metadata: run_metadata: 12 rows where experiment.library_layout = "SINGLE", experiment.library_selection = "PCR" and tissue_curation

12 rows where experiment.library_layout = "SINGLE", experiment.library_selection = "PCR" and tissue_curation_coarse = "Nervous System"

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.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
52216	52216	SRR9164636	SRX5937422	SRS4850458	SRP199963	PRJNA541414	Danio rerio Raw sequence reads	PRJNA541414	Other	In most vertebrates including zebrafish the hypothalamicserotonergic cerebrospinal fluid contacting CSF c cells constitutea prominent population. In contrast to the hindbrain serotonergicneurons little is known about the development and function of thesecells. Here we identify fibroblast growth factor Fgf 3 as the main Fgfligand controlling the ontogeny of serotonergic CSF c cells. We showthat fgf3 positively regulates the number of serotonergic CSF c cells as well as a subset of dopaminergic and neuroendocrine cells in theposterior hypothalamus via control of proliferation and cell survival.Further expression of the ETS domain transcription factor etv5b isdownregulated post fgf3 impairment. Previous findings identifiedetv5b as critical for the proliferation of serotonergic progenitors in thehypothalamus and therefore we now suggest that Fgf3 acts via etv5bduring early development to ultimately control the number of matureserotonergic CSF c cells. Moreover our analysis of the developinghypothalamic transcriptome shows that the expression of fgf3 isupregulated upon fgf3 loss of function suggesting activation of a self compensatory mechanism. Together these results highlight Fgf3 in anovel context as part of a signalling pathway of critical importance forhypothalamic development.	wt +/+ 3dpf 3	wt +/+ 3dpf 3	filename:L1700046 Probe 20 plus plus 3dpf 1 2.fq.gz\|strain:Tuebingen\|dev stage:embryo\|sex:not determined\|tissue:hypothalamus\|BioSampleModel:Model organism or animal	wt +/+ 3dpf 3	wt +/+ 3dpf 3	wt +/+ 3dpf 3	library preparation was performed according to the Illumina TruSeq stranded mRNA Samples Preparation Guide with 100 ng of input RNA and 15 PCR cycles	RNA-Seq	TRANSCRIPTOMIC	PCR	SINGLE	ILLUMINA	NextSeq 500	SRP199963	L1700046_Probe_20_plus_plus_3dpf_1_2.fq.gz	fastq	2506233674.0	16597574.0	L1700046 Probe 20 plus plus 3dpf 1 2.fq.gz	0:151 1:0	A:634000443;C:604069545;G:613398240;T:654463196;N:302250	151	634000443	604069545	613398240	654463196	302250	SRX5937422	SRS4850458	SRA892447	University of Wuerzburg\|Department for Physiological Chemistry	University of Wuerzburg	1	0.96178	0.07984	0.72125	0.48053	151	B	usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	bulk	unknown	unknown	Germany	2019-05-31	Larval	Larval	Brain	Nervous System
52217	52217	SRR9164637	SRX5937421	SRS4850457	SRP199963	PRJNA541414	Danio rerio Raw sequence reads	PRJNA541414	Other	In most vertebrates including zebrafish the hypothalamicserotonergic cerebrospinal fluid contacting CSF c cells constitutea prominent population. In contrast to the hindbrain serotonergicneurons little is known about the development and function of thesecells. Here we identify fibroblast growth factor Fgf 3 as the main Fgfligand controlling the ontogeny of serotonergic CSF c cells. We showthat fgf3 positively regulates the number of serotonergic CSF c cells as well as a subset of dopaminergic and neuroendocrine cells in theposterior hypothalamus via control of proliferation and cell survival.Further expression of the ETS domain transcription factor etv5b isdownregulated post fgf3 impairment. Previous findings identifiedetv5b as critical for the proliferation of serotonergic progenitors in thehypothalamus and therefore we now suggest that Fgf3 acts via etv5bduring early development to ultimately control the number of matureserotonergic CSF c cells. Moreover our analysis of the developinghypothalamic transcriptome shows that the expression of fgf3 isupregulated upon fgf3 loss of function suggesting activation of a self compensatory mechanism. Together these results highlight Fgf3 in anovel context as part of a signalling pathway of critical importance forhypothalamic development.	wt +/+ 3dpf 2	wt +/+ 3dpf 2	filename:L1700052 Probe 14 plus plus 3dpf 4.fq.gz\|strain:Tuebingen\|dev stage:embryo\|sex:not determined\|tissue:hypothalamus\|BioSampleModel:Model organism or animal	wt +/+ 3dpf 2	wt +/+ 3dpf 2	wt +/+ 3dpf 2	library preparation was performed according to the Illumina TruSeq stranded mRNA Samples Preparation Guide with 100 ng of input RNA and 15 PCR cycles	RNA-Seq	TRANSCRIPTOMIC	PCR	SINGLE	ILLUMINA	NextSeq 500	SRP199963	L1700052_Probe_14_plus_plus_3dpf_4.fq.gz	fastq	2552457794.0	16903694.0	L1700052 Probe 14 plus plus 3dpf 4.fq.gz	0:151 1:0	A:645631711;C:614227022;G:612129428;T:680168081;N:301552	151	645631711	614227022	612129428	680168081	301552	SRX5937421	SRS4850457	SRA892447	University of Wuerzburg\|Department for Physiological Chemistry	University of Wuerzburg	1	0.96269	0.07747	0.71871	0.48604	151	B	usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	bulk	unknown	unknown	Germany	2019-05-31	Larval	Larval	Brain	Nervous System
52218	52218	SRR9164638	SRX5937420	SRS4850456	SRP199963	PRJNA541414	Danio rerio Raw sequence reads	PRJNA541414	Other	In most vertebrates including zebrafish the hypothalamicserotonergic cerebrospinal fluid contacting CSF c cells constitutea prominent population. In contrast to the hindbrain serotonergicneurons little is known about the development and function of thesecells. Here we identify fibroblast growth factor Fgf 3 as the main Fgfligand controlling the ontogeny of serotonergic CSF c cells. We showthat fgf3 positively regulates the number of serotonergic CSF c cells as well as a subset of dopaminergic and neuroendocrine cells in theposterior hypothalamus via control of proliferation and cell survival.Further expression of the ETS domain transcription factor etv5b isdownregulated post fgf3 impairment. Previous findings identifiedetv5b as critical for the proliferation of serotonergic progenitors in thehypothalamus and therefore we now suggest that Fgf3 acts via etv5bduring early development to ultimately control the number of matureserotonergic CSF c cells. Moreover our analysis of the developinghypothalamic transcriptome shows that the expression of fgf3 isupregulated upon fgf3 loss of function suggesting activation of a self compensatory mechanism. Together these results highlight Fgf3 in anovel context as part of a signalling pathway of critical importance forhypothalamic development.	fgf3t24152 / 7dpf 2	fgf3t24152 / 7dpf 2	filename:L1700048 Probe 22 minus minus 7dpf 4 5.fq.gz\|strain:Tuebingen\|dev stage:embryo\|sex:not determined\|tissue:hypothalamus\|BioSampleModel:Model organism or animal	fgf3t24152 / 7dpf 2	fgf3t24152 / 7dpf 2	fgf3t24152 / 7dpf 2	library preparation was performed according to the Illumina TruSeq stranded mRNA Samples Preparation Guide with 100 ng of input RNA and 15 PCR cycles	RNA-Seq	TRANSCRIPTOMIC	PCR	SINGLE	ILLUMINA	NextSeq 500	SRP199963	L1700048_Probe_22_minus_minus_7dpf_4_5.fq.gz	fastq	2516535951.0	16665801.0	L1700048 Probe 22 minus minus 7dpf 4 5.fq.gz	0:151 1:0	A:660865986;C:587075382;G:595275252;T:673011628;N:307703	151	660865986	587075382	595275252	673011628	307703	SRX5937420	SRS4850456	SRA892447	University of Wuerzburg\|Department for Physiological Chemistry	University of Wuerzburg	1	0.9567	0.10788	0.7134	0.51087	151	B	usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	bulk	unknown	unknown	Germany	2019-05-31	Larval	Larval	Brain	Nervous System
52219	52219	SRR9164639	SRX5937419	SRS4850455	SRP199963	PRJNA541414	Danio rerio Raw sequence reads	PRJNA541414	Other	In most vertebrates including zebrafish the hypothalamicserotonergic cerebrospinal fluid contacting CSF c cells constitutea prominent population. In contrast to the hindbrain serotonergicneurons little is known about the development and function of thesecells. Here we identify fibroblast growth factor Fgf 3 as the main Fgfligand controlling the ontogeny of serotonergic CSF c cells. We showthat fgf3 positively regulates the number of serotonergic CSF c cells as well as a subset of dopaminergic and neuroendocrine cells in theposterior hypothalamus via control of proliferation and cell survival.Further expression of the ETS domain transcription factor etv5b isdownregulated post fgf3 impairment. Previous findings identifiedetv5b as critical for the proliferation of serotonergic progenitors in thehypothalamus and therefore we now suggest that Fgf3 acts via etv5bduring early development to ultimately control the number of matureserotonergic CSF c cells. Moreover our analysis of the developinghypothalamic transcriptome shows that the expression of fgf3 isupregulated upon fgf3 loss of function suggesting activation of a self compensatory mechanism. Together these results highlight Fgf3 in anovel context as part of a signalling pathway of critical importance forhypothalamic development.	fgf3t24152 / 7dpf 1	fgf3t24152 / 7dpf 1	filename:L1700047 Probe 21 minus minus 7dpf 1 2.fq.gz\|strain:Tuebingen\|dev stage:embryo\|sex:not determined\|tissue:hypothalamus\|BioSampleModel:Model organism or animal	fgf3t24152 / 7dpf 1	fgf3t24152 / 7dpf 1	fgf3t24152 / 7dpf 1	library preparation was performed according to the Illumina TruSeq stranded mRNA Samples Preparation Guide with 100 ng of input RNA and 15 PCR cycles	RNA-Seq	TRANSCRIPTOMIC	PCR	SINGLE	ILLUMINA	NextSeq 500	SRP199963	L1700047_Probe_21_minus_minus_7dpf_1_2.fq.gz	fastq	2466014673.0	16331223.0	L1700047 Probe 21 minus minus 7dpf 1 2.fq.gz	0:151 1:0	A:625570716;C:591147110;G:589476430;T:659526551;N:293866	151	625570716	591147110	589476430	659526551	293866	SRX5937419	SRS4850455	SRA892447	University of Wuerzburg\|Department for Physiological Chemistry	University of Wuerzburg	1	0.95779	0.09881	0.71206	0.49427	151	B	usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	bulk	unknown	unknown	Germany	2019-05-31	Larval	Larval	Brain	Nervous System
52220	52220	SRR9164640	SRX5937418	SRS4850454	SRP199963	PRJNA541414	Danio rerio Raw sequence reads	PRJNA541414	Other	In most vertebrates including zebrafish the hypothalamicserotonergic cerebrospinal fluid contacting CSF c cells constitutea prominent population. In contrast to the hindbrain serotonergicneurons little is known about the development and function of thesecells. Here we identify fibroblast growth factor Fgf 3 as the main Fgfligand controlling the ontogeny of serotonergic CSF c cells. We showthat fgf3 positively regulates the number of serotonergic CSF c cells as well as a subset of dopaminergic and neuroendocrine cells in theposterior hypothalamus via control of proliferation and cell survival.Further expression of the ETS domain transcription factor etv5b isdownregulated post fgf3 impairment. Previous findings identifiedetv5b as critical for the proliferation of serotonergic progenitors in thehypothalamus and therefore we now suggest that Fgf3 acts via etv5bduring early development to ultimately control the number of matureserotonergic CSF c cells. Moreover our analysis of the developinghypothalamic transcriptome shows that the expression of fgf3 isupregulated upon fgf3 loss of function suggesting activation of a self compensatory mechanism. Together these results highlight Fgf3 in anovel context as part of a signalling pathway of critical importance forhypothalamic development.	fgf3t24152 / 3dpf 2	fgf3t24152 / 3dpf 2	filename:L1700045 Probe 19 minus minus 3dpf 3 4 5.fq.gz\|strain:Tuebingen\|dev stage:embryo\|sex:not determined\|tissue:hypothalamus\|BioSampleModel:Model organism or animal	fgf3t24152 / 3dpf 2	fgf3t24152 / 3dpf 2	fgf3t24152 / 3dpf 2	library preparation was performed according to the Illumina TruSeq stranded mRNA Samples Preparation Guide with 100 ng of input RNA and 15 PCR cycles	RNA-Seq	TRANSCRIPTOMIC	PCR	SINGLE	ILLUMINA	NextSeq 500	SRP199963	L1700045_Probe_19_minus_minus_3dpf_3_4_5.fq.gz	fastq	2409258605.0	15955355.0	L1700045 Probe 19 minus minus 3dpf 3 4 5.fq.gz	0:151 1:0	A:608760544;C:578294028;G:574909172;T:647001344;N:293517	151	608760544	578294028	574909172	647001344	293517	SRX5937418	SRS4850454	SRA892447	University of Wuerzburg\|Department for Physiological Chemistry	University of Wuerzburg	1	0.96392	0.07974	0.71467	0.47801	151	B	usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	bulk	unknown	unknown	Germany	2019-05-31	Larval	Larval	Brain	Nervous System
52221	52221	SRR9164641	SRX5937417	SRS4850453	SRP199963	PRJNA541414	Danio rerio Raw sequence reads	PRJNA541414	Other	In most vertebrates including zebrafish the hypothalamicserotonergic cerebrospinal fluid contacting CSF c cells constitutea prominent population. In contrast to the hindbrain serotonergicneurons little is known about the development and function of thesecells. Here we identify fibroblast growth factor Fgf 3 as the main Fgfligand controlling the ontogeny of serotonergic CSF c cells. We showthat fgf3 positively regulates the number of serotonergic CSF c cells as well as a subset of dopaminergic and neuroendocrine cells in theposterior hypothalamus via control of proliferation and cell survival.Further expression of the ETS domain transcription factor etv5b isdownregulated post fgf3 impairment. Previous findings identifiedetv5b as critical for the proliferation of serotonergic progenitors in thehypothalamus and therefore we now suggest that Fgf3 acts via etv5bduring early development to ultimately control the number of matureserotonergic CSF c cells. Moreover our analysis of the developinghypothalamic transcriptome shows that the expression of fgf3 isupregulated upon fgf3 loss of function suggesting activation of a self compensatory mechanism. Together these results highlight Fgf3 in anovel context as part of a signalling pathway of critical importance forhypothalamic development.	fgf3t24152 / 3dpf 1	fgf3t24152 / 3dpf 1	filename:L1700044 Probe 1 minus minus 3dpf 1.fq.gz\|strain:Tuebingen\|dev stage:embryo\|sex:not determined\|tissue:hypothalamus\|BioSampleModel:Model organism or animal	fgf3t24152 / 3dpf 1	fgf3t24152 / 3dpf 1	fgf3t24152 / 3dpf 1	library preparation was performed according to the Illumina TruSeq stranded mRNA Samples Preparation Guide with 100 ng of input RNA and 15 PCR cycles	RNA-Seq	TRANSCRIPTOMIC	PCR	SINGLE	ILLUMINA	NextSeq 500	SRP199963	L1700044_Probe_1_minus_minus_3dpf_1.fq.gz	fastq	2424787596.0	16058196.0	L1700044 Probe 1 minus minus 3dpf 1.fq.gz	0:151 1:0	A:605667403;C:588658821;G:580998119;T:649175582;N:287671	151	605667403	588658821	580998119	649175582	287671	SRX5937417	SRS4850453	SRA892447	University of Wuerzburg\|Department for Physiological Chemistry	University of Wuerzburg	1	0.96678	0.07043	0.72151	0.4886	151	B	usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	bulk	unknown	unknown	Germany	2019-05-31	Larval	Larval	Brain	Nervous System
52222	52222	SRR9164642	SRX5937416	SRS4850452	SRP199963	PRJNA541414	Danio rerio Raw sequence reads	PRJNA541414	Other	In most vertebrates including zebrafish the hypothalamicserotonergic cerebrospinal fluid contacting CSF c cells constitutea prominent population. In contrast to the hindbrain serotonergicneurons little is known about the development and function of thesecells. Here we identify fibroblast growth factor Fgf 3 as the main Fgfligand controlling the ontogeny of serotonergic CSF c cells. We showthat fgf3 positively regulates the number of serotonergic CSF c cells as well as a subset of dopaminergic and neuroendocrine cells in theposterior hypothalamus via control of proliferation and cell survival.Further expression of the ETS domain transcription factor etv5b isdownregulated post fgf3 impairment. Previous findings identifiedetv5b as critical for the proliferation of serotonergic progenitors in thehypothalamus and therefore we now suggest that Fgf3 acts via etv5bduring early development to ultimately control the number of matureserotonergic CSF c cells. Moreover our analysis of the developinghypothalamic transcriptome shows that the expression of fgf3 isupregulated upon fgf3 loss of function suggesting activation of a self compensatory mechanism. Together these results highlight Fgf3 in anovel context as part of a signalling pathway of critical importance forhypothalamic development.	wt +/+ 7dpf 3	wt +/+ 7dpf 3	filename:L1700055 Probe 16 plus plus 7dpf 4.fq.gz\|strain:Tuebingen\|dev stage:embryo\|sex:not determined\|tissue:hypothalamus\|BioSampleModel:Model organism or animal	wt +/+ 7dpf 3	wt +/+ 7dpf 3	wt +/+ 7dpf 3	library preparation was performed according to the Illumina TruSeq stranded mRNA Samples Preparation Guide with 100 ng of input RNA and 15 PCR cycles	RNA-Seq	TRANSCRIPTOMIC	PCR	SINGLE	ILLUMINA	NextSeq 500	SRP199963	L1700055_Probe_16_plus_plus_7dpf_4.fq.gz	fastq	2406426147.0	15936597.0	L1700055 Probe 16 plus plus 7dpf 4.fq.gz	0:151 1:0	A:621628027;C:570510169;G:570560525;T:643440348;N:287078	151	621628027	570510169	570560525	643440348	287078	SRX5937416	SRS4850452	SRA892447	University of Wuerzburg\|Department for Physiological Chemistry	University of Wuerzburg	1	0.95873	0.09322	0.70849	0.50116	151	B	usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	bulk	unknown	unknown	Germany	2019-05-31	Larval	Larval	Brain	Nervous System
52223	52223	SRR9164643	SRX5937415	SRS4850451	SRP199963	PRJNA541414	Danio rerio Raw sequence reads	PRJNA541414	Other	In most vertebrates including zebrafish the hypothalamicserotonergic cerebrospinal fluid contacting CSF c cells constitutea prominent population. In contrast to the hindbrain serotonergicneurons little is known about the development and function of thesecells. Here we identify fibroblast growth factor Fgf 3 as the main Fgfligand controlling the ontogeny of serotonergic CSF c cells. We showthat fgf3 positively regulates the number of serotonergic CSF c cells as well as a subset of dopaminergic and neuroendocrine cells in theposterior hypothalamus via control of proliferation and cell survival.Further expression of the ETS domain transcription factor etv5b isdownregulated post fgf3 impairment. Previous findings identifiedetv5b as critical for the proliferation of serotonergic progenitors in thehypothalamus and therefore we now suggest that Fgf3 acts via etv5bduring early development to ultimately control the number of matureserotonergic CSF c cells. Moreover our analysis of the developinghypothalamic transcriptome shows that the expression of fgf3 isupregulated upon fgf3 loss of function suggesting activation of a self compensatory mechanism. Together these results highlight Fgf3 in anovel context as part of a signalling pathway of critical importance forhypothalamic development.	wt +/+ 7dpf 2	wt +/+ 7dpf 2	filename:L1700054 Probe 11 plus plus 7dpf 2.fq.gz\|strain:Tuebingen\|dev stage:embryo\|sex:not determined\|tissue:hypothalamus\|BioSampleModel:Model organism or animal	wt +/+ 7dpf 2	wt +/+ 7dpf 2	wt +/+ 7dpf 2	library preparation was performed according to the Illumina TruSeq stranded mRNA Samples Preparation Guide with 100 ng of input RNA and 15 PCR cycles	RNA-Seq	TRANSCRIPTOMIC	PCR	SINGLE	ILLUMINA	NextSeq 500	SRP199963	L1700054_Probe_11_plus_plus_7dpf_2.fq.gz	fastq	2388621586.0	15818686.0	L1700054 Probe 11 plus plus 7dpf 2.fq.gz	0:151 1:0	A:604867119;C:572969413;G:574552382;T:635946570;N:286102	151	604867119	572969413	574552382	635946570	286102	SRX5937415	SRS4850451	SRA892447	University of Wuerzburg\|Department for Physiological Chemistry	University of Wuerzburg	1	0.9601	0.08858	0.71226	0.4818	151	B	usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	bulk	unknown	unknown	Germany	2019-05-31	Larval	Larval	Brain	Nervous System
52224	52224	SRR9164644	SRX5937414	SRS4850450	SRP199963	PRJNA541414	Danio rerio Raw sequence reads	PRJNA541414	Other	In most vertebrates including zebrafish the hypothalamicserotonergic cerebrospinal fluid contacting CSF c cells constitutea prominent population. In contrast to the hindbrain serotonergicneurons little is known about the development and function of thesecells. Here we identify fibroblast growth factor Fgf 3 as the main Fgfligand controlling the ontogeny of serotonergic CSF c cells. We showthat fgf3 positively regulates the number of serotonergic CSF c cells as well as a subset of dopaminergic and neuroendocrine cells in theposterior hypothalamus via control of proliferation and cell survival.Further expression of the ETS domain transcription factor etv5b isdownregulated post fgf3 impairment. Previous findings identifiedetv5b as critical for the proliferation of serotonergic progenitors in thehypothalamus and therefore we now suggest that Fgf3 acts via etv5bduring early development to ultimately control the number of matureserotonergic CSF c cells. Moreover our analysis of the developinghypothalamic transcriptome shows that the expression of fgf3 isupregulated upon fgf3 loss of function suggesting activation of a self compensatory mechanism. Together these results highlight Fgf3 in anovel context as part of a signalling pathway of critical importance forhypothalamic development.	wt +/+ 3dpf 1	wt +/+ 3dpf 1	filename:L1700051 Probe 6 plus plus 3dpf 3.fq.gz\|strain:Tuebingen\|dev stage:embryo\|sex:not determined\|tissue:hypothalamus\|BioSampleModel:Model organism or animal	wt +/+ 3dpf 1	wt +/+ 3dpf 1	wt +/+ 3dpf 1	library preparation was performed according to the Illumina TruSeq stranded mRNA Samples Preparation Guide with 100 ng of input RNA and 15 PCR cycles	RNA-Seq	TRANSCRIPTOMIC	PCR	SINGLE	ILLUMINA	NextSeq 500	SRP199963	L1700051_Probe_6_plus_plus_3dpf_3.fq.gz	fastq	2516841877.0	16667827.0	L1700051 Probe 6 plus plus 3dpf 3.fq.gz	0:151 1:0	A:638504042;C:602279329;G:599178016;T:676575909;N:304581	151	638504042	602279329	599178016	676575909	304581	SRX5937414	SRS4850450	SRA892447	University of Wuerzburg\|Department for Physiological Chemistry	University of Wuerzburg	1	0.96561	0.07463	0.72054	0.48315	151	B	usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	bulk	unknown	unknown	Germany	2019-05-31	Larval	Larval	Brain	Nervous System
52225	52225	SRR9164645	SRX5937413	SRS4850449	SRP199963	PRJNA541414	Danio rerio Raw sequence reads	PRJNA541414	Other	In most vertebrates including zebrafish the hypothalamicserotonergic cerebrospinal fluid contacting CSF c cells constitutea prominent population. In contrast to the hindbrain serotonergicneurons little is known about the development and function of thesecells. Here we identify fibroblast growth factor Fgf 3 as the main Fgfligand controlling the ontogeny of serotonergic CSF c cells. We showthat fgf3 positively regulates the number of serotonergic CSF c cells as well as a subset of dopaminergic and neuroendocrine cells in theposterior hypothalamus via control of proliferation and cell survival.Further expression of the ETS domain transcription factor etv5b isdownregulated post fgf3 impairment. Previous findings identifiedetv5b as critical for the proliferation of serotonergic progenitors in thehypothalamus and therefore we now suggest that Fgf3 acts via etv5bduring early development to ultimately control the number of matureserotonergic CSF c cells. Moreover our analysis of the developinghypothalamic transcriptome shows that the expression of fgf3 isupregulated upon fgf3 loss of function suggesting activation of a self compensatory mechanism. Together these results highlight Fgf3 in anovel context as part of a signalling pathway of critical importance forhypothalamic development.	wt +/+ 7dpf 1	wt +/+ 7dpf 1	filename:L1700049 Probe 23 plus plus 7dpf 1 3.fq.gz\|strain:Tuebingen\|dev stage:embryo\|sex:not determined\|tissue:hypothalamus\|BioSampleModel:Model organism or animal	wt +/+ 7dpf 1	wt +/+ 7dpf 1	wt +/+ 7dpf 1	library preparation was performed according to the Illumina TruSeq stranded mRNA Samples Preparation Guide with 100 ng of input RNA and 15 PCR cycles	RNA-Seq	TRANSCRIPTOMIC	PCR	SINGLE	ILLUMINA	NextSeq 500	SRP199963	L1700049_Probe_23_plus_plus_7dpf_1_3.fq.gz	fastq	2811795311.0	18621161.0	L1700049 Probe 23 plus plus 7dpf 1 3.fq.gz	0:151 1:0	A:718804998;C:669270370;G:672469872;T:750915840;N:334231	151	718804998	669270370	672469872	750915840	334231	SRX5937413	SRS4850449	SRA892447	University of Wuerzburg\|Department for Physiological Chemistry	University of Wuerzburg	1	0.95734	0.09739	0.71256	0.48704	151	B	usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	bulk	unknown	unknown	Germany	2019-05-31	Larval	Larval	Brain	Nervous System
52226	52226	SRR9164646	SRX5937412	SRS4850448	SRP199963	PRJNA541414	Danio rerio Raw sequence reads	PRJNA541414	Other	In most vertebrates including zebrafish the hypothalamicserotonergic cerebrospinal fluid contacting CSF c cells constitutea prominent population. In contrast to the hindbrain serotonergicneurons little is known about the development and function of thesecells. Here we identify fibroblast growth factor Fgf 3 as the main Fgfligand controlling the ontogeny of serotonergic CSF c cells. We showthat fgf3 positively regulates the number of serotonergic CSF c cells as well as a subset of dopaminergic and neuroendocrine cells in theposterior hypothalamus via control of proliferation and cell survival.Further expression of the ETS domain transcription factor etv5b isdownregulated post fgf3 impairment. Previous findings identifiedetv5b as critical for the proliferation of serotonergic progenitors in thehypothalamus and therefore we now suggest that Fgf3 acts via etv5bduring early development to ultimately control the number of matureserotonergic CSF c cells. Moreover our analysis of the developinghypothalamic transcriptome shows that the expression of fgf3 isupregulated upon fgf3 loss of function suggesting activation of a self compensatory mechanism. Together these results highlight Fgf3 in anovel context as part of a signalling pathway of critical importance forhypothalamic development.	fgf3t24152 / 7dpf 3	fgf3t24152 / 7dpf 3	filename:L1700053 Probe 9 minus minus 7dpf 3.fq.gz\|strain:Tuebingen\|dev stage:embryo\|sex:not determined\|tissue:hypothalamus\|BioSampleModel:Model organism or animal	fgf3t24152 / 7dpf 3	fgf3t24152 / 7dpf 3	fgf3t24152 / 7dpf 3	library preparation was performed according to the Illumina TruSeq stranded mRNA Samples Preparation Guide with 100 ng of input RNA and 15 PCR cycles	RNA-Seq	TRANSCRIPTOMIC	PCR	SINGLE	ILLUMINA	NextSeq 500	SRP199963	L1700053_Probe_9_minus_minus_7dpf_3.fq.gz	fastq	2201563390.0	14579890.0	L1700053 Probe 9 minus minus 7dpf 3.fq.gz	0:151 1:0	A:559541557;C:523434389;G:527775051;T:590547674;N:264719	151	559541557	523434389	527775051	590547674	264719	SRX5937412	SRS4850448	SRA892447	University of Wuerzburg\|Department for Physiological Chemistry	University of Wuerzburg	1	0.95732	0.09772	0.70678	0.49199	151	B	usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	bulk	unknown	unknown	Germany	2019-05-31	Larval	Larval	Brain	Nervous System
52227	52227	SRR9164647	SRX5937411	SRS4850447	SRP199963	PRJNA541414	Danio rerio Raw sequence reads	PRJNA541414	Other	In most vertebrates including zebrafish the hypothalamicserotonergic cerebrospinal fluid contacting CSF c cells constitutea prominent population. In contrast to the hindbrain serotonergicneurons little is known about the development and function of thesecells. Here we identify fibroblast growth factor Fgf 3 as the main Fgfligand controlling the ontogeny of serotonergic CSF c cells. We showthat fgf3 positively regulates the number of serotonergic CSF c cells as well as a subset of dopaminergic and neuroendocrine cells in theposterior hypothalamus via control of proliferation and cell survival.Further expression of the ETS domain transcription factor etv5b isdownregulated post fgf3 impairment. Previous findings identifiedetv5b as critical for the proliferation of serotonergic progenitors in thehypothalamus and therefore we now suggest that Fgf3 acts via etv5bduring early development to ultimately control the number of matureserotonergic CSF c cells. Moreover our analysis of the developinghypothalamic transcriptome shows that the expression of fgf3 isupregulated upon fgf3 loss of function suggesting activation of a self compensatory mechanism. Together these results highlight Fgf3 in anovel context as part of a signalling pathway of critical importance forhypothalamic development.	fgf3t24152 / 3dpf 3	fgf3t24152 / 3dpf 3	filename:L1700050 Probe 2 minus minus 3dpf 2.fq.gz\|strain:Tuebingen\|dev stage:embryo\|sex:not determined\|tissue:hypothalamus\|BioSampleModel:Model organism or animal	fgf3t24152 / 3dpf 3	fgf3t24152 / 3dpf 3	fgf3t24152 / 3dpf 3	library preparation was performed according to the Illumina TruSeq stranded mRNA Samples Preparation Guide with 100 ng of input RNA and 15 PCR cycles	RNA-Seq	TRANSCRIPTOMIC	PCR	SINGLE	ILLUMINA	NextSeq 500	SRP199963	L1700050_Probe_2_minus_minus_3dpf_2.fq.gz	fastq	2555431890.0	16923390.0	L1700050 Probe 2 minus minus 3dpf 2.fq.gz	0:151 1:0	A:649509144;C:614610346;G:607297438;T:683712219;N:302743	151	649509144	614610346	607297438	683712219	302743	SRX5937411	SRS4850447	SRA892447	University of Wuerzburg\|Department for Physiological Chemistry	University of Wuerzburg	1	0.96502	0.07688	0.72381	0.4855	151	B	usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	bulk	unknown	unknown	Germany	2019-05-31	Larval	Larval	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");;