{"database": "metadata", "table": "run_metadata", "rows": [[75613, "SRR24740774", "SRX20518080", "SRS17828036", "SRP439616", "PRJNA976345", "An organ specific angiogenic control mechanism for endothelial tailoring", "GSE233488", "Transcriptome Analysis", "To address the role of endothelial Wnt/\u00df catenin signaling in CNS angiogenesis  we compared the bulk transcriptomes of WT and Wnt/\u00df catenin signaling deficient PHBC endothelial cells  prior to CNS vascular invasion. To this end  we used three approaches to abrogate endothelial Wnt/\u00df catenin signaling: Morpholino mediated knock down of gpr124  reck or wnt7aa. We find that the expression of mmp25b is decreased in PHBC endothelial cells of all Wnt/\u00df catenin signaling deficient conditions as compared to the WT controls. Overall design: Tgfli1:Gal4ubs3;UAS:Kaederk8 embryos were injected at the single cell stage with Morpholinos targeting gpr124  reck  or wnt7aa. Prior to CNS vascular invasion 30 hpf  PHBC endothelial cells expressing the Kaede fluorescent protein  were photoconverted shifting green towards red fluorescence by exposere to a 405 nm laser nanobeam  specifically at the level of the PHBC. Subsequent embryo dissociation and FACS allowed for isolation of PHBC endothelial cells. RNA extraction and sequencing was performed on 4 samples per condition  each containing photoconverted PHBC endothelial cells of 80 embryos.", null, "pubmed:38570687", null, "PHBC endothelial cells 30 hpf  wnt7aa MO 1", "GSM7429338", null, "source name:Vascular endothelium|tissue:Vascular endothelium|cell line:PHBC endothelial cells|Stage:30 hpf|cell type:Endothelial cells|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8|genotype:wnt7aa MO|treatment:photoconverted|geo loc name:missing|collection date:missing", "PHBC endothelial cells 30 hpf  wnt7aa MO 1", "The resulting raw reads were assessed for quality  adapter content  and duplication rates with FastQC. Trimmomatic version 0.33 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter \u201c\u2014outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.5.1 tool from the Subread package84. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers activities at the Universal Protein Resource UniProt. Assembly: DanRer10 Supplementary files format and content: library size normlized counts", "Vascular endothelium", null, "RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250\u2013500\u2009pg total RNA was used as input for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.", null, "tissue:Vascular endothelium|cell line:PHBC endothelial cells|Stage:30 hpf|cell type:Endothelial cells|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8|genotype:wnt7aa MO|treatment:photoconverted", "GSM7429338", "GSM7429338: PHBC endothelial cells 30 hpf  wnt7aa MO 1; Danio rerio; RNA Seq", "GSM7429338 r1", "GSM7429338", "1", "RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250\u2013500\u2009pg total RNA was used as input for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP439616", null, "loader:fastq load.py", "F1_MO_wnt7aa_R1.fastq.gz F1_MO_wnt7aa_R2.fastq.gz", "fastq fastq", 2134056620.0, 14319615.0, "GSM7429338 r1", null, "A:574764769;C:489478372;G:488808981;T:579820041;N:1184457", null, null, null, null, 574764769, 489478372, 488808981, 579820041, 1184457, "SRX20518080", "SRS17828036", "SRA1644604", "MPI for heart and lung research", "MPI for heart and lung research", 2, 0.90992, 0.91125, 0.15485, 0.15169, 0.77126, 0.77352, 0.52889, 0.52569, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2023-05-25", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"]], "columns": ["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"], "primary_keys": ["rowid"], "primary_key_values": ["75613"], "units": {}, "query_ms": 8.770505999564193}