nde1KO	strain:nde1KO\|dev stage:2mpf\|sex:male\|tissue:brain\|BioSampleModel:Model organism or animal	RNA seq of nde1 ko Danio rerio brain	B2	B2	RNA seq transcriptome librariy was prepared following TruSeqTM RNA sample preparation Kit from Illumina San Diego CA using 5g of total RNA. Shortly messenger RNA was isolated according to polyA selection method by oligodT beads and then fragmented by fragmentation buffer firstly. Secondly double stranded cDNA was synthesized using a SuperScript double stranded cDNA synthesis kit Invitrogen CA with random hexamer primers Illumina. Then the synthesized cDNA was subjected to end repair phosphorylation and A base addition according to Illuminas library construction protocol. Libraries were size selected for cDNA target fragments of 200300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. post quantified by TBS380 paired end RNA seq sequencing library was sequenced with the Illumina HiSeq 4000 2 150bp read length.	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP343978	B2.R1.fastq.gz B2.R2.fastq.gz	fastq fastq	8547028538.0	28301419.0	B2.R1.fastq.gz	0:151 1:151	A:2378598350;C:1891330158;G:1921569124;T:2355455648;N:75258	151	151	2378598350	1891330158	1921569124	2355455648	75258	SRX12875365	SRS10818487			Children's Hospital of Fudan University	2	0.94029	0.92534	0.13616	0.13373	0.68949	0.69219	0.47948	0.48398	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	China	2021-11-01	Juvenile	Juvenile	Brain	Nervous System
66834	66834	SRR16674683	SRX12875364	SRS10818488	SRP343978	PRJNA776712	RNA seq analysis of nde1 mutant zebrafish	PRJNA776712	Other	We perform RNA sequencing to detect defferential expressed genes of nde1 deficiency mutant zebrafish brains compared to wild type.		brain WT	strain:TU\|dev stage:2mpf\|sex:male\|tissue:brain\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio brain	B7	B7	RNA seq transcriptome librariy was prepared following TruSeqTM RNA sample preparation Kit from Illumina San Diego CA using 5g of total RNA. Shortly messenger RNA was isolated according to polyA selection method by oligodT beads and then fragmented by fragmentation buffer firstly. Secondly double stranded cDNA was synthesized using a SuperScript double stranded cDNA synthesis kit Invitrogen CA with random hexamer primers Illumina. Then the synthesized cDNA was subjected to end repair phosphorylation and A base addition according to Illuminas library construction protocol. Libraries were size selected for cDNA target fragments of 200300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. post quantified by TBS380 paired end RNA seq sequencing library was sequenced with the Illumina HiSeq 4000 2 150bp read length.	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP343978	B7.R1.fastq.gz B7.R2.fastq.gz	fastq fastq	6685388496.0	22137048.0	B7.R1.fastq.gz	0:151 1:151	A:1860264075;C:1483831512;G:1503216220;T:1838014556;N:62133	151	151	1860264075	1483831512	1503216220	1838014556	62133	SRX12875364	SRS10818488			Children's Hospital of Fudan University	2	0.94254	0.93341	0.13834	0.13689	0.69355	0.69755	0.49201	0.49217	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	China	2021-11-01	Juvenile	Juvenile	Brain	Nervous System
66835	66835	SRR16674684	SRX12875363	SRS10818488	SRP343978	PRJNA776712	RNA seq analysis of nde1 mutant zebrafish	PRJNA776712	Other	We perform RNA sequencing to detect defferential expressed genes of nde1 deficiency mutant zebrafish brains compared to wild type.		brain WT	strain:TU\|dev stage:2mpf\|sex:male\|tissue:brain\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio brain	B4	B4	RNA seq transcriptome librariy was prepared following TruSeqTM RNA sample preparation Kit from Illumina San Diego CA using 5g of total RNA. Shortly messenger RNA was isolated according to polyA selection method by oligodT beads and then fragmented by fragmentation buffer firstly. Secondly double stranded cDNA was synthesized using a SuperScript double stranded cDNA synthesis kit Invitrogen CA with random hexamer primers Illumina. Then the synthesized cDNA was subjected to end repair phosphorylation and A base addition according to Illuminas library construction protocol. Libraries were size selected for cDNA target fragments of 200300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. post quantified by TBS380 paired end RNA seq sequencing library was sequenced with the Illumina HiSeq 4000 2 150bp read length.	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP343978	B4.R1.fastq.gz B4.R2.fastq.gz	fastq fastq	7546711220.0	24989110.0	B4.R1.fastq.gz	0:151 1:151	A:2099092660;C:1670910951;G:1699960602;T:2076680479;N:66528	151	151	2099092660	1670910951	1699960602	2076680479	66528	SRX12875363	SRS10818488			Children's Hospital of Fudan University	2	0.94254	0.92745	0.13347	0.13114	0.69225	0.69424	0.48413	0.49124	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	China	2021-11-01	Juvenile	Juvenile	Brain	Nervous System
66836	66836	SRR16674685	SRX12875362	SRS10818488	SRP343978	PRJNA776712	RNA seq analysis of nde1 mutant zebrafish	PRJNA776712	Other	We perform RNA sequencing to detect defferential expressed genes of nde1 deficiency mutant zebrafish brains compared to wild type.		brain WT	strain:TU\|dev stage:2mpf\|sex:male\|tissue:brain\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio brain	B1	B1	RNA seq transcriptome librariy was prepared following TruSeqTM RNA sample preparation Kit from Illumina San Diego CA using 5g of total RNA. Shortly messenger RNA was isolated according to polyA selection method by oligodT beads and then fragmented by fragmentation buffer firstly. Secondly double stranded cDNA was synthesized using a SuperScript double stranded cDNA synthesis kit Invitrogen CA with random hexamer primers Illumina. Then the synthesized cDNA was subjected to end repair phosphorylation and A base addition according to Illuminas library construction protocol. Libraries were size selected for cDNA target fragments of 200300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. post quantified by TBS380 paired end RNA seq sequencing library was sequenced with the Illumina HiSeq 4000 2 150bp read length.	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP343978	B1.R1.fastq.gz B1.R2.fastq.gz	fastq fastq	6758464342.0	22379021.0	B1.R1.fastq.gz	0:151 1:151	A:1881676275;C:1495234309;G:1519420774;T:1862074223;N:58761	151	151	1881676275	1495234309	1519420774	1862074223	58761	SRX12875362	SRS10818488			Children's Hospital of Fudan University	2	0.94263	0.92421	0.13676	0.13324	0.69505	0.697	0.48389	0.48239	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	China	2021-11-02	Juvenile	Juvenile	Brain	Nervous System
68554	68554	SRR18010263	SRX14164590	SRS11988750	SRP359660	PRJNA806676	Transcriptome analysis of nomo1 homologous deficiency zebrafish	PRJNA806676	Other	This analysis revealed transcriptome level changes of brain of nomo1 homologous deficiency zebrafish.		nomo1	strain:nomo / \|dev stage:2mpf\|sex:male\|tissue:brain\|BioSampleModel:Model organism or animal	RNA seq of Danio rario: nomo1	nomo	nomo	RNA seq transcriptome librariy was prepared following TruSeqTM RNA sample preparation Kit from Illumina San Diego CA using 5g of total RNA. Shortly messenger RNA was isolated according to polyA selection method by oligodT beads and then fragmented by fragmentation buffer firstly. Secondly double stranded cDNA was synthesized using a SuperScript double stranded cDNA synthesis kit Invitrogen CA with random hexamer primers Illumina. Then the synthesized cDNA was subjected to end repair phosphorylation and A base addition according to Illuminas library construction protocol. Libraries were size selected for cDNA target fragments of 200300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. post quantified by TBS380 paired end RNA seq sequencing library was sequenced with the Illumina HiSeq 4000 2 150bp read length.	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP359660	NOMO_1.fq.gz NOMO_2.fq.gz	fastq fastq	7423945800.0	24746486.0	NOMO 1.fq.gz	0:150 1:150	A:2079187833;C:1643658691;G:1652867282;T:2048199003;N:32991	150	150	2079187833	1643658691	1652867282	2048199003	32991	SRX14164590	SRS11988750			Children's Hospital of Fudan University	2	0.93796	0.93625	0.16379	0.1632	0.69643	0.69842	0.48865	0.48976	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	China	2022-02-13	Juvenile	Juvenile	Brain	Nervous System
68555	68555	SRR18010264	SRX14164589	SRS11988749	SRP359660	PRJNA806676	Transcriptome analysis of nomo1 homologous deficiency zebrafish	PRJNA806676	Other	This analysis revealed transcriptome level changes of brain of nomo1 homologous deficiency zebrafish.		WT	strain:tu\|dev stage:2mpf\|sex:male\|tissue:brain\|BioSampleModel:Model organism or animal	RNA seq of Danio rario: TU	TU	TU	RNA seq transcriptome librariy was prepared following TruSeqTM RNA sample preparation Kit from Illumina San Diego CA using 5g of total RNA. Shortly messenger RNA was isolated according to polyA selection method by oligodT beads and then fragmented by fragmentation buffer firstly. Secondly double stranded cDNA was synthesized using a SuperScript double stranded cDNA synthesis kit Invitrogen CA with random hexamer primers Illumina. Then the synthesized cDNA was subjected to end repair phosphorylation and A base addition according to Illuminas library construction protocol. Libraries were size selected for cDNA target fragments of 200300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. post quantified by TBS380 paired end RNA seq sequencing library was sequenced with the Illumina HiSeq 4000 2 150bp read length.	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP359660	TU_1.fq.gz TU_2.fq.gz	fastq fastq	7981027200.0	26603424.0	TU 1.fq.gz	0:150 1:150	A:2246332345;C:1756444706;G:1767372264;T:2210842856;N:35029	150	150	2246332345	1756444706	1767372264	2210842856	35029	SRX14164589	SRS11988749			Children's Hospital of Fudan University	2	0.93375	0.93291	0.17081	0.17028	0.69755	0.69875	0.48942	0.49405	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	China	2022-02-13	Juvenile	Juvenile	Brain	Nervous System

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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");;