run_metadata: 52216
This data as json
| rowid | run.accession | experiment.accession | sample.accession | study.accession | bioproject | study.title | study.alias | study.type | study.abstract | study.attributes | study.PMIDs | sample.description | sample.title | sample.alias | sample.centername | sample.attributes | GEOsample.title | GEOsample.dataprocessing | GEOsample.source | GEOsample.treatmentprotocol | GEOsample.extractprotocol | GEOsample.growthprotocol | 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.title | run.attributes | run.filename | run.semantic_name | run.total_bases | run.total_spots | run.alias | run.read_lengths | run.base_counts | run.r1_length | run.r2_length | run.r3_length | run.r4_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 | tech_variant | submission.bioprojectsource.country | earliest_date | devstage_curation | devstage_curation_coarse | tissue_curation | tissue_curation_coarse |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 | 0 | 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 |