metadata: run_metadata: 12 rows where experiment.library_selection = "unspecified" and tissue_curation

12 rows where experiment.library_selection = "unspecified" and tissue_curation_coarse = "Sensory System"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	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.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.nofeature_rate.mate1	seqdetective.sparsity.mate1	seqdetective.pos_strand_rate.mate1	seqdetective.readlen.mate1	seqdetective.judgement.mate1	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
67683	67683	SRR17235493	SRX13414611	SRS11316492	SRP350846	PRJNA789116	RNAseq of Bbs1 KO Zebrafish larval eyes	PRJNA789116	Other	Bardet Biedl syndrome BBS is a ciliopathy characterized by retinal dystrophy intellectual disability polydactyly obesity and renal anomalies. In photoreceptors PR light sensation occurs in outer segments OSs which are specialized primary cilia. BBS1 the major BBS gene is part of a protein complex called BBSome which is involved in intracellular protein transport. However the precise function of BBS1/BBSome in controlling ciliary content in PRs remains unclear. To investigate the transcriptional consequences of a dysfunctional BBSome we established a new bbs1 zebrafish mutant. We conducted an eye specific RNAseq experiment using 5 dpf and 10 dpf maternal zygotic mutants and their heterozygous unaffected siblings as control. Differential expression analysis was used to investigate the expression levels at 5 and 10 days.	BBS1 MUT 10dpf S1	strain:Bbs1ka742\|age:10dpf\|dev stage:Larvae\|sex:not applicable\|tissue:Eye\|genotype: / \|Paired group:D\|BioSampleModel:Model organism or animal	RNA Seq of Danio Rerio: larval bbs1 mutant eye	BBS1 MUT 10dpf S1	BBS1 MUT 10dpf S1	TruSeq Stranded Total RNA Library Prep Gold	RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP350846	fasta file:Danio rerio.GRCz11.dna.primary assembly.fa\|assembly:GCA 000002035.4	BBS1_MUT_10dpf_S4_merged.bam Danio_rerio.GRCz11.dna.primary_assembly.fa	bam bam	3635985845.0	36892654.0	BBS1 MUT 10dpf S4 merged.bam	0:98.56	A:951181543;C:805662797;G:846180468;T:1032919946;N:41091	98	951181543	805662797	846180468	1032919946	41091	SRX13414611	SRS11316492	SRA1343787	University of Zurich (UZH)\|Molecular Life Science	University of Zurich (UZH)	1	0.93818	0.32197	0.69451	0.47394	101	B	usable mapping rate	illumina	novaseq_era	unknown	unknown	trueseq	bulk	bulk	bulk	Switzerland	2021-12-15	Larval	Larval	Eye	Sensory System
67684	67684	SRR17235494	SRX13414610	SRS11316490	SRP350846	PRJNA789116	RNAseq of Bbs1 KO Zebrafish larval eyes	PRJNA789116	Other	Bardet Biedl syndrome BBS is a ciliopathy characterized by retinal dystrophy intellectual disability polydactyly obesity and renal anomalies. In photoreceptors PR light sensation occurs in outer segments OSs which are specialized primary cilia. BBS1 the major BBS gene is part of a protein complex called BBSome which is involved in intracellular protein transport. However the precise function of BBS1/BBSome in controlling ciliary content in PRs remains unclear. To investigate the transcriptional consequences of a dysfunctional BBSome we established a new bbs1 zebrafish mutant. We conducted an eye specific RNAseq experiment using 5 dpf and 10 dpf maternal zygotic mutants and their heterozygous unaffected siblings as control. Differential expression analysis was used to investigate the expression levels at 5 and 10 days.	BBS1 CTRL 10dpf S3	strain:Bbs1ka742\|age:10dpf\|dev stage:Larvae\|sex:not applicable\|tissue:Eye\|genotype:+/ \|Paired group:F\|BioSampleModel:Model organism or animal	RNA Seq of Danio Rerio: larval bbs1 mutant eye	BBS1 CTRL 10dpf S3	BBS1 CTRL 10dpf S3	TruSeq Stranded Total RNA Library Prep Gold	RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP350846	fasta file:Danio rerio.GRCz11.dna.primary assembly.fa\|assembly:GCA 000002035.4	BBS1_CTRL_10dpf_S6_merged.bam Danio_rerio.GRCz11.dna.primary_assembly.fa	bam bam	3130875298.0	31620050.0	BBS1 CTRL 10dpf S6 merged.bam	0:99.02	A:814143728;C:694726254;G:728135378;T:893834285;N:35653	99	814143728	694726254	728135378	893834285	35653	SRX13414610	SRS11316490	SRA1343787	University of Zurich (UZH)\|Molecular Life Science	University of Zurich (UZH)	1	0.94014	0.33329	0.69735	0.47408	101	B	usable mapping rate	illumina	novaseq_era	unknown	unknown	trueseq	bulk	bulk	bulk	Switzerland	2021-12-15	Larval	Larval	Eye	Sensory System
67685	67685	SRR17235495	SRX13414609	SRS11316491	SRP350846	PRJNA789116	RNAseq of Bbs1 KO Zebrafish larval eyes	PRJNA789116	Other	Bardet Biedl syndrome BBS is a ciliopathy characterized by retinal dystrophy intellectual disability polydactyly obesity and renal anomalies. In photoreceptors PR light sensation occurs in outer segments OSs which are specialized primary cilia. BBS1 the major BBS gene is part of a protein complex called BBSome which is involved in intracellular protein transport. However the precise function of BBS1/BBSome in controlling ciliary content in PRs remains unclear. To investigate the transcriptional consequences of a dysfunctional BBSome we established a new bbs1 zebrafish mutant. We conducted an eye specific RNAseq experiment using 5 dpf and 10 dpf maternal zygotic mutants and their heterozygous unaffected siblings as control. Differential expression analysis was used to investigate the expression levels at 5 and 10 days.	BBS1 CTRL 10dpf S2	strain:Bbs1ka742\|age:10dpf\|dev stage:Larvae\|sex:not applicable\|tissue:Eye\|genotype:+/ \|Paired group:E\|BioSampleModel:Model organism or animal	RNA Seq of Danio Rerio: larval bbs1 mutant eye	BBS1 CTRL 10dpf S2	BBS1 CTRL 10dpf S2	TruSeq Stranded Total RNA Library Prep Gold	RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP350846	fasta file:Danio rerio.GRCz11.dna.primary assembly.fa\|assembly:GCA 000002035.4	BBS1_CTRL_10dpf_S5_merged.bam Danio_rerio.GRCz11.dna.primary_assembly.fa	bam bam	3062763746.0	31000736.0	BBS1 CTRL 10dpf S5 merged.bam	0:98.80	A:786649223;C:679725108;G:723425238;T:872929361;N:34816	98	786649223	679725108	723425238	872929361	34816	SRX13414609	SRS11316491	SRA1343787	University of Zurich (UZH)\|Molecular Life Science	University of Zurich (UZH)	1	0.94626	0.26532	0.68793	0.46861	101	B	usable mapping rate	illumina	novaseq_era	unknown	unknown	trueseq	bulk	bulk	bulk	Switzerland	2021-12-15	Larval	Larval	Eye	Sensory System
67686	67686	SRR17235496	SRX13414608	SRS11316489	SRP350846	PRJNA789116	RNAseq of Bbs1 KO Zebrafish larval eyes	PRJNA789116	Other	Bardet Biedl syndrome BBS is a ciliopathy characterized by retinal dystrophy intellectual disability polydactyly obesity and renal anomalies. In photoreceptors PR light sensation occurs in outer segments OSs which are specialized primary cilia. BBS1 the major BBS gene is part of a protein complex called BBSome which is involved in intracellular protein transport. However the precise function of BBS1/BBSome in controlling ciliary content in PRs remains unclear. To investigate the transcriptional consequences of a dysfunctional BBSome we established a new bbs1 zebrafish mutant. We conducted an eye specific RNAseq experiment using 5 dpf and 10 dpf maternal zygotic mutants and their heterozygous unaffected siblings as control. Differential expression analysis was used to investigate the expression levels at 5 and 10 days.	BBS1 Ctrl 10dpf S1	strain:Bbs1ka742\|age:10dpf\|dev stage:Larvae\|sex:not applicable\|tissue:Eye\|genotype:+/ \|Paired group:D\|BioSampleModel:Model organism or animal	RNA Seq of Danio Rerio: larval bbs1 mutant eye	BBS1 Ctrl 10dpf S1	BBS1 Ctrl 10dpf S1	TruSeq Stranded Total RNA Library Prep Gold	RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP350846	fasta file:Danio rerio.GRCz11.dna.primary assembly.fa\|assembly:GCA 000002035.4	BBS1_CTRL_10dpf_S4_merged.bam Danio_rerio.GRCz11.dna.primary_assembly.fa	bam bam	4388386557.0	44385344.0	BBS1 CTRL 10dpf S4 merged.bam	0:98.87	A:1141948730;C:979155774;G:1019331809;T:1247901031;N:49213	98	1141948730	979155774	1019331809	1247901031	49213	SRX13414608	SRS11316489	SRA1343787	University of Zurich (UZH)\|Molecular Life Science	University of Zurich (UZH)	1	0.94326	0.28573	0.69296	0.47244	101	B	usable mapping rate	illumina	novaseq_era	unknown	unknown	trueseq	bulk	bulk	bulk	Switzerland	2021-12-15	Larval	Larval	Eye	Sensory System
67687	67687	SRR17235497	SRX13414607	SRS11316488	SRP350846	PRJNA789116	RNAseq of Bbs1 KO Zebrafish larval eyes	PRJNA789116	Other	Bardet Biedl syndrome BBS is a ciliopathy characterized by retinal dystrophy intellectual disability polydactyly obesity and renal anomalies. In photoreceptors PR light sensation occurs in outer segments OSs which are specialized primary cilia. BBS1 the major BBS gene is part of a protein complex called BBSome which is involved in intracellular protein transport. However the precise function of BBS1/BBSome in controlling ciliary content in PRs remains unclear. To investigate the transcriptional consequences of a dysfunctional BBSome we established a new bbs1 zebrafish mutant. We conducted an eye specific RNAseq experiment using 5 dpf and 10 dpf maternal zygotic mutants and their heterozygous unaffected siblings as control. Differential expression analysis was used to investigate the expression levels at 5 and 10 days.	BBS1 MUT 5dpf S3	strain:Bbs1ka742\|age:5dpf\|dev stage:Larvae\|sex:not applicable\|tissue:Eye\|genotype: / \|Paired group:C\|BioSampleModel:Model organism or animal	RNA Seq of Danio Rerio: larval bbs1 mutant eye	BBS1 MUT 5dpf S3	BBS1 MUT 5dpf S3	TruSeq Stranded Total RNA Library Prep Gold	RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP350846	fasta file:Danio rerio.GRCz11.dna.primary assembly.fa\|assembly:GCA 000002035.4	BBS1_MUT_5dpf_S3_merged.bam Danio_rerio.GRCz11.dna.primary_assembly.fa	bam bam	3030482374.0	30617366.0	BBS1 MUT 5dpf S3 merged.bam	0:98.98	A:813926164;C:646079228;G:694857531;T:875585698;N:33753	98	813926164	646079228	694857531	875585698	33753	SRX13414607	SRS11316488	SRA1343787	University of Zurich (UZH)\|Molecular Life Science	University of Zurich (UZH)	1	0.92861	0.41464	0.69051	0.49332	101	B	usable mapping rate	illumina	novaseq_era	unknown	unknown	trueseq	bulk	bulk	bulk	Switzerland	2021-12-15	Larval	Larval	Eye	Sensory System
67688	67688	SRR17235498	SRX13414606	SRS11316487	SRP350846	PRJNA789116	RNAseq of Bbs1 KO Zebrafish larval eyes	PRJNA789116	Other	Bardet Biedl syndrome BBS is a ciliopathy characterized by retinal dystrophy intellectual disability polydactyly obesity and renal anomalies. In photoreceptors PR light sensation occurs in outer segments OSs which are specialized primary cilia. BBS1 the major BBS gene is part of a protein complex called BBSome which is involved in intracellular protein transport. However the precise function of BBS1/BBSome in controlling ciliary content in PRs remains unclear. To investigate the transcriptional consequences of a dysfunctional BBSome we established a new bbs1 zebrafish mutant. We conducted an eye specific RNAseq experiment using 5 dpf and 10 dpf maternal zygotic mutants and their heterozygous unaffected siblings as control. Differential expression analysis was used to investigate the expression levels at 5 and 10 days.	BBS1 MUT 5dpf S2	strain:Bbs1ka742\|age:5dpf\|dev stage:Larvae\|sex:not applicable\|tissue:Eye\|genotype: / \|Paired group:B\|BioSampleModel:Model organism or animal	RNA Seq of Danio Rerio: larval bbs1 mutant eye	BBS1 MUT 5dpf S2	BBS1 MUT 5dpf S2	TruSeq Stranded Total RNA Library Prep Gold	RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP350846	fasta file:Danio rerio.GRCz11.dna.primary assembly.fa\|assembly:GCA 000002035.4	BBS1_MUT_5dpf_S2_merged.bam Danio_rerio.GRCz11.dna.primary_assembly.fa	bam bam	3714404169.0	37505417.0	BBS1 MUT 5dpf S2 merged.bam	0:99.04	A:968857332;C:821571707;G:867307403;T:1056625911;N:41816	99	968857332	821571707	867307403	1056625911	41816	SRX13414606	SRS11316487	SRA1343787	University of Zurich (UZH)\|Molecular Life Science	University of Zurich (UZH)	1	0.93912	0.32694	0.68781	0.48549	101	B	usable mapping rate	illumina	novaseq_era	unknown	unknown	trueseq	bulk	bulk	bulk	Switzerland	2021-12-15	Larval	Larval	Eye	Sensory System
67689	67689	SRR17235499	SRX13414605	SRS11316486	SRP350846	PRJNA789116	RNAseq of Bbs1 KO Zebrafish larval eyes	PRJNA789116	Other	Bardet Biedl syndrome BBS is a ciliopathy characterized by retinal dystrophy intellectual disability polydactyly obesity and renal anomalies. In photoreceptors PR light sensation occurs in outer segments OSs which are specialized primary cilia. BBS1 the major BBS gene is part of a protein complex called BBSome which is involved in intracellular protein transport. However the precise function of BBS1/BBSome in controlling ciliary content in PRs remains unclear. To investigate the transcriptional consequences of a dysfunctional BBSome we established a new bbs1 zebrafish mutant. We conducted an eye specific RNAseq experiment using 5 dpf and 10 dpf maternal zygotic mutants and their heterozygous unaffected siblings as control. Differential expression analysis was used to investigate the expression levels at 5 and 10 days.	BBS1 MUT 5dpf S1	strain:Bbs1ka742\|age:5dpf\|dev stage:Larvae\|sex:not applicable\|tissue:Eye\|genotype: / \|Paired group:A\|BioSampleModel:Model organism or animal	RNA Seq of Danio Rerio: larval bbs1 mutant eye	BBS1 MUT 5dpf S1	BBS1 MUT 5dpf S1	TruSeq Stranded Total RNA Library Prep Gold	RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP350846	fasta file:Danio rerio.GRCz11.dna.primary assembly.fa\|assembly:GCA 000002035.4	BBS1_MUT_5dpf_S1_merged.bam Danio_rerio.GRCz11.dna.primary_assembly.fa	bam bam	3699896449.0	37382583.0	BBS1 MUT 5dpf S1 merged.bam	0:98.97	A:977907912;C:830475992;G:855441672;T:1036029492;N:41381	98	977907912	830475992	855441672	1036029492	41381	SRX13414605	SRS11316486	SRA1343787	University of Zurich (UZH)\|Molecular Life Science	University of Zurich (UZH)	1	0.93133	0.40806	0.69562	0.5114	101	B	usable mapping rate	illumina	novaseq_era	unknown	unknown	trueseq	bulk	bulk	bulk	Switzerland	2021-12-15	Larval	Larval	Eye	Sensory System
67690	67690	SRR17235500	SRX13414604	SRS11316485	SRP350846	PRJNA789116	RNAseq of Bbs1 KO Zebrafish larval eyes	PRJNA789116	Other	Bardet Biedl syndrome BBS is a ciliopathy characterized by retinal dystrophy intellectual disability polydactyly obesity and renal anomalies. In photoreceptors PR light sensation occurs in outer segments OSs which are specialized primary cilia. BBS1 the major BBS gene is part of a protein complex called BBSome which is involved in intracellular protein transport. However the precise function of BBS1/BBSome in controlling ciliary content in PRs remains unclear. To investigate the transcriptional consequences of a dysfunctional BBSome we established a new bbs1 zebrafish mutant. We conducted an eye specific RNAseq experiment using 5 dpf and 10 dpf maternal zygotic mutants and their heterozygous unaffected siblings as control. Differential expression analysis was used to investigate the expression levels at 5 and 10 days.	BBS1 CTRL 5dpf S3	strain:Bbs1ka742\|age:5dpf\|dev stage:Larvae\|sex:not applicable\|tissue:Eye\|genotype:+/ \|Paired group:C\|BioSampleModel:Model organism or animal	RNA Seq of Danio Rerio: larval bbs1 mutant eye	BBS1 CTRL 5dpf S3	BBS1 CTRL 5dpf S3	TruSeq Stranded Total RNA Library Prep Gold	RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP350846	fasta file:Danio rerio.GRCz11.dna.primary assembly.fa\|assembly:GCA 000002035.4	BBS1_CTRL_5dpf_S3_merged.bam Danio_rerio.GRCz11.dna.primary_assembly.fa	bam bam	3505192259.0	35384389.0	BBS1 CTRL 5dpf S3 merged.bam	0:99.06	A:910433958;C:775887812;G:822289434;T:996540997;N:40058	99	910433958	775887812	822289434	996540997	40058	SRX13414604	SRS11316485	SRA1343787	University of Zurich (UZH)\|Molecular Life Science	University of Zurich (UZH)	1	0.94274	0.28843	0.68678	0.47383	101	B	usable mapping rate	illumina	novaseq_era	unknown	unknown	trueseq	bulk	bulk	bulk	Switzerland	2021-12-15	Larval	Larval	Eye	Sensory System
67691	67691	SRR17235501	SRX13414603	SRS11316483	SRP350846	PRJNA789116	RNAseq of Bbs1 KO Zebrafish larval eyes	PRJNA789116	Other	Bardet Biedl syndrome BBS is a ciliopathy characterized by retinal dystrophy intellectual disability polydactyly obesity and renal anomalies. In photoreceptors PR light sensation occurs in outer segments OSs which are specialized primary cilia. BBS1 the major BBS gene is part of a protein complex called BBSome which is involved in intracellular protein transport. However the precise function of BBS1/BBSome in controlling ciliary content in PRs remains unclear. To investigate the transcriptional consequences of a dysfunctional BBSome we established a new bbs1 zebrafish mutant. We conducted an eye specific RNAseq experiment using 5 dpf and 10 dpf maternal zygotic mutants and their heterozygous unaffected siblings as control. Differential expression analysis was used to investigate the expression levels at 5 and 10 days.	BBS1 MUT 10dpf S3	strain:Bbs1ka742\|age:10dpf\|dev stage:Larvae\|sex:not applicable\|tissue:Eye\|genotype: / \|Paired group:F\|BioSampleModel:Model organism or animal	RNA Seq of Danio Rerio: larval bbs1 mutant eye	BBS1 MUT 10dpf S3	BBS1 MUT 10dpf S3	TruSeq Stranded Total RNA Library Prep Gold	RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP350846	fasta file:Danio rerio.GRCz11.dna.primary assembly.fa\|assembly:GCA 000002035.4	BBS1_MUT_10dpf_S6_merged.bam Danio_rerio.GRCz11.dna.primary_assembly.fa	bam bam	3821277753.0	38662066.0	BBS1 MUT 10dpf S6 merged.bam	0:98.84	A:1019329287;C:820362185;G:870436357;T:1111106893;N:43031	98	1019329287	820362185	870436357	1111106893	43031	SRX13414603	SRS11316483	SRA1343787	University of Zurich (UZH)\|Molecular Life Science	University of Zurich (UZH)	1	0.93021	0.40772	0.70019	0.47824	101	B	usable mapping rate	illumina	novaseq_era	unknown	unknown	trueseq	bulk	bulk	bulk	Switzerland	2021-12-15	Larval	Larval	Eye	Sensory System
67692	67692	SRR17235502	SRX13414602	SRS11316484	SRP350846	PRJNA789116	RNAseq of Bbs1 KO Zebrafish larval eyes	PRJNA789116	Other	Bardet Biedl syndrome BBS is a ciliopathy characterized by retinal dystrophy intellectual disability polydactyly obesity and renal anomalies. In photoreceptors PR light sensation occurs in outer segments OSs which are specialized primary cilia. BBS1 the major BBS gene is part of a protein complex called BBSome which is involved in intracellular protein transport. However the precise function of BBS1/BBSome in controlling ciliary content in PRs remains unclear. To investigate the transcriptional consequences of a dysfunctional BBSome we established a new bbs1 zebrafish mutant. We conducted an eye specific RNAseq experiment using 5 dpf and 10 dpf maternal zygotic mutants and their heterozygous unaffected siblings as control. Differential expression analysis was used to investigate the expression levels at 5 and 10 days.	BBS1 MUT 10dpf S2	strain:Bbs1ka742\|age:10dpf\|dev stage:Larvae\|sex:not applicable\|tissue:Eye\|genotype: / \|Paired group:E\|BioSampleModel:Model organism or animal	RNA Seq of Danio Rerio: larval bbs1 mutant eye	BBS1 MUT 10dpf S2	BBS1 MUT 10dpf S2	TruSeq Stranded Total RNA Library Prep Gold	RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP350846	fasta file:Danio rerio.GRCz11.dna.primary assembly.fa\|assembly:GCA 000002035.4	BBS1_MUT_10dpf_S5_merged.bam Danio_rerio.GRCz11.dna.primary_assembly.fa	bam bam	2747848263.0	27781273.0	BBS1 MUT 10dpf S5 merged.bam	0:98.91	A:726140802;C:605265574;G:628347573;T:788063451;N:30863	98	726140802	605265574	628347573	788063451	30863	SRX13414602	SRS11316484	SRA1343787	University of Zurich (UZH)\|Molecular Life Science	University of Zurich (UZH)	1	0.93216	0.39301	0.70009	0.50624	101	B	usable mapping rate	illumina	novaseq_era	unknown	unknown	trueseq	bulk	bulk	bulk	Switzerland	2021-12-15	Larval	Larval	Eye	Sensory System
67693	67693	SRR17235503	SRX13414601	SRS11316482	SRP350846	PRJNA789116	RNAseq of Bbs1 KO Zebrafish larval eyes	PRJNA789116	Other	Bardet Biedl syndrome BBS is a ciliopathy characterized by retinal dystrophy intellectual disability polydactyly obesity and renal anomalies. In photoreceptors PR light sensation occurs in outer segments OSs which are specialized primary cilia. BBS1 the major BBS gene is part of a protein complex called BBSome which is involved in intracellular protein transport. However the precise function of BBS1/BBSome in controlling ciliary content in PRs remains unclear. To investigate the transcriptional consequences of a dysfunctional BBSome we established a new bbs1 zebrafish mutant. We conducted an eye specific RNAseq experiment using 5 dpf and 10 dpf maternal zygotic mutants and their heterozygous unaffected siblings as control. Differential expression analysis was used to investigate the expression levels at 5 and 10 days.	BBS1 CTRL 5dpf S2	strain:Bbs1ka742\|age:5dpf\|dev stage:Larvae\|sex:not applicable\|tissue:Eye\|genotype:+/ \|Paired group:B\|BioSampleModel:Model organism or animal	RNA Seq of Danio Rerio: larval bbs1 mutant eye	BBS1 CTRL 5dpf S2	BBS1 CTRL 5dpf S2	TruSeq Stranded Total RNA Library Prep Gold	RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP350846	fasta file:Danio rerio.GRCz11.dna.primary assembly.fa\|assembly:GCA 000002035.4	BBS1_CTRL_5dpf_S2_merged.bam Danio_rerio.GRCz11.dna.primary_assembly.fa	bam bam	3371457502.0	33990750.0	BBS1 CTRL 5dpf S2 merged.bam	0:99.19	A:865249225;C:752466820;G:799272800;T:954431124;N:37533	99	865249225	752466820	799272800	954431124	37533	SRX13414601	SRS11316482	SRA1343787	University of Zurich (UZH)\|Molecular Life Science	University of Zurich (UZH)	1	0.94297	0.30382	0.68523	0.49502	101	B	usable mapping rate	illumina	novaseq_era	unknown	unknown	trueseq	bulk	bulk	bulk	Switzerland	2021-12-15	Larval	Larval	Eye	Sensory System
67694	67694	SRR17235504	SRX13414600	SRS11316481	SRP350846	PRJNA789116	RNAseq of Bbs1 KO Zebrafish larval eyes	PRJNA789116	Other	Bardet Biedl syndrome BBS is a ciliopathy characterized by retinal dystrophy intellectual disability polydactyly obesity and renal anomalies. In photoreceptors PR light sensation occurs in outer segments OSs which are specialized primary cilia. BBS1 the major BBS gene is part of a protein complex called BBSome which is involved in intracellular protein transport. However the precise function of BBS1/BBSome in controlling ciliary content in PRs remains unclear. To investigate the transcriptional consequences of a dysfunctional BBSome we established a new bbs1 zebrafish mutant. We conducted an eye specific RNAseq experiment using 5 dpf and 10 dpf maternal zygotic mutants and their heterozygous unaffected siblings as control. Differential expression analysis was used to investigate the expression levels at 5 and 10 days.	BBS1 CTRL 5dpf S1	strain:Bbs1ka742\|age:5dpf\|dev stage:Larvae\|sex:not applicable\|tissue:Eye\|genotype:+/ \|Paired group:A\|BioSampleModel:Model organism or animal	RNA Seq of Danio Rerio: larval bbs1 mutant eye	BBS1 CTRL 5dpf S1	BBS1 CTRL 5dpf S1	TruSeq Stranded Total RNA Library Prep Gold	RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP350846	fasta file:Danio rerio.GRCz11.dna.primary assembly.fa\|assembly:GCA 000002035.4	BBS1_CTRL_5dpf_S1_merged.bam Danio_rerio.GRCz11.dna.primary_assembly.fa	bam bam	3243942424.0	32951170.0	BBS1 CTRL 5dpf S1 merged.bam	0:98.45	A:886651528;C:694664952;G:729637645;T:932951711;N:36588	98	886651528	694664952	729637645	932951711	36588	SRX13414600	SRS11316481	SRA1343787	University of Zurich (UZH)\|Molecular Life Science	University of Zurich (UZH)	1	0.92662	0.42838	0.69404	0.48808	101	B	usable mapping rate	illumina	novaseq_era	unknown	unknown	trueseq	bulk	bulk	bulk	Switzerland	2021-12-15	Larval	Larval	Eye	Sensory 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");;